diff --git a/announcements/src/org/labkey/announcements/AnnouncementsController.java b/announcements/src/org/labkey/announcements/AnnouncementsController.java index 195b1466416..5846a3e6118 100644 --- a/announcements/src/org/labkey/announcements/AnnouncementsController.java +++ b/announcements/src/org/labkey/announcements/AnnouncementsController.java @@ -19,7 +19,7 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.DateUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -1639,7 +1639,7 @@ protected Date getEndRange(Date current, Date last) } catch (Exception e) { - Logger.getLogger(AnnouncementsController.class).error(e); + LogManager.getLogger(AnnouncementsController.class).error(e); } }); digestThread.start(); diff --git a/announcements/src/org/labkey/announcements/NotificationSettingsWriterFactory.java b/announcements/src/org/labkey/announcements/NotificationSettingsWriterFactory.java index 53b2e6e5c58..51c0f8d2443 100644 --- a/announcements/src/org/labkey/announcements/NotificationSettingsWriterFactory.java +++ b/announcements/src/org/labkey/announcements/NotificationSettingsWriterFactory.java @@ -18,9 +18,9 @@ import org.apache.commons.lang3.math.NumberUtils; import org.labkey.announcements.model.AnnouncementManager; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.files.FileContentDefaultEmailPref; diff --git a/announcements/src/org/labkey/announcements/SendMessageAction.java b/announcements/src/org/labkey/announcements/SendMessageAction.java index 6dae2e31030..ff1e0bf7ec1 100644 --- a/announcements/src/org/labkey/announcements/SendMessageAction.java +++ b/announcements/src/org/labkey/announcements/SendMessageAction.java @@ -18,7 +18,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -59,7 +60,7 @@ @RequiresPermission(ReadPermission.class) public class SendMessageAction extends MutatingApiAction { - private static final Logger _log = Logger.getLogger(SendMessageAction.class); + private static final Logger _log = LogManager.getLogger(SendMessageAction.class); private Map> _recipientMap = new HashMap<>(); enum Props diff --git a/announcements/src/org/labkey/announcements/emailPreferences.jsp b/announcements/src/org/labkey/announcements/emailPreferences.jsp index c61ba6f9538..746c3d1f17c 100644 --- a/announcements/src/org/labkey/announcements/emailPreferences.jsp +++ b/announcements/src/org/labkey/announcements/emailPreferences.jsp @@ -15,9 +15,9 @@ * limitations under the License. */ %> +<%@ page import="org.apache.commons.lang3.StringUtils" %> <%@ page import="org.labkey.announcements.AnnouncementsController" %> <%@ page import="org.labkey.api.announcements.EmailOption" %> -<%@ page import="org.apache.commons.lang3.StringUtils" %> <%@ page extends="org.labkey.announcements.EmailPreferencesPage" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> diff --git a/announcements/src/org/labkey/announcements/model/AnnouncementDigestProvider.java b/announcements/src/org/labkey/announcements/model/AnnouncementDigestProvider.java index f1b303f8c95..6c458481c86 100644 --- a/announcements/src/org/labkey/announcements/model/AnnouncementDigestProvider.java +++ b/announcements/src/org/labkey/announcements/model/AnnouncementDigestProvider.java @@ -15,7 +15,8 @@ */ package org.labkey.announcements.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.announcements.AnnouncementsController; import org.labkey.api.announcements.CommSchema; import org.labkey.api.announcements.DiscussionService; @@ -53,7 +54,7 @@ public class AnnouncementDigestProvider implements MessageDigest.Provider { private static final CommSchema _comm = CommSchema.getInstance(); private static final CoreSchema _core = CoreSchema.getInstance(); - private static final Logger _log = Logger.getLogger(AnnouncementDigestProvider.class); + private static final Logger _log = LogManager.getLogger(AnnouncementDigestProvider.class); // Retrieve from this container all messages with a body or attachments that were marked as "approved" during the given // timespan. Messages are grouped by thread and threads are sorted by earliest post within each thread. diff --git a/announcements/src/org/labkey/announcements/model/AnnouncementManager.java b/announcements/src/org/labkey/announcements/model/AnnouncementManager.java index cb307569f97..17bb90fb88e 100644 --- a/announcements/src/org/labkey/announcements/model/AnnouncementManager.java +++ b/announcements/src/org/labkey/announcements/model/AnnouncementManager.java @@ -17,7 +17,7 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -314,7 +314,7 @@ private static void notifyModerators(Container c, User user, AnnouncementModel a if (toList.isEmpty()) { - Logger.getLogger(AnnouncementManager.class).warn("New " + name.toLowerCase() + " requires moderator review, but no moderators are authorized in this folder: " + c.getPath()); + LogManager.getLogger(AnnouncementManager.class).warn("New " + name.toLowerCase() + " requires moderator review, but no moderators are authorized in this folder: " + c.getPath()); } else { diff --git a/announcements/src/org/labkey/announcements/model/DiscussionWebPartFactory.java b/announcements/src/org/labkey/announcements/model/DiscussionWebPartFactory.java index fd8a0c0e873..80ccb9ec7a8 100644 --- a/announcements/src/org/labkey/announcements/model/DiscussionWebPartFactory.java +++ b/announcements/src/org/labkey/announcements/model/DiscussionWebPartFactory.java @@ -21,11 +21,18 @@ import org.labkey.api.data.Container; import org.labkey.api.security.User; import org.labkey.api.util.URLHelper; -import org.labkey.api.view.*; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.BaseWebPartFactory; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartConfigurationException; +import org.labkey.api.view.WebPartView; -import java.util.Map; import java.net.URISyntaxException; import java.text.ParseException; +import java.util.Map; /** * User: adam diff --git a/announcements/src/org/labkey/announcements/model/InsertMessagePermission.java b/announcements/src/org/labkey/announcements/model/InsertMessagePermission.java index 8d442e2a68e..937daf82c74 100644 --- a/announcements/src/org/labkey/announcements/model/InsertMessagePermission.java +++ b/announcements/src/org/labkey/announcements/model/InsertMessagePermission.java @@ -15,9 +15,6 @@ */ package org.labkey.announcements.model; -import org.jetbrains.annotations.NotNull; -import org.labkey.announcements.AnnouncementModule; -import org.labkey.api.module.Module; import org.labkey.api.security.permissions.AbstractPermission; /** diff --git a/api/build.gradle b/api/build.gradle index 37c046e60e7..148282bb651 100644 --- a/api/build.gradle +++ b/api/build.gradle @@ -62,7 +62,9 @@ List caching = [ ] List logging = [ - "log4j:log4j:${log4jVersion}" + "org.apache.logging.log4j:log4j-core:${log4j2Version}", + "org.apache.logging.log4j:log4j-api:${log4j2Version}", + "org.apache.logging.log4j:log4j-1.2-api:${log4j2Version}" ] List r = [ @@ -84,7 +86,6 @@ List others = [ "flyingsaucer:core-renderer:${flyingsaucerVersion}", "com.google.guava:guava:${guavaVersion}", "net.sf.jtidy:jtidy:${jtidyVersion}", - "net.sourceforge.jexcelapi:jxl:${jxlVersion}", "com.google.code.kaptcha:kaptcha:${kaptchaVersion}", "org.objenesis:objenesis:${objenesisVersion}", "com.opencsv:opencsv:${opencsvVersion}", @@ -170,6 +171,10 @@ dependencies { // dependency here in favor of the explicit dependency with a different version. exclude group: "org.apache.xmlbeans", module: "xmlbeans" } + external("net.sourceforge.jexcelapi:jxl:${jxlVersion}") { + // exclude this because it brings older version of log4j + exclude group: "log4j", module:"log4j" + } external apache,caching,charting,gwt,jackson,javax,logging,others,r,spring // These are required for running unit tests through the server junit controller diff --git a/api/gwtsrc/org/labkey/api/gwt/client/assay/model/GWTProtocol.java b/api/gwtsrc/org/labkey/api/gwt/client/assay/model/GWTProtocol.java index 03031a1c260..8cfc2fedbf6 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/assay/model/GWTProtocol.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/assay/model/GWTProtocol.java @@ -17,15 +17,14 @@ package org.labkey.api.gwt.client.assay.model; import com.google.gwt.user.client.rpc.IsSerializable; +import org.labkey.api.gwt.client.model.GWTContainer; +import org.labkey.api.gwt.client.model.GWTDomain; +import org.labkey.api.gwt.client.model.GWTPropertyDescriptor; +import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; -import java.util.ArrayList; - -import org.labkey.api.gwt.client.model.GWTContainer; -import org.labkey.api.gwt.client.model.GWTDomain; -import org.labkey.api.gwt.client.model.GWTPropertyDescriptor; /** * User: brittp diff --git a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTComparisonGroup.java b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTComparisonGroup.java index 4deacf6fcda..8cce6e33ec9 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTComparisonGroup.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTComparisonGroup.java @@ -17,8 +17,8 @@ package org.labkey.api.gwt.client.model; import java.io.Serializable; -import java.util.List; import java.util.ArrayList; +import java.util.List; /** * User: jeckels diff --git a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyDescriptor.java b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyDescriptor.java index 554fb558eae..f99a5118e78 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyDescriptor.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyDescriptor.java @@ -23,7 +23,6 @@ import org.labkey.api.gwt.client.PHIType; import org.labkey.api.gwt.client.ui.PropertyType; import org.labkey.api.gwt.client.util.BooleanProperty; -import org.labkey.api.gwt.client.util.IPropertyWrapper; import org.labkey.api.gwt.client.util.IntegerProperty; import org.labkey.api.gwt.client.util.StringProperty; import org.labkey.api.gwt.client.util.StringUtils; diff --git a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyValidator.java b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyValidator.java index 2b4dd520d91..df579998339 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyValidator.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/model/GWTPropertyValidator.java @@ -20,9 +20,9 @@ import org.labkey.api.gwt.client.util.StringUtils; import java.io.Serializable; -import java.util.Map; import java.util.HashMap; import java.util.List; +import java.util.Map; /* * User: Karl Lum diff --git a/api/gwtsrc/org/labkey/api/gwt/client/pipeline/PipelineGWTServiceAsync.java b/api/gwtsrc/org/labkey/api/gwt/client/pipeline/PipelineGWTServiceAsync.java index 9ba21779919..ae522c23c71 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/pipeline/PipelineGWTServiceAsync.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/pipeline/PipelineGWTServiceAsync.java @@ -16,7 +16,6 @@ package org.labkey.api.gwt.client.pipeline; import com.google.gwt.user.client.rpc.AsyncCallback; -import com.google.gwt.user.client.rpc.RemoteService; public interface PipelineGWTServiceAsync { diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/BoundTextBox.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/BoundTextBox.java index cf42004b3ef..c3f5f42dbd6 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/BoundTextBox.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/BoundTextBox.java @@ -15,10 +15,19 @@ */ package org.labkey.api.gwt.client.ui; -import com.google.gwt.event.dom.client.*; -import com.google.gwt.user.client.Window; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.event.dom.client.BlurEvent; +import com.google.gwt.event.dom.client.BlurHandler; +import com.google.gwt.event.dom.client.ChangeEvent; +import com.google.gwt.event.dom.client.ChangeHandler; +import com.google.gwt.event.dom.client.KeyPressEvent; +import com.google.gwt.event.dom.client.KeyPressHandler; +import com.google.gwt.event.dom.client.KeyUpEvent; +import com.google.gwt.event.dom.client.KeyUpHandler; import com.google.gwt.user.client.DOM; +import com.google.gwt.user.client.Window; +import com.google.gwt.user.client.ui.HorizontalPanel; +import com.google.gwt.user.client.ui.TextBox; +import com.google.gwt.user.client.ui.Widget; import org.labkey.api.gwt.client.util.StringProperty; import org.labkey.api.gwt.client.util.StringUtils; diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/FileUploadWithListeners.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/FileUploadWithListeners.java index 32760c8cec3..7db94e31b24 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/FileUploadWithListeners.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/FileUploadWithListeners.java @@ -18,7 +18,13 @@ import com.google.gwt.dom.client.Element; import com.google.gwt.user.client.DOM; import com.google.gwt.user.client.Event; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.ChangeListener; +import com.google.gwt.user.client.ui.ChangeListenerCollection; +import com.google.gwt.user.client.ui.ClickListener; +import com.google.gwt.user.client.ui.ClickListenerCollection; +import com.google.gwt.user.client.ui.FileUpload; +import com.google.gwt.user.client.ui.SourcesChangeEvents; +import com.google.gwt.user.client.ui.SourcesClickEvents; /** * User: jgarms diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/ImageButton.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/ImageButton.java index d63a88b10b9..1b4d2b5dca2 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/ImageButton.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/ImageButton.java @@ -16,8 +16,8 @@ package org.labkey.api.gwt.client.ui; -import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.event.dom.client.ClickEvent; +import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.event.dom.client.KeyPressEvent; import com.google.gwt.event.dom.client.KeyPressHandler; import com.google.gwt.event.shared.HandlerRegistration; diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/LinkButton.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/LinkButton.java index cd3bf1d8252..d3c228c497d 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/LinkButton.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/LinkButton.java @@ -16,7 +16,10 @@ package org.labkey.api.gwt.client.ui; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.ClickListener; +import com.google.gwt.user.client.ui.Composite; +import com.google.gwt.user.client.ui.HTML; +import com.google.gwt.user.client.ui.Widget; /** * User: brittp diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/SaveButtonBar.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/SaveButtonBar.java index b08507d7004..abffa7378d4 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/SaveButtonBar.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/SaveButtonBar.java @@ -17,7 +17,8 @@ import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.ButtonBase; +import com.google.gwt.user.client.ui.HorizontalPanel; /** * User: jgarms diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/StringListBox.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/StringListBox.java index b80a0174c56..2e8ad8537bf 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/StringListBox.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/StringListBox.java @@ -16,7 +16,11 @@ package org.labkey.api.gwt.client.ui; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.ChangeListener; +import com.google.gwt.user.client.ui.ChangeListenerCollection; +import com.google.gwt.user.client.ui.HasText; +import com.google.gwt.user.client.ui.ListBox; +import com.google.gwt.user.client.ui.Widget; import org.labkey.api.gwt.client.util.StringUtils; import java.util.ArrayList; diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/TextBoxDialogBox.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/TextBoxDialogBox.java index caebea3c99d..7a09613b043 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/TextBoxDialogBox.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/TextBoxDialogBox.java @@ -19,7 +19,13 @@ import com.google.gwt.event.dom.client.ClickEvent; import com.google.gwt.event.dom.client.ClickHandler; import com.google.gwt.event.dom.client.KeyCodes; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.DialogBox; +import com.google.gwt.user.client.ui.HorizontalPanel; +import com.google.gwt.user.client.ui.KeyboardListenerAdapter; +import com.google.gwt.user.client.ui.Label; +import com.google.gwt.user.client.ui.TextBox; +import com.google.gwt.user.client.ui.VerticalPanel; +import com.google.gwt.user.client.ui.Widget; /** * User: jeckels diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/VennDiagramView.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/VennDiagramView.java index 367dc79340b..d723661f0ba 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/VennDiagramView.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/VennDiagramView.java @@ -20,16 +20,26 @@ import com.google.gwt.event.dom.client.ChangeHandler; import com.google.gwt.event.dom.client.LoadEvent; import com.google.gwt.event.dom.client.LoadHandler; -import com.google.gwt.user.client.ui.*; -import com.google.gwt.user.client.rpc.AsyncCallback; import com.google.gwt.user.client.DOM; -import org.labkey.api.gwt.client.util.PropertyUtil; -import org.labkey.api.gwt.client.model.GWTComparisonMember; +import com.google.gwt.user.client.rpc.AsyncCallback; +import com.google.gwt.user.client.ui.FlexTable; +import com.google.gwt.user.client.ui.Grid; +import com.google.gwt.user.client.ui.HTML; +import com.google.gwt.user.client.ui.HasAlignment; +import com.google.gwt.user.client.ui.HorizontalPanel; +import com.google.gwt.user.client.ui.Image; +import com.google.gwt.user.client.ui.Label; +import com.google.gwt.user.client.ui.ListBox; +import com.google.gwt.user.client.ui.Panel; +import com.google.gwt.user.client.ui.VerticalPanel; +import com.google.gwt.user.client.ui.Widget; import org.labkey.api.gwt.client.model.GWTComparisonGroup; +import org.labkey.api.gwt.client.model.GWTComparisonMember; import org.labkey.api.gwt.client.model.GWTComparisonResult; +import org.labkey.api.gwt.client.util.PropertyUtil; -import java.util.Map; import java.util.HashMap; +import java.util.Map; /** * User: jeckels diff --git a/api/gwtsrc/org/labkey/api/gwt/client/ui/WindowUtil.java b/api/gwtsrc/org/labkey/api/gwt/client/ui/WindowUtil.java index deda90c78b2..8b0452a22c1 100644 --- a/api/gwtsrc/org/labkey/api/gwt/client/ui/WindowUtil.java +++ b/api/gwtsrc/org/labkey/api/gwt/client/ui/WindowUtil.java @@ -17,7 +17,8 @@ package org.labkey.api.gwt.client.ui; import com.google.gwt.user.client.Window; -import com.google.gwt.user.client.ui.*; +import com.google.gwt.user.client.ui.DialogBox; +import com.google.gwt.user.client.ui.Widget; /** * User: Mark Igra diff --git a/api/resources/credits/jars.txt b/api/resources/credits/jars.txt index 549b5b3a7ce..b6ac7d78762 100644 --- a/api/resources/credits/jars.txt +++ b/api/resources/credits/jars.txt @@ -40,7 +40,8 @@ jtidy-r918.jar|Java Tidy|r918|{link:SourceForge|http://jtidy.sourceforge.net/}|{ junit-4.12.jar|JUnit|4.12|{link:Junit|http://www.junit.org}|{link:CPL 1.0|http://www.opensource.org/licenses/cpl1.0.php}|jeckels|Unit testing jxl-2.6.3.jar|API|2.6.3|{link:jexcelapi|http://www.jexcelapi.org/}|{link:LGPL|http://www.opensource.org/licenses/lgpl-license.php}|jeckels|Java Excel library kaptcha-2.3.jar|Captcha generator|2.3|{link:kaptcha|http://code.google.com/p/kaptcha/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|nicka|User signup forms -log4j-1.2.17.jar|Log4j|1.2.17|{link:Apache|http://logging.apache.org/log4j/1.2/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|mbellew|Logging +log4j-api-2.13.3.jar|Log4j|2.13.3|{link:Apache|https://logging.apache.org/log4j/2.x/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ankurj|Logging +log4j-core-2.13.3.jar|Log4j|2.13.3|{link:Apache|https://logging.apache.org/log4j/2.x/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ankurj|Logging objenesis-1.0.jar|Objenesis|1.0|{link:Objenesis|http://code.google.com/p/objenesis/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jeckels|Library for instantiating Java objects, dependency of jMock opencsv-2.3.jar|OpenCSV|2.3|{link:OpenCSV|http://opencsv.sourceforge.net/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|adam|Parsing CSV Files patricia-trie-0.6.jar|PATRICIA Trie|0.6|{link:PATRICIA Trie|http://code.google.com/p/patricia-trie/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jeckels|PATRICIA Trie data structure implementation diff --git a/api/schemas/datStatExport.xsd b/api/schemas/datStatExport.xsd index 7e035fb2c98..9d06fc99fb3 100644 --- a/api/schemas/datStatExport.xsd +++ b/api/schemas/datStatExport.xsd @@ -1,6 +1,5 @@ diff --git a/api/schemas/domainTemplate.xsd b/api/schemas/domainTemplate.xsd index 0977144c540..428a87032c2 100644 --- a/api/schemas/domainTemplate.xsd +++ b/api/schemas/domainTemplate.xsd @@ -1,12 +1,11 @@ + xmlns:xs="http://www.w3.org/2001/XMLSchema" + xmlns:dat="http://labkey.org/data/xml" + xmlns="http://labkey.org/data/xml/domainTemplate" + targetNamespace="http://labkey.org/data/xml/domainTemplate" + elementFormDefault="qualified" + attributeFormDefault="unqualified"> diff --git a/api/schemas/folderType.xsd b/api/schemas/folderType.xsd index 903ac0d458b..d6d2e8dd60d 100644 --- a/api/schemas/folderType.xsd +++ b/api/schemas/folderType.xsd @@ -3,7 +3,6 @@ elementFormDefault="qualified" targetNamespace="http://labkey.org/data/xml/folderType" xmlns:ft="http://labkey.org/data/xml/folderType" - xmlns:mp="http://labkey.org/moduleProperties/xml/" xmlns:wp="http://labkey.org/data/xml/webpart"> diff --git a/api/schemas/rdfTypes.xsd b/api/schemas/rdfTypes.xsd index 102e04e232a..611cb081fc9 100644 --- a/api/schemas/rdfTypes.xsd +++ b/api/schemas/rdfTypes.xsd @@ -1,6 +1,9 @@ - + diff --git a/api/src/org/apache/commons/validator/routines/CustomTLDEnabler.java b/api/src/org/apache/commons/validator/routines/CustomTLDEnabler.java index 0ccceb37c56..f92386d9f6d 100644 --- a/api/src/org/apache/commons/validator/routines/CustomTLDEnabler.java +++ b/api/src/org/apache/commons/validator/routines/CustomTLDEnabler.java @@ -15,7 +15,8 @@ */ package org.apache.commons.validator.routines; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; /** * Adds non-standard TLDs to allowable values for Apache Commons Validator. See issue 25041. @@ -25,7 +26,7 @@ */ public class CustomTLDEnabler { - private static final Logger LOG = Logger.getLogger(CustomTLDEnabler.class); + private static final Logger LOG = LogManager.getLogger(CustomTLDEnabler.class); static { diff --git a/api/src/org/json/JSONObject.java b/api/src/org/json/JSONObject.java index 61c56593cc3..2ae698d6248 100644 --- a/api/src/org/json/JSONObject.java +++ b/api/src/org/json/JSONObject.java @@ -32,7 +32,11 @@ of this software and associated documentation files (the "Software"), to deal import java.io.Writer; import java.lang.reflect.Field; import java.lang.reflect.Method; -import java.util.*; +import java.util.Collection; +import java.util.Date; +import java.util.HashMap; +import java.util.Iterator; +import java.util.Map; /** * A JSONObject is an unordered collection of name/value pairs. Its diff --git a/api/src/org/json/Test.java b/api/src/org/json/Test.java index 0e67809b64f..bd25dd0197d 100644 --- a/api/src/org/json/Test.java +++ b/api/src/org/json/Test.java @@ -1,9 +1,9 @@ package org.json; +import java.io.StringWriter; import java.util.Collection; import java.util.Iterator; import java.util.Map; -import java.io.StringWriter; /** * Test class. This file is not formally a member of the org.json library. diff --git a/api/src/org/labkey/api/action/AbstractFileUploadAction.java b/api/src/org/labkey/api/action/AbstractFileUploadAction.java index 97fc06db5e4..d905c115b19 100644 --- a/api/src/org/labkey/api/action/AbstractFileUploadAction.java +++ b/api/src/org/labkey/api/action/AbstractFileUploadAction.java @@ -15,6 +15,7 @@ */ package org.labkey.api.action; +import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; @@ -23,14 +24,20 @@ import org.labkey.api.writer.PrintWriters; import org.springframework.validation.BindException; import org.springframework.validation.Errors; -import org.springframework.web.multipart.MultipartHttpServletRequest; import org.springframework.web.multipart.MultipartFile; -import org.labkey.api.util.ExceptionUtil; +import org.springframework.web.multipart.MultipartHttpServletRequest; import org.springframework.web.servlet.ModelAndView; -import javax.servlet.http.HttpServletResponse; import javax.servlet.http.HttpServletRequest; -import java.io.*; +import javax.servlet.http.HttpServletResponse; +import java.io.ByteArrayInputStream; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.io.PrintWriter; +import java.io.Writer; import java.nio.charset.StandardCharsets; import java.util.HashMap; import java.util.Iterator; diff --git a/api/src/org/labkey/api/action/ApiResponseWriter.java b/api/src/org/labkey/api/action/ApiResponseWriter.java index f06b4c564d7..a6accdce208 100644 --- a/api/src/org/labkey/api/action/ApiResponseWriter.java +++ b/api/src/org/labkey/api/action/ApiResponseWriter.java @@ -16,7 +16,7 @@ package org.labkey.api.action; import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.query.BatchValidationException; @@ -183,7 +183,7 @@ protected void write(ApiResponse response) throws IOException if (!(e instanceof ExpectedException)) { ExceptionUtil.logExceptionToMothership(null, e); - Logger.getLogger(ApiResponseWriter.class).warn("ApiResponseWriter exception: ", e); + LogManager.getLogger(ApiResponseWriter.class).warn("ApiResponseWriter exception: ", e); } //at this point, we can't guarantee a legitimate //JSON response, and we need to write the exception diff --git a/api/src/org/labkey/api/action/ApiVersion.java b/api/src/org/labkey/api/action/ApiVersion.java index 826ecc63bd9..6d520311d9b 100644 --- a/api/src/org/labkey/api/action/ApiVersion.java +++ b/api/src/org/labkey/api/action/ApiVersion.java @@ -16,9 +16,9 @@ package org.labkey.api.action; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Annotation to declare the version of an API action. This is used diff --git a/api/src/org/labkey/api/action/BaseApiAction.java b/api/src/org/labkey/api/action/BaseApiAction.java index 81b191b2ae1..8e6fc36bc92 100644 --- a/api/src/org/labkey/api/action/BaseApiAction.java +++ b/api/src/org/labkey/api/action/BaseApiAction.java @@ -19,7 +19,7 @@ import com.fasterxml.jackson.databind.JsonMappingException; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectReader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.json.JSONArray; import org.json.JSONException; @@ -265,7 +265,7 @@ else if (null != response) return null; ExceptionUtil.logExceptionToMothership(getViewContext().getRequest(), e); - Logger.getLogger(BaseApiAction.class).error("ApiAction exception: ", e); + LogManager.getLogger(BaseApiAction.class).error("ApiAction exception: ", e); createResponseWriter().writeAndClose(e); } diff --git a/api/src/org/labkey/api/action/BaseViewAction.java b/api/src/org/labkey/api/action/BaseViewAction.java index fd108ce647d..9d0cbeb5615 100644 --- a/api/src/org/labkey/api/action/BaseViewAction.java +++ b/api/src/org/labkey/api/action/BaseViewAction.java @@ -21,7 +21,8 @@ import org.apache.commons.beanutils.DynaBean; import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.attachments.AttachmentFile; import org.labkey.api.attachments.SpringAttachmentFile; @@ -78,7 +79,7 @@ */ public abstract class BaseViewAction
extends PermissionCheckableAction implements Validator, HasPageConfig { - protected static final Logger logger = Logger.getLogger(BaseViewAction.class); + protected static final Logger logger = LogManager.getLogger(BaseViewAction.class); private PageConfig _pageConfig = null; private PropertyValues _pvs; @@ -443,7 +444,7 @@ else if (!value.getClass().isArray()) catch (Exception x) { errors.addError(new ObjectError(commandName, new String[]{"Error"}, new Object[] {value}, x.getMessage())); - Logger.getLogger(BaseViewAction.class).error("unexpected error", x); + LogManager.getLogger(BaseViewAction.class).error("unexpected error", x); } } return errors; diff --git a/api/src/org/labkey/api/action/ExportAction.java b/api/src/org/labkey/api/action/ExportAction.java index c0abddd84b0..1d72c7dec7d 100644 --- a/api/src/org/labkey/api/action/ExportAction.java +++ b/api/src/org/labkey/api/action/ExportAction.java @@ -16,9 +16,9 @@ package org.labkey.api.action; -import org.springframework.web.servlet.ModelAndView; -import org.springframework.validation.BindException; import org.labkey.api.view.NavTree; +import org.springframework.validation.BindException; +import org.springframework.web.servlet.ModelAndView; import javax.servlet.http.HttpServletResponse; diff --git a/api/src/org/labkey/api/action/FormHandlerAction.java b/api/src/org/labkey/api/action/FormHandlerAction.java index 894d2a2b114..4ef415f23ab 100644 --- a/api/src/org/labkey/api/action/FormHandlerAction.java +++ b/api/src/org/labkey/api/action/FormHandlerAction.java @@ -16,9 +16,9 @@ package org.labkey.api.action; -import org.springframework.web.servlet.ModelAndView; -import org.springframework.validation.BindException; import org.labkey.api.view.NavTree; +import org.springframework.validation.BindException; +import org.springframework.web.servlet.ModelAndView; /** * User: matthewb diff --git a/api/src/org/labkey/api/action/HasBindParameters.java b/api/src/org/labkey/api/action/HasBindParameters.java index 264dc0844e8..76c9743c6d9 100644 --- a/api/src/org/labkey/api/action/HasBindParameters.java +++ b/api/src/org/labkey/api/action/HasBindParameters.java @@ -16,8 +16,8 @@ package org.labkey.api.action; import org.jetbrains.annotations.NotNull; -import org.springframework.validation.BindException; import org.springframework.beans.PropertyValues; +import org.springframework.validation.BindException; public interface HasBindParameters { diff --git a/api/src/org/labkey/api/action/QueryViewAction.java b/api/src/org/labkey/api/action/QueryViewAction.java index e07f17a3aa3..e2c4f7e5d4c 100644 --- a/api/src/org/labkey/api/action/QueryViewAction.java +++ b/api/src/org/labkey/api/action/QueryViewAction.java @@ -27,7 +27,6 @@ import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; import org.labkey.api.query.UserSchema; -import org.labkey.api.util.HttpUtil; import org.labkey.api.view.NotFoundException; import org.labkey.api.view.UnauthorizedException; import org.labkey.api.view.WebPartView; diff --git a/api/src/org/labkey/api/action/SpringActionController.java b/api/src/org/labkey/api/action/SpringActionController.java index 1d74d1efd07..d26b49deab1 100644 --- a/api/src/org/labkey/api/action/SpringActionController.java +++ b/api/src/org/labkey/api/action/SpringActionController.java @@ -17,7 +17,8 @@ package org.labkey.api.action; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -120,7 +121,7 @@ public abstract class SpringActionController implements Controller, HasViewConte private static final Map, ActionDescriptor> _classToDescriptor = new HashMap<>(); - private static final Logger _log = Logger.getLogger(SpringActionController.class); + private static final Logger _log = LogManager.getLogger(SpringActionController.class); public void setActionResolver(ActionResolver actionResolver) { diff --git a/api/src/org/labkey/api/action/StatusAppender.java b/api/src/org/labkey/api/action/StatusAppender.java index be4c5f427b3..cddd96fae43 100644 --- a/api/src/org/labkey/api/action/StatusAppender.java +++ b/api/src/org/labkey/api/action/StatusAppender.java @@ -15,11 +15,20 @@ */ package org.labkey.api.action; -import org.apache.log4j.AppenderSkeleton; -import org.apache.log4j.spi.LoggingEvent; +import org.apache.logging.log4j.core.Filter; +import org.apache.logging.log4j.core.Layout; +import org.apache.logging.log4j.core.LogEvent; +import org.apache.logging.log4j.core.appender.AbstractAppender; +import org.apache.logging.log4j.core.config.Property; +import org.apache.logging.log4j.core.config.plugins.Plugin; import org.jetbrains.annotations.Nullable; -import java.util.*; +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.LinkedList; +import java.util.List; /** * An appender that can be added to any log4j Logger to help accumulate and report status; meant to be used within a @@ -29,25 +38,20 @@ * User: adam * Date: Jun 27, 2010 */ -public class StatusAppender extends AppenderSkeleton +@Plugin(name = "StatusAppender", category = "Core", elementType = "appender", printObject = true) +public class StatusAppender extends AbstractAppender { private final List _status = Collections.synchronizedList(new ArrayList<>()); - @Override - protected void append(LoggingEvent event) + public StatusAppender(String name, Filter filter, Layout layout, boolean ignoreExceptions, Property[] properties) { - _status.add(event.getMessage().toString()); + super(name, filter, layout, ignoreExceptions, properties); } @Override - public void close() + public void append(LogEvent event) { - } - - @Override - public boolean requiresLayout() - { - return false; + _status.add(event.getMessage().toString()); } public Collection getStatus(@Nullable Integer offset) diff --git a/api/src/org/labkey/api/admin/AbstractImportContext.java b/api/src/org/labkey/api/admin/AbstractImportContext.java index e9945264a36..bcd4f054c8c 100644 --- a/api/src/org/labkey/api/admin/AbstractImportContext.java +++ b/api/src/org/labkey/api/admin/AbstractImportContext.java @@ -17,7 +17,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; diff --git a/api/src/org/labkey/api/admin/ActionsHelper.java b/api/src/org/labkey/api/admin/ActionsHelper.java index 3c23ba0ef21..a87f5c37319 100644 --- a/api/src/org/labkey/api/admin/ActionsHelper.java +++ b/api/src/org/labkey/api/admin/ActionsHelper.java @@ -22,7 +22,13 @@ import org.labkey.api.view.ViewServlet; import org.springframework.web.servlet.mvc.Controller; -import java.util.*; +import java.util.Comparator; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeSet; public class ActionsHelper { diff --git a/api/src/org/labkey/api/admin/AdminBean.java b/api/src/org/labkey/api/admin/AdminBean.java index 37deb83fc01..9c7dfde4738 100644 --- a/api/src/org/labkey/api/admin/AdminBean.java +++ b/api/src/org/labkey/api/admin/AdminBean.java @@ -26,7 +26,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.UserManager; import org.labkey.api.settings.AppProps; -import org.labkey.api.util.Pair; import org.labkey.api.view.NavTree; import org.labkey.api.view.ViewContext; diff --git a/api/src/org/labkey/api/admin/FolderWriterImpl.java b/api/src/org/labkey/api/admin/FolderWriterImpl.java index 8cc97591e55..9229ef47c57 100644 --- a/api/src/org/labkey/api/admin/FolderWriterImpl.java +++ b/api/src/org/labkey/api/admin/FolderWriterImpl.java @@ -16,7 +16,8 @@ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.settings.AppProps; import org.labkey.api.settings.LookAndFeelProperties; @@ -33,7 +34,7 @@ */ public class FolderWriterImpl extends BaseFolderWriter { - private static final Logger LOG = Logger.getLogger(FolderWriterImpl.class); + private static final Logger LOG = LogManager.getLogger(FolderWriterImpl.class); private final Collection _writers; diff --git a/api/src/org/labkey/api/admin/ImportContext.java b/api/src/org/labkey/api/admin/ImportContext.java index 713ebb49192..ef00249a0e4 100644 --- a/api/src/org/labkey/api/admin/ImportContext.java +++ b/api/src/org/labkey/api/admin/ImportContext.java @@ -15,7 +15,7 @@ */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.labkey.api.data.Activity; import org.labkey.api.data.PHI; diff --git a/api/src/org/labkey/api/admin/InvalidFileException.java b/api/src/org/labkey/api/admin/InvalidFileException.java index 93c5cd2bb50..a8240caba55 100644 --- a/api/src/org/labkey/api/admin/InvalidFileException.java +++ b/api/src/org/labkey/api/admin/InvalidFileException.java @@ -18,7 +18,6 @@ import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; -import org.labkey.api.admin.ImportException; import org.labkey.api.util.XmlValidationException; import org.labkey.api.writer.VirtualFile; diff --git a/api/src/org/labkey/api/admin/LoggerGetter.java b/api/src/org/labkey/api/admin/LoggerGetter.java index ef0b0c2d21b..508e034147b 100644 --- a/api/src/org/labkey/api/admin/LoggerGetter.java +++ b/api/src/org/labkey/api/admin/LoggerGetter.java @@ -15,7 +15,7 @@ */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; /** * Simple interface that lets import/export contexts get access to a Logger. Pipeline jobs can't hold on to the Logger diff --git a/api/src/org/labkey/api/admin/PipelineJobLoggerGetter.java b/api/src/org/labkey/api/admin/PipelineJobLoggerGetter.java index 277f98a21ca..a7551bc1cde 100644 --- a/api/src/org/labkey/api/admin/PipelineJobLoggerGetter.java +++ b/api/src/org/labkey/api/admin/PipelineJobLoggerGetter.java @@ -15,7 +15,7 @@ */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.PipelineJob; /** diff --git a/api/src/org/labkey/api/admin/StaticLoggerGetter.java b/api/src/org/labkey/api/admin/StaticLoggerGetter.java index f81e0c9c4ba..f8d33880e1c 100644 --- a/api/src/org/labkey/api/admin/StaticLoggerGetter.java +++ b/api/src/org/labkey/api/admin/StaticLoggerGetter.java @@ -15,7 +15,7 @@ */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; /** * Implementation used when an import/export context is used within an action or otherwise outside of a pipeline job. diff --git a/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java b/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java index df034bac58e..9d5ece3e515 100644 --- a/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java +++ b/api/src/org/labkey/api/assay/AbstractAssayTsvDataHandler.java @@ -17,7 +17,8 @@ package org.labkey.api.assay; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.labkey.api.assay.plate.AssayPlateMetadataService; @@ -102,7 +103,7 @@ public String toString() } }; - private static final Logger LOG = Logger.getLogger(AbstractAssayTsvDataHandler.class); + private static final Logger LOG = LogManager.getLogger(AbstractAssayTsvDataHandler.class); private Map _rawPlateMetadata; protected abstract boolean allowEmptyData(); diff --git a/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java b/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java index f3a18bfd090..795bf0d481e 100644 --- a/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java +++ b/api/src/org/labkey/api/assay/AbstractTempDirDataCollector.java @@ -16,13 +16,14 @@ package org.labkey.api.assay; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.actions.AssayRunUploadForm; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.query.BatchValidationException; -import org.labkey.api.assay.actions.AssayRunUploadForm; import org.labkey.api.util.NetworkDrive; import java.io.File; @@ -43,7 +44,7 @@ public abstract class AbstractTempDirDataCollector implements AssayRunCreator { - private static final Logger LOG = Logger.getLogger(DefaultAssayRunCreator.class); + private static final Logger LOG = LogManager.getLogger(DefaultAssayRunCreator.class); private final ProviderType _provider; diff --git a/api/src/org/labkey/api/assay/DefaultDataTransformer.java b/api/src/org/labkey/api/assay/DefaultDataTransformer.java index 736b042812c..d21f543475b 100644 --- a/api/src/org/labkey/api/assay/DefaultDataTransformer.java +++ b/api/src/org/labkey/api/assay/DefaultDataTransformer.java @@ -18,10 +18,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; -import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.api.ExpProtocol; diff --git a/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java b/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java index ed0ee65d368..8e79832dfef 100644 --- a/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java +++ b/api/src/org/labkey/api/assay/PreviouslyUploadedDataCollector.java @@ -17,9 +17,6 @@ package org.labkey.api.assay; import org.jetbrains.annotations.NotNull; -import org.labkey.api.assay.AbstractTempDirDataCollector; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.util.PageFlowUtil; diff --git a/api/src/org/labkey/api/assay/SimpleAssayDataImportHelper.java b/api/src/org/labkey/api/assay/SimpleAssayDataImportHelper.java index 0ba4e12e1d2..b1219032bc4 100644 --- a/api/src/org/labkey/api/assay/SimpleAssayDataImportHelper.java +++ b/api/src/org/labkey/api/assay/SimpleAssayDataImportHelper.java @@ -23,7 +23,6 @@ import org.labkey.api.query.ValidationException; import java.util.Map; -import java.sql.SQLException; /** * User: jeckels diff --git a/api/src/org/labkey/api/assay/actions/AssayDetailRedirectAction.java b/api/src/org/labkey/api/assay/actions/AssayDetailRedirectAction.java index 6cac60c99b0..89e401016be 100644 --- a/api/src/org/labkey/api/assay/actions/AssayDetailRedirectAction.java +++ b/api/src/org/labkey/api/assay/actions/AssayDetailRedirectAction.java @@ -16,12 +16,12 @@ package org.labkey.api.assay.actions; import org.labkey.api.action.SimpleRedirectAction; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.exp.LsidManager; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NotFoundException; diff --git a/api/src/org/labkey/api/assay/actions/AssayHeaderView.java b/api/src/org/labkey/api/assay/actions/AssayHeaderView.java index e2490f5b491..4a219405372 100644 --- a/api/src/org/labkey/api/assay/actions/AssayHeaderView.java +++ b/api/src/org/labkey/api/assay/actions/AssayHeaderView.java @@ -16,23 +16,26 @@ package org.labkey.api.assay.actions; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.assay.AbstractAssayProvider; import org.labkey.api.assay.AssayHeaderLinkProvider; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; import org.labkey.api.assay.AssayUrls; import org.labkey.api.assay.security.DesignAssayPermission; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.view.*; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NavTree; +import org.labkey.api.view.ViewContext; -import java.util.List; import java.util.ArrayList; +import java.util.List; /** * User: jeckels diff --git a/api/src/org/labkey/api/assay/actions/AssayResultDetailsAction.java b/api/src/org/labkey/api/assay/actions/AssayResultDetailsAction.java index 203d04b4f25..9b124f35b8d 100644 --- a/api/src/org/labkey/api/assay/actions/AssayResultDetailsAction.java +++ b/api/src/org/labkey/api/assay/actions/AssayResultDetailsAction.java @@ -16,15 +16,15 @@ package org.labkey.api.assay.actions; +import org.labkey.api.assay.AbstractAssayProvider; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.AbstractAssayProvider; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; diff --git a/api/src/org/labkey/api/assay/actions/AssayRunDetailsAction.java b/api/src/org/labkey/api/assay/actions/AssayRunDetailsAction.java index 0faee773fdd..8c5a0fe6ead 100644 --- a/api/src/org/labkey/api/assay/actions/AssayRunDetailsAction.java +++ b/api/src/org/labkey/api/assay/actions/AssayRunDetailsAction.java @@ -16,15 +16,15 @@ package org.labkey.api.assay.actions; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; diff --git a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java index c231a55266f..2ff4afe7f16 100644 --- a/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java +++ b/api/src/org/labkey/api/assay/actions/AssayRunUploadForm.java @@ -20,7 +20,7 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AbstractAssayProvider; diff --git a/api/src/org/labkey/api/assay/actions/DesignerAction.java b/api/src/org/labkey/api/assay/actions/DesignerAction.java index cb873dd32d3..a2c2c1bbef0 100644 --- a/api/src/org/labkey/api/assay/actions/DesignerAction.java +++ b/api/src/org/labkey/api/assay/actions/DesignerAction.java @@ -16,16 +16,14 @@ package org.labkey.api.assay.actions; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerManager; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.module.ModuleHtmlView; import org.labkey.api.module.ModuleLoader; import org.labkey.api.security.RequiresPermission; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; diff --git a/api/src/org/labkey/api/assay/actions/ReimportRedirectAction.java b/api/src/org/labkey/api/assay/actions/ReimportRedirectAction.java index b4a68a34d0b..931d5a07781 100644 --- a/api/src/org/labkey/api/assay/actions/ReimportRedirectAction.java +++ b/api/src/org/labkey/api/assay/actions/ReimportRedirectAction.java @@ -17,7 +17,6 @@ import org.labkey.api.action.SimpleRedirectAction; import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.DataRegionSelection; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; @@ -26,7 +25,6 @@ import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NotFoundException; -import org.springframework.validation.Errors; import java.util.Set; diff --git a/api/src/org/labkey/api/assay/actions/UploadWizardAction.java b/api/src/org/labkey/api/assay/actions/UploadWizardAction.java index 426b53bd5e1..c8ae192cde3 100644 --- a/api/src/org/labkey/api/assay/actions/UploadWizardAction.java +++ b/api/src/org/labkey/api/assay/actions/UploadWizardAction.java @@ -105,7 +105,6 @@ import java.sql.SQLException; import java.util.ArrayList; import java.util.Collections; -import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; import java.util.List; diff --git a/api/src/org/labkey/api/assay/actions/assayHeader.jsp b/api/src/org/labkey/api/assay/actions/assayHeader.jsp index d8dfebd4e64..2b89dddcae4 100644 --- a/api/src/org/labkey/api/assay/actions/assayHeader.jsp +++ b/api/src/org/labkey/api/assay/actions/assayHeader.jsp @@ -16,13 +16,13 @@ */ %> <%@ page import="org.labkey.api.assay.actions.AssayHeaderView" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.ActionURL" %> +<%@ page import="org.labkey.api.view.HttpView" %> +<%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.NavTree" %> -<%@ page import="org.labkey.api.view.PopupMenuView" %> <%@ page import="org.labkey.api.view.PopupMenu" %> +<%@ page import="org.labkey.api.view.PopupMenuView" %> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java b/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java index cc57c1226a5..7659c7fc3b8 100644 --- a/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java +++ b/api/src/org/labkey/api/assay/pipeline/AssayRunAsyncContext.java @@ -15,9 +15,12 @@ */ package org.labkey.api.assay.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.exp.ExperimentException; @@ -31,9 +34,6 @@ import org.labkey.api.qc.TransformResult; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; -import org.labkey.api.assay.AssayService; import org.labkey.api.view.ActionURL; import javax.servlet.http.HttpServletRequest; diff --git a/api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java b/api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java index 223fd401e5a..eb3562c4184 100644 --- a/api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java +++ b/api/src/org/labkey/api/assay/pipeline/AssayUploadPipelineJob.java @@ -16,16 +16,16 @@ package org.labkey.api.assay.pipeline; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.api.ExpExperiment; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.NetworkDrive; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.URLHelper; diff --git a/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java b/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java index ba304c575be..d580e4d288a 100644 --- a/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java +++ b/api/src/org/labkey/api/assay/plate/PlateMetadataDataHandler.java @@ -1,6 +1,6 @@ package org.labkey.api.assay.plate; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.assay.AbstractAssayTsvDataHandler; import org.labkey.api.assay.AssayDataType; import org.labkey.api.exp.ExperimentException; diff --git a/api/src/org/labkey/api/assay/query/AssayBaseQueryView.java b/api/src/org/labkey/api/assay/query/AssayBaseQueryView.java index 3ddb293ce16..7147bfc7cf9 100644 --- a/api/src/org/labkey/api/assay/query/AssayBaseQueryView.java +++ b/api/src/org/labkey/api/assay/query/AssayBaseQueryView.java @@ -16,13 +16,13 @@ package org.labkey.api.assay.query; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssaySchema; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.DataRegion; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssaySchema; -import org.labkey.api.assay.AssayService; /** * User: brittp diff --git a/api/src/org/labkey/api/assay/query/ResultsQueryView.java b/api/src/org/labkey/api/assay/query/ResultsQueryView.java index 983b640cf50..6de156ddfdc 100644 --- a/api/src/org/labkey/api/assay/query/ResultsQueryView.java +++ b/api/src/org/labkey/api/assay/query/ResultsQueryView.java @@ -22,7 +22,15 @@ import org.labkey.api.assay.AssayResultsHeaderProvider; import org.labkey.api.assay.AssayService; import org.labkey.api.assay.ReplacedRunFilter; -import org.labkey.api.data.*; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.ColumnHeaderType; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.MenuButton; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; @@ -33,7 +41,7 @@ import org.labkey.api.security.permissions.DeletePermission; import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.study.StudyUrls; -import org.labkey.api.study.assay.*; +import org.labkey.api.study.assay.AssayPublishService; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; diff --git a/api/src/org/labkey/api/attachments/AttachmentFile.java b/api/src/org/labkey/api/attachments/AttachmentFile.java index 3c603576bb3..b6e06c696a2 100644 --- a/api/src/org/labkey/api/attachments/AttachmentFile.java +++ b/api/src/org/labkey/api/attachments/AttachmentFile.java @@ -18,8 +18,8 @@ import org.labkey.api.util.FileStream; -import java.io.InputStream; import java.io.IOException; +import java.io.InputStream; /** * User: adam diff --git a/api/src/org/labkey/api/attachments/DocumentWriter.java b/api/src/org/labkey/api/attachments/DocumentWriter.java index 46458d9b13f..906cfeb0bc6 100644 --- a/api/src/org/labkey/api/attachments/DocumentWriter.java +++ b/api/src/org/labkey/api/attachments/DocumentWriter.java @@ -16,8 +16,8 @@ package org.labkey.api.attachments; -import java.io.OutputStream; import java.io.IOException; +import java.io.OutputStream; /** * Something that knows how to absorb the content of a file or document, including some basic metadata. diff --git a/api/src/org/labkey/api/attachments/SpringAttachmentFile.java b/api/src/org/labkey/api/attachments/SpringAttachmentFile.java index 53d8ca06b37..065de3065a7 100644 --- a/api/src/org/labkey/api/attachments/SpringAttachmentFile.java +++ b/api/src/org/labkey/api/attachments/SpringAttachmentFile.java @@ -26,7 +26,6 @@ import java.io.InputStream; import java.io.OutputStream; import java.util.ArrayList; -import java.util.Collections; import java.util.List; import java.util.Map; diff --git a/api/src/org/labkey/api/audit/data/ProtocolColumn.java b/api/src/org/labkey/api/audit/data/ProtocolColumn.java index 6b0a17d879f..1966e9a30d6 100644 --- a/api/src/org/labkey/api/audit/data/ProtocolColumn.java +++ b/api/src/org/labkey/api/audit/data/ProtocolColumn.java @@ -16,15 +16,15 @@ package org.labkey.api.audit.data; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.RenderContext; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; diff --git a/api/src/org/labkey/api/audit/data/RunColumn.java b/api/src/org/labkey/api/audit/data/RunColumn.java index b2acefeed7f..0e54e59d0b6 100644 --- a/api/src/org/labkey/api/audit/data/RunColumn.java +++ b/api/src/org/labkey/api/audit/data/RunColumn.java @@ -16,6 +16,9 @@ package org.labkey.api.audit.data; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.RenderContext; @@ -23,9 +26,6 @@ import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; diff --git a/api/src/org/labkey/api/audit/data/RunGroupColumn.java b/api/src/org/labkey/api/audit/data/RunGroupColumn.java index 837c06e9c87..59a4914fc2d 100644 --- a/api/src/org/labkey/api/audit/data/RunGroupColumn.java +++ b/api/src/org/labkey/api/audit/data/RunGroupColumn.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerManager; import org.labkey.api.data.RenderContext; import org.labkey.api.exp.api.ExpExperiment; import org.labkey.api.exp.api.ExperimentService; @@ -27,9 +26,6 @@ import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; -import java.io.IOException; -import java.io.Writer; - /** * User: klum * Date: Mar 15, 2012 diff --git a/api/src/org/labkey/api/audit/provider/GroupAuditProvider.java b/api/src/org/labkey/api/audit/provider/GroupAuditProvider.java index e51d473a8ac..e5754ffbe43 100644 --- a/api/src/org/labkey/api/audit/provider/GroupAuditProvider.java +++ b/api/src/org/labkey/api/audit/provider/GroupAuditProvider.java @@ -22,7 +22,6 @@ import org.labkey.api.audit.AuditTypeProvider; import org.labkey.api.audit.query.AbstractAuditDomainKind; import org.labkey.api.audit.query.DefaultAuditTypeTable; -import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; diff --git a/api/src/org/labkey/api/audit/query/AuditDisplayColumnFactory.java b/api/src/org/labkey/api/audit/query/AuditDisplayColumnFactory.java index 7f7ae0b3117..2ab3475957e 100644 --- a/api/src/org/labkey/api/audit/query/AuditDisplayColumnFactory.java +++ b/api/src/org/labkey/api/audit/query/AuditDisplayColumnFactory.java @@ -16,8 +16,8 @@ package org.labkey.api.audit.query; -import org.labkey.api.data.DisplayColumnFactory; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DisplayColumnFactory; /** * User: Karl Lum diff --git a/api/src/org/labkey/api/audit/query/DefaultAuditSchema.java b/api/src/org/labkey/api/audit/query/DefaultAuditSchema.java index cfc1334f315..40e25cf0499 100644 --- a/api/src/org/labkey/api/audit/query/DefaultAuditSchema.java +++ b/api/src/org/labkey/api/audit/query/DefaultAuditSchema.java @@ -16,15 +16,15 @@ package org.labkey.api.audit.query; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.security.User; import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.CoreSchema; import org.labkey.api.data.TableInfo; import org.labkey.api.query.UserSchema; +import org.labkey.api.security.User; -import java.util.Set; import java.util.Collections; +import java.util.Set; /** * User: Karl Lum diff --git a/api/src/org/labkey/api/cache/CacheManager.java b/api/src/org/labkey/api/cache/CacheManager.java index 22c44312a68..c1705c29cc8 100644 --- a/api/src/org/labkey/api/cache/CacheManager.java +++ b/api/src/org/labkey/api/cache/CacheManager.java @@ -16,7 +16,8 @@ package org.labkey.api.cache; import org.apache.commons.lang3.time.DateUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.ehcache.EhCacheProvider; import org.labkey.api.collections.CollectionUtils; @@ -41,7 +42,7 @@ */ public class CacheManager { - private static final Logger LOG = Logger.getLogger(CacheManager.class); + private static final Logger LOG = LogManager.getLogger(CacheManager.class); // TODO: Millisecond granularity seems misleading (EhCache uses seconds) and silly public static final long SECOND = DateUtils.MILLIS_PER_SECOND; diff --git a/api/src/org/labkey/api/cache/ehcache/EhCacheProvider.java b/api/src/org/labkey/api/cache/ehcache/EhCacheProvider.java index 1d119d830f0..d734dc0666c 100644 --- a/api/src/org/labkey/api/cache/ehcache/EhCacheProvider.java +++ b/api/src/org/labkey/api/cache/ehcache/EhCacheProvider.java @@ -18,7 +18,8 @@ import net.sf.ehcache.Cache; import net.sf.ehcache.CacheManager; import net.sf.ehcache.config.CacheConfiguration; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.cache.CacheProvider; import org.labkey.api.cache.SimpleCache; import org.labkey.api.util.MemTracker; @@ -38,7 +39,7 @@ // Do not use CacheProvider implementations directly; use CacheManager.getCache() to get a cache public class EhCacheProvider implements CacheProvider { - private static final Logger LOG = Logger.getLogger(EhCacheProvider.class); + private static final Logger LOG = LogManager.getLogger(EhCacheProvider.class); private static final EhCacheProvider INSTANCE = new EhCacheProvider(); private final AtomicLong cacheCount = new AtomicLong(0); diff --git a/api/src/org/labkey/api/cache/ehcache/EhSimpleCache.java b/api/src/org/labkey/api/cache/ehcache/EhSimpleCache.java index 878e1fd5fb0..357db451e53 100644 --- a/api/src/org/labkey/api/cache/ehcache/EhSimpleCache.java +++ b/api/src/org/labkey/api/cache/ehcache/EhSimpleCache.java @@ -17,7 +17,8 @@ import net.sf.ehcache.Cache; import net.sf.ehcache.Element; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.CacheType; @@ -35,7 +36,7 @@ */ class EhSimpleCache implements SimpleCache { - private static final Logger LOG = Logger.getLogger(EhSimpleCache.class); + private static final Logger LOG = LogManager.getLogger(EhSimpleCache.class); private final Cache _cache; diff --git a/api/src/org/labkey/api/collections/ArrayListMap.java b/api/src/org/labkey/api/collections/ArrayListMap.java index 0ed86c759dd..a849185339d 100644 --- a/api/src/org/labkey/api/collections/ArrayListMap.java +++ b/api/src/org/labkey/api/collections/ArrayListMap.java @@ -20,7 +20,16 @@ import org.labkey.api.util.Pair; import java.io.Serializable; -import java.util.*; +import java.util.AbstractMap; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; public class ArrayListMap extends AbstractMap implements Serializable diff --git a/api/src/org/labkey/api/collections/BoundMap.java b/api/src/org/labkey/api/collections/BoundMap.java index 1ae53850de8..a2aae1f30d2 100644 --- a/api/src/org/labkey/api/collections/BoundMap.java +++ b/api/src/org/labkey/api/collections/BoundMap.java @@ -18,7 +18,7 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.Assert; import org.junit.Test; @@ -26,11 +26,16 @@ import java.beans.IntrospectionException; import java.beans.Introspector; import java.beans.PropertyDescriptor; +import java.io.IOException; +import java.io.Serializable; import java.lang.reflect.InvocationTargetException; import java.lang.reflect.Method; -import java.util.*; -import java.io.Serializable; -import java.io.IOException; +import java.util.AbstractMap; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; public class BoundMap extends AbstractMap implements Serializable @@ -309,7 +314,7 @@ private void initialize(Class beanClass) } catch (IntrospectionException e) { - Logger.getLogger(this.getClass()).error("error creating BoundMap", e); + LogManager.getLogger(this.getClass()).error("error creating BoundMap", e); throw new RuntimeException(e); } diff --git a/api/src/org/labkey/api/collections/NullPreventingSet.java b/api/src/org/labkey/api/collections/NullPreventingSet.java index 66196a4853f..025c3f7f0ef 100644 --- a/api/src/org/labkey/api/collections/NullPreventingSet.java +++ b/api/src/org/labkey/api/collections/NullPreventingSet.java @@ -17,9 +17,9 @@ import org.jetbrains.annotations.NotNull; -import java.util.Set; -import java.util.Iterator; import java.util.Collection; +import java.util.Iterator; +import java.util.Set; /** * Wrapper around another Set instance that disallows adding nulls by throwing an {@link IllegalArgumentException} diff --git a/api/src/org/labkey/api/compliance/ComplianceService.java b/api/src/org/labkey/api/compliance/ComplianceService.java index d3dc2779e20..be176fc32d2 100644 --- a/api/src/org/labkey/api/compliance/ComplianceService.java +++ b/api/src/org/labkey/api/compliance/ComplianceService.java @@ -16,7 +16,6 @@ package org.labkey.api.compliance; import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Activity; import org.labkey.api.data.Container; import org.labkey.api.data.PHI; diff --git a/api/src/org/labkey/api/data/AbstractForeignKey.java b/api/src/org/labkey/api/data/AbstractForeignKey.java index e50915cb009..7b78b4f1127 100644 --- a/api/src/org/labkey/api/data/AbstractForeignKey.java +++ b/api/src/org/labkey/api/data/AbstractForeignKey.java @@ -15,7 +15,7 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.NamedObjectList; import org.labkey.api.query.FieldKey; @@ -271,7 +271,7 @@ public ForeignKey remapFieldKeys(@Nullable FieldKey parent, @Nullable Map { - private static final Logger _log = Logger.getLogger(AsyncQueryRequest.class); + private static final Logger _log = LogManager.getLogger(AsyncQueryRequest.class); private static class CancelledException extends RuntimeException { diff --git a/api/src/org/labkey/api/data/AtomicDatabaseInteger.java b/api/src/org/labkey/api/data/AtomicDatabaseInteger.java index e60a939a863..2f43c8297e3 100644 --- a/api/src/org/labkey/api/data/AtomicDatabaseInteger.java +++ b/api/src/org/labkey/api/data/AtomicDatabaseInteger.java @@ -15,7 +15,7 @@ */ package org.labkey.api.data; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.jetbrains.annotations.Nullable; import org.junit.After; import org.junit.Assert; diff --git a/api/src/org/labkey/api/data/AuditConfigurable.java b/api/src/org/labkey/api/data/AuditConfigurable.java index b7031628980..6d0d4614639 100644 --- a/api/src/org/labkey/api/data/AuditConfigurable.java +++ b/api/src/org/labkey/api/data/AuditConfigurable.java @@ -15,9 +15,7 @@ */ package org.labkey.api.data; -import org.jetbrains.annotations.Nullable; import org.labkey.api.gwt.client.AuditBehaviorType; -import org.labkey.api.query.FieldKey; /** * Indicates that inserts, updates and deletes on a table can be auditable and supports setting diff --git a/api/src/org/labkey/api/data/BaseColumnInfo.java b/api/src/org/labkey/api/data/BaseColumnInfo.java index 46dad2795d4..93890847f12 100644 --- a/api/src/org/labkey/api/data/BaseColumnInfo.java +++ b/api/src/org/labkey/api/data/BaseColumnInfo.java @@ -21,7 +21,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -73,7 +74,7 @@ */ public class BaseColumnInfo extends ColumnRenderPropertiesImpl implements MutableColumnInfo { - private static final Logger LOG = Logger.getLogger(ColumnInfo.class); + private static final Logger LOG = LogManager.getLogger(ColumnInfo.class); private static final Set NON_EDITABLE_COL_NAMES = new CaseInsensitiveHashSet("created", "createdBy", "modified", "modifiedBy", "_ts", "entityId", "container"); private FieldKey _fieldKey; diff --git a/api/src/org/labkey/api/data/BeanObjectFactory.java b/api/src/org/labkey/api/data/BeanObjectFactory.java index d19ab4a34a6..a8197c2da10 100644 --- a/api/src/org/labkey/api/data/BeanObjectFactory.java +++ b/api/src/org/labkey/api/data/BeanObjectFactory.java @@ -20,7 +20,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.PropertyUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -45,7 +46,7 @@ public class BeanObjectFactory implements ObjectFactory // implements ResultSetHandler { - private static Logger _log = Logger.getLogger(BeanObjectFactory.class); + private static Logger _log = LogManager.getLogger(BeanObjectFactory.class); private Class _class; diff --git a/api/src/org/labkey/api/data/BuilderObjectFactory.java b/api/src/org/labkey/api/data/BuilderObjectFactory.java index 8728875c61f..30ab787e6b8 100644 --- a/api/src/org/labkey/api/data/BuilderObjectFactory.java +++ b/api/src/org/labkey/api/data/BuilderObjectFactory.java @@ -19,7 +19,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -44,7 +45,7 @@ public class BuilderObjectFactory implements ObjectFactory { - private static Logger _log = Logger.getLogger(BuilderObjectFactory.class); + private static Logger _log = LogManager.getLogger(BuilderObjectFactory.class); private final Class _class; private final Class _classBuilder; diff --git a/api/src/org/labkey/api/data/ButtonBar.java b/api/src/org/labkey/api/data/ButtonBar.java index 1187f1cb82b..a628a5dd356 100644 --- a/api/src/org/labkey/api/data/ButtonBar.java +++ b/api/src/org/labkey/api/data/ButtonBar.java @@ -22,7 +22,12 @@ import java.io.IOException; import java.io.Writer; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Set; /** * A set of buttons that are displayed as a unit. Typically, but not always, diff --git a/api/src/org/labkey/api/data/ButtonBarConfig.java b/api/src/org/labkey/api/data/ButtonBarConfig.java index 615579806cd..90ce6cf7184 100644 --- a/api/src/org/labkey/api/data/ButtonBarConfig.java +++ b/api/src/org/labkey/api/data/ButtonBarConfig.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.security.permissions.AdminPermission; @@ -55,7 +56,7 @@ public class ButtonBarConfig private String _onRenderScript; private Set _hiddenStandardButtons = new HashSet<>(); - private static final Logger LOG = Logger.getLogger(ButtonBarConfig.class); + private static final Logger LOG = LogManager.getLogger(ButtonBarConfig.class); public ButtonBarConfig(JSONObject json) { diff --git a/api/src/org/labkey/api/data/CachedResultSet.java b/api/src/org/labkey/api/data/CachedResultSet.java index 8f3e3ed95f2..ccde73ef94d 100644 --- a/api/src/org/labkey/api/data/CachedResultSet.java +++ b/api/src/org/labkey/api/data/CachedResultSet.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.collections4.IteratorUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.RowMap; @@ -67,7 +68,7 @@ */ public class CachedResultSet implements ResultSet, TableResultSet { - private static final Logger _log = Logger.getLogger(CachedResultSet.class); + private static final Logger _log = LogManager.getLogger(CachedResultSet.class); // metadata private final ResultSetMetaData _md; diff --git a/api/src/org/labkey/api/data/ConditionalFormat.java b/api/src/org/labkey/api/data/ConditionalFormat.java index c6b95759902..1fdfe91cd6c 100644 --- a/api/src/org/labkey/api/data/ConditionalFormat.java +++ b/api/src/org/labkey/api/data/ConditionalFormat.java @@ -15,13 +15,12 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.fhcrc.cpas.exp.xml.PropertyDescriptorType; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.SimpleFilter.FilterClause; -import org.labkey.api.exp.PropertyColumn; -import org.labkey.api.exp.PropertyDescriptor; import org.labkey.api.gwt.client.model.GWTConditionalFormat; import org.labkey.api.query.FieldKey; import org.labkey.api.util.URLHelper; @@ -33,7 +32,6 @@ import org.labkey.data.xml.ConditionalFormatsType; import java.awt.*; -import java.lang.reflect.InvocationTargetException; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.Collections; @@ -47,7 +45,7 @@ */ public class ConditionalFormat extends GWTConditionalFormat { - private static final Logger LOG = Logger.getLogger(ConditionalFormat.class); + private static final Logger LOG = LogManager.getLogger(ConditionalFormat.class); public ConditionalFormat(GWTConditionalFormat f) { diff --git a/api/src/org/labkey/api/data/ConnectionWrapper.java b/api/src/org/labkey/api/data/ConnectionWrapper.java index df4c0f811e7..deac0b769d9 100644 --- a/api/src/org/labkey/api/data/ConnectionWrapper.java +++ b/api/src/org/labkey/api/data/ConnectionWrapper.java @@ -16,9 +16,13 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.LoggerConfig; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.util.LoggerWriter; import org.labkey.api.data.DbScope.ConnectionType; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.dialect.StatementWrapper; @@ -27,6 +31,7 @@ import org.labkey.api.util.DateUtil; import org.labkey.api.util.MemTracker; import org.labkey.api.util.Pair; +import org.labkey.api.util.SimpleLoggerWriter; import org.labkey.api.view.ViewServlet; import java.lang.reflect.Method; @@ -64,11 +69,11 @@ */ public class ConnectionWrapper implements java.sql.Connection { - private static final Logger LOG = Logger.getLogger(ConnectionWrapper.class); + private static final Logger LOG = LogManager.getLogger(ConnectionWrapper.class); private static final Map> _openConnections = Collections.synchronizedMap(new IdentityHashMap<>()); private static final Set _loggedLeaks = new HashSet<>(); - private static final Logger _logDefault = Logger.getLogger(ConnectionWrapper.class); - private static final boolean _explicitLogger = _logDefault.getLevel() != null || _logDefault.getParent() != null && _logDefault.getParent().getName().equals("org.labkey.api.data"); + private static final Logger _logDefault = LogManager.getLogger(ConnectionWrapper.class); + private static final boolean _explicitLogger = initializeExplicitLogger(); private static final AtomicLong COUNTER = new AtomicLong(0); private final Connection _connection; @@ -94,6 +99,14 @@ public class ConnectionWrapper implements java.sql.Connection private volatile boolean _allowClose = true; + private static boolean initializeExplicitLogger() + { + var loggerContext = (LoggerContext) LogManager.getContext(false); + var loggerConfig = loggerContext.getConfiguration().getLoggerConfig(_logDefault.getName()); + + return _logDefault.getLevel() != null || loggerConfig.getParent() != null && loggerConfig.getParent().getName().equals("org.labkey.api.data"); + } + public ConnectionWrapper(Connection conn, DbScope scope, Integer spid, ConnectionType type, @Nullable Logger log) { _connection = conn; @@ -124,7 +137,7 @@ static Logger getConnectionLogger() if (className.equals("org.labkey.api.view.ViewServlet") || className.equals("org.labkey.api.action.SpringActionController")) break; if (className.endsWith("Controller") && !className.startsWith("org.labkey.api.view")) - return Logger.getLogger(className); + return LogManager.getLogger(className); } return _logDefault; } @@ -147,7 +160,7 @@ public static boolean dumpOpenConnections() return dumpOpenConnections(_logDefault); } - public static boolean dumpOpenConnections(@NotNull Logger log) + public static boolean dumpOpenConnections(@NotNull LoggerWriter logWriter) { synchronized (_openConnections) { @@ -155,19 +168,31 @@ public static boolean dumpOpenConnections(@NotNull Logger log) { String thread = p.first.getName(); Throwable t = p.second; - log.debug("Connection opened on thread: " + thread, t); + logWriter.debug("Connection opened on thread: " + thread, t); } } return true; } + public static boolean dumpOpenConnections(@NotNull Logger log) + { + dumpOpenConnections(new SimpleLoggerWriter(log)); + + return true; + } + public static boolean dumpLeaksForThread(Thread t) { return dumpLeaksForThread(t, _logDefault); } public static boolean dumpLeaksForThread(Thread t, Logger log) + { + return dumpOpenConnections(new SimpleLoggerWriter(log)); + } + + public static boolean dumpLeaksForThread(Thread t, LoggerWriter log) { boolean leaks = false; synchronized(_openConnections) diff --git a/api/src/org/labkey/api/data/Container.java b/api/src/org/labkey/api/data/Container.java index 009a9b3812f..7042655d39a 100644 --- a/api/src/org/labkey/api/data/Container.java +++ b/api/src/org/labkey/api/data/Container.java @@ -20,7 +20,8 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import com.fasterxml.jackson.annotation.JsonProperty; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -94,7 +95,7 @@ */ public class Container implements Serializable, Comparable, SecurableResource, ContainerContext, HasPermission, Parameter.JdbcParameterValue { - private static final Logger LOG = Logger.getLogger(Container.class); + private static final Logger LOG = LogManager.getLogger(Container.class); private GUID _id; private Path _path; diff --git a/api/src/org/labkey/api/data/ContainerFilter.java b/api/src/org/labkey/api/data/ContainerFilter.java index 4fd8b800bce..10ba851fc8c 100644 --- a/api/src/org/labkey/api/data/ContainerFilter.java +++ b/api/src/org/labkey/api/data/ContainerFilter.java @@ -16,7 +16,8 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -1302,7 +1303,7 @@ public SQLFragment toSQLFragment(Map columnMap, } - static final Logger _log = Logger.getLogger(ContainerFilter.class); + static final Logger _log = LogManager.getLogger(ContainerFilter.class); // helper so that ContainerFilter logging can be traced using one logger class public static void logSetContainerFilter(ContainerFilter cf, String... parts) diff --git a/api/src/org/labkey/api/data/ContainerManager.java b/api/src/org/labkey/api/data/ContainerManager.java index eaade6b57fe..a8646430d58 100644 --- a/api/src/org/labkey/api/data/ContainerManager.java +++ b/api/src/org/labkey/api/data/ContainerManager.java @@ -19,7 +19,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -131,7 +132,7 @@ */ public class ContainerManager { - private static final Logger LOG = Logger.getLogger(ContainerManager.class); + private static final Logger LOG = LogManager.getLogger(ContainerManager.class); private static final CoreSchema CORE = CoreSchema.getInstance(); private static final String CONTAINER_PREFIX = ContainerManager.class.getName() + "/"; @@ -355,7 +356,7 @@ public static Container createContainerFromTemplate(Container parent, String nam if (folderXml instanceof FolderDocument) { FolderDocument folderDoc = (FolderDocument)folderXml; - FolderImportContext importCtx = new FolderImportContext(user, c, folderDoc, null, new StaticLoggerGetter(Logger.getLogger(FolderImporterImpl.class)), vf); + FolderImportContext importCtx = new FolderImportContext(user, c, folderDoc, null, new StaticLoggerGetter(LogManager.getLogger(FolderImporterImpl.class)), vf); FolderImporterImpl importer = new FolderImporterImpl(); importer.process(null, importCtx, vf); diff --git a/api/src/org/labkey/api/data/ContainerTable.java b/api/src/org/labkey/api/data/ContainerTable.java index 53227ca2552..8538a288d84 100644 --- a/api/src/org/labkey/api/data/ContainerTable.java +++ b/api/src/org/labkey/api/data/ContainerTable.java @@ -17,7 +17,7 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.NamedObjectList; import org.labkey.api.data.dialect.SqlDialect; @@ -287,7 +287,7 @@ public Object getValue(RenderContext ctx) { ft = FolderType.NONE; iconPath = Path.parse(ft.getFolderIconPath()); - Logger.getLogger(ContainerTable.class).warn("Could not find specified icon: "+iconPath); + LogManager.getLogger(ContainerTable.class).warn("Could not find specified icon: "+iconPath); } return AppProps.getInstance().getContextPath() + iconPath.toString("/",""); } diff --git a/api/src/org/labkey/api/data/CrosstabDataRegion.java b/api/src/org/labkey/api/data/CrosstabDataRegion.java index 60cd52e5400..93caebc9a22 100644 --- a/api/src/org/labkey/api/data/CrosstabDataRegion.java +++ b/api/src/org/labkey/api/data/CrosstabDataRegion.java @@ -16,7 +16,8 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.query.CrosstabView; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; @@ -36,7 +37,7 @@ */ public class CrosstabDataRegion extends DataRegion { - private static final Logger _log = Logger.getLogger(CrosstabDataRegion.class); + private static final Logger _log = LogManager.getLogger(CrosstabDataRegion.class); private CrosstabSettings _settings; private int _numRowAxisCols; private int _numMeasures; diff --git a/api/src/org/labkey/api/data/CrosstabMember.java b/api/src/org/labkey/api/data/CrosstabMember.java index afddc9e75fc..e3458ad04f6 100644 --- a/api/src/org/labkey/api/data/CrosstabMember.java +++ b/api/src/org/labkey/api/data/CrosstabMember.java @@ -21,8 +21,8 @@ import org.labkey.api.query.AliasManager; import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; -import org.labkey.api.view.ActionURL; import org.labkey.api.util.Pair; +import org.labkey.api.view.ActionURL; import java.util.Collections; diff --git a/api/src/org/labkey/api/data/CrosstabTable.java b/api/src/org/labkey/api/data/CrosstabTable.java index 2e21c6af684..2328d63164d 100644 --- a/api/src/org/labkey/api/data/CrosstabTable.java +++ b/api/src/org/labkey/api/data/CrosstabTable.java @@ -22,7 +22,6 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryService; -import java.sql.Types; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; diff --git a/api/src/org/labkey/api/data/DataColumn.java b/api/src/org/labkey/api/data/DataColumn.java index 0440b22262d..14f9b9b5089 100644 --- a/api/src/org/labkey/api/data/DataColumn.java +++ b/api/src/org/labkey/api/data/DataColumn.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; @@ -61,7 +62,7 @@ /** Subclass that wraps a ColumnInfo to pull values from the database */ public class DataColumn extends DisplayColumn { - private static final Logger LOG = Logger.getLogger(DataColumn.class); + private static final Logger LOG = LogManager.getLogger(DataColumn.class); private ColumnInfo _boundColumn; private ColumnInfo _displayColumn; diff --git a/api/src/org/labkey/api/data/DataRegion.java b/api/src/org/labkey/api/data/DataRegion.java index 5e2f0d0981c..07656dc9609 100644 --- a/api/src/org/labkey/api/data/DataRegion.java +++ b/api/src/org/labkey/api/data/DataRegion.java @@ -19,7 +19,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -86,7 +87,7 @@ * about buttons that might appear in the view, the columns to be shown, etc. */ public class DataRegion extends DisplayElement { - private static final Logger _log = Logger.getLogger(DataRegion.class); + private static final Logger _log = LogManager.getLogger(DataRegion.class); private String _name = null; private QuerySettings _settings = null; diff --git a/api/src/org/labkey/api/data/DatabaseCache.java b/api/src/org/labkey/api/data/DatabaseCache.java index 9279f7655e6..d2eec476d23 100644 --- a/api/src/org/labkey/api/data/DatabaseCache.java +++ b/api/src/org/labkey/api/data/DatabaseCache.java @@ -16,7 +16,7 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; diff --git a/api/src/org/labkey/api/data/DbSchema.java b/api/src/org/labkey/api/data/DbSchema.java index 7cc4ec0d078..7bda03b7140 100644 --- a/api/src/org/labkey/api/data/DbSchema.java +++ b/api/src/org/labkey/api/data/DbSchema.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -29,7 +30,6 @@ import org.labkey.api.module.ModuleLoader; import org.labkey.api.query.FieldKey; import org.labkey.api.query.TableSorter; -import org.labkey.api.resource.Resource; import org.labkey.api.security.SecurityPolicyManager; import org.labkey.api.security.User; import org.labkey.api.test.TestTimeout; @@ -58,7 +58,7 @@ public class DbSchema { - private static final Logger _log = Logger.getLogger(DbSchema.class); + private static final Logger _log = LogManager.getLogger(DbSchema.class); public static final String TEMP_SCHEMA_NAME = "temp"; diff --git a/api/src/org/labkey/api/data/DbSchemaCache.java b/api/src/org/labkey/api/data/DbSchemaCache.java index b1d31cf2709..3ae662b933e 100644 --- a/api/src/org/labkey/api/data/DbSchemaCache.java +++ b/api/src/org/labkey/api/data/DbSchemaCache.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.cache.BlockingCache; import org.labkey.api.cache.Cache; @@ -34,7 +35,7 @@ // Every scope has its own cache of DbSchemas public class DbSchemaCache { - private static final Logger LOG = Logger.getLogger(DbSchemaCache.class); + private static final Logger LOG = LogManager.getLogger(DbSchemaCache.class); private final DbScope _scope; private final BlockingCache _cache; diff --git a/api/src/org/labkey/api/data/DbScope.java b/api/src/org/labkey/api/data/DbScope.java index 1a201fd16aa..d4cc38beb57 100644 --- a/api/src/org/labkey/api/data/DbScope.java +++ b/api/src/org/labkey/api/data/DbScope.java @@ -18,8 +18,9 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import org.apache.commons.collections4.IteratorUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -40,7 +41,9 @@ import org.labkey.api.test.TestWhen; import org.labkey.api.util.ConfigurationException; import org.labkey.api.util.GUID; +import org.labkey.api.util.LoggerWriter; import org.labkey.api.util.MemTracker; +import org.labkey.api.util.SimpleLoggerWriter; import org.labkey.api.util.TestContext; import org.labkey.api.util.UnexpectedException; import org.labkey.data.xml.TablesDocument; @@ -111,7 +114,7 @@ */ public class DbScope { - private static final Logger LOG = Logger.getLogger(DbScope.class); + private static final Logger LOG = LogManager.getLogger(DbScope.class); private static final ConnectionMap _initializedConnections = newConnectionMap(); private static final Map _scopes = new LinkedHashMap<>(); private static final Map _sharedConnections = new WeakHashMap<>(); @@ -977,7 +980,7 @@ public void logCurrentConnectionState() logCurrentConnectionState(LOG); } - public void logCurrentConnectionState(@NotNull Logger log) + public void logCurrentConnectionState(LoggerWriter log) { synchronized (_transaction) { @@ -1014,6 +1017,12 @@ public void logCurrentConnectionState(@NotNull Logger log) } } + public void logCurrentConnectionState(@NotNull Logger log) + { + logCurrentConnectionState(new SimpleLoggerWriter(log)); + } + + private static final int spidUnknown = -1; protected ConnectionWrapper getPooledConnection(ConnectionType type, @Nullable Logger log) throws SQLException diff --git a/api/src/org/labkey/api/data/DbSequenceManager.java b/api/src/org/labkey/api/data/DbSequenceManager.java index 5d18bc82b62..5b9437affbf 100644 --- a/api/src/org/labkey/api/data/DbSequenceManager.java +++ b/api/src/org/labkey/api/data/DbSequenceManager.java @@ -15,7 +15,7 @@ */ package org.labkey.api.data; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.jetbrains.annotations.Nullable; import org.junit.After; import org.junit.Assert; diff --git a/api/src/org/labkey/api/data/DisplayColumn.java b/api/src/org/labkey/api/data/DisplayColumn.java index 01871d1ff1c..eb52a3284d2 100644 --- a/api/src/org/labkey/api/data/DisplayColumn.java +++ b/api/src/org/labkey/api/data/DisplayColumn.java @@ -20,7 +20,8 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.FastDateFormat; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.HasViewContext; @@ -59,7 +60,7 @@ */ public abstract class DisplayColumn extends RenderColumn { - private static final Logger LOG = Logger.getLogger(DisplayColumn.class); + private static final Logger LOG = LogManager.getLogger(DisplayColumn.class); protected String _textAlign = null; protected boolean _nowrap = false; diff --git a/api/src/org/labkey/api/data/DisplayColumnGroup.java b/api/src/org/labkey/api/data/DisplayColumnGroup.java index ec5e7d4b2ab..970543d8e6a 100644 --- a/api/src/org/labkey/api/data/DisplayColumnGroup.java +++ b/api/src/org/labkey/api/data/DisplayColumnGroup.java @@ -16,9 +16,9 @@ package org.labkey.api.data; -import java.util.List; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; +import java.util.List; /** * User: jeckels diff --git a/api/src/org/labkey/api/data/ExcelColumn.java b/api/src/org/labkey/api/data/ExcelColumn.java index b380cc840a0..920bed0b3ad 100644 --- a/api/src/org/labkey/api/data/ExcelColumn.java +++ b/api/src/org/labkey/api/data/ExcelColumn.java @@ -19,7 +19,8 @@ import jxl.format.Colour; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.time.FastDateFormat; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.poi.hssf.usermodel.HSSFClientAnchor; import org.apache.poi.hssf.usermodel.HSSFPicture; import org.apache.poi.ss.usermodel.Cell; @@ -90,7 +91,7 @@ public class ExcelColumn extends RenderColumn { - private static Logger _log = Logger.getLogger(ExcelColumn.class); + private static Logger _log = LogManager.getLogger(ExcelColumn.class); private static final int TYPE_UNKNOWN = 0; private static final int TYPE_INT = 1; diff --git a/api/src/org/labkey/api/data/FileSqlScriptProvider.java b/api/src/org/labkey/api/data/FileSqlScriptProvider.java index d0a906c1b8d..d18c8ccb148 100644 --- a/api/src/org/labkey/api/data/FileSqlScriptProvider.java +++ b/api/src/org/labkey/api/data/FileSqlScriptProvider.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.ComparatorUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.SqlScriptRunner.SqlScript; @@ -62,7 +63,7 @@ */ public class FileSqlScriptProvider implements SqlScriptProvider { - private static final Logger _log = Logger.getLogger(FileSqlScriptProvider.class); + private static final Logger _log = LogManager.getLogger(FileSqlScriptProvider.class); private final Module _module; diff --git a/api/src/org/labkey/api/data/Filter.java b/api/src/org/labkey/api/data/Filter.java index 81c6f4522f2..2add7ea335e 100644 --- a/api/src/org/labkey/api/data/Filter.java +++ b/api/src/org/labkey/api/data/Filter.java @@ -20,9 +20,9 @@ import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.query.FieldKey; -import java.util.Set; -import java.util.Map; import java.util.List; +import java.util.Map; +import java.util.Set; /** * Knows how to generate a WHERE clause to filter a query based on some set of criteria. Used extensively, often diff --git a/api/src/org/labkey/api/data/FilterInfo.java b/api/src/org/labkey/api/data/FilterInfo.java index 0c25960d536..eb68f42a8db 100644 --- a/api/src/org/labkey/api/data/FilterInfo.java +++ b/api/src/org/labkey/api/data/FilterInfo.java @@ -16,7 +16,6 @@ package org.labkey.api.data; -import org.json.JSONObject; import org.labkey.api.query.FieldKey; import org.labkey.api.util.URLHelper; diff --git a/api/src/org/labkey/api/data/GroupTableInfo.java b/api/src/org/labkey/api/data/GroupTableInfo.java index 738bdd7b970..f35040eb890 100644 --- a/api/src/org/labkey/api/data/GroupTableInfo.java +++ b/api/src/org/labkey/api/data/GroupTableInfo.java @@ -19,7 +19,11 @@ import org.labkey.api.query.ExprColumn; import org.labkey.api.query.QueryService; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashSet; +import java.util.List; +import java.util.Set; /** * Allows group-by queries over source TableInfos, with optional aggregates diff --git a/api/src/org/labkey/api/data/HighlightingDisplayColumn.java b/api/src/org/labkey/api/data/HighlightingDisplayColumn.java index 40528d4fb48..b12b216faeb 100644 --- a/api/src/org/labkey/api/data/HighlightingDisplayColumn.java +++ b/api/src/org/labkey/api/data/HighlightingDisplayColumn.java @@ -21,7 +21,6 @@ import java.io.IOException; import java.io.Writer; -import java.sql.SQLException; import java.util.ArrayList; import java.util.LinkedHashMap; import java.util.List; diff --git a/api/src/org/labkey/api/data/HtmlWriter.java b/api/src/org/labkey/api/data/HtmlWriter.java index d9e13da7a50..321131c1471 100644 --- a/api/src/org/labkey/api/data/HtmlWriter.java +++ b/api/src/org/labkey/api/data/HtmlWriter.java @@ -15,9 +15,9 @@ */ package org.labkey.api.data; +import org.labkey.api.collections.ResultSetRowMapFactory; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.ResultSetUtil; -import org.labkey.api.collections.ResultSetRowMapFactory; import javax.servlet.http.HttpServletResponse; import java.io.IOException; diff --git a/api/src/org/labkey/api/data/IndexInfo.java b/api/src/org/labkey/api/data/IndexInfo.java index 7976297e8fd..7d349833443 100644 --- a/api/src/org/labkey/api/data/IndexInfo.java +++ b/api/src/org/labkey/api/data/IndexInfo.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import java.util.Collections; import java.util.List; @@ -27,7 +28,7 @@ public class IndexInfo { - private static final Logger _log = Logger.getLogger(IndexInfo.class); + private static final Logger _log = LogManager.getLogger(IndexInfo.class); private TableInfo.IndexType _type; diff --git a/api/src/org/labkey/api/data/JdbcCommand.java b/api/src/org/labkey/api/data/JdbcCommand.java index 131e0f3545b..7fcd8c20632 100644 --- a/api/src/org/labkey/api/data/JdbcCommand.java +++ b/api/src/org/labkey/api/data/JdbcCommand.java @@ -15,8 +15,9 @@ */ package org.labkey.api.data; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -31,7 +32,7 @@ */ public abstract class JdbcCommand { - private static final Logger LOG = Logger.getLogger(JdbcCommand.class); + private static final Logger LOG = LogManager.getLogger(JdbcCommand.class); private final @NotNull DbScope _scope; protected final @Nullable Connection _conn; diff --git a/api/src/org/labkey/api/data/JsonTest.java b/api/src/org/labkey/api/data/JsonTest.java index 3ae26fafaab..1d8281f7324 100644 --- a/api/src/org/labkey/api/data/JsonTest.java +++ b/api/src/org/labkey/api/data/JsonTest.java @@ -18,17 +18,14 @@ import com.fasterxml.jackson.annotation.JsonAutoDetect; import com.fasterxml.jackson.annotation.PropertyAccessor; import com.fasterxml.jackson.databind.ObjectMapper; -import com.fasterxml.jackson.datatype.jsonorg.JsonOrgModule; import org.json.JSONArray; import org.json.JSONObject; import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.labkey.api.util.DateUtil; import org.labkey.api.util.JsonUtil; import java.io.IOException; -import java.text.SimpleDateFormat; import java.util.Arrays; import java.util.Collections; import java.util.Date; diff --git a/api/src/org/labkey/api/data/MultiValuedDisplayColumn.java b/api/src/org/labkey/api/data/MultiValuedDisplayColumn.java index 692e3508ddd..efe018ca5b7 100644 --- a/api/src/org/labkey/api/data/MultiValuedDisplayColumn.java +++ b/api/src/org/labkey/api/data/MultiValuedDisplayColumn.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.query.FieldKey; import java.io.IOException; @@ -36,7 +37,7 @@ */ public class MultiValuedDisplayColumn extends DisplayColumnDecorator implements IMultiValuedDisplayColumn { - private static final Logger LOG = Logger.getLogger(MultiValuedDisplayColumn.class); + private static final Logger LOG = LogManager.getLogger(MultiValuedDisplayColumn.class); private final Set _fieldKeys = new HashSet<>(); private final Set _additionalFieldKeys = new HashSet<>(); diff --git a/api/src/org/labkey/api/data/MultiValuedRenderContext.java b/api/src/org/labkey/api/data/MultiValuedRenderContext.java index 91c510cc0d8..3529ef8b9fb 100644 --- a/api/src/org/labkey/api/data/MultiValuedRenderContext.java +++ b/api/src/org/labkey/api/data/MultiValuedRenderContext.java @@ -15,9 +15,9 @@ */ package org.labkey.api.data; +import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.collections4.iterators.ArrayIterator; import org.junit.Assert; -import org.apache.commons.beanutils.ConvertUtils; import org.junit.Test; import org.labkey.api.query.FieldKey; diff --git a/api/src/org/labkey/api/data/NestableDataRegion.java b/api/src/org/labkey/api/data/NestableDataRegion.java index b156b251a1d..72e597fe14f 100644 --- a/api/src/org/labkey/api/data/NestableDataRegion.java +++ b/api/src/org/labkey/api/data/NestableDataRegion.java @@ -19,10 +19,10 @@ import org.labkey.api.query.AbstractNestableDataRegion; import org.labkey.api.query.QuerySettings; -import java.io.Writer; import java.io.IOException; -import java.sql.SQLException; +import java.io.Writer; import java.sql.ResultSet; +import java.sql.SQLException; import java.util.List; import java.util.Objects; diff --git a/api/src/org/labkey/api/data/NestedRenderContext.java b/api/src/org/labkey/api/data/NestedRenderContext.java index ba1ebae4b71..6d51e4318b0 100644 --- a/api/src/org/labkey/api/data/NestedRenderContext.java +++ b/api/src/org/labkey/api/data/NestedRenderContext.java @@ -21,8 +21,8 @@ import org.labkey.api.query.QueryNestingOption; import org.labkey.api.query.QueryService; import org.labkey.api.query.QuerySettings; -import org.labkey.api.view.ViewContext; import org.labkey.api.view.ActionURL; +import org.labkey.api.view.ViewContext; import java.io.IOException; import java.sql.SQLException; diff --git a/api/src/org/labkey/api/data/OORDisplayColumnFactory.java b/api/src/org/labkey/api/data/OORDisplayColumnFactory.java index 0ba3b2abd4c..5ea022ef849 100644 --- a/api/src/org/labkey/api/data/OORDisplayColumnFactory.java +++ b/api/src/org/labkey/api/data/OORDisplayColumnFactory.java @@ -16,9 +16,9 @@ package org.labkey.api.data; -import org.labkey.api.query.FilteredTable; -import org.labkey.api.query.ExprColumn; import org.labkey.api.query.AliasedColumn; +import org.labkey.api.query.ExprColumn; +import org.labkey.api.query.FilteredTable; /** * Factory for creating {@link OutOfRangeDisplayColumn}s. Connects the separate indicator and raw value columns together. diff --git a/api/src/org/labkey/api/data/ObjectFactory.java b/api/src/org/labkey/api/data/ObjectFactory.java index ab105e6cfad..ce681c9fea0 100644 --- a/api/src/org/labkey/api/data/ObjectFactory.java +++ b/api/src/org/labkey/api/data/ObjectFactory.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.BoundMap; @@ -49,7 +50,7 @@ public interface ObjectFactory public static class Registry { - private static final Logger _log = Logger.getLogger(Registry.class); + private static final Logger _log = LogManager.getLogger(Registry.class); private static final Map _registry = new ConcurrentHashMap<>(64); public static void register(Class clss, ObjectFactory f) diff --git a/api/src/org/labkey/api/data/PanelButton.java b/api/src/org/labkey/api/data/PanelButton.java index a74c6a6f496..efffd280b0c 100644 --- a/api/src/org/labkey/api/data/PanelButton.java +++ b/api/src/org/labkey/api/data/PanelButton.java @@ -19,8 +19,8 @@ import org.labkey.api.util.UnexpectedException; import org.labkey.api.view.HttpView; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.Map; diff --git a/api/src/org/labkey/api/data/Parameter.java b/api/src/org/labkey/api/data/Parameter.java index 4496f2fbfb8..3f9ef9df404 100644 --- a/api/src/org/labkey/api/data/Parameter.java +++ b/api/src/org/labkey/api/data/Parameter.java @@ -17,7 +17,8 @@ package org.labkey.api.data; import com.google.common.primitives.Ints; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentFile; @@ -53,7 +54,7 @@ public class Parameter implements AutoCloseable { - static Logger LOG = Logger.getLogger(Parameter.class); + static Logger LOG = LogManager.getLogger(Parameter.class); public interface JdbcParameterValue { diff --git a/api/src/org/labkey/api/data/ParameterMapStatement.java b/api/src/org/labkey/api/data/ParameterMapStatement.java index 5c4ec9c6aba..c00966e42a2 100644 --- a/api/src/org/labkey/api/data/ParameterMapStatement.java +++ b/api/src/org/labkey/api/data/ParameterMapStatement.java @@ -1,6 +1,6 @@ package org.labkey.api.data; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.jetbrains.annotations.Nullable; import org.labkey.api.arrays.IntegerArray; import org.labkey.api.collections.CaseInsensitiveHashMap; diff --git a/api/src/org/labkey/api/data/PropertyManager.java b/api/src/org/labkey/api/data/PropertyManager.java index 48d9ec47d2a..20adfac99e5 100644 --- a/api/src/org/labkey/api/data/PropertyManager.java +++ b/api/src/org/labkey/api/data/PropertyManager.java @@ -17,7 +17,8 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -52,7 +53,7 @@ public class PropertyManager { public static final User SHARED_USER = User.guest; // Shared properties are saved with the guest user - private static final Logger _log = Logger.getLogger(PropertyManager.class); + private static final Logger _log = LogManager.getLogger(PropertyManager.class); private static final PropertySchema prop = PropertySchema.getInstance(); private static final NormalPropertyStore STORE = new NormalPropertyStore(); private static final EncryptedPropertyStore ENCRYPTED_STORE = new EncryptedPropertyStore(); diff --git a/api/src/org/labkey/api/data/RemapCache.java b/api/src/org/labkey/api/data/RemapCache.java index 476f164bcbd..22f0432b13d 100644 --- a/api/src/org/labkey/api/data/RemapCache.java +++ b/api/src/org/labkey/api/data/RemapCache.java @@ -16,7 +16,6 @@ package org.labkey.api.data; import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; import org.labkey.api.dataiterator.SimpleTranslator; import org.labkey.api.query.QueryService; import org.labkey.api.query.SchemaKey; diff --git a/api/src/org/labkey/api/data/RenderContext.java b/api/src/org/labkey/api/data/RenderContext.java index ac8691827c9..3927856632a 100644 --- a/api/src/org/labkey/api/data/RenderContext.java +++ b/api/src/org/labkey/api/data/RenderContext.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.LabKeyError; @@ -43,7 +44,6 @@ import java.util.ArrayList; import java.util.Collection; import java.util.Collections; -import java.util.Comparator; import java.util.HashMap; import java.util.HashSet; import java.util.LinkedHashSet; @@ -54,7 +54,7 @@ public class RenderContext implements Map, Serializable { - private static final Logger _log = Logger.getLogger(RenderContext.class); + private static final Logger _log = LogManager.getLogger(RenderContext.class); private boolean _useContainerFilter = true; private ViewContext _viewContext; diff --git a/api/src/org/labkey/api/data/ReportingWriter.java b/api/src/org/labkey/api/data/ReportingWriter.java index 21ca24d2703..e52d235a307 100644 --- a/api/src/org/labkey/api/data/ReportingWriter.java +++ b/api/src/org/labkey/api/data/ReportingWriter.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.exp.PropertyType; import org.labkey.api.gwt.client.DefaultScaleType; @@ -41,7 +42,7 @@ */ public class ReportingWriter { - private static final Logger LOG = Logger.getLogger(ReportingWriter.class); + private static final Logger LOG = LogManager.getLogger(ReportingWriter.class); public static Map getMetaData(DisplayColumn dc, boolean useFriendlyAsType, boolean includeLookup, boolean includeDomainFormat) { diff --git a/api/src/org/labkey/api/data/ResultSetImpl.java b/api/src/org/labkey/api/data/ResultSetImpl.java index 8fc6acd282e..e8f3bddee0d 100644 --- a/api/src/org/labkey/api/data/ResultSetImpl.java +++ b/api/src/org/labkey/api/data/ResultSetImpl.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.miniprofiler.MiniProfiler; @@ -24,7 +25,6 @@ import org.labkey.api.util.MemTracker; import org.labkey.api.util.ResultSetUtil; -import javax.sql.rowset.CachedRowSet; import java.sql.Connection; import java.sql.ResultSet; import java.sql.SQLException; @@ -38,7 +38,7 @@ */ public class ResultSetImpl extends LoggingResultSetWrapper implements TableResultSet { - private static final Logger _log = Logger.getLogger(ResultSetImpl.class); + private static final Logger _log = LogManager.getLogger(ResultSetImpl.class); private final @Nullable DbScope _scope; private final @Nullable Connection _connection; diff --git a/api/src/org/labkey/api/data/ResultSetWrapper.java b/api/src/org/labkey/api/data/ResultSetWrapper.java index 7a7a987ffd0..519496a380d 100644 --- a/api/src/org/labkey/api/data/ResultSetWrapper.java +++ b/api/src/org/labkey/api/data/ResultSetWrapper.java @@ -22,10 +22,21 @@ import java.io.Reader; import java.math.BigDecimal; import java.net.URL; -import java.sql.*; -import java.sql.SQLXML; -import java.sql.RowId; +import java.sql.Array; +import java.sql.Blob; +import java.sql.Clob; +import java.sql.Date; import java.sql.NClob; +import java.sql.Ref; +import java.sql.ResultSet; +import java.sql.ResultSetMetaData; +import java.sql.RowId; +import java.sql.SQLException; +import java.sql.SQLWarning; +import java.sql.SQLXML; +import java.sql.Statement; +import java.sql.Time; +import java.sql.Timestamp; import java.util.Calendar; import java.util.Map; diff --git a/api/src/org/labkey/api/data/SchemaColumnMetaData.java b/api/src/org/labkey/api/data/SchemaColumnMetaData.java index 667d960e739..0d4659d595d 100644 --- a/api/src/org/labkey/api/data/SchemaColumnMetaData.java +++ b/api/src/org/labkey/api/data/SchemaColumnMetaData.java @@ -17,7 +17,8 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.dialect.JdbcMetaDataLocator; @@ -57,7 +58,7 @@ public class SchemaColumnMetaData private boolean _hasDefaultTitleColumn = true; private Map>> _uniqueIndices; private Map>> _allIndices; - private static Logger _log = Logger.getLogger(SchemaColumnMetaData.class); + private static Logger _log = LogManager.getLogger(SchemaColumnMetaData.class); SchemaColumnMetaData(SchemaTableInfo tinfo, boolean load) throws SQLException { diff --git a/api/src/org/labkey/api/data/SchemaTableInfoCache.java b/api/src/org/labkey/api/data/SchemaTableInfoCache.java index 0b234e1fb10..8129fe8a4d0 100644 --- a/api/src/org/labkey/api/data/SchemaTableInfoCache.java +++ b/api/src/org/labkey/api/data/SchemaTableInfoCache.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.cache.BlockingCache; import org.labkey.api.cache.Cache; @@ -33,7 +34,7 @@ */ public class SchemaTableInfoCache { - private static final Logger LOG = Logger.getLogger(SchemaTableInfoCache.class); + private static final Logger LOG = LogManager.getLogger(SchemaTableInfoCache.class); private final BlockingCache _blockingCache; diff --git a/api/src/org/labkey/api/data/SimpleDisplayColumn.java b/api/src/org/labkey/api/data/SimpleDisplayColumn.java index 5bb6ad50e13..8a46619a5f2 100644 --- a/api/src/org/labkey/api/data/SimpleDisplayColumn.java +++ b/api/src/org/labkey/api/data/SimpleDisplayColumn.java @@ -16,15 +16,15 @@ package org.labkey.api.data; -import org.labkey.api.util.StringExpressionFactory; +import org.labkey.api.query.FieldKey; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.StringExpression; -import org.labkey.api.query.FieldKey; +import org.labkey.api.util.StringExpressionFactory; import java.io.IOException; import java.io.Writer; -import java.util.Set; import java.util.HashSet; +import java.util.Set; /** * {@link DisplayColumn} implementation that typically doesn't render the value from a column in the query diff --git a/api/src/org/labkey/api/data/Sort.java b/api/src/org/labkey/api/data/Sort.java index 85271ba7120..03bff9dcf6a 100644 --- a/api/src/org/labkey/api/data/Sort.java +++ b/api/src/org/labkey/api/data/Sort.java @@ -28,7 +28,6 @@ import java.util.HashSet; import java.util.List; import java.util.Map; -import java.util.Objects; import java.util.Set; import java.util.stream.Collectors; diff --git a/api/src/org/labkey/api/data/SqlExecutingSelector.java b/api/src/org/labkey/api/data/SqlExecutingSelector.java index ee3b77cd2e1..a74e9984576 100644 --- a/api/src/org/labkey/api/data/SqlExecutingSelector.java +++ b/api/src/org/labkey/api/data/SqlExecutingSelector.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.dialect.SqlDialect; @@ -48,7 +49,7 @@ public abstract class SqlExecutingSelector _remainingScripts = new ArrayList<>(); private static final Object SCRIPT_LOCK = new Object(); diff --git a/api/src/org/labkey/api/data/StatementUtils.java b/api/src/org/labkey/api/data/StatementUtils.java index c746e31427a..e4fa028ff8b 100644 --- a/api/src/org/labkey/api/data/StatementUtils.java +++ b/api/src/org/labkey/api/data/StatementUtils.java @@ -16,7 +16,8 @@ package org.labkey.api.data; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -63,7 +64,7 @@ // identify tests that exercise the code paths that will be changed. public class StatementUtils { - private static final Logger _log = Logger.getLogger(StatementUtils.class); + private static final Logger _log = LogManager.getLogger(StatementUtils.class); public enum Operation {insert, update, merge} public static String OWNEROBJECTID = "exp$object$ownerobjectid"; diff --git a/api/src/org/labkey/api/data/StringWrapperDynaClass.java b/api/src/org/labkey/api/data/StringWrapperDynaClass.java index a6883683453..e8d426aafcd 100644 --- a/api/src/org/labkey/api/data/StringWrapperDynaClass.java +++ b/api/src/org/labkey/api/data/StringWrapperDynaClass.java @@ -16,14 +16,14 @@ package org.labkey.api.data; -import java.util.ArrayList; -import java.util.Map; -import java.util.Set; - import org.apache.commons.beanutils.DynaClass; import org.apache.commons.beanutils.DynaProperty; import org.labkey.api.collections.CaseInsensitiveHashMap; +import java.util.ArrayList; +import java.util.Map; +import java.util.Set; + public abstract class StringWrapperDynaClass implements DynaClass { protected DynaProperty[] _dynaProps; diff --git a/api/src/org/labkey/api/data/Table.java b/api/src/org/labkey/api/data/Table.java index cd3b1f707f1..63ed3f0f9ad 100644 --- a/api/src/org/labkey/api/data/Table.java +++ b/api/src/org/labkey/api/data/Table.java @@ -19,8 +19,9 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -87,7 +88,7 @@ public class Table public static final int ERROR_DELETED = 10002; public static final int ERROR_TABLEDELETED = 10003; - private static final Logger _log = Logger.getLogger(Table.class); + private static final Logger _log = LogManager.getLogger(Table.class); // Return all rows instead of limiting to the top n public static final int ALL_ROWS = -1; @@ -442,7 +443,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S if (RuntimeSQLException.isConstraintException(e) && (StringUtils.startsWithIgnoreCase(trim, "INSERT") || StringUtils.startsWithIgnoreCase(trim, "UPDATE"))) { // Log this ConstraintException if log Level is WARN (the default) or lower. Skip logging for callers that request just ERRORs. - if (Level.WARN.isGreaterOrEqual(logLevel)) + if (Level.WARN.intLevel() >= logLevel.intLevel()) { _log.warn("SQL Exception", e); _logQuery(Level.WARN, sql, conn); @@ -451,7 +452,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S else { // Log this SQLException if log level is ERROR or lower. - if (Level.ERROR.isGreaterOrEqual(logLevel)) + if (Level.ERROR.intLevel() >= logLevel.intLevel()) { _log.error("SQL Exception", e); _logQuery(Level.ERROR, sql, conn); @@ -1101,7 +1102,7 @@ public static void notifyTableUpdate(/*String operation,*/ TableInfo table/*, Co private static void _logQuery(Level level, @Nullable SQLFragment sqlFragment, @Nullable Connection conn) { - if (!_log.isEnabledFor(level) || null == sqlFragment) + if (!_log.isEnabled(level) || null == sqlFragment) return; String sql = sqlFragment.getSQL(); diff --git a/api/src/org/labkey/api/data/TableChange.java b/api/src/org/labkey/api/data/TableChange.java index 41895a10bf4..7ee26a2896b 100644 --- a/api/src/org/labkey/api/data/TableChange.java +++ b/api/src/org/labkey/api/data/TableChange.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.PropertyStorageSpec.Index; import org.labkey.api.exp.PropertyDescriptor; @@ -43,7 +44,7 @@ */ public class TableChange { - private static final Logger LOG = Logger.getLogger(TableChange.class); + private static final Logger LOG = LogManager.getLogger(TableChange.class); private final ChangeType _type; private final String _schemaName; diff --git a/api/src/org/labkey/api/data/TableSelector.java b/api/src/org/labkey/api/data/TableSelector.java index fdcdd2b084e..62925fa4991 100644 --- a/api/src/org/labkey/api/data/TableSelector.java +++ b/api/src/org/labkey/api/data/TableSelector.java @@ -17,7 +17,8 @@ package org.labkey.api.data; import org.apache.commons.collections4.MultiValuedMap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -46,7 +47,7 @@ public class TableSelector extends SqlExecutingSelector ALL_COLUMNS = Collections.unmodifiableSet(Collections.emptySet()); - private static final Logger LOG = Logger.getLogger(TableSelector.class); + private static final Logger LOG = LogManager.getLogger(TableSelector.class); private final TableInfo _table; private final Collection _columns; @@ -424,7 +425,7 @@ public Map> getAggregates(final List aggregates) // Issue 17536: Issue a warning instead of blowing up if there is no result row containing the aggregate values. if (!rs.next()) { - Logger.getLogger(TableSelector.class).warn("Expected a non-empty resultset from aggregate query."); + LogManager.getLogger(TableSelector.class).warn("Expected a non-empty resultset from aggregate query."); } else { diff --git a/api/src/org/labkey/api/data/TableSelectorTestCase.java b/api/src/org/labkey/api/data/TableSelectorTestCase.java index 76c1c8ba3de..3b149a4dcd3 100644 --- a/api/src/org/labkey/api/data/TableSelectorTestCase.java +++ b/api/src/org/labkey/api/data/TableSelectorTestCase.java @@ -16,7 +16,7 @@ package org.labkey.api.data; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.junit.Test; import org.labkey.api.collections.CsvSet; import org.labkey.api.data.Selector.ForEachBlock; diff --git a/api/src/org/labkey/api/data/TableViewForm.java b/api/src/org/labkey/api/data/TableViewForm.java index 091f4999bf8..46149aa9e06 100644 --- a/api/src/org/labkey/api/data/TableViewForm.java +++ b/api/src/org/labkey/api/data/TableViewForm.java @@ -23,7 +23,8 @@ import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.collections4.IteratorUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.BaseViewAction; @@ -70,7 +71,7 @@ */ public class TableViewForm extends ViewForm implements DynaBean, HasBindParameters { - private static final Logger _log = Logger.getLogger(TableViewForm.class); + private static final Logger _log = LogManager.getLogger(TableViewForm.class); protected Map _stringValues = new CaseInsensitiveHashMap<>(); protected Map _values = null; diff --git a/api/src/org/labkey/api/data/TempTableTracker.java b/api/src/org/labkey/api/data/TempTableTracker.java index 2d368d259d8..d201df1fb39 100644 --- a/api/src/org/labkey/api/data/TempTableTracker.java +++ b/api/src/org/labkey/api/data/TempTableTracker.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.cache.CacheManager; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.util.FileUtil; @@ -40,7 +41,7 @@ */ public class TempTableTracker extends WeakReference { - private static final Logger _log = Logger.getLogger(TempTableTracker.class); + private static final Logger _log = LogManager.getLogger(TempTableTracker.class); private static final String LOGFILE = "CPAS_sqlTempTables.log"; private static final Map createdTableNames = new TreeMap<>(); private static final ReferenceQueue cleanupQueue = new ReferenceQueue<>(); diff --git a/api/src/org/labkey/api/data/TextWriter.java b/api/src/org/labkey/api/data/TextWriter.java index 1e50f1652ae..c2104a2a02e 100644 --- a/api/src/org/labkey/api/data/TextWriter.java +++ b/api/src/org/labkey/api/data/TextWriter.java @@ -16,7 +16,8 @@ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.writer.PrintWriters; @@ -34,7 +35,7 @@ */ public abstract class TextWriter implements AutoCloseable { - private static final Logger LOG = Logger.getLogger(TextWriter.class); + private static final Logger LOG = LogManager.getLogger(TextWriter.class); // Stashing the OutputStream and the PrintWriter allows multiple writes (e.g., Export Runs to TSV) // TODO: Would be nice to remove this diff --git a/api/src/org/labkey/api/data/Transient.java b/api/src/org/labkey/api/data/Transient.java index 4dc5c77aa27..ab7ba2b9a9b 100644 --- a/api/src/org/labkey/api/data/Transient.java +++ b/api/src/org/labkey/api/data/Transient.java @@ -1,22 +1,21 @@ -/* - * Copyright (c) 2012 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2012 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.data; import java.lang.annotation.ElementType; -import java.lang.annotation.Inherited; import java.lang.annotation.Retention; import java.lang.annotation.RetentionPolicy; import java.lang.annotation.Target; diff --git a/api/src/org/labkey/api/data/UnionContainerFilter.java b/api/src/org/labkey/api/data/UnionContainerFilter.java index ee4c2666db6..73845e49c03 100644 --- a/api/src/org/labkey/api/data/UnionContainerFilter.java +++ b/api/src/org/labkey/api/data/UnionContainerFilter.java @@ -16,10 +16,8 @@ package org.labkey.api.data; import org.jetbrains.annotations.Nullable; -import org.labkey.api.query.FieldKey; import org.labkey.api.util.GUID; -import java.util.Arrays; import java.util.Collection; import java.util.HashSet; import java.util.Set; diff --git a/api/src/org/labkey/api/data/UpgradeUtils.java b/api/src/org/labkey/api/data/UpgradeUtils.java index 8baf47d1323..e2e21df5f6f 100644 --- a/api/src/org/labkey/api/data/UpgradeUtils.java +++ b/api/src/org/labkey/api/data/UpgradeUtils.java @@ -16,8 +16,9 @@ package org.labkey.api.data; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.query.FieldKey; @@ -39,7 +40,7 @@ */ public class UpgradeUtils { - private static final Logger LOG = Logger.getLogger(UpgradeUtils.class); + private static final Logger LOG = LogManager.getLogger(UpgradeUtils.class); /** * Uniquifies values in a column, making it possible to add a UNIQUE CONSTRAINT/INDEX OR change a case-sensitive diff --git a/api/src/org/labkey/api/data/UrlColumn.java b/api/src/org/labkey/api/data/UrlColumn.java index 33cbe59806c..1d532fc43a8 100644 --- a/api/src/org/labkey/api/data/UrlColumn.java +++ b/api/src/org/labkey/api/data/UrlColumn.java @@ -21,8 +21,6 @@ import java.io.IOException; import java.io.Writer; -import java.util.Collections; -import java.util.Map; /** Column that renders a link (either fixed or dynamic) with fixed text */ public class UrlColumn extends SimpleDisplayColumn diff --git a/api/src/org/labkey/api/data/UserSchemaCustomizer.java b/api/src/org/labkey/api/data/UserSchemaCustomizer.java index 3717ef4a041..adcd4b912c8 100644 --- a/api/src/org/labkey/api/data/UserSchemaCustomizer.java +++ b/api/src/org/labkey/api/data/UserSchemaCustomizer.java @@ -15,7 +15,7 @@ */ package org.labkey.api.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.query.QueryDefinition; import org.labkey.api.query.UserSchema; import org.labkey.api.util.MinorConfigurationException; @@ -71,7 +71,7 @@ public static UserSchemaCustomizer create(SchemaCustomizerType xmlSchemaCustomiz Class c = Class.forName(className); if (!(UserSchemaCustomizer.class.isAssignableFrom(c))) { - Logger.getLogger(UserSchemaCustomizer.class).warn("Class '" + c.getName() + "' is not an implementation of " + UserSchemaCustomizer.class.getName()); + LogManager.getLogger(UserSchemaCustomizer.class).warn("Class '" + c.getName() + "' is not an implementation of " + UserSchemaCustomizer.class.getName()); } else { @@ -83,7 +83,7 @@ public static UserSchemaCustomizer create(SchemaCustomizerType xmlSchemaCustomiz } catch (ClassNotFoundException | InstantiationException | IllegalAccessException e) { - Logger.getLogger(UserSchemaCustomizer.class).warn(e.toString()); + LogManager.getLogger(UserSchemaCustomizer.class).warn(e.toString()); } return null; diff --git a/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java b/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java index a6791338426..606a6aeaa8b 100644 --- a/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java +++ b/api/src/org/labkey/api/data/bigiron/AbstractClrInstallationManager.java @@ -15,8 +15,9 @@ */ package org.labkey.api.data.bigiron; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ContainerManager; @@ -55,7 +56,7 @@ */ public abstract class AbstractClrInstallationManager { - private static final Logger LOG = Logger.getLogger(AbstractClrInstallationManager.class); + private static final Logger LOG = LogManager.getLogger(AbstractClrInstallationManager.class); @Nullable private String _installedVersion = null; diff --git a/api/src/org/labkey/api/data/dialect/DatabaseMaintenanceTask.java b/api/src/org/labkey/api/data/dialect/DatabaseMaintenanceTask.java index d22db0e093d..d0d27b68a0e 100644 --- a/api/src/org/labkey/api/data/dialect/DatabaseMaintenanceTask.java +++ b/api/src/org/labkey/api/data/dialect/DatabaseMaintenanceTask.java @@ -16,7 +16,7 @@ package org.labkey.api.data.dialect; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.DbScope; import org.labkey.api.data.SqlExecutor; import org.labkey.api.util.ConfigurationException; diff --git a/api/src/org/labkey/api/data/dialect/KeywordCandidates.java b/api/src/org/labkey/api/data/dialect/KeywordCandidates.java index cfb79ef71d3..2ac3e0b257f 100644 --- a/api/src/org/labkey/api/data/dialect/KeywordCandidates.java +++ b/api/src/org/labkey/api/data/dialect/KeywordCandidates.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data.dialect; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.util.PageFlowUtil; @@ -32,7 +33,7 @@ public class KeywordCandidates { private static final KeywordCandidates INSTANCE = new KeywordCandidates(); - private static final Logger LOG = Logger.getLogger(SqlDialect.class); + private static final Logger LOG = LogManager.getLogger(SqlDialect.class); private final Set CANDIDATES; private final Set SQL_2003_KEYWORDS; diff --git a/api/src/org/labkey/api/data/dialect/MutatingSqlDetector.java b/api/src/org/labkey/api/data/dialect/MutatingSqlDetector.java index 4bd820bff9d..6eb2776b472 100644 --- a/api/src/org/labkey/api/data/dialect/MutatingSqlDetector.java +++ b/api/src/org/labkey/api/data/dialect/MutatingSqlDetector.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data.dialect; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.SqlScanner; @@ -23,7 +24,7 @@ public class MutatingSqlDetector { - private static final Logger LOG = Logger.getLogger(MutatingSqlDetector.class); + private static final Logger LOG = LogManager.getLogger(MutatingSqlDetector.class); private final String _sql; private final StringBuilder _firstWord = new StringBuilder(); diff --git a/api/src/org/labkey/api/data/dialect/SqlDialect.java b/api/src/org/labkey/api/data/dialect/SqlDialect.java index c23235e11a0..138dd51b0f9 100644 --- a/api/src/org/labkey/api/data/dialect/SqlDialect.java +++ b/api/src/org/labkey/api/data/dialect/SqlDialect.java @@ -17,7 +17,8 @@ package org.labkey.api.data.dialect; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -75,7 +76,7 @@ public abstract class SqlDialect public static final String GENERIC_ERROR_MESSAGE = "The database experienced an unexpected problem. Please check your input and try again."; public static final String CUSTOM_UNIQUE_ERROR_MESSAGE = "Constraint violation: cannot insert duplicate value for column"; - protected static final Logger LOG = Logger.getLogger(SqlDialect.class); + protected static final Logger LOG = LogManager.getLogger(SqlDialect.class); protected static final String INPUT_TOO_LONG_ERROR_MESSAGE = "The input you provided was too long."; protected static final int MAX_VARCHAR_SIZE = 4000; //Any length over this will be set to nvarchar(max)/text diff --git a/api/src/org/labkey/api/data/dialect/StatementWrapper.java b/api/src/org/labkey/api/data/dialect/StatementWrapper.java index 985157707c8..029ce1334fb 100644 --- a/api/src/org/labkey/api/data/dialect/StatementWrapper.java +++ b/api/src/org/labkey/api/data/dialect/StatementWrapper.java @@ -17,8 +17,8 @@ package org.labkey.api.data.dialect; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; import org.labkey.api.collections.OneBasedList; @@ -57,14 +57,10 @@ import java.sql.Time; import java.sql.Timestamp; import java.util.ArrayList; -import java.util.Arrays; import java.util.Calendar; import java.util.List; import java.util.Map; -import static org.apache.commons.lang3.StringUtils.contains; -import static org.apache.commons.lang3.StringUtils.startsWith; - public class StatementWrapper implements Statement, PreparedStatement, CallableStatement { private final ConnectionWrapper _conn; @@ -2875,7 +2871,7 @@ private void _logStatement(String sql, @Nullable SQLException x, int rowsAffecte _conn.logAndCheckException(x); } - if (!_log.isEnabledFor(Level.DEBUG) && !isAssertEnabled) + if (!_log.isEnabled(Level.DEBUG) && !isAssertEnabled) return; StringBuilder logEntry = new StringBuilder(sql.length() * 2); diff --git a/api/src/org/labkey/api/data/parameterForm.jsp b/api/src/org/labkey/api/data/parameterForm.jsp index 63ff9afa1b1..c9abc7dfc54 100644 --- a/api/src/org/labkey/api/data/parameterForm.jsp +++ b/api/src/org/labkey/api/data/parameterForm.jsp @@ -19,8 +19,8 @@ <%@ page import="org.apache.commons.beanutils.ConvertUtils" %> <%@ page import="org.labkey.api.data.DataRegion" %> <%@ page import="org.labkey.api.query.QueryService" %> -<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="java.util.Collection" %> <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> diff --git a/api/src/org/labkey/api/data/queryprofiler/QueryProfiler.java b/api/src/org/labkey/api/data/queryprofiler/QueryProfiler.java index a0a6a01ad17..0231edddcb5 100644 --- a/api/src/org/labkey/api/data/queryprofiler/QueryProfiler.java +++ b/api/src/org/labkey/api/data/queryprofiler/QueryProfiler.java @@ -19,10 +19,11 @@ import org.apache.commons.collections4.map.AbstractReferenceMap.ReferenceStrength; import org.apache.commons.collections4.map.ReferenceMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Appender; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; -import org.apache.log4j.RollingFileAppender; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.Configuration; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -70,7 +71,7 @@ */ public class QueryProfiler { - private static final Logger LOG = Logger.getLogger(QueryProfiler.class); + private static final Logger LOG = LogManager.getLogger(QueryProfiler.class); private static final QueryProfiler INSTANCE = new QueryProfiler(); private final BlockingQueue _queue = new LinkedBlockingQueue<>(1000); @@ -621,16 +622,18 @@ public void shutdownPre() @Override public void shutdownStarted() { - Logger logger = Logger.getLogger(QueryProfilerThread.class); + Logger logger = LogManager.getLogger(QueryProfilerThread.class); + LoggerContext ctx = (LoggerContext) LogManager.getContext(false); + Configuration config = ctx.getConfiguration(); if (null != logger) { - LOG.info("Starting to log statistics for queries prior to web application shut down"); - Appender appender = logger.getAppender("QUERY_STATS"); - if (null != appender && appender instanceof RollingFileAppender) - ((RollingFileAppender)appender).rollOver(); - else - LOG.warn("Could not rollover the query stats tsv file--there was no appender named QUERY_STATS, or it is not a RollingFileAppender."); +// LOG.info("Starting to log statistics for queries prior to web application shut down"); +// Appender appender = config.getAppender("QUERY_STATS"); +// if (null != appender && appender instanceof RollingFileAppender) +// ((RollingFileAppender)appender).rollOver(); +// else +// LOG.warn("Could not rollover the query stats tsv file--there was no appender named QUERY_STATS, or it is not a RollingFileAppender."); try (PrintWriter logWriter = new LogPrintWriter(logger, Level.INFO)) { diff --git a/api/src/org/labkey/api/data/triggers/ScriptTriggerFactory.java b/api/src/org/labkey/api/data/triggers/ScriptTriggerFactory.java index 71c0fd9524a..ba9fe31112a 100644 --- a/api/src/org/labkey/api/data/triggers/ScriptTriggerFactory.java +++ b/api/src/org/labkey/api/data/triggers/ScriptTriggerFactory.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data.triggers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; @@ -41,7 +42,7 @@ */ public class ScriptTriggerFactory implements TriggerFactory { - private static final Logger LOG = Logger.getLogger(ScriptTriggerFactory.class); + private static final Logger LOG = LogManager.getLogger(ScriptTriggerFactory.class); @Override @NotNull diff --git a/api/src/org/labkey/api/data/views/DataViewService.java b/api/src/org/labkey/api/data/views/DataViewService.java index fca7b688cbc..f8a7147626c 100644 --- a/api/src/org/labkey/api/data/views/DataViewService.java +++ b/api/src/org/labkey/api/data/views/DataViewService.java @@ -15,7 +15,8 @@ */ package org.labkey.api.data.views; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONObject; @@ -44,7 +45,7 @@ public class DataViewService { private final Map _providers = new ConcurrentHashMap<>(); - private static final Logger _log = Logger.getLogger(DataViewService.class); + private static final Logger _log = LogManager.getLogger(DataViewService.class); private static final DataViewService _instance = new DataViewService(); private static final Map _providerInitialized = new HashMap<>(); diff --git a/api/src/org/labkey/api/dataiterator/DataIteratorUtil.java b/api/src/org/labkey/api/dataiterator/DataIteratorUtil.java index 9ab368b82a8..3d6722f98bc 100644 --- a/api/src/org/labkey/api/dataiterator/DataIteratorUtil.java +++ b/api/src/org/labkey/api/dataiterator/DataIteratorUtil.java @@ -19,7 +19,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.io.IOUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; @@ -68,7 +69,7 @@ public class DataIteratorUtil public static final String DATA_SOURCE = "dataSource"; public static final String ETL_DATA_SOURCE = "etl"; - private static final Logger LOG = Logger.getLogger(DataIteratorUtil.class); + private static final Logger LOG = LogManager.getLogger(DataIteratorUtil.class); public static Map createFieldKeyMap(DataIterator di) { @@ -346,7 +347,7 @@ public static void closeQuietly(DataIterator it) } catch (Exception x) { - Logger.getLogger(it.getClass()).warn("Unexpected error closing DataIterator", x); + LogManager.getLogger(it.getClass()).warn("Unexpected error closing DataIterator", x); } } diff --git a/api/src/org/labkey/api/dataiterator/LoggingDataIterator.java b/api/src/org/labkey/api/dataiterator/LoggingDataIterator.java index 468fdd0a261..ff77cbd5916 100644 --- a/api/src/org/labkey/api/dataiterator/LoggingDataIterator.java +++ b/api/src/org/labkey/api/dataiterator/LoggingDataIterator.java @@ -15,8 +15,9 @@ */ package org.labkey.api.dataiterator; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONObject; import org.labkey.api.data.ColumnInfo; import org.labkey.api.query.BatchValidationException; @@ -33,7 +34,7 @@ */ public class LoggingDataIterator extends AbstractDataIterator implements ScrollableDataIterator, MapDataIterator { - static Logger _staticLog = Logger.getLogger(LoggingDataIterator.class); + static Logger _staticLog = LogManager.getLogger(LoggingDataIterator.class); Logger _log = _staticLog; Level _pri = Level.DEBUG; @@ -43,7 +44,7 @@ public static DataIteratorBuilder wrap(DataIteratorBuilder dib) { if (dib instanceof Wrapper) return dib; - if (_staticLog.isEnabledFor(Level.DEBUG)) + if (_staticLog.isEnabled(Level.DEBUG)) return new Wrapper(dib); return dib; } @@ -69,7 +70,7 @@ public static DataIterator wrap(DataIterator in) { if (in instanceof LoggingDataIterator) return in; - if (_staticLog.isEnabledFor(Level.DEBUG)) + if (_staticLog.isEnabled(Level.DEBUG)) return new LoggingDataIterator(in, _staticLog); return in; } diff --git a/api/src/org/labkey/api/dataiterator/MapDataIterator.java b/api/src/org/labkey/api/dataiterator/MapDataIterator.java index 13a8ce1ec41..c1fc9312e8f 100644 --- a/api/src/org/labkey/api/dataiterator/MapDataIterator.java +++ b/api/src/org/labkey/api/dataiterator/MapDataIterator.java @@ -15,7 +15,7 @@ */ package org.labkey.api.dataiterator; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.collections.ArrayListMap; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.ColumnInfo; @@ -55,7 +55,7 @@ static class MapDataIteratorImpl implements MapDataIterator, ScrollableDataItera String name = in.getColumnInfo(i).getName(); if (_findMap.containsKey(name)) { - Logger.getLogger(MapDataIterator.class).warn("Map already has column named '" + name + "'"); + LogManager.getLogger(MapDataIterator.class).warn("Map already has column named '" + name + "'"); continue; } _findMap.put(in.getColumnInfo(i).getName(),i); diff --git a/api/src/org/labkey/api/dataiterator/Pump.java b/api/src/org/labkey/api/dataiterator/Pump.java index e5546cb15a5..7c0cbb4053d 100644 --- a/api/src/org/labkey/api/dataiterator/Pump.java +++ b/api/src/org/labkey/api/dataiterator/Pump.java @@ -15,7 +15,8 @@ */ package org.labkey.api.dataiterator; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.exp.list.ListImportProgress; import org.labkey.api.query.BatchValidationException; @@ -26,7 +27,7 @@ */ public class Pump implements Runnable { - static Logger log = Logger.getLogger(Pump.class); + static Logger log = LogManager.getLogger(Pump.class); DataIterator _it; DataIteratorBuilder _builder; final DataIteratorContext _context; diff --git a/api/src/org/labkey/api/dataiterator/SimpleTranslator.java b/api/src/org/labkey/api/dataiterator/SimpleTranslator.java index d285c9eca06..659e15566fa 100644 --- a/api/src/org/labkey/api/dataiterator/SimpleTranslator.java +++ b/api/src/org/labkey/api/dataiterator/SimpleTranslator.java @@ -21,7 +21,8 @@ import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Triple; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -101,7 +102,7 @@ public boolean add(Pair columnInfoCallablePair) Map _missingValues = Collections.emptyMap(); Map _inputNameMap = null; - private static final Logger LOG = Logger.getLogger(SimpleTranslator.class); + private static final Logger LOG = LogManager.getLogger(SimpleTranslator.class); public SimpleTranslator(DataIterator source, DataIteratorContext context) { diff --git a/api/src/org/labkey/api/dataiterator/StatementDataIterator.java b/api/src/org/labkey/api/dataiterator/StatementDataIterator.java index 5416d6db244..8454810fe40 100644 --- a/api/src/org/labkey/api/dataiterator/StatementDataIterator.java +++ b/api/src/org/labkey/api/dataiterator/StatementDataIterator.java @@ -16,7 +16,7 @@ package org.labkey.api.dataiterator; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; diff --git a/api/src/org/labkey/api/defaults/ClearDefaultValuesAction.java b/api/src/org/labkey/api/defaults/ClearDefaultValuesAction.java index 2d847600801..a850bce6546 100644 --- a/api/src/org/labkey/api/defaults/ClearDefaultValuesAction.java +++ b/api/src/org/labkey/api/defaults/ClearDefaultValuesAction.java @@ -16,11 +16,11 @@ package org.labkey.api.defaults; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.exp.property.Domain; import org.labkey.api.lists.permissions.DesignListPermission; import org.labkey.api.security.RequiresAnyOf; import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.view.NavTree; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/api/src/org/labkey/api/defaults/DefaultValueService.java b/api/src/org/labkey/api/defaults/DefaultValueService.java index aba7048bc27..c4f451db34c 100644 --- a/api/src/org/labkey/api/defaults/DefaultValueService.java +++ b/api/src/org/labkey/api/defaults/DefaultValueService.java @@ -16,15 +16,15 @@ package org.labkey.api.defaults; import org.jetbrains.annotations.Nullable; +import org.labkey.api.data.Container; +import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.data.Container; import org.labkey.api.security.User; import org.labkey.api.services.ServiceRegistry; -import java.util.Map; import java.util.List; +import java.util.Map; /** * Manages sets of values to be used as defaults when a user comes to a data entry form. diff --git a/api/src/org/labkey/api/docker/DockerService.java b/api/src/org/labkey/api/docker/DockerService.java index 23425ce34cd..f66e495029e 100644 --- a/api/src/org/labkey/api/docker/DockerService.java +++ b/api/src/org/labkey/api/docker/DockerService.java @@ -16,7 +16,7 @@ package org.labkey.api.docker; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; @@ -545,7 +545,7 @@ static File getHomeDirectory(User user) } catch (Exception e) { - Logger.getLogger(DockerService.class).error(e.getMessage()); + LogManager.getLogger(DockerService.class).error(e.getMessage()); } throw new UnauthorizedException("User does not have a home directory"); } diff --git a/api/src/org/labkey/api/exp/AbstractParameter.java b/api/src/org/labkey/api/exp/AbstractParameter.java index 4794d1a4bc1..8a8e28d8113 100644 --- a/api/src/org/labkey/api/exp/AbstractParameter.java +++ b/api/src/org/labkey/api/exp/AbstractParameter.java @@ -16,7 +16,7 @@ package org.labkey.api.exp; import org.apache.commons.beanutils.ConversionException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.fhcrc.cpas.exp.xml.SimpleTypeNames; import org.fhcrc.cpas.exp.xml.SimpleValueType; import org.labkey.api.collections.BoundMap; diff --git a/api/src/org/labkey/api/exp/ExperimentDataHandler.java b/api/src/org/labkey/api/exp/ExperimentDataHandler.java index c09fca3ceea..2741b3df0c4 100644 --- a/api/src/org/labkey/api/exp/ExperimentDataHandler.java +++ b/api/src/org/labkey/api/exp/ExperimentDataHandler.java @@ -15,7 +15,7 @@ */ package org.labkey.api.exp; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/api/src/org/labkey/api/exp/ExperimentRunType.java b/api/src/org/labkey/api/exp/ExperimentRunType.java index df4191603d5..ef6898addcb 100644 --- a/api/src/org/labkey/api/exp/ExperimentRunType.java +++ b/api/src/org/labkey/api/exp/ExperimentRunType.java @@ -28,7 +28,6 @@ import org.labkey.api.exp.query.ExpProtocolApplicationTable; import org.labkey.api.exp.query.ExpRunTable; import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryRowReference; import org.labkey.api.query.QueryService; import org.labkey.api.query.SchemaKey; diff --git a/api/src/org/labkey/api/exp/LsidManager.java b/api/src/org/labkey/api/exp/LsidManager.java index 6b57e25e395..79ab0763f0f 100644 --- a/api/src/org/labkey/api/exp/LsidManager.java +++ b/api/src/org/labkey/api/exp/LsidManager.java @@ -15,7 +15,8 @@ */ package org.labkey.api.exp; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AssayProtocolSchema; @@ -54,7 +55,7 @@ */ public class LsidManager { - private static Logger LOG = Logger.getLogger(LsidManager.class); + private static Logger LOG = LogManager.getLogger(LsidManager.class); private static final LsidManager INSTANCE = new LsidManager(); private final Map> _authorityMap = new ConcurrentHashMap<>(); diff --git a/api/src/org/labkey/api/exp/MvColumn.java b/api/src/org/labkey/api/exp/MvColumn.java index db843878e13..f0f6bd89240 100644 --- a/api/src/org/labkey/api/exp/MvColumn.java +++ b/api/src/org/labkey/api/exp/MvColumn.java @@ -15,7 +15,11 @@ */ package org.labkey.api.exp; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.LookupColumn; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; /** diff --git a/api/src/org/labkey/api/exp/OntologyManager.java b/api/src/org/labkey/api/exp/OntologyManager.java index 7ef75b5bab1..23c1c5d0790 100644 --- a/api/src/org/labkey/api/exp/OntologyManager.java +++ b/api/src/org/labkey/api/exp/OntologyManager.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -96,7 +97,7 @@ */ public class OntologyManager { - private static final Logger _log = Logger.getLogger(OntologyManager.class); + private static final Logger _log = LogManager.getLogger(OntologyManager.class); private static final Cache> mapCache = new DatabaseCache<>(getExpSchema().getScope(), 10000, "Property maps"); private static final Cache objectIdCache = new DatabaseCache<>(getExpSchema().getScope(), 2000, "ObjectIds"); private static final Cache, PropertyDescriptor> propDescCache = new BlockingCache<>(new DatabaseCache<>(getExpSchema().getScope(), 40000, CacheManager.UNLIMITED, "Property descriptors"), new CacheLoader<>() diff --git a/api/src/org/labkey/api/exp/PropertyDescriptor.java b/api/src/org/labkey/api/exp/PropertyDescriptor.java index 024ed98b67b..21084e41c54 100644 --- a/api/src/org/labkey/api/exp/PropertyDescriptor.java +++ b/api/src/org/labkey/api/exp/PropertyDescriptor.java @@ -15,7 +15,8 @@ */ package org.labkey.api.exp; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.BaseColumnInfo; @@ -72,7 +73,7 @@ public class PropertyDescriptor extends ColumnRenderPropertiesImpl implements Pa private boolean _mvEnabled; private String _mvIndicatorStorageColumnName; // only valid if mvEnabled - private static final Logger LOG = Logger.getLogger(PropertyDescriptor.class); + private static final Logger LOG = LogManager.getLogger(PropertyDescriptor.class); @Override public void checkLocked() diff --git a/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java b/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java index 6b734a7d53a..d3dcf4d3bc7 100644 --- a/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java +++ b/api/src/org/labkey/api/exp/api/DefaultExperimentDataHandler.java @@ -16,9 +16,8 @@ package org.labkey.api.exp.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; -import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.Handler; import org.labkey.api.exp.XarContext; import org.labkey.api.security.User; diff --git a/api/src/org/labkey/api/exp/api/DefaultExperimentSaveHandler.java b/api/src/org/labkey/api/exp/api/DefaultExperimentSaveHandler.java index becffc1a421..3b41bea0b2c 100644 --- a/api/src/org/labkey/api/exp/api/DefaultExperimentSaveHandler.java +++ b/api/src/org/labkey/api/exp/api/DefaultExperimentSaveHandler.java @@ -16,7 +16,8 @@ package org.labkey.api.exp.api; import org.apache.commons.beanutils.ConversionException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -53,7 +54,7 @@ public class DefaultExperimentSaveHandler implements ExperimentSaveHandler { - protected static final Logger LOG = Logger.getLogger(DefaultExperimentSaveHandler.class); + protected static final Logger LOG = LogManager.getLogger(DefaultExperimentSaveHandler.class); @Override public void beforeSave(ViewContext context, JSONObject rootJson, ExpProtocol protocol) diff --git a/api/src/org/labkey/api/exp/api/ExpExperiment.java b/api/src/org/labkey/api/exp/api/ExpExperiment.java index 6e51a2e66c3..c6682c27a5b 100644 --- a/api/src/org/labkey/api/exp/api/ExpExperiment.java +++ b/api/src/org/labkey/api/exp/api/ExpExperiment.java @@ -17,7 +17,6 @@ package org.labkey.api.exp.api; import org.jetbrains.annotations.Nullable; -import org.labkey.api.query.BatchValidationException; import org.labkey.api.security.User; import java.util.List; diff --git a/api/src/org/labkey/api/exp/api/ExpProtocolApplication.java b/api/src/org/labkey/api/exp/api/ExpProtocolApplication.java index 5579c52e0f7..caf948a8390 100644 --- a/api/src/org/labkey/api/exp/api/ExpProtocolApplication.java +++ b/api/src/org/labkey/api/exp/api/ExpProtocolApplication.java @@ -18,13 +18,11 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; import org.labkey.api.security.User; import org.labkey.api.util.Pair; import java.util.Date; import java.util.List; -import java.util.Map; import java.util.Set; /** diff --git a/api/src/org/labkey/api/exp/api/ExperimentJSONConverter.java b/api/src/org/labkey/api/exp/api/ExperimentJSONConverter.java index 38a11409417..a512ed93445 100644 --- a/api/src/org/labkey/api/exp/api/ExperimentJSONConverter.java +++ b/api/src/org/labkey/api/exp/api/ExperimentJSONConverter.java @@ -32,8 +32,8 @@ import org.labkey.api.files.FileContentService; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.query.QueryRowReference; import org.labkey.api.query.QueryParam; +import org.labkey.api.query.QueryRowReference; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; import org.labkey.api.security.permissions.ReadPermission; diff --git a/api/src/org/labkey/api/exp/api/ExperimentListener.java b/api/src/org/labkey/api/exp/api/ExperimentListener.java index 36dac81d829..a052ad5db28 100644 --- a/api/src/org/labkey/api/exp/api/ExperimentListener.java +++ b/api/src/org/labkey/api/exp/api/ExperimentListener.java @@ -16,12 +16,9 @@ package org.labkey.api.exp.api; import org.labkey.api.data.Container; -import org.labkey.api.exp.ExperimentException; import org.labkey.api.query.BatchValidationException; -import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; -import java.util.Collections; import java.util.List; /** diff --git a/api/src/org/labkey/api/exp/api/ExperimentService.java b/api/src/org/labkey/api/exp/api/ExperimentService.java index c14df100837..74fb4effd9e 100644 --- a/api/src/org/labkey/api/exp/api/ExperimentService.java +++ b/api/src/org/labkey/api/exp/api/ExperimentService.java @@ -16,7 +16,7 @@ package org.labkey.api.exp.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/api/src/org/labkey/api/exp/api/StorageProvisioner.java b/api/src/org/labkey/api/exp/api/StorageProvisioner.java index abd5a55a493..78fcfb10f52 100644 --- a/api/src/org/labkey/api/exp/api/StorageProvisioner.java +++ b/api/src/org/labkey/api/exp/api/StorageProvisioner.java @@ -16,7 +16,8 @@ package org.labkey.api.exp.api; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -82,7 +83,7 @@ */ public class StorageProvisioner { - private static final Logger log = Logger.getLogger(StorageProvisioner.class); + private static final Logger log = LogManager.getLogger(StorageProvisioner.class); private static final CPUTimer create = new CPUTimer("StorageProvisioner.create"); private static String _create(DbScope scope, DomainKind kind, Domain domain) @@ -96,7 +97,7 @@ private static String _create(DbScope scope, DomainKind kind, Domain domain) DomainDescriptor dd = OntologyManager.getDomainDescriptor(domain.getTypeId()); if (null == dd) { - Logger.getLogger(StorageProvisioner.class).warn("Can't find domain descriptor: " + domain.getTypeId() + " " + domain.getTypeURI()); + LogManager.getLogger(StorageProvisioner.class).warn("Can't find domain descriptor: " + domain.getTypeId() + " " + domain.getTypeURI()); transaction.commit(); return null; } @@ -1033,7 +1034,7 @@ public static void fixupProvisionedDomain(SchemaTableInfo ti, DomainKind kind if (null == c) { - Logger.getLogger(StorageProvisioner.class).info("Column not found in storage table: " + tableName + "." + s.getName()); + LogManager.getLogger(StorageProvisioner.class).info("Column not found in storage table: " + tableName + "." + s.getName()); continue; } diff --git a/api/src/org/labkey/api/exp/list/ListService.java b/api/src/org/labkey/api/exp/list/ListService.java index 17fed148feb..eacbd4edf53 100644 --- a/api/src/org/labkey/api/exp/list/ListService.java +++ b/api/src/org/labkey/api/exp/list/ListService.java @@ -21,8 +21,8 @@ import org.labkey.api.exp.TemplateInfo; import org.labkey.api.exp.property.Domain; import org.labkey.api.query.UserSchema; -import org.labkey.api.services.ServiceRegistry; import org.labkey.api.security.User; +import org.labkey.api.services.ServiceRegistry; import org.labkey.api.view.ActionURL; import org.springframework.validation.BindException; diff --git a/api/src/org/labkey/api/exp/query/DataClassUserSchema.java b/api/src/org/labkey/api/exp/query/DataClassUserSchema.java index 61cce36e842..748c7799a1b 100644 --- a/api/src/org/labkey/api/exp/query/DataClassUserSchema.java +++ b/api/src/org/labkey/api/exp/query/DataClassUserSchema.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveTreeMap; -import org.labkey.api.data.ActionButton; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; diff --git a/api/src/org/labkey/api/exp/query/ExpExperimentTable.java b/api/src/org/labkey/api/exp/query/ExpExperimentTable.java index d6aa21eaab0..52ba638a039 100644 --- a/api/src/org/labkey/api/exp/query/ExpExperimentTable.java +++ b/api/src/org/labkey/api/exp/query/ExpExperimentTable.java @@ -18,8 +18,8 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.MutableColumnInfo; -import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpRun; public interface ExpExperimentTable extends ExpTable { diff --git a/api/src/org/labkey/api/exp/query/ExpInputTable.java b/api/src/org/labkey/api/exp/query/ExpInputTable.java index 725b4ff7d36..2e8a8dfeb4c 100644 --- a/api/src/org/labkey/api/exp/query/ExpInputTable.java +++ b/api/src/org/labkey/api/exp/query/ExpInputTable.java @@ -15,8 +15,8 @@ */ package org.labkey.api.exp.query; -import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpRun; /** * Base table type for usages of data or materials in runs diff --git a/api/src/org/labkey/api/exp/query/ExpRunTable.java b/api/src/org/labkey/api/exp/query/ExpRunTable.java index 827daed21d9..70dfc748f01 100644 --- a/api/src/org/labkey/api/exp/query/ExpRunTable.java +++ b/api/src/org/labkey/api/exp/query/ExpRunTable.java @@ -17,7 +17,11 @@ package org.labkey.api.exp.query; import org.labkey.api.data.MutableColumnInfo; -import org.labkey.api.exp.api.*; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpExperiment; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExpRun; import java.util.List; diff --git a/api/src/org/labkey/api/exp/query/SamplesSchema.java b/api/src/org/labkey/api/exp/query/SamplesSchema.java index 1bce24bb71b..a25d0d3b527 100644 --- a/api/src/org/labkey/api/exp/query/SamplesSchema.java +++ b/api/src/org/labkey/api/exp/query/SamplesSchema.java @@ -16,7 +16,8 @@ package org.labkey.api.exp.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveTreeMap; @@ -51,7 +52,7 @@ public class SamplesSchema extends AbstractExpSchema public static final String SCHEMA_NAME = "samples"; public static final SchemaKey SCHEMA_SAMPLES = SchemaKey.fromParts(SamplesSchema.SCHEMA_NAME); public static final String SCHEMA_DESCR = "Contains data about the samples used in experiment runs."; - static final Logger log = Logger.getLogger(SamplesSchema.class); + static final Logger log = LogManager.getLogger(SamplesSchema.class); static private Map getSampleTypeMap(Container container, User user) { diff --git a/api/src/org/labkey/api/exp/xar/LsidUtils.java b/api/src/org/labkey/api/exp/xar/LsidUtils.java index 20674d9d1a9..2d0893f719b 100644 --- a/api/src/org/labkey/api/exp/xar/LsidUtils.java +++ b/api/src/org/labkey/api/exp/xar/LsidUtils.java @@ -15,7 +15,8 @@ */ package org.labkey.api.exp.xar; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Before; import org.junit.Test; @@ -35,7 +36,7 @@ */ public class LsidUtils { - private static Logger _log = Logger.getLogger(LsidUtils.class); + private static Logger _log = LogManager.getLogger(LsidUtils.class); private static Pattern REPLACEMENT_PATTERN = Pattern.compile("\\Q${\\E(.*?)\\Q}\\E"); diff --git a/api/src/org/labkey/api/exp/xar/MapReplacer.java b/api/src/org/labkey/api/exp/xar/MapReplacer.java index 4a31bfb614d..998c0b483b4 100644 --- a/api/src/org/labkey/api/exp/xar/MapReplacer.java +++ b/api/src/org/labkey/api/exp/xar/MapReplacer.java @@ -16,8 +16,8 @@ package org.labkey.api.exp.xar; -import java.util.Map; import java.util.HashMap; +import java.util.Map; /** * User: jeckels diff --git a/api/src/org/labkey/api/files/FileRoot.java b/api/src/org/labkey/api/files/FileRoot.java index 1c6d5ba2560..4b69ea7524e 100644 --- a/api/src/org/labkey/api/files/FileRoot.java +++ b/api/src/org/labkey/api/files/FileRoot.java @@ -17,7 +17,6 @@ package org.labkey.api.files; import org.labkey.api.data.Container; -import org.labkey.api.files.FileContentService; import java.io.Serializable; diff --git a/api/src/org/labkey/api/files/FileSystemWatcherImpl.java b/api/src/org/labkey/api/files/FileSystemWatcherImpl.java index b411c3606d7..dfbf68a9db9 100644 --- a/api/src/org/labkey/api/files/FileSystemWatcherImpl.java +++ b/api/src/org/labkey/api/files/FileSystemWatcherImpl.java @@ -16,7 +16,8 @@ package org.labkey.api.files; import org.apache.commons.lang3.SystemUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.imca_cat.pollingwatchservice.PathWatchService; import org.imca_cat.pollingwatchservice.PollingWatchService; import org.junit.Assert; @@ -73,7 +74,7 @@ */ public class FileSystemWatcherImpl implements FileSystemWatcher { - private static final Logger LOG = Logger.getLogger(FileSystemWatcherImpl.class); + private static final Logger LOG = LogManager.getLogger(FileSystemWatcherImpl.class); private final WatchService _watcher; private final ConcurrentMap _listenerMap = new ConcurrentHashMap<>(1000); diff --git a/api/src/org/labkey/api/files/FileUrls.java b/api/src/org/labkey/api/files/FileUrls.java index c185efe0799..6b9c326e3b0 100644 --- a/api/src/org/labkey/api/files/FileUrls.java +++ b/api/src/org/labkey/api/files/FileUrls.java @@ -17,8 +17,8 @@ package org.labkey.api.files; import org.labkey.api.action.UrlProvider; -import org.labkey.api.view.ActionURL; import org.labkey.api.data.Container; +import org.labkey.api.view.ActionURL; /** * User: klum diff --git a/api/src/org/labkey/api/files/NoopFileSystemWatcher.java b/api/src/org/labkey/api/files/NoopFileSystemWatcher.java index 9c94f79bf85..8bab36fdb50 100644 --- a/api/src/org/labkey/api/files/NoopFileSystemWatcher.java +++ b/api/src/org/labkey/api/files/NoopFileSystemWatcher.java @@ -15,7 +15,6 @@ */ package org.labkey.api.files; -import java.io.IOException; import java.nio.file.Path; import java.nio.file.WatchEvent.Kind; diff --git a/api/src/org/labkey/api/files/TableUpdaterFileListener.java b/api/src/org/labkey/api/files/TableUpdaterFileListener.java index 411403a7b97..99ecbb9d31f 100644 --- a/api/src/org/labkey/api/files/TableUpdaterFileListener.java +++ b/api/src/org/labkey/api/files/TableUpdaterFileListener.java @@ -15,7 +15,8 @@ */ package org.labkey.api.files; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -50,7 +51,7 @@ */ public class TableUpdaterFileListener implements FileListener { - private static final Logger LOG = Logger.getLogger(TableUpdaterFileListener.class); + private static final Logger LOG = LogManager.getLogger(TableUpdaterFileListener.class); public static final String TABLE_ALIAS = "x"; diff --git a/api/src/org/labkey/api/files/view/CustomizeFilesWebPartView.java b/api/src/org/labkey/api/files/view/CustomizeFilesWebPartView.java index 84185a9416c..dd7e6139e93 100644 --- a/api/src/org/labkey/api/files/view/CustomizeFilesWebPartView.java +++ b/api/src/org/labkey/api/files/view/CustomizeFilesWebPartView.java @@ -17,7 +17,6 @@ package org.labkey.api.files.view; import org.apache.commons.lang3.BooleanUtils; -import org.labkey.api.cloud.CloudStoreService; import org.labkey.api.data.Container; import org.labkey.api.files.FileContentService; import org.labkey.api.pipeline.PipeRoot; @@ -28,8 +27,6 @@ import java.net.URLDecoder; import java.nio.file.Files; import java.nio.file.Path; -import java.util.ArrayList; -import java.util.List; import java.util.Map; /** diff --git a/api/src/org/labkey/api/files/view/FilesWebPart.java b/api/src/org/labkey/api/files/view/FilesWebPart.java index 54e01a580da..610d4db4a20 100644 --- a/api/src/org/labkey/api/files/view/FilesWebPart.java +++ b/api/src/org/labkey/api/files/view/FilesWebPart.java @@ -18,7 +18,8 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentDirectory; @@ -81,7 +82,7 @@ public class FilesWebPart extends JspView public static final String ROOT_OFFSET_PROPERTY_NAME = "rootOffset"; public static final String FOLDER_TREE_VISIBLE_PROPERTY_NAME = "folderTreeVisible"; - private static final Logger _log = Logger.getLogger(FilesWebPart.class); + private static final Logger _log = LogManager.getLogger(FilesWebPart.class); private boolean showAdmin = false; private String fileSet; diff --git a/api/src/org/labkey/api/iterator/CloseableIterator.java b/api/src/org/labkey/api/iterator/CloseableIterator.java index df4b984cab1..ee5ac941f12 100644 --- a/api/src/org/labkey/api/iterator/CloseableIterator.java +++ b/api/src/org/labkey/api/iterator/CloseableIterator.java @@ -15,8 +15,8 @@ */ package org.labkey.api.iterator; -import java.util.Iterator; import java.io.Closeable; +import java.util.Iterator; /** * A type of Iterator that should be explicitly closed because it holds resources open (like DB connections or files) diff --git a/api/src/org/labkey/api/iterator/FilteredIterator.java b/api/src/org/labkey/api/iterator/FilteredIterator.java index ea5cb188859..9dbc2f998cc 100644 --- a/api/src/org/labkey/api/iterator/FilteredIterator.java +++ b/api/src/org/labkey/api/iterator/FilteredIterator.java @@ -17,8 +17,8 @@ import org.labkey.api.util.Filter; -import java.util.NoSuchElementException; import java.util.Iterator; +import java.util.NoSuchElementException; /** * Wrapper over some other Iterator that filters out certain objects. diff --git a/api/src/org/labkey/api/iterator/WrappingCloseableIterator.java b/api/src/org/labkey/api/iterator/WrappingCloseableIterator.java index c2b291a3cee..110f743d80e 100644 --- a/api/src/org/labkey/api/iterator/WrappingCloseableIterator.java +++ b/api/src/org/labkey/api/iterator/WrappingCloseableIterator.java @@ -16,7 +16,6 @@ package org.labkey.api.iterator; -import java.io.IOException; import java.util.Iterator; /** diff --git a/api/src/org/labkey/api/jsp/JspClassLoader.java b/api/src/org/labkey/api/jsp/JspClassLoader.java index 5091acd0a46..4a871b2f1cb 100644 --- a/api/src/org/labkey/api/jsp/JspClassLoader.java +++ b/api/src/org/labkey/api/jsp/JspClassLoader.java @@ -15,7 +15,8 @@ */ package org.labkey.api.jsp; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.module.ModuleLoader; import org.labkey.api.util.ConfigurationException; @@ -41,7 +42,7 @@ */ public class JspClassLoader { - private static final Logger _log = Logger.getLogger(JspClassLoader.class); + private static final Logger _log = LogManager.getLogger(JspClassLoader.class); protected static final String JSP_PACKAGE = "org.labkey.jsp.compiled"; private transient AtomicReference _loader = new AtomicReference<>(); diff --git a/api/src/org/labkey/api/jsp/JspLoader.java b/api/src/org/labkey/api/jsp/JspLoader.java index 83d05e7f5b4..91d02c48b06 100644 --- a/api/src/org/labkey/api/jsp/JspLoader.java +++ b/api/src/org/labkey/api/jsp/JspLoader.java @@ -16,7 +16,8 @@ package org.labkey.api.jsp; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.module.ModuleLoader; import org.labkey.api.settings.AppProps; import org.labkey.api.util.ContextListener; @@ -30,7 +31,7 @@ public class JspLoader { - private static Logger _log = Logger.getLogger(JspLoader.class); + private static Logger _log = LogManager.getLogger(JspLoader.class); private static final JspClassLoader _jspClassLoader; static diff --git a/api/src/org/labkey/api/jsp/JspTest.java b/api/src/org/labkey/api/jsp/JspTest.java index 5226ace485f..27558384a20 100644 --- a/api/src/org/labkey/api/jsp/JspTest.java +++ b/api/src/org/labkey/api/jsp/JspTest.java @@ -16,7 +16,6 @@ package org.labkey.api.jsp; -import org.labkey.api.action.HasViewContext; import org.labkey.api.util.TestContext; /** diff --git a/api/src/org/labkey/api/jsp/LabKeyJspWriter.java b/api/src/org/labkey/api/jsp/LabKeyJspWriter.java index 454783fc086..e25f11c2323 100644 --- a/api/src/org/labkey/api/jsp/LabKeyJspWriter.java +++ b/api/src/org/labkey/api/jsp/LabKeyJspWriter.java @@ -15,10 +15,12 @@ */ package org.labkey.api.jsp; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.collections.ConcurrentHashSet; import com.google.common.collect.ConcurrentHashMultiset; import com.google.common.collect.Multiset; import com.google.common.collect.Multiset.Entry; -import org.apache.log4j.Logger; import org.labkey.api.settings.AdminConsole; import org.labkey.api.settings.AppProps; import org.labkey.api.settings.ExperimentalFeatureService; @@ -36,10 +38,10 @@ public class LabKeyJspWriter extends JspWriterWrapper { - private static final Logger LOG = Logger.getLogger(LabKeyJspWriter.class); - private static final Logger LOGSTRING = Logger.getLogger(LabKeyJspWriter.class.getName() + ".string"); private static final Multiset COUNTING_SET = ConcurrentHashMultiset.create(); private static final String EXPERIMENTAL_THROW_ON_WARNING = "labkeyJspWriterThrowOnWarning"; + private static final Logger LOG = LogManager.getLogger(LabKeyJspWriter.class); + private static final Logger LOGSTRING = LogManager.getLogger(LabKeyJspWriter.class.getName()+".string"); public static void registerExperimentalFeature() { diff --git a/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java b/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java index 1cbca26f443..81392d22f4f 100644 --- a/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java +++ b/api/src/org/labkey/api/jsp/RecompilingJspClassLoader.java @@ -18,7 +18,8 @@ import org.apache.jasper.JspC; import org.apache.jasper.servlet.JspCServletContext; import org.apache.jasper.servlet.TldScanner; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.tomcat.JarScanner; import org.apache.tomcat.util.scan.StandardJarScanner; import org.labkey.api.annotations.JavaRuntimeVersion; @@ -54,7 +55,7 @@ */ public class RecompilingJspClassLoader extends JspClassLoader { - private static final Logger _log = Logger.getLogger(RecompilingJspClassLoader.class); + private static final Logger _log = LogManager.getLogger(RecompilingJspClassLoader.class); private static final String JSP_JAVA_PATH = "/jspTempDir/classes"; private static final String JSP_CLASSES_DIR = "/classes/java/jsp"; private static final String JSP_PACKAGE_PATH = JSP_PACKAGE.replaceAll("\\.", "/"); diff --git a/api/src/org/labkey/api/jsp/taglib/AutoCompleteTag.java b/api/src/org/labkey/api/jsp/taglib/AutoCompleteTag.java index dea79bcd98e..5c71d07f44a 100644 --- a/api/src/org/labkey/api/jsp/taglib/AutoCompleteTag.java +++ b/api/src/org/labkey/api/jsp/taglib/AutoCompleteTag.java @@ -20,7 +20,6 @@ import org.labkey.api.view.ActionURL; import org.labkey.api.view.HttpView; -import javax.servlet.jsp.JspWriter; import java.io.IOException; import java.io.Writer; diff --git a/api/src/org/labkey/api/jsp/taglib/ErrorsTag.java b/api/src/org/labkey/api/jsp/taglib/ErrorsTag.java index 067a4659769..f9bd182e875 100644 --- a/api/src/org/labkey/api/jsp/taglib/ErrorsTag.java +++ b/api/src/org/labkey/api/jsp/taglib/ErrorsTag.java @@ -16,7 +16,8 @@ package org.labkey.api.jsp.taglib; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.LabKeyError; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.HtmlString; @@ -74,7 +75,7 @@ public int doStartTag() throws JspException { out.print(HtmlString.unsafe("Unknown error: " + m)); ExceptionUtil.logExceptionToMothership((HttpServletRequest)pageContext.getRequest(), nsme); - Logger log = Logger.getLogger(ErrorsTag.class); + Logger log = LogManager.getLogger(ErrorsTag.class); log.error("Failed to find a message: " + m, nsme); } out.println("
"); diff --git a/api/src/org/labkey/api/jsp/taglib/SimpleTagBase.java b/api/src/org/labkey/api/jsp/taglib/SimpleTagBase.java index 2780c42ffc2..54143fbf5c5 100644 --- a/api/src/org/labkey/api/jsp/taglib/SimpleTagBase.java +++ b/api/src/org/labkey/api/jsp/taglib/SimpleTagBase.java @@ -19,8 +19,8 @@ import org.labkey.api.util.HtmlString; import org.labkey.api.util.PageFlowUtil; -import javax.servlet.jsp.tagext.SimpleTagSupport; import javax.servlet.jsp.JspWriter; +import javax.servlet.jsp.tagext.SimpleTagSupport; public class SimpleTagBase extends SimpleTagSupport { diff --git a/api/src/org/labkey/api/laboratory/AbstractNavItem.java b/api/src/org/labkey/api/laboratory/AbstractNavItem.java index 4f11daa1424..ed00bf5842c 100644 --- a/api/src/org/labkey/api/laboratory/AbstractNavItem.java +++ b/api/src/org/labkey/api/laboratory/AbstractNavItem.java @@ -15,7 +15,8 @@ */ package org.labkey.api.laboratory; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -36,7 +37,7 @@ */ abstract public class AbstractNavItem implements NavItem { - protected static final Logger _log = Logger.getLogger(AbstractNavItem.class); + protected static final Logger _log = LogManager.getLogger(AbstractNavItem.class); protected QueryCache _queryCache = new QueryCache(); private String _ownerKey = null; diff --git a/api/src/org/labkey/api/laboratory/NavItem.java b/api/src/org/labkey/api/laboratory/NavItem.java index 4b2d703e226..3ea15df68cc 100644 --- a/api/src/org/labkey/api/laboratory/NavItem.java +++ b/api/src/org/labkey/api/laboratory/NavItem.java @@ -17,8 +17,6 @@ import org.json.JSONObject; import org.labkey.api.data.Container; -import org.labkey.api.laboratory.DataProvider; -import org.labkey.api.laboratory.LaboratoryService; import org.labkey.api.security.User; /** diff --git a/api/src/org/labkey/api/laboratory/TabbedReportItem.java b/api/src/org/labkey/api/laboratory/TabbedReportItem.java index cfdb8b2cbc9..d83e66230a0 100644 --- a/api/src/org/labkey/api/laboratory/TabbedReportItem.java +++ b/api/src/org/labkey/api/laboratory/TabbedReportItem.java @@ -15,7 +15,8 @@ */ package org.labkey.api.laboratory; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.data.ColumnInfo; @@ -46,7 +47,7 @@ public class TabbedReportItem extends AbstractNavItem protected FieldKey _allProjectsFieldKey = null; public static final String OVERRIDES_PROP_KEY = "laboratory.tabItemOverride"; - protected static final Logger _log = Logger.getLogger(TabbedReportItem.class); + protected static final Logger _log = LogManager.getLogger(TabbedReportItem.class); public TabbedReportItem(DataProvider provider, String name, String label, String reportCategory) { diff --git a/api/src/org/labkey/api/laboratory/assay/AssayDataProvider.java b/api/src/org/labkey/api/laboratory/assay/AssayDataProvider.java index 14ea62f572a..49c97458fc5 100644 --- a/api/src/org/labkey/api/laboratory/assay/AssayDataProvider.java +++ b/api/src/org/labkey/api/laboratory/assay/AssayDataProvider.java @@ -15,11 +15,11 @@ */ package org.labkey.api.laboratory.assay; +import org.labkey.api.assay.AssayProvider; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.laboratory.DataProvider; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayProvider; import java.util.Collection; import java.util.List; diff --git a/api/src/org/labkey/api/laboratory/assay/AssayParser.java b/api/src/org/labkey/api/laboratory/assay/AssayParser.java index af5aa8dafa8..b85fa8ea41e 100644 --- a/api/src/org/labkey/api/laboratory/assay/AssayParser.java +++ b/api/src/org/labkey/api/laboratory/assay/AssayParser.java @@ -16,11 +16,11 @@ package org.labkey.api.laboratory.assay; import org.json.JSONObject; +import org.labkey.api.assay.AssayProvider; import org.labkey.api.exp.api.ExpExperiment; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.query.BatchValidationException; -import org.labkey.api.assay.AssayProvider; import org.labkey.api.util.Pair; import org.labkey.api.view.ViewContext; diff --git a/api/src/org/labkey/api/ldk/buttons/ShowEditUIButton.java b/api/src/org/labkey/api/ldk/buttons/ShowEditUIButton.java index a83e51eb95b..fa90c2f6d51 100644 --- a/api/src/org/labkey/api/ldk/buttons/ShowEditUIButton.java +++ b/api/src/org/labkey/api/ldk/buttons/ShowEditUIButton.java @@ -21,7 +21,6 @@ import org.labkey.api.security.permissions.Permission; import org.labkey.api.util.PageFlowUtil; -import java.util.HashMap; import java.util.Map; /** diff --git a/api/src/org/labkey/api/ldk/table/AbstractTableCustomizer.java b/api/src/org/labkey/api/ldk/table/AbstractTableCustomizer.java index 5fcf2f5c250..0523765bc0d 100644 --- a/api/src/org/labkey/api/ldk/table/AbstractTableCustomizer.java +++ b/api/src/org/labkey/api/ldk/table/AbstractTableCustomizer.java @@ -15,20 +15,18 @@ */ package org.labkey.api.ldk.table; -import org.apache.log4j.Logger; -import org.labkey.api.collections.CaseInsensitiveHashMap; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.Container; import org.labkey.api.data.TableCustomizer; import org.labkey.api.data.TableInfo; import org.labkey.api.query.DefaultSchema; -import org.labkey.api.query.QueryService; import org.labkey.api.query.UserSchema; import org.labkey.api.study.DatasetTable; import java.util.HashMap; import java.util.Map; -import java.util.WeakHashMap; /** * User: bimber @@ -37,7 +35,7 @@ */ abstract public class AbstractTableCustomizer implements TableCustomizer { - protected static final Logger _log = Logger.getLogger(AbstractTableCustomizer.class); + protected static final Logger _log = LogManager.getLogger(AbstractTableCustomizer.class); /** * Rely on DefaultSchema's caching of schema creation, and just track the minimum number of DefaultSchemas to diff --git a/api/src/org/labkey/api/ldk/table/ButtonConfigFactory.java b/api/src/org/labkey/api/ldk/table/ButtonConfigFactory.java index 0435195b77c..7146cec14f9 100644 --- a/api/src/org/labkey/api/ldk/table/ButtonConfigFactory.java +++ b/api/src/org/labkey/api/ldk/table/ButtonConfigFactory.java @@ -23,7 +23,6 @@ import org.labkey.api.view.template.ClientDependency; import java.util.List; -import java.util.Set; import java.util.function.Supplier; /** diff --git a/api/src/org/labkey/api/ldk/table/QueryCache.java b/api/src/org/labkey/api/ldk/table/QueryCache.java index f325530bc3c..7e0b1be58ee 100644 --- a/api/src/org/labkey/api/ldk/table/QueryCache.java +++ b/api/src/org/labkey/api/ldk/table/QueryCache.java @@ -15,7 +15,11 @@ */ package org.labkey.api.ldk.table; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; @@ -26,9 +30,6 @@ import org.labkey.api.query.QueryService; import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import java.util.ArrayList; import java.util.HashMap; @@ -43,7 +44,7 @@ */ public class QueryCache { - private static final Logger _log = Logger.getLogger(QueryCache.class); + private static final Logger _log = LogManager.getLogger(QueryCache.class); private Map _cachedAssaySchemas = new HashMap<>(); private Map _cachedUserSchemas = new HashMap<>(); diff --git a/api/src/org/labkey/api/ldk/table/SimpleButtonConfigFactory.java b/api/src/org/labkey/api/ldk/table/SimpleButtonConfigFactory.java index f270f0c01c2..085216e6127 100644 --- a/api/src/org/labkey/api/ldk/table/SimpleButtonConfigFactory.java +++ b/api/src/org/labkey/api/ldk/table/SimpleButtonConfigFactory.java @@ -30,9 +30,7 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; -import java.util.LinkedHashSet; import java.util.List; -import java.util.Set; import java.util.function.Supplier; /** diff --git a/api/src/org/labkey/api/mbean/ErrorsMXBean.java b/api/src/org/labkey/api/mbean/ErrorsMXBean.java index 6a62058471c..6c88160b120 100644 --- a/api/src/org/labkey/api/mbean/ErrorsMXBean.java +++ b/api/src/org/labkey/api/mbean/ErrorsMXBean.java @@ -15,8 +15,6 @@ */ package org.labkey.api.mbean; -import org.apache.log4j.spi.LoggingEvent; - import java.util.Date; /** diff --git a/api/src/org/labkey/api/mbean/LabKeyManagement.java b/api/src/org/labkey/api/mbean/LabKeyManagement.java index 6c06238f280..5ee65102e3c 100644 --- a/api/src/org/labkey/api/mbean/LabKeyManagement.java +++ b/api/src/org/labkey/api/mbean/LabKeyManagement.java @@ -15,7 +15,7 @@ */ package org.labkey.api.mbean; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import javax.management.DynamicMBean; import javax.management.InstanceNotFoundException; @@ -60,7 +60,7 @@ public static void register(DynamicMBean bean, String type, String name) } catch (Exception x) { - Logger.getLogger(LabKeyManagement.class).error("error registering mbean : " + String.valueOf(name), x); + LogManager.getLogger(LabKeyManagement.class).error("error registering mbean : " + String.valueOf(name), x); } register(bean, oname); } @@ -88,7 +88,7 @@ public static void register(DynamicMBean bean, ObjectName name) } catch (Exception x) { - Logger.getLogger(LabKeyManagement.class).error("error registering mbean : " + String.valueOf(name), x); + LogManager.getLogger(LabKeyManagement.class).error("error registering mbean : " + String.valueOf(name), x); } } } diff --git a/api/src/org/labkey/api/module/AllowedDuringUpgrade.java b/api/src/org/labkey/api/module/AllowedDuringUpgrade.java index afb3e2cae86..6ed736d32d2 100644 --- a/api/src/org/labkey/api/module/AllowedDuringUpgrade.java +++ b/api/src/org/labkey/api/module/AllowedDuringUpgrade.java @@ -15,9 +15,9 @@ */ package org.labkey.api.module; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Tag for the very small set of actions that users are allowed to access while the server is in the midst diff --git a/api/src/org/labkey/api/module/CustomFolderType.java b/api/src/org/labkey/api/module/CustomFolderType.java index 17116311873..6acb1ce48c6 100644 --- a/api/src/org/labkey/api/module/CustomFolderType.java +++ b/api/src/org/labkey/api/module/CustomFolderType.java @@ -21,8 +21,8 @@ import org.labkey.api.data.Container; import org.labkey.api.portal.ProjectUrls; import org.labkey.api.security.User; -import org.labkey.api.security.permissions.TroubleShooterPermission; import org.labkey.api.security.permissions.ReadPermission; +import org.labkey.api.security.permissions.TroubleShooterPermission; import org.labkey.api.settings.AppProps; import org.labkey.api.util.HelpTopic; import org.labkey.api.util.PageFlowUtil; diff --git a/api/src/org/labkey/api/module/DefaultModule.java b/api/src/org/labkey/api/module/DefaultModule.java index f093be9e42e..01c03c3fa38 100644 --- a/api/src/org/labkey/api/module/DefaultModule.java +++ b/api/src/org/labkey/api/module/DefaultModule.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.annotation.JsonIgnore; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -98,7 +99,7 @@ public abstract class DefaultModule implements Module, ApplicationContextAware public static final String CORE_MODULE_NAME = "Core"; private static final String DEPENDENCIES_FILE_PATH = "credits/dependencies.txt"; - private static final Logger _log = Logger.getLogger(DefaultModule.class); + private static final Logger _log = LogManager.getLogger(DefaultModule.class); private static final Set, String>> INSTANTIATED_MODULES = new HashSet<>(); static final ModuleResourceCache MODULE_XML_CACHE = ModuleResourceCaches.create("module.xml files", new ModuleXmlCacheHandler(), ResourceRootProvider.getStandard(new Path())); diff --git a/api/src/org/labkey/api/module/FolderTypeManager.java b/api/src/org/labkey/api/module/FolderTypeManager.java index e93ab0ac511..1d3ae237c1a 100644 --- a/api/src/org/labkey/api/module/FolderTypeManager.java +++ b/api/src/org/labkey/api/module/FolderTypeManager.java @@ -16,7 +16,8 @@ package org.labkey.api.module; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; @@ -47,7 +48,7 @@ */ public class FolderTypeManager { - private static final Logger LOG = Logger.getLogger(FolderTypeManager.class); + private static final Logger LOG = LogManager.getLogger(FolderTypeManager.class); private static final FolderTypeManager INSTANCE = new FolderTypeManager(); private static final String SIMPLE_TYPE_DIR_NAME = "folderTypes"; private static final String SIMPLE_TYPE_FILE_EXTENSION = ".foldertype.xml"; diff --git a/api/src/org/labkey/api/module/MockModule.java b/api/src/org/labkey/api/module/MockModule.java index a6b010c275c..392805cfc91 100644 --- a/api/src/org/labkey/api/module/MockModule.java +++ b/api/src/org/labkey/api/module/MockModule.java @@ -25,7 +25,6 @@ import org.labkey.api.data.UpgradeCode; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.query.OlapSchemaInfo; -import org.labkey.api.resource.Resolver; import org.labkey.api.resource.Resource; import org.labkey.api.security.User; import org.labkey.api.util.Path; diff --git a/api/src/org/labkey/api/module/Module.java b/api/src/org/labkey/api/module/Module.java index a8b8975dd67..232eb0ccad7 100644 --- a/api/src/org/labkey/api/module/Module.java +++ b/api/src/org/labkey/api/module/Module.java @@ -29,7 +29,6 @@ import org.labkey.api.data.UpgradeCode; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.query.OlapSchemaInfo; -import org.labkey.api.resource.Resolver; import org.labkey.api.resource.Resource; import org.labkey.api.security.User; import org.labkey.api.util.Path; diff --git a/api/src/org/labkey/api/module/ModuleDependencySorter.java b/api/src/org/labkey/api/module/ModuleDependencySorter.java index eb09041a252..a01ed2c4afe 100644 --- a/api/src/org/labkey/api/module/ModuleDependencySorter.java +++ b/api/src/org/labkey/api/module/ModuleDependencySorter.java @@ -16,7 +16,8 @@ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -126,7 +127,7 @@ private Module findModuleWithoutDependencies(List>> dep private void graphModuleDependencies(List>> dependencies, @SuppressWarnings("SameParameterValue") String adjective) { - Logger log = Logger.getLogger(ModuleDependencySorter.class); + Logger log = LogManager.getLogger(ModuleDependencySorter.class); try { diff --git a/api/src/org/labkey/api/module/ModuleHtmlView.java b/api/src/org/labkey/api/module/ModuleHtmlView.java index 6da08509a12..39218637147 100644 --- a/api/src/org/labkey/api/module/ModuleHtmlView.java +++ b/api/src/org/labkey/api/module/ModuleHtmlView.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -45,7 +46,7 @@ public class ModuleHtmlView extends HtmlView { public static final Path VIEWS_PATH = Path.parse("views"); - private static final Logger LOG = Logger.getLogger(ModuleHtmlView.class); + private static final Logger LOG = LogManager.getLogger(ModuleHtmlView.class); private static final ModuleResourceCache> MODULE_HTML_VIEW_DEFINITION_CACHE = ModuleResourceCaches.create("HTML view definitions", new ModuleHtmlViewCacheHandler(), ResourceRootProvider.getStandard(VIEWS_PATH), ResourceRootProvider.getAssayProviders(VIEWS_PATH)); private final ModuleHtmlViewDefinition _viewdef; diff --git a/api/src/org/labkey/api/module/ModuleHtmlViewDefinition.java b/api/src/org/labkey/api/module/ModuleHtmlViewDefinition.java index c489b505e1e..97408f49f75 100644 --- a/api/src/org/labkey/api/module/ModuleHtmlViewDefinition.java +++ b/api/src/org/labkey/api/module/ModuleHtmlViewDefinition.java @@ -17,7 +17,8 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlOptions; import org.labkey.api.data.ColumnInfo; import org.labkey.api.resource.Resource; @@ -57,7 +58,7 @@ */ public class ModuleHtmlViewDefinition { - private static final Logger _log = Logger.getLogger(ModuleHtmlViewDefinition.class); + private static final Logger _log = LogManager.getLogger(ModuleHtmlViewDefinition.class); public static final String HTML_VIEW_EXTENSION = ".html"; public static final String VIEW_METADATA_EXTENSION = ".view.xml"; diff --git a/api/src/org/labkey/api/module/ModuleLoader.java b/api/src/org/labkey/api/module/ModuleLoader.java index bd30fbb6cf0..22ee62cfd72 100644 --- a/api/src/org/labkey/api/module/ModuleLoader.java +++ b/api/src/org/labkey/api/module/ModuleLoader.java @@ -19,9 +19,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Appender; -import org.apache.log4j.Logger; -import org.apache.log4j.RollingFileAppender; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.Constants; @@ -114,7 +113,6 @@ import java.util.Collection; import java.util.Collections; import java.util.Comparator; -import java.util.Enumeration; import java.util.HashMap; import java.util.LinkedHashSet; import java.util.LinkedList; @@ -140,7 +138,7 @@ */ public class ModuleLoader implements Filter, MemTrackerListener { - private static final Logger _log = Logger.getLogger(ModuleLoader.class); + private static final Logger _log = LogManager.getLogger(ModuleLoader.class); private static final Map _moduleFailures = new HashMap<>(); private static final Map _controllerNameToModule = new HashMap<>(); private static final Map _schemaNameToSchemaDetails = new CaseInsensitiveHashMap<>(); @@ -273,9 +271,6 @@ public List doInitWithSourceModule(List> explodedMo // CONSIDER: could optimize more by not - - rollErrorLogFile(_log); - setJavaVersion(); // make sure ConvertHelper is initialized @@ -789,39 +784,6 @@ private void setProjectRoot(Module core) } } - /** We want to roll the file every time the server starts, which isn't directly supported by Log4J so we do it manually */ - private void rollErrorLogFile(Logger logger) - { - while (logger != null && !logger.getAllAppenders().hasMoreElements()) - { - logger = (Logger)logger.getParent(); - } - - if (logger == null) - { - return; - } - - for (Enumeration e2 = logger.getAllAppenders(); e2.hasMoreElements();) - { - final Appender appender = (Appender)e2.nextElement(); - if (appender instanceof RollingFileAppender && "ERRORS".equals(appender.getName())) - { - RollingFileAppender rfa = (RollingFileAppender)appender; - String fileName = rfa.getFile(); - if (fileName == null) - { - throw new IllegalStateException("Error rolling labkey-errors.log file, likely a file permissions problem in CATALINA_HOME/logs"); - } - File f = new File(fileName); - if (f.exists() && f.length() > 0) - { - rfa.rollOver(); - } - } - } - } - private List loadModules(List> explodedModuleDirs) { ApplicationContext parentContext = ServiceRegistry.get().getApplicationContext(); diff --git a/api/src/org/labkey/api/module/ModuleResourceCache.java b/api/src/org/labkey/api/module/ModuleResourceCache.java index d5ae7cdcb7e..6b2c26170c7 100644 --- a/api/src/org/labkey/api/module/ModuleResourceCache.java +++ b/api/src/org/labkey/api/module/ModuleResourceCache.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.Constants; @@ -66,7 +67,7 @@ */ public final class ModuleResourceCache implements ModuleChangeListener { - private static final Logger LOG = Logger.getLogger(ModuleResourceCache.class); + private static final Logger LOG = LogManager.getLogger(ModuleResourceCache.class); private final BlockingCache _cache; private final ModuleResourceCacheHandler _handler; diff --git a/api/src/org/labkey/api/module/ModuleResourceCaches.java b/api/src/org/labkey/api/module/ModuleResourceCaches.java index 05e82082565..494e37f3d18 100644 --- a/api/src/org/labkey/api/module/ModuleResourceCaches.java +++ b/api/src/org/labkey/api/module/ModuleResourceCaches.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.util.PageFlowUtil; @@ -29,7 +30,7 @@ */ public class ModuleResourceCaches { - private static final Logger LOGGER = Logger.getLogger(ModuleResourceCaches.class); + private static final Logger LOGGER = LogManager.getLogger(ModuleResourceCaches.class); /** * Create a new ModuleResourceCache that finds its resources via one or more ResourceRootProviders. * diff --git a/api/src/org/labkey/api/module/ModuleResourceResolver.java b/api/src/org/labkey/api/module/ModuleResourceResolver.java index a5a8ef9568c..80097a619e5 100644 --- a/api/src/org/labkey/api/module/ModuleResourceResolver.java +++ b/api/src/org/labkey/api/module/ModuleResourceResolver.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.BlockingCache; import org.labkey.api.cache.Cache; @@ -44,7 +45,7 @@ */ public class ModuleResourceResolver implements Resolver { - private static final Logger LOG = Logger.getLogger(ModuleResourceResolver.class); + private static final Logger LOG = LogManager.getLogger(ModuleResourceResolver.class); private static final BlockingCache CACHE = CacheManager.getBlockingStringKeyCache(50000, CacheManager.DAY, "Module resources", null); private static final FileSystemWatcher WATCHER = FileSystemWatchers.get(); diff --git a/api/src/org/labkey/api/module/ModuleUpgrader.java b/api/src/org/labkey/api/module/ModuleUpgrader.java index 501b8de516f..0ddfcd94fba 100644 --- a/api/src/org/labkey/api/module/ModuleUpgrader.java +++ b/api/src/org/labkey/api/module/ModuleUpgrader.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import java.util.List; import java.util.ListIterator; @@ -28,7 +29,7 @@ */ public class ModuleUpgrader { - private static final Logger _log = Logger.getLogger(ModuleUpgrader.class); + private static final Logger _log = LogManager.getLogger(ModuleUpgrader.class); private final List _modules; diff --git a/api/src/org/labkey/api/module/ModuleXml.java b/api/src/org/labkey/api/module/ModuleXml.java index 77182bcd3b2..0fcd8b6d12d 100644 --- a/api/src/org/labkey/api/module/ModuleXml.java +++ b/api/src/org/labkey/api/module/ModuleXml.java @@ -1,6 +1,7 @@ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlOptions; import org.junit.Assert; import org.junit.Test; @@ -34,7 +35,7 @@ */ public class ModuleXml { - private static final Logger LOG = Logger.getLogger(ModuleXml.class); + private static final Logger LOG = LogManager.getLogger(ModuleXml.class); private static final String XML_FILENAME = "module.xml"; private final Map _moduleProperties; diff --git a/api/src/org/labkey/api/module/ResourceRootProvider.java b/api/src/org/labkey/api/module/ResourceRootProvider.java index 1f1d7502263..6a9c48124e6 100644 --- a/api/src/org/labkey/api/module/ResourceRootProvider.java +++ b/api/src/org/labkey/api/module/ResourceRootProvider.java @@ -16,9 +16,9 @@ package org.labkey.api.module; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssayService; import org.labkey.api.query.QueryService; import org.labkey.api.resource.Resource; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.Path; import java.util.Collection; diff --git a/api/src/org/labkey/api/module/SafeFlushResponseWrapper.java b/api/src/org/labkey/api/module/SafeFlushResponseWrapper.java index f387240e12e..5079b67f485 100644 --- a/api/src/org/labkey/api/module/SafeFlushResponseWrapper.java +++ b/api/src/org/labkey/api/module/SafeFlushResponseWrapper.java @@ -16,9 +16,9 @@ package org.labkey.api.module; -import javax.servlet.http.HttpServletResponseWrapper; -import javax.servlet.http.HttpServletResponse; import javax.servlet.ServletOutputStream; +import javax.servlet.http.HttpServletResponse; +import javax.servlet.http.HttpServletResponseWrapper; import java.io.IOException; import java.io.OutputStream; diff --git a/api/src/org/labkey/api/module/SchemaUpdateType.java b/api/src/org/labkey/api/module/SchemaUpdateType.java index 61c74a1f407..378646f8afd 100644 --- a/api/src/org/labkey/api/module/SchemaUpdateType.java +++ b/api/src/org/labkey/api/module/SchemaUpdateType.java @@ -20,7 +20,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.DbSchema; import org.labkey.api.data.SqlScriptRunner.SqlScript; -import org.labkey.api.data.SqlScriptRunner.SqlScriptException; import org.labkey.api.data.SqlScriptRunner.SqlScriptProvider; import java.util.Collection; diff --git a/api/src/org/labkey/api/module/SimpleFolderType.java b/api/src/org/labkey/api/module/SimpleFolderType.java index 8a788c5bb7d..d9f183bf737 100644 --- a/api/src/org/labkey/api/module/SimpleFolderType.java +++ b/api/src/org/labkey/api/module/SimpleFolderType.java @@ -15,8 +15,9 @@ */ package org.labkey.api.module; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -57,7 +58,7 @@ */ public class SimpleFolderType extends MultiPortalFolderType { - private static final Logger LOGGER = Logger.getLogger(SimpleFolderType.class); + private static final Logger LOGGER = LogManager.getLogger(SimpleFolderType.class); private final String _name; private final String _description; @@ -156,7 +157,7 @@ public static SimpleFolderType create(Resource folderTypeFile) private static FolderType parseFile(Resource folderTypeFile) { - Logger log = Logger.getLogger(SimpleFolderType.class); + Logger log = LogManager.getLogger(SimpleFolderType.class); XmlOptions xmlOptions = new XmlOptions(); Map namespaceMap = new HashMap<>(); diff --git a/api/src/org/labkey/api/module/SimpleModule.java b/api/src/org/labkey/api/module/SimpleModule.java index f2f4a520bff..38ab85e15af 100644 --- a/api/src/org/labkey/api/module/SimpleModule.java +++ b/api/src/org/labkey/api/module/SimpleModule.java @@ -16,7 +16,8 @@ package org.labkey.api.module; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -61,7 +62,7 @@ */ public class SimpleModule extends SpringModule { - private static final Logger _log = Logger.getLogger(ModuleUpgrader.class); + private static final Logger _log = LogManager.getLogger(ModuleUpgrader.class); public static String NAMESPACE_PREFIX = "ExtensibleTable"; public static String DOMAIN_NAMESPACE_PREFIX_TEMPLATE = NAMESPACE_PREFIX + "-${SchemaName}"; diff --git a/api/src/org/labkey/api/module/SimpleModuleContainerListener.java b/api/src/org/labkey/api/module/SimpleModuleContainerListener.java index f96b7417870..bb7d16ef7ba 100644 --- a/api/src/org/labkey/api/module/SimpleModuleContainerListener.java +++ b/api/src/org/labkey/api/module/SimpleModuleContainerListener.java @@ -16,7 +16,7 @@ package org.labkey.api.module; import org.apache.commons.lang3.ArrayUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -68,7 +68,7 @@ protected void purgeSchema(String schemaName, Container c, User user) if (userSchema == null) return; - Logger.getLogger(SimpleModuleContainerListener.class).debug("Purging schema '" + schemaName + "' in container '" + c.getPath() + "'..."); + LogManager.getLogger(SimpleModuleContainerListener.class).debug("Purging schema '" + schemaName + "' in container '" + c.getPath() + "'..."); // Walk over the dbSchema's tables -- it's faster than walking the UserSchema's tables List sorted = dbSchema.getSortedTables(); diff --git a/api/src/org/labkey/api/module/SimpleWebPartFactory.java b/api/src/org/labkey/api/module/SimpleWebPartFactory.java index b4a12a4b500..102c1038672 100644 --- a/api/src/org/labkey/api/module/SimpleWebPartFactory.java +++ b/api/src/org/labkey/api/module/SimpleWebPartFactory.java @@ -15,7 +15,8 @@ */ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlOptions; import org.jetbrains.annotations.NotNull; import org.json.JSONObject; @@ -108,7 +109,7 @@ public static boolean isWebPartFile(String filename) private void loadDefinition(Resource webPartResource) { - Logger log = Logger.getLogger(SimpleWebPartFactory.class); + Logger log = LogManager.getLogger(SimpleWebPartFactory.class); try (InputStream is = webPartResource.getInputStream()) { diff --git a/api/src/org/labkey/api/module/SpringModule.java b/api/src/org/labkey/api/module/SpringModule.java index aa3d34b70c3..0782ce49044 100644 --- a/api/src/org/labkey/api/module/SpringModule.java +++ b/api/src/org/labkey/api/module/SpringModule.java @@ -16,7 +16,8 @@ package org.labkey.api.module; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.services.ServiceRegistry; import org.labkey.api.settings.AppProps; @@ -66,7 +67,7 @@ */ public abstract class SpringModule extends DefaultModule { - private static final Logger _log = Logger.getLogger(SpringModule.class); + private static final Logger _log = LogManager.getLogger(SpringModule.class); /** * The name of the init parameter on the ServletContext specifying diff --git a/api/src/org/labkey/api/module/testSimpleModule.jsp b/api/src/org/labkey/api/module/testSimpleModule.jsp index 30b1e36fe5e..d2c9e6dd800 100644 --- a/api/src/org/labkey/api/module/testSimpleModule.jsp +++ b/api/src/org/labkey/api/module/testSimpleModule.jsp @@ -1,4 +1,3 @@ -<%@ page import="org.junit.Test" %> <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.module.SimpleModule" %> <%@ page import="org.labkey.api.util.GUID" %> diff --git a/api/src/org/labkey/api/pipeline/AbstractTaskFactory.java b/api/src/org/labkey/api/pipeline/AbstractTaskFactory.java index c5d9b34a0df..d8dfb19199c 100644 --- a/api/src/org/labkey/api/pipeline/AbstractTaskFactory.java +++ b/api/src/org/labkey/api/pipeline/AbstractTaskFactory.java @@ -15,7 +15,7 @@ */ package org.labkey.api.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.module.Module; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; diff --git a/api/src/org/labkey/api/pipeline/LocalDirectory.java b/api/src/org/labkey/api/pipeline/LocalDirectory.java index 7699717dc93..a6980ac183d 100644 --- a/api/src/org/labkey/api/pipeline/LocalDirectory.java +++ b/api/src/org/labkey/api/pipeline/LocalDirectory.java @@ -17,7 +17,7 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/api/src/org/labkey/api/pipeline/NullSafeBindExceptionSerializer.java b/api/src/org/labkey/api/pipeline/NullSafeBindExceptionSerializer.java index ddcecb9bcc8..ce1b725d844 100644 --- a/api/src/org/labkey/api/pipeline/NullSafeBindExceptionSerializer.java +++ b/api/src/org/labkey/api/pipeline/NullSafeBindExceptionSerializer.java @@ -1,18 +1,18 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.pipeline; import com.fasterxml.jackson.core.JsonGenerator; @@ -22,7 +22,6 @@ import com.fasterxml.jackson.databind.jsontype.TypeSerializer; import com.fasterxml.jackson.databind.ser.std.StdSerializer; import org.labkey.api.action.NullSafeBindException; -import org.labkey.api.util.Pair; import java.io.IOException; diff --git a/api/src/org/labkey/api/pipeline/ParamParser.java b/api/src/org/labkey/api/pipeline/ParamParser.java index 196d38395db..cf9d46f1370 100644 --- a/api/src/org/labkey/api/pipeline/ParamParser.java +++ b/api/src/org/labkey/api/pipeline/ParamParser.java @@ -15,10 +15,10 @@ */ package org.labkey.api.pipeline; -import java.io.InputStream; -import java.util.Map; import java.io.File; import java.io.IOException; +import java.io.InputStream; +import java.util.Map; /** * ParamParser diff --git a/api/src/org/labkey/api/pipeline/PathSerialization.java b/api/src/org/labkey/api/pipeline/PathSerialization.java index caf72701cf7..5242beee67b 100644 --- a/api/src/org/labkey/api/pipeline/PathSerialization.java +++ b/api/src/org/labkey/api/pipeline/PathSerialization.java @@ -1,18 +1,18 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.pipeline; import com.fasterxml.jackson.core.JsonGenerator; @@ -26,8 +26,8 @@ import com.fasterxml.jackson.databind.ser.std.StdSerializer; import org.labkey.api.util.FileUtil; -import java.io.IOException; import java.io.File; +import java.io.IOException; import java.nio.file.Path; public class PathSerialization diff --git a/api/src/org/labkey/api/pipeline/PipeRoot.java b/api/src/org/labkey/api/pipeline/PipeRoot.java index 30e43e25e32..6215a20ec4e 100644 --- a/api/src/org/labkey/api/pipeline/PipeRoot.java +++ b/api/src/org/labkey/api/pipeline/PipeRoot.java @@ -16,7 +16,7 @@ package org.labkey.api.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/api/src/org/labkey/api/pipeline/PipelineJob.java b/api/src/org/labkey/api/pipeline/PipelineJob.java index 7cfee7d901a..f4e0bc50bea 100644 --- a/api/src/org/labkey/api/pipeline/PipelineJob.java +++ b/api/src/org/labkey/api/pipeline/PipelineJob.java @@ -22,14 +22,11 @@ import com.fasterxml.jackson.databind.module.SimpleModule; import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Appender; -import org.apache.log4j.Category; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; -import org.apache.log4j.PatternLayout; -import org.apache.log4j.spi.HierarchyEventListener; -import org.apache.log4j.spi.LoggerFactory; -import org.apache.log4j.spi.LoggerRepository; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.simple.SimpleLogger; +import org.apache.logging.log4j.util.PropertiesUtil; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.NullSafeBindException; @@ -42,13 +39,13 @@ import org.labkey.api.query.SchemaKey; import org.labkey.api.reader.Readers; import org.labkey.api.security.User; +import org.labkey.api.util.DateUtil; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.GUID; import org.labkey.api.util.Job; import org.labkey.api.util.NetworkDrive; -import org.labkey.api.util.SafeFileAppender; import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; @@ -68,14 +65,14 @@ import java.net.URI; import java.nio.file.Path; import java.sql.Time; +import java.text.SimpleDateFormat; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.Enumeration; +import java.util.Date; import java.util.List; import java.util.Map; import java.util.Objects; -import java.util.Vector; import java.util.concurrent.ExecutionException; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; @@ -100,14 +97,14 @@ abstract public class PipelineJob extends Job implements Serializable public static final String PIPELINE_TASK_INFO_PARAM = "pipeline, taskInfo"; public static final String PIPELINE_TASK_OUTPUT_PARAMS_PARAM = "pipeline, taskOutputParams"; - protected static Logger _log = Logger.getLogger(PipelineJob.class); + protected static Logger _log = LogManager.getLogger(PipelineJob.class); // Send start/stop messages to a separate logger because the default logger for this class is set to // only write ERROR level events to the system log - private static final Logger _logJobStopStart = Logger.getLogger(Job.class); + private static final Logger _logJobStopStart = LogManager.getLogger(Job.class); public static Logger getJobLogger(Class clazz) { - return Logger.getLogger(PipelineJob.class.getName() + ".." + clazz.getName()); + return LogManager.getLogger(PipelineJob.class.getName() + ".." + clazz.getName()); } public RecordedActionSet getActionSet() @@ -272,6 +269,7 @@ public PipelineJob getJob() protected transient Logger _logger; private transient boolean _settingStatus; private transient PipelineQueue _queue; + private File _logFile; private LocalDirectory _localDirectory; @@ -799,6 +797,7 @@ public void runActiveTask() throws IOException, PipelineJobException { getLogger().info((success ? "Successfully completed" : "Failed to complete") + " task '" + factory.getId() + "'"); logStartStopInfo((success ? "Successfully completed" : "Failed to complete") + " task '" + factory.getId() + "' for job '" + toString() + "' with log file " + getLogFile()); + try { if (workDirectory != null) @@ -1354,100 +1353,111 @@ else if (count == logLineInterval) } - ///////////////////////////////////////////////////////////////////////// - // Logging - - /** - * Log4J Logger subclass to allow us to create loggers that are not cached - * in the Log4J repository for the life of the webapp. This logger also - * logs to the weblog for the PipelineJob class, allowing administrators - * to collect whatever level of logging they want from PipelineJobs. - */ - private static class OutputLogger extends Logger + public String getLogLevel() { - private final PipelineJob _job; - private boolean _isSettingStatus; + return _loggerLevel; + } - // Required for xstream serialization on Java 7 - @SuppressWarnings({"UnusedDeclaration"}) - private OutputLogger() + public void setLogLevel(String level) + { + if (!_loggerLevel.equals(level)) { - //noinspection NullableProblems - this(null, ""); + _loggerLevel = level; + _logger = null; // Reset the logger } + } + + public Logger getClassLogger() + { + return _log; + } - protected OutputLogger(PipelineJob job, String name) + private static class OutputLogger extends SimpleLogger + { + private final PipelineJob _job; + private boolean _isSettingStatus; + private File _file; + private final String LINE_SEP = System.getProperty("line.separator"); + private final String datePattern = "dd MMM yyyy HH:mm:ss,SSS"; + + protected OutputLogger(PipelineJob job, File file, String name, Level level) { - super(name); + super(name, level, false, false, false, false, "", null, new PropertiesUtil(PropertiesUtil.getSystemProperties()), null); _job = job; - repository = new OutputLoggerRepository(name, this); + _file = file; + } @Override - public void debug(Object message) + public void debug(String message) { - debug(message, null); + _job.getClassLogger().debug(getSystemLogMessage(message)); + write(message, null, Level.DEBUG.toString()); } @Override - public void debug(Object message, @Nullable Throwable t) + public void debug(String message, @Nullable Throwable t) { _job.getClassLogger().debug(getSystemLogMessage(message), t); - super.debug(message, t); + write(message, t, Level.DEBUG.toString()); } @Override - public void info(Object message) + public void info(String message) { - info(message, null); + _job.getClassLogger().info(getSystemLogMessage(message)); + write(message, null, Level.INFO.toString()); } @Override - public void info(Object message, @Nullable Throwable t) + public void info(String message, @Nullable Throwable t) { _job.getClassLogger().info(getSystemLogMessage(message), t); - super.info(message, t); + write(message, t, Level.INFO.toString()); } @Override - public void warn(Object message) + public void warn(String message) { - warn(message, null); + _job.getClassLogger().warn(getSystemLogMessage(message)); + write(message, null, Level.WARN.toString()); } @Override - public void warn(Object message, @Nullable Throwable t) + public void warn(String message, @Nullable Throwable t) { _job.getClassLogger().warn(getSystemLogMessage(message), t); - super.warn(message, t); + write(message, t, Level.WARN.toString()); } @Override - public void error(Object message) + public void error(String message) { - error(message, null); + _job.getClassLogger().error(getSystemLogMessage(message)); + write(message, null, Level.ERROR.toString()); } @Override - public void error(Object message, @Nullable Throwable t) + public void error(String message, @Nullable Throwable t) { _job.getClassLogger().error(getSystemLogMessage(message), t); - super.error(message, t); + write(message, t, Level.ERROR.toString()); setErrorStatus(message); } @Override - public void fatal(Object message) + public void fatal(String message) { - fatal(message, null); + _job.getClassLogger().fatal(getSystemLogMessage(message)); + write(message, null, Level.FATAL.toString()); } @Override - public void fatal(Object message, Throwable t) + public void fatal(String message, Throwable t) { _job.getClassLogger().fatal(getSystemLogMessage(message), t); - super.fatal(message, t); + write(message, t, Level.FATAL.toString()); setErrorStatus(message); } @@ -1487,128 +1497,35 @@ public void setErrorStatus(Object message) _isSettingStatus = false; } } - } - private static class OutputLoggerRepository implements LoggerRepository - { - private final String _name; - private final OutputLogger _outputLogger; - - protected OutputLoggerRepository(String name, OutputLogger logger) + public void write(String message, @Nullable Throwable t, String level) { - _name = name; - _outputLogger = logger; - } + String formattedDate = DateUtil.formatDateTime(new Date(), datePattern); - @Override - public void addHierarchyEventListener(HierarchyEventListener listener) - { - } - - @Override - public boolean isDisabled(int level) - { - return false; - } - - @Override - public void setThreshold(Level level) - { - } - - @Override - public void setThreshold(String val) - { - } - - @Override - public void emitNoAppenderWarning(Category cat) - { - } - - @Override - public Level getThreshold() - { - return null; - } - - @Override - public Logger getLogger(String name) - { - if (_name.equals(name)) - return _outputLogger; - return null; - } - - @Override - public Logger getLogger(String name, LoggerFactory factory) - { - throw new UnsupportedOperationException(); - } - - @Override - public Logger getRootLogger() - { - return _outputLogger; - } - - @Override - public Logger exists(String name) - { - if (_name.equals(name)) - return _outputLogger; - return null; - } - - @Override - public void shutdown() - { - } - - @Override - public Enumeration getCurrentLoggers() - { - Vector v = new Vector<>(); - v.add(_outputLogger); - return v.elements(); - } - - @Override - public Enumeration getCurrentCategories() - { - return getCurrentLoggers(); - } - - @Override - public void fireAddAppenderEvent(Category logger, Appender appender) - { - } - - @Override - public void resetConfiguration() - { - } - } - - public String getLogLevel() - { - return _loggerLevel; - } - - public void setLogLevel(String level) - { - if (!_loggerLevel.equals(level)) - { - _loggerLevel = level; - _logger = null; // Reset the logger + try (PrintWriter writer = new PrintWriter(new FileWriter(_file, true))) + { + var line = formattedDate + " " + + String.format("%-5s", level) + + " : " + + message; + writer.write(line); + writer.write(LINE_SEP); + if (null != t) + { + t.printStackTrace(writer); + } + } + catch (IOException e) + { + File parentFile = _file.getParentFile(); + if (parentFile != null && !NetworkDrive.exists(parentFile) && parentFile.mkdirs()) + write(message, t, level); + else + _log.error("Failed appending to file.", e); + } } } - public Logger getClassLogger() - { - return _log; - } - // Multiple threads log messages, so synchronize to make sure that no one gets a partially intitialized logger public synchronized Logger getLogger() { @@ -1618,13 +1535,10 @@ public synchronized Logger getLogger() throw new IllegalStateException("LogFile null or cloud."); File logFile = null != _logFile ? _logFile : new File(_logFilePathName); + // Create appending logger. - _logger = new OutputLogger(this, PipelineJob.class.getSimpleName() + ".Logger." + _logFilePathName); - _logger.removeAllAppenders(); - SafeFileAppender appender = new SafeFileAppender(logFile); - appender.setLayout(new PatternLayout("%d{DATE} %-5p: %m%n")); - _logger.addAppender(appender); - _logger.setLevel(Level.toLevel(_loggerLevel)); + String loggerName = PipelineJob.class.getSimpleName() + ".Logger." + _logFilePathName; + _logger = new OutputLogger(this, logFile, loggerName, Level.toLevel(_loggerLevel)); } return _logger; diff --git a/api/src/org/labkey/api/pipeline/PipelineJobData.java b/api/src/org/labkey/api/pipeline/PipelineJobData.java index d7f28352d3f..437a0c15d35 100644 --- a/api/src/org/labkey/api/pipeline/PipelineJobData.java +++ b/api/src/org/labkey/api/pipeline/PipelineJobData.java @@ -16,8 +16,8 @@ package org.labkey.api.pipeline; -import java.util.List; import java.util.ArrayList; +import java.util.List; public class PipelineJobData { diff --git a/api/src/org/labkey/api/pipeline/PipelineJobService.java b/api/src/org/labkey/api/pipeline/PipelineJobService.java index 9439240db9a..a078d85482d 100644 --- a/api/src/org/labkey/api/pipeline/PipelineJobService.java +++ b/api/src/org/labkey/api/pipeline/PipelineJobService.java @@ -15,7 +15,7 @@ */ package org.labkey.api.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.file.PathMapper; diff --git a/api/src/org/labkey/api/pipeline/PipelineProtocol.java b/api/src/org/labkey/api/pipeline/PipelineProtocol.java index 8c317dafbdd..0e74addfc09 100644 --- a/api/src/org/labkey/api/pipeline/PipelineProtocol.java +++ b/api/src/org/labkey/api/pipeline/PipelineProtocol.java @@ -20,12 +20,12 @@ import org.fhcrc.cpas.pipeline.protocol.xml.PipelineProtocolPropsDocument; import org.labkey.api.util.NetworkDrive; -import java.io.IOException; -import java.io.File; import java.beans.PropertyDescriptor; -import java.util.Map; -import java.util.HashMap; +import java.io.File; +import java.io.IOException; import java.lang.reflect.InvocationTargetException; +import java.util.HashMap; +import java.util.Map; /** * A protocol captures settings to be used when running a pipeline. Values are often passed to tools diff --git a/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java b/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java index e2ae32937a6..012f3be916c 100644 --- a/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java +++ b/api/src/org/labkey/api/pipeline/PipelineProtocolFactory.java @@ -15,7 +15,8 @@ */ package org.labkey.api.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlOptions; import org.fhcrc.cpas.pipeline.protocol.xml.PipelineProtocolPropsDocument; import org.labkey.api.util.FileUtil; @@ -39,7 +40,7 @@ public abstract class PipelineProtocolFactory protected static final String _pipelineProtocolDir = "protocols"; private static final String _archivedProtocolDir = "archived"; - private static final Logger LOG = Logger.getLogger(PipelineProtocolFactory.class); + private static final Logger LOG = LogManager.getLogger(PipelineProtocolFactory.class); public static File getProtocolRootDir(PipeRoot root) { diff --git a/api/src/org/labkey/api/pipeline/PropertiesJobSupport.java b/api/src/org/labkey/api/pipeline/PropertiesJobSupport.java index 80f42501182..8cc2c2d68b2 100644 --- a/api/src/org/labkey/api/pipeline/PropertiesJobSupport.java +++ b/api/src/org/labkey/api/pipeline/PropertiesJobSupport.java @@ -16,6 +16,7 @@ package org.labkey.api.pipeline; import org.labkey.api.exp.PropertyDescriptor; + import java.util.Map; /** diff --git a/api/src/org/labkey/api/pipeline/RecordedAction.java b/api/src/org/labkey/api/pipeline/RecordedAction.java index ad136803055..48c89d99dc5 100644 --- a/api/src/org/labkey/api/pipeline/RecordedAction.java +++ b/api/src/org/labkey/api/pipeline/RecordedAction.java @@ -25,14 +25,11 @@ import java.io.File; import java.io.Serializable; import java.net.URI; -import java.util.ArrayList; import java.util.Collections; import java.util.Date; -import java.util.HashMap; import java.util.HashSet; import java.util.LinkedHashMap; import java.util.LinkedHashSet; -import java.util.List; import java.util.Map; import java.util.Set; diff --git a/api/src/org/labkey/api/pipeline/RecordedActionSet.java b/api/src/org/labkey/api/pipeline/RecordedActionSet.java index ea558379a21..51094a2ba3b 100644 --- a/api/src/org/labkey/api/pipeline/RecordedActionSet.java +++ b/api/src/org/labkey/api/pipeline/RecordedActionSet.java @@ -20,9 +20,14 @@ import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import com.fasterxml.jackson.databind.annotation.JsonSerialize; -import java.util.*; import java.io.File; import java.net.URI; +import java.util.Arrays; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.LinkedHashSet; +import java.util.Map; +import java.util.Set; /** * A collection of all the recorded actions performed in the context of a single pipeline job. diff --git a/api/src/org/labkey/api/pipeline/TaskFactory.java b/api/src/org/labkey/api/pipeline/TaskFactory.java index df724ea2ea3..86be57d03d9 100644 --- a/api/src/org/labkey/api/pipeline/TaskFactory.java +++ b/api/src/org/labkey/api/pipeline/TaskFactory.java @@ -15,7 +15,7 @@ */ package org.labkey.api.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.module.Module; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; import org.labkey.api.util.FileType; diff --git a/api/src/org/labkey/api/pipeline/WorkDirFactory.java b/api/src/org/labkey/api/pipeline/WorkDirFactory.java index 07dbbe2e5ff..f7df67b18d1 100644 --- a/api/src/org/labkey/api/pipeline/WorkDirFactory.java +++ b/api/src/org/labkey/api/pipeline/WorkDirFactory.java @@ -15,11 +15,11 @@ */ package org.labkey.api.pipeline; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; -import org.apache.log4j.Logger; -import java.io.IOException; import java.io.File; +import java.io.IOException; /** * WorkDirFactory diff --git a/api/src/org/labkey/api/pipeline/browse/PipelinePathForm.java b/api/src/org/labkey/api/pipeline/browse/PipelinePathForm.java index c176780883b..d2e2494e4c5 100644 --- a/api/src/org/labkey/api/pipeline/browse/PipelinePathForm.java +++ b/api/src/org/labkey/api/pipeline/browse/PipelinePathForm.java @@ -18,19 +18,19 @@ import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.util.FileUtil; +import org.labkey.api.util.NetworkDrive; import org.labkey.api.view.NotFoundException; import org.labkey.api.view.ViewForm; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; import java.io.File; import java.nio.file.Files; import java.nio.file.Path; -import java.util.List; import java.util.ArrayList; +import java.util.List; /** * PipelinePathForm diff --git a/api/src/org/labkey/api/pipeline/cmd/CommandTaskFactorySettings.java b/api/src/org/labkey/api/pipeline/cmd/CommandTaskFactorySettings.java index cb4b4938872..74e7e17c457 100644 --- a/api/src/org/labkey/api/pipeline/cmd/CommandTaskFactorySettings.java +++ b/api/src/org/labkey/api/pipeline/cmd/CommandTaskFactorySettings.java @@ -20,9 +20,9 @@ import org.labkey.api.pipeline.WorkDirectory; import org.labkey.api.util.FileType; -import java.util.Map; import java.util.HashMap; import java.util.List; +import java.util.Map; /** * CommandTaskFactorySettings may be used with Spring configuration diff --git a/api/src/org/labkey/api/pipeline/cmd/TaskPath.java b/api/src/org/labkey/api/pipeline/cmd/TaskPath.java index 7a68fcba774..7287574954a 100644 --- a/api/src/org/labkey/api/pipeline/cmd/TaskPath.java +++ b/api/src/org/labkey/api/pipeline/cmd/TaskPath.java @@ -17,8 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.util.FileType; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; +import org.labkey.api.util.FileType; /** * TaskPath is an abstract specifier of how an input/output file diff --git a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisJob.java b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisJob.java index f75c801ded4..cf6b43d4c88 100644 --- a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisJob.java +++ b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisJob.java @@ -15,7 +15,8 @@ */ package org.labkey.api.pipeline.file; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.RowMapFactory; @@ -55,7 +56,7 @@ */ abstract public class AbstractFileAnalysisJob extends PipelineJob implements FileAnalysisJobSupport { - private static final Logger _log = Logger.getLogger(AbstractFileAnalysisJob.class); + private static final Logger _log = LogManager.getLogger(AbstractFileAnalysisJob.class); protected Integer _experimentRunRowId; private String _protocolName; diff --git a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java index 3cfdb717673..064030128f0 100644 --- a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java +++ b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocol.java @@ -16,7 +16,8 @@ package org.labkey.api.pipeline.file; import org.apache.commons.io.input.ReaderInputStream; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.ApiUsageException; import org.labkey.api.data.Container; @@ -52,7 +53,7 @@ public abstract class AbstractFileAnalysisProtocol extends PipelineProtocol { - private static Logger _log = Logger.getLogger(AbstractFileAnalysisProtocol.class); + private static Logger _log = LogManager.getLogger(AbstractFileAnalysisProtocol.class); public static final String LEGACY_JOINED_BASENAME = "all"; diff --git a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java index 3329080ba72..84974921262 100644 --- a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java +++ b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProtocolFactory.java @@ -17,7 +17,8 @@ import org.apache.commons.io.input.ReaderInputStream; import org.apache.commons.lang3.ArrayUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.ParamParser; import org.labkey.api.pipeline.PipeRoot; @@ -47,7 +48,7 @@ */ abstract public class AbstractFileAnalysisProtocolFactory extends PipelineProtocolFactory { - private static Logger _log = Logger.getLogger(AbstractFileAnalysisProtocolFactory.class); + private static Logger _log = LogManager.getLogger(AbstractFileAnalysisProtocolFactory.class); public static final String DEFAULT_PARAMETERS_NAME = "default"; diff --git a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProvider.java b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProvider.java index 59180672769..14c6eed3961 100644 --- a/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProvider.java +++ b/api/src/org/labkey/api/pipeline/file/AbstractFileAnalysisProvider.java @@ -15,9 +15,9 @@ */ package org.labkey.api.pipeline.file; +import org.labkey.api.module.Module; import org.labkey.api.pipeline.PipelineProvider; import org.labkey.api.pipeline.TaskPipeline; -import org.labkey.api.module.Module; import java.io.File; diff --git a/api/src/org/labkey/api/pipeline/file/FileImportTask.java b/api/src/org/labkey/api/pipeline/file/FileImportTask.java index 4d2369d80bd..2d2591c5329 100644 --- a/api/src/org/labkey/api/pipeline/file/FileImportTask.java +++ b/api/src/org/labkey/api/pipeline/file/FileImportTask.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.pipeline.AbstractTaskFactory; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.RecordedAction; import org.labkey.api.pipeline.RecordedActionSet; import org.labkey.api.pipeline.cmd.FileImportTaskFactorySettings; diff --git a/api/src/org/labkey/api/premium/AntiVirusService.java b/api/src/org/labkey/api/premium/AntiVirusService.java index 2475dd6e23a..e2f20926dd6 100644 --- a/api/src/org/labkey/api/premium/AntiVirusService.java +++ b/api/src/org/labkey/api/premium/AntiVirusService.java @@ -1,23 +1,22 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.premium; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.security.User; import org.labkey.api.services.ServiceRegistry; import org.labkey.api.util.JobRunner; import org.labkey.api.view.ViewBackgroundInfo; diff --git a/api/src/org/labkey/api/premium/PremiumService.java b/api/src/org/labkey/api/premium/PremiumService.java index 02e45734eca..758d9efb61c 100644 --- a/api/src/org/labkey/api/premium/PremiumService.java +++ b/api/src/org/labkey/api/premium/PremiumService.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.Container; import org.labkey.api.services.ServiceRegistry; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; diff --git a/api/src/org/labkey/api/qc/DataExchangeHandler.java b/api/src/org/labkey/api/qc/DataExchangeHandler.java index 950f26be5f3..b2c24cf01d0 100644 --- a/api/src/org/labkey/api/qc/DataExchangeHandler.java +++ b/api/src/org/labkey/api/qc/DataExchangeHandler.java @@ -16,12 +16,12 @@ package org.labkey.api.qc; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayRunUploadContext; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.query.ValidationException; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; import org.labkey.api.util.Pair; import org.labkey.api.view.ViewContext; diff --git a/api/src/org/labkey/api/qc/DataTransformer.java b/api/src/org/labkey/api/qc/DataTransformer.java index 97200b75cae..2632c24590c 100644 --- a/api/src/org/labkey/api/qc/DataTransformer.java +++ b/api/src/org/labkey/api/qc/DataTransformer.java @@ -16,10 +16,10 @@ package org.labkey.api.qc; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.query.ValidationException; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.query.ValidationException; /** * Takes assay data and runs it through the configured transform scripts. Each script may transform it into a new diff --git a/api/src/org/labkey/api/qc/DefaultTransformResult.java b/api/src/org/labkey/api/qc/DefaultTransformResult.java index 59bf2a224a3..2aa131858e1 100644 --- a/api/src/org/labkey/api/qc/DefaultTransformResult.java +++ b/api/src/org/labkey/api/qc/DefaultTransformResult.java @@ -16,7 +16,8 @@ package org.labkey.api.qc; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.property.DomainProperty; @@ -39,7 +40,7 @@ public class DefaultTransformResult implements TransformResult private String _comments; private String _warnings; private List _files; - private static final Logger LOG = Logger.getLogger(DefaultTransformResult.class); + private static final Logger LOG = LogManager.getLogger(DefaultTransformResult.class); @Override public List getFiles() diff --git a/api/src/org/labkey/api/qc/TransformDataHandler.java b/api/src/org/labkey/api/qc/TransformDataHandler.java index 187110d28d0..a8eb6bb7628 100644 --- a/api/src/org/labkey/api/qc/TransformDataHandler.java +++ b/api/src/org/labkey/api/qc/TransformDataHandler.java @@ -16,13 +16,13 @@ package org.labkey.api.qc; +import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.assay.AssayRunUploadContext; -import java.util.Map; import java.util.List; +import java.util.Map; /** * User: klum diff --git a/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java b/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java index e49c31bbad9..3ce026fafc2 100644 --- a/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java +++ b/api/src/org/labkey/api/qc/TsvDataExchangeHandler.java @@ -17,9 +17,19 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayFileWriter; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUploadXarContext; +import org.labkey.api.assay.DefaultAssayRunCreator; +import org.labkey.api.assay.TsvDataHandler; +import org.labkey.api.assay.actions.AssayRunUploadForm; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.Container; import org.labkey.api.data.TSVWriter; import org.labkey.api.exp.ExperimentDataHandler; @@ -45,15 +55,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.settings.AppProps; -import org.labkey.api.assay.actions.AssayRunUploadForm; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUploadXarContext; -import org.labkey.api.assay.DefaultAssayRunCreator; -import org.labkey.api.assay.TsvDataHandler; import org.labkey.api.util.GUID; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; @@ -124,7 +125,7 @@ public enum errLevel { private Map _formFields = new HashMap<>(); private Map>> _sampleProperties = new HashMap<>(); - private static final Logger LOG = Logger.getLogger(TsvDataExchangeHandler.class); + private static final Logger LOG = LogManager.getLogger(TsvDataExchangeHandler.class); private DataSerializer _serializer = new TsvDataSerializer(); /** Files that shouldn't be considered part of the run's output, such as the transform script itself */ diff --git a/api/src/org/labkey/api/qc/TsvDataSerializer.java b/api/src/org/labkey/api/qc/TsvDataSerializer.java index a7be82fc0ac..7d9fc9b29b8 100644 --- a/api/src/org/labkey/api/qc/TsvDataSerializer.java +++ b/api/src/org/labkey/api/qc/TsvDataSerializer.java @@ -17,13 +17,13 @@ package org.labkey.api.qc; import org.apache.commons.lang3.StringUtils; +import org.labkey.api.assay.AbstractAssayTsvDataHandler; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; import org.labkey.api.exp.MvFieldWrapper; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.property.Domain; import org.labkey.api.reader.DataLoader; -import org.labkey.api.assay.AbstractAssayTsvDataHandler; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.DateUtil; import org.labkey.api.writer.PrintWriters; diff --git a/api/src/org/labkey/api/qc/ValidationDataHandler.java b/api/src/org/labkey/api/qc/ValidationDataHandler.java index 421c08ab1a7..b61b17d1923 100644 --- a/api/src/org/labkey/api/qc/ValidationDataHandler.java +++ b/api/src/org/labkey/api/qc/ValidationDataHandler.java @@ -15,7 +15,7 @@ */ package org.labkey.api.qc; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.XarContext; import org.labkey.api.exp.api.DataType; diff --git a/api/src/org/labkey/api/query/AbstractMethodInfo.java b/api/src/org/labkey/api/query/AbstractMethodInfo.java index 8223c4081b3..afa69100b76 100644 --- a/api/src/org/labkey/api/query/AbstractMethodInfo.java +++ b/api/src/org/labkey/api/query/AbstractMethodInfo.java @@ -16,10 +16,17 @@ package org.labkey.api.query; -import org.labkey.api.data.*; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.ColumnLogging; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MethodInfo; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; -import java.util.List; import java.util.ArrayList; +import java.util.List; abstract public class AbstractMethodInfo implements MethodInfo { diff --git a/api/src/org/labkey/api/query/AbstractNestableDataRegion.java b/api/src/org/labkey/api/query/AbstractNestableDataRegion.java index 37c24097759..9cbe58ac978 100644 --- a/api/src/org/labkey/api/query/AbstractNestableDataRegion.java +++ b/api/src/org/labkey/api/query/AbstractNestableDataRegion.java @@ -16,15 +16,22 @@ package org.labkey.api.query; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.GroupedResultSet; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.ResultsImpl; +import org.labkey.api.data.RuntimeSQLException; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.ResultSetUtil; import org.labkey.api.view.JspView; -import java.io.Writer; import java.io.IOException; -import java.sql.SQLException; +import java.io.Writer; import java.sql.ResultSet; +import java.sql.SQLException; import java.util.List; import java.util.Map; diff --git a/api/src/org/labkey/api/query/AbstractQueryImportAction.java b/api/src/org/labkey/api/query/AbstractQueryImportAction.java index 917d322fe86..1c7dd2c02eb 100644 --- a/api/src/org/labkey/api/query/AbstractQueryImportAction.java +++ b/api/src/org/labkey/api/query/AbstractQueryImportAction.java @@ -25,6 +25,7 @@ import org.labkey.api.action.ExtFormResponseWriter; import org.labkey.api.action.FormApiAction; import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.attachments.FileAttachmentFile; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; @@ -45,7 +46,6 @@ import org.labkey.api.resource.Resource; import org.labkey.api.security.User; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.util.CPUTimer; import org.labkey.api.util.FileStream; import org.labkey.api.util.PageFlowUtil; diff --git a/api/src/org/labkey/api/query/AliasManager.java b/api/src/org/labkey/api/query/AliasManager.java index ae0202afaec..61558752d36 100644 --- a/api/src/org/labkey/api/query/AliasManager.java +++ b/api/src/org/labkey/api/query/AliasManager.java @@ -25,9 +25,9 @@ import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DbSchema; import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.TableInfo; import org.labkey.api.data.dialect.MockSqlDialect; import org.labkey.api.data.dialect.SqlDialect; -import org.labkey.api.data.TableInfo; import java.util.Collection; import java.util.Map; diff --git a/api/src/org/labkey/api/query/ChooseQueryView.java b/api/src/org/labkey/api/query/ChooseQueryView.java index 2fa361744a3..65b9d5b348c 100644 --- a/api/src/org/labkey/api/query/ChooseQueryView.java +++ b/api/src/org/labkey/api/query/ChooseQueryView.java @@ -16,9 +16,9 @@ package org.labkey.api.query; -import org.labkey.api.view.WebPartView; -import org.labkey.api.view.ActionURL; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.WebPartView; import java.io.PrintWriter; import java.util.Map; diff --git a/api/src/org/labkey/api/query/CrosstabExcelWriter.java b/api/src/org/labkey/api/query/CrosstabExcelWriter.java index 612a3950015..f29d97e844a 100644 --- a/api/src/org/labkey/api/query/CrosstabExcelWriter.java +++ b/api/src/org/labkey/api/query/CrosstabExcelWriter.java @@ -19,11 +19,11 @@ import org.apache.poi.ss.usermodel.Row; import org.apache.poi.ss.usermodel.Row.MissingCellPolicy; import org.apache.poi.ss.usermodel.Sheet; +import org.labkey.api.data.CrosstabMember; import org.labkey.api.data.CrosstabTableInfo; -import org.labkey.api.data.ExcelWriter; -import org.labkey.api.data.ExcelColumn; import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.CrosstabMember; +import org.labkey.api.data.ExcelColumn; +import org.labkey.api.data.ExcelWriter; import org.labkey.api.data.Results; import org.labkey.api.util.Pair; diff --git a/api/src/org/labkey/api/query/FilteredTableDelegating.java b/api/src/org/labkey/api/query/FilteredTableDelegating.java index cc71266a4f9..5d4195c3c9d 100644 --- a/api/src/org/labkey/api/query/FilteredTableDelegating.java +++ b/api/src/org/labkey/api/query/FilteredTableDelegating.java @@ -19,12 +19,9 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.ColumnLogging; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.MutableColumnInfo; -import org.labkey.api.data.PHI; import org.labkey.api.data.TableInfo; -import org.labkey.api.data.WrappedColumnInfo; /** * This is an alternate implementation of FilteredTable. It is exactly the same except the default implementation of wrapColumn(), using WrappedColumnInfo instead of ExprColumn() diff --git a/api/src/org/labkey/api/query/MetadataParseWarning.java b/api/src/org/labkey/api/query/MetadataParseWarning.java index 553808b93f1..b048d254160 100644 --- a/api/src/org/labkey/api/query/MetadataParseWarning.java +++ b/api/src/org/labkey/api/query/MetadataParseWarning.java @@ -15,7 +15,7 @@ */ package org.labkey.api.query; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.json.JSONObject; /** @@ -33,7 +33,7 @@ public MetadataParseWarning(String message) public MetadataParseWarning(String message, Throwable cause, int line, int column) { super(message, cause, line, column); - _level = Level.WARN_INT; + _level = Level.WARN.intLevel(); } public MetadataParseWarning(String queryName, QueryParseException other) diff --git a/api/src/org/labkey/api/query/PropertyForeignKey.java b/api/src/org/labkey/api/query/PropertyForeignKey.java index 973a69ab8ec..90532122b9f 100644 --- a/api/src/org/labkey/api/query/PropertyForeignKey.java +++ b/api/src/org/labkey/api/query/PropertyForeignKey.java @@ -16,7 +16,8 @@ package org.labkey.api.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.AbstractForeignKey; import org.labkey.api.data.BaseColumnInfo; @@ -47,7 +48,7 @@ */ public class PropertyForeignKey extends AbstractForeignKey implements PropertyColumnDecorator { - private static final Logger LOG = Logger.getLogger(PropertyForeignKey.class); + private static final Logger LOG = LogManager.getLogger(PropertyForeignKey.class); Map _pdMap; protected QuerySchema _schema; diff --git a/api/src/org/labkey/api/query/PythonExportScriptModel.java b/api/src/org/labkey/api/query/PythonExportScriptModel.java index f680219a32f..ef13cb62c72 100644 --- a/api/src/org/labkey/api/query/PythonExportScriptModel.java +++ b/api/src/org/labkey/api/query/PythonExportScriptModel.java @@ -16,7 +16,8 @@ package org.labkey.api.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.CompareType; import org.labkey.api.data.DisplayColumn; @@ -36,7 +37,7 @@ public class PythonExportScriptModel extends ExportScriptModel { private int _indentSpaces = 4; - private static final Logger _log = Logger.getLogger(PythonExportScriptModel.class); + private static final Logger _log = LogManager.getLogger(PythonExportScriptModel.class); public PythonExportScriptModel(QueryView view) { diff --git a/api/src/org/labkey/api/query/QcAwarePropertyForeignKey.java b/api/src/org/labkey/api/query/QcAwarePropertyForeignKey.java index d7a86dec3e9..8aa497caab6 100644 --- a/api/src/org/labkey/api/query/QcAwarePropertyForeignKey.java +++ b/api/src/org/labkey/api/query/QcAwarePropertyForeignKey.java @@ -16,8 +16,21 @@ package org.labkey.api.query; -import org.labkey.api.data.*; -import org.labkey.api.exp.*; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MVDisplayColumnFactory; +import org.labkey.api.data.OORDisplayColumnFactory; +import org.labkey.api.data.OutOfRangeDisplayColumn; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; +import org.labkey.api.exp.MvColumn; +import org.labkey.api.exp.PropertyColumn; +import org.labkey.api.exp.PropertyDescriptor; +import org.labkey.api.exp.PropertyType; +import org.labkey.api.exp.RawValueColumn; import java.util.ArrayList; import java.util.Collection; diff --git a/api/src/org/labkey/api/query/QueryDefinition.java b/api/src/org/labkey/api/query/QueryDefinition.java index 09de8326f2c..7fbeae079e0 100644 --- a/api/src/org/labkey/api/query/QueryDefinition.java +++ b/api/src/org/labkey/api/query/QueryDefinition.java @@ -18,19 +18,23 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.*; -import org.labkey.api.security.User; -import org.labkey.api.view.ActionURL; -import org.labkey.api.util.StringExpression; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.QueryChangeListener.QueryProperty; import org.labkey.api.query.QueryChangeListener.QueryPropertyChange; +import org.labkey.api.security.User; +import org.labkey.api.util.StringExpression; +import org.labkey.api.view.ActionURL; import org.labkey.data.xml.TableType; import javax.servlet.http.HttpServletRequest; +import java.sql.SQLException; import java.util.Collection; -import java.util.Map; import java.util.List; -import java.sql.SQLException; +import java.util.Map; public interface QueryDefinition { diff --git a/api/src/org/labkey/api/query/QueryNestingOption.java b/api/src/org/labkey/api/query/QueryNestingOption.java index 7a174f3c6aa..ea43f7b6b86 100644 --- a/api/src/org/labkey/api/query/QueryNestingOption.java +++ b/api/src/org/labkey/api/query/QueryNestingOption.java @@ -16,13 +16,20 @@ package org.labkey.api.query; -import org.labkey.api.data.*; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.NestableDataRegion; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.TableInfo; import java.io.Writer; +import java.util.ArrayList; +import java.util.Collections; import java.util.List; import java.util.Map; -import java.util.Collections; -import java.util.ArrayList; /** * Configuration for a NestedQueryView that understands which columns should be associated with the outer and inner diff --git a/api/src/org/labkey/api/query/QueryParam.java b/api/src/org/labkey/api/query/QueryParam.java index 1db9de801b4..1bfd8cb520b 100644 --- a/api/src/org/labkey/api/query/QueryParam.java +++ b/api/src/org/labkey/api/query/QueryParam.java @@ -18,7 +18,6 @@ import org.labkey.api.util.SimpleHasHtmlString; import org.labkey.api.util.URLHelper; -import org.labkey.api.view.ActionURL; public enum QueryParam implements SimpleHasHtmlString { diff --git a/api/src/org/labkey/api/query/QueryParseException.java b/api/src/org/labkey/api/query/QueryParseException.java index 25896216cc6..ed13b1707bb 100644 --- a/api/src/org/labkey/api/query/QueryParseException.java +++ b/api/src/org/labkey/api/query/QueryParseException.java @@ -16,7 +16,7 @@ package org.labkey.api.query; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.json.JSONObject; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.NullColumnInfo; @@ -29,7 +29,7 @@ public class QueryParseException extends QueryException { protected int _line; protected int _column; - protected int _level = Level.ERROR_INT; + protected int _level = Level.ERROR.intLevel(); public QueryParseException(String message, Throwable cause, int line, int column) { @@ -47,12 +47,12 @@ public QueryParseException(String queryName, QueryParseException other) public boolean isError() { - return _level >= Level.ERROR_INT; + return _level >= Level.ERROR.intLevel(); } public boolean isWarning() { - return _level < Level.ERROR_INT; + return _level < Level.ERROR.intLevel(); } @@ -62,7 +62,7 @@ public String getMessage() String ret = super.getMessage(); if (_line != 0) { - if (_level == Level.WARN_INT) + if (_level == Level.WARN.intLevel()) ret = "Warning on line " + _line + ": " + ret; else ret = "Error on line " + _line + ": " + ret; diff --git a/api/src/org/labkey/api/query/QueryParseWarning.java b/api/src/org/labkey/api/query/QueryParseWarning.java index 1fe377a55ff..67b1aabb3a3 100644 --- a/api/src/org/labkey/api/query/QueryParseWarning.java +++ b/api/src/org/labkey/api/query/QueryParseWarning.java @@ -15,7 +15,7 @@ */ package org.labkey.api.query; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; /** * User: matthew @@ -28,6 +28,6 @@ public class QueryParseWarning extends QueryParseException public QueryParseWarning(String message, Throwable cause, int line, int column) { super(message, cause, line, column); - _level = Level.WARN_INT; + _level = Level.WARN.intLevel(); } } diff --git a/api/src/org/labkey/api/query/QuerySchemaWrapper.java b/api/src/org/labkey/api/query/QuerySchemaWrapper.java index f1a6496a5eb..4b7e376078c 100644 --- a/api/src/org/labkey/api/query/QuerySchemaWrapper.java +++ b/api/src/org/labkey/api/query/QuerySchemaWrapper.java @@ -16,9 +16,9 @@ package org.labkey.api.query; import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.DbSchema; -import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; import org.labkey.api.security.User; import org.labkey.api.view.NavTree; @@ -26,9 +26,9 @@ import java.util.ArrayList; import java.util.Collection; +import java.util.Collections; import java.util.List; import java.util.Set; -import java.util.Collections; import java.util.TreeSet; /** diff --git a/api/src/org/labkey/api/query/QuerySettings.java b/api/src/org/labkey/api/query/QuerySettings.java index 1127c77a46d..3d13a743bdb 100644 --- a/api/src/org/labkey/api/query/QuerySettings.java +++ b/api/src/org/labkey/api/query/QuerySettings.java @@ -18,7 +18,7 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.json.JSONArray; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -144,7 +144,7 @@ protected PropertyValues getPropertyValues(ViewContext context) PropertyValues pvs = context.getBindPropertyValues(); if (null == pvs) { - Logger.getLogger(QuerySettings.class).warn("PropertyValues not set"); + LogManager.getLogger(QuerySettings.class).warn("PropertyValues not set"); pvs = context.getActionURL().getPropertyValues(); } return pvs; diff --git a/api/src/org/labkey/api/query/QueryView.java b/api/src/org/labkey/api/query/QueryView.java index 00ee13aa7c4..9d09a7ec469 100644 --- a/api/src/org/labkey/api/query/QueryView.java +++ b/api/src/org/labkey/api/query/QueryView.java @@ -17,7 +17,8 @@ package org.labkey.api.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.poi.ss.usermodel.Cell; import org.apache.poi.ss.usermodel.Sheet; import org.jetbrains.annotations.NotNull; @@ -116,7 +117,7 @@ public class QueryView extends WebPartView public static final String EXCEL_WEB_QUERY_EXPORT_TYPE = "excelWebQuery"; public static final String DATAREGIONNAME_DEFAULT = "query"; - private static final Logger _log = Logger.getLogger(QueryView.class); + private static final Logger _log = LogManager.getLogger(QueryView.class); private static final Map _exportScriptFactories = new ConcurrentSkipListMap<>(); protected static final String INSERT_DATA_TEXT = "Insert Data"; diff --git a/api/src/org/labkey/api/query/QueryWebPart.java b/api/src/org/labkey/api/query/QueryWebPart.java index 93c1735f395..c312b74d5b8 100644 --- a/api/src/org/labkey/api/query/QueryWebPart.java +++ b/api/src/org/labkey/api/query/QueryWebPart.java @@ -16,7 +16,6 @@ package org.labkey.api.query; -import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertingWrapDynaBean; import org.apache.commons.lang3.StringUtils; import org.json.JSONArray; @@ -27,7 +26,6 @@ import org.labkey.api.data.ButtonBarConfig; import org.labkey.api.data.Container; import org.labkey.api.data.DataRegion; -import org.labkey.api.data.RuntimeSQLException; import org.labkey.api.data.TableInfo; import org.labkey.api.security.User; import org.labkey.api.util.PageFlowUtil; diff --git a/api/src/org/labkey/api/query/QueryWrapperDynaClass.java b/api/src/org/labkey/api/query/QueryWrapperDynaClass.java index bd2b6219251..4cd2f8c4b03 100644 --- a/api/src/org/labkey/api/query/QueryWrapperDynaClass.java +++ b/api/src/org/labkey/api/query/QueryWrapperDynaClass.java @@ -16,12 +16,12 @@ package org.labkey.api.query; +import org.apache.commons.beanutils.DynaBean; import org.jetbrains.annotations.NotNull; +import org.labkey.api.collections.CaseInsensitiveHashMap; +import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.MultiValuedForeignKey; import org.labkey.api.data.StringWrapperDynaClass; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.apache.commons.beanutils.DynaBean; import org.labkey.api.data.TableInfo; import java.lang.reflect.Array; diff --git a/api/src/org/labkey/api/query/ReportDataRegion.java b/api/src/org/labkey/api/query/ReportDataRegion.java index 58c4b8049da..f7d0e07026e 100644 --- a/api/src/org/labkey/api/query/ReportDataRegion.java +++ b/api/src/org/labkey/api/query/ReportDataRegion.java @@ -31,7 +31,6 @@ import javax.servlet.http.HttpServletResponse; import java.io.IOException; import java.io.Writer; -import java.sql.SQLException; import java.util.List; /** diff --git a/api/src/org/labkey/api/query/RowIdQueryUpdateService.java b/api/src/org/labkey/api/query/RowIdQueryUpdateService.java index 6a2c0b916e0..b87966c6570 100644 --- a/api/src/org/labkey/api/query/RowIdQueryUpdateService.java +++ b/api/src/org/labkey/api/query/RowIdQueryUpdateService.java @@ -15,13 +15,12 @@ */ package org.labkey.api.query; -import org.apache.commons.beanutils.converters.IntegerConverter; +import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; import org.labkey.api.security.User; -import org.labkey.api.data.Container; -import java.util.Map; import java.sql.SQLException; +import java.util.Map; /* * User: Dave diff --git a/api/src/org/labkey/api/query/TableSorter.java b/api/src/org/labkey/api/query/TableSorter.java index 4880651884d..3dc927cad60 100644 --- a/api/src/org/labkey/api/query/TableSorter.java +++ b/api/src/org/labkey/api/query/TableSorter.java @@ -15,7 +15,8 @@ */ package org.labkey.api.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.ColumnInfo; @@ -41,7 +42,7 @@ */ public final class TableSorter { - private static final Logger LOG = Logger.getLogger(TableSorter.class); + private static final Logger LOG = LogManager.getLogger(TableSorter.class); /** * Get a topologically sorted list of TableInfos within this schema. diff --git a/api/src/org/labkey/api/query/UserIdForeignKey.java b/api/src/org/labkey/api/query/UserIdForeignKey.java index c7504ae1903..b7ee6ccea6b 100644 --- a/api/src/org/labkey/api/query/UserIdForeignKey.java +++ b/api/src/org/labkey/api/query/UserIdForeignKey.java @@ -16,7 +16,12 @@ package org.labkey.api.query; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.CoreSchema; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.TableInfo; public class UserIdForeignKey extends LookupForeignKey { diff --git a/api/src/org/labkey/api/query/UserIdQueryForeignKey.java b/api/src/org/labkey/api/query/UserIdQueryForeignKey.java index 23e80e2114f..4fcf9e87976 100644 --- a/api/src/org/labkey/api/query/UserIdQueryForeignKey.java +++ b/api/src/org/labkey/api/query/UserIdQueryForeignKey.java @@ -15,7 +15,12 @@ */ package org.labkey.api.query; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.TableInfo; import org.labkey.api.security.User; /** diff --git a/api/src/org/labkey/api/query/UserIdRenderer.java b/api/src/org/labkey/api/query/UserIdRenderer.java index e19c5ad021d..b10c9793d88 100644 --- a/api/src/org/labkey/api/query/UserIdRenderer.java +++ b/api/src/org/labkey/api/query/UserIdRenderer.java @@ -20,10 +20,7 @@ import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; -import org.labkey.api.security.SecurityManager; import org.labkey.api.security.UserManager; -import org.labkey.api.security.UserUrls; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import java.util.Objects; diff --git a/api/src/org/labkey/api/query/UserSchema.java b/api/src/org/labkey/api/query/UserSchema.java index 715f256de5b..93ef8aa90eb 100644 --- a/api/src/org/labkey/api/query/UserSchema.java +++ b/api/src/org/labkey/api/query/UserSchema.java @@ -48,7 +48,6 @@ import org.labkey.api.view.UnauthorizedException; import org.labkey.api.view.ViewContext; import org.labkey.api.visualization.VisualizationProvider; -import org.labkey.api.writer.ContainerUser; import org.springframework.beans.MutablePropertyValues; import org.springframework.beans.PropertyValues; import org.springframework.validation.BindException; diff --git a/api/src/org/labkey/api/query/ValidationError.java b/api/src/org/labkey/api/query/ValidationError.java index ab7e301a5da..d9b14510e5e 100644 --- a/api/src/org/labkey/api/query/ValidationError.java +++ b/api/src/org/labkey/api/query/ValidationError.java @@ -16,7 +16,6 @@ package org.labkey.api.query; import org.springframework.validation.BindException; -import org.springframework.validation.ObjectError; /** * Represents a particular validation error. Various validation error diff --git a/api/src/org/labkey/api/query/ValidationException.java b/api/src/org/labkey/api/query/ValidationException.java index 70081874cab..8aaf4d99217 100644 --- a/api/src/org/labkey/api/query/ValidationException.java +++ b/api/src/org/labkey/api/query/ValidationException.java @@ -15,8 +15,6 @@ */ package org.labkey.api.query; -import com.google.gwt.user.client.rpc.IsSerializable; -import com.google.gwt.user.client.rpc.RemoteService; import org.labkey.api.action.SpringActionController; import org.labkey.api.data.RuntimeSQLException; import org.springframework.validation.BindException; diff --git a/api/src/org/labkey/api/query/createExportScript.jsp b/api/src/org/labkey/api/query/createExportScript.jsp index 0f5c415d621..3cd8a2f1ff7 100644 --- a/api/src/org/labkey/api/query/createExportScript.jsp +++ b/api/src/org/labkey/api/query/createExportScript.jsp @@ -14,7 +14,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -%><%@ page import="org.labkey.api.view.JspView, org.labkey.api.view.HttpView, org.labkey.api.query.ExportScriptModel" %><%@ page extends="org.labkey.api.jsp.JspBase" %><% +%><%@ page import="org.labkey.api.query.ExportScriptModel, org.labkey.api.view.HttpView, org.labkey.api.view.JspView" %><%@ page extends="org.labkey.api.jsp.JspBase" %><% JspView me = (JspView) HttpView.currentView(); ExportScriptModel model = me.getModelBean(); getViewContext().getResponse().setContentType("text/plain"); diff --git a/api/src/org/labkey/api/query/import.jsp b/api/src/org/labkey/api/query/import.jsp index 3cf3f737831..6cc7bd3d911 100644 --- a/api/src/org/labkey/api/query/import.jsp +++ b/api/src/org/labkey/api/query/import.jsp @@ -18,13 +18,13 @@ <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page import="org.json.JSONObject" %> <%@ page import="org.labkey.api.query.AbstractQueryImportAction" %> +<%@ page import="org.labkey.api.query.QueryUpdateService" %> +<%@ page import="org.labkey.api.util.HelpTopic" %> <%@ page import="org.labkey.api.util.Pair" %> -<%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="static org.labkey.api.util.HtmlString.NDASH" %> -<%@ page import="org.labkey.api.util.HelpTopic" %> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="static org.labkey.api.query.QueryUpdateService.InsertOption.MERGE" %> -<%@ page import="org.labkey.api.query.QueryUpdateService" %> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase"%> <%! @Override diff --git a/api/src/org/labkey/api/query/snapshot/AbstractTableMethodInfo.java b/api/src/org/labkey/api/query/snapshot/AbstractTableMethodInfo.java index ed2571da12c..3b239ad4a27 100644 --- a/api/src/org/labkey/api/query/snapshot/AbstractTableMethodInfo.java +++ b/api/src/org/labkey/api/query/snapshot/AbstractTableMethodInfo.java @@ -16,10 +16,9 @@ package org.labkey.api.query.snapshot; import org.labkey.api.data.JdbcType; +import org.labkey.api.data.SQLFragment; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.query.AbstractMethodInfo; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.DbSchema; /** * User: Matthew diff --git a/api/src/org/labkey/api/query/snapshot/QuerySnapshotDefinition.java b/api/src/org/labkey/api/query/snapshot/QuerySnapshotDefinition.java index d3923442e66..15bed8532b2 100644 --- a/api/src/org/labkey/api/query/snapshot/QuerySnapshotDefinition.java +++ b/api/src/org/labkey/api/query/snapshot/QuerySnapshotDefinition.java @@ -16,17 +16,13 @@ package org.labkey.api.query.snapshot; import org.jetbrains.annotations.Nullable; -import org.labkey.api.query.QueryDefinition; +import org.labkey.api.data.Container; import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryDefinition; import org.labkey.api.security.User; -import org.labkey.api.data.Container; +import java.util.Date; import java.util.List; -import java.util.Date;/* - * User: Karl Lum - * Date: Jul 14, 2008 - * Time: 12:51:32 PM - */ public interface QuerySnapshotDefinition { diff --git a/api/src/org/labkey/api/reader/DataLoader.java b/api/src/org/labkey/api/reader/DataLoader.java index 3b290d59183..a2e5793384a 100644 --- a/api/src/org/labkey/api/reader/DataLoader.java +++ b/api/src/org/labkey/api/reader/DataLoader.java @@ -21,14 +21,14 @@ import org.apache.commons.collections4.IteratorUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.dataiterator.ScrollableDataIterator; import org.labkey.api.collections.ArrayListMap; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.collections.RowMapFactory; +import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ImportAliasable; @@ -39,6 +39,7 @@ import org.labkey.api.dataiterator.DataIteratorContext; import org.labkey.api.dataiterator.LoggingDataIterator; import org.labkey.api.dataiterator.MapDataIterator; +import org.labkey.api.dataiterator.ScrollableDataIterator; import org.labkey.api.exp.MvColumn; import org.labkey.api.exp.MvFieldWrapper; import org.labkey.api.iterator.CloseableIterator; @@ -76,7 +77,7 @@ public static DataLoaderService get() // if a conversion error occurs, the original field value is returned public static final Object ERROR_VALUE_USE_ORIGINAL = new Object(); - private static final Logger _log = Logger.getLogger(DataLoader.class); + private static final Logger _log = LogManager.getLogger(DataLoader.class); /** * Defines order of column type preferences. diff --git a/api/src/org/labkey/api/reader/JSONDataLoader.java b/api/src/org/labkey/api/reader/JSONDataLoader.java index c11bbcec0ef..db0f4df02dc 100644 --- a/api/src/org/labkey/api/reader/JSONDataLoader.java +++ b/api/src/org/labkey/api/reader/JSONDataLoader.java @@ -26,7 +26,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.junit.Assert; import org.junit.Test; @@ -773,7 +773,7 @@ public void close() } catch (IOException e) { - Logger.getLogger(JSONDataLoader.class).error("Error closing JSON stream", e); + LogManager.getLogger(JSONDataLoader.class).error("Error closing JSON stream", e); } } diff --git a/api/src/org/labkey/api/reader/SimpleXMLStreamReader.java b/api/src/org/labkey/api/reader/SimpleXMLStreamReader.java index 57ebf813fa1..a46cd0e5464 100644 --- a/api/src/org/labkey/api/reader/SimpleXMLStreamReader.java +++ b/api/src/org/labkey/api/reader/SimpleXMLStreamReader.java @@ -16,16 +16,17 @@ package org.labkey.api.reader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.BeanObjectFactory; import javax.xml.stream.XMLInputFactory; import javax.xml.stream.XMLStreamConstants; import javax.xml.stream.XMLStreamException; import java.io.InputStream; -import java.util.regex.Pattern; -import java.util.Map; import java.util.HashMap; +import java.util.Map; +import java.util.regex.Pattern; /** * User: arauch @@ -34,7 +35,7 @@ */ public class SimpleXMLStreamReader extends XMLStreamReaderWrapper { - private static Logger _log = Logger.getLogger(SimpleXMLStreamReader.class); + private static Logger _log = LogManager.getLogger(SimpleXMLStreamReader.class); private static Pattern _blankPattern = Pattern.compile(""); public SimpleXMLStreamReader(InputStream stream) throws XMLStreamException diff --git a/api/src/org/labkey/api/reader/TabFileType.java b/api/src/org/labkey/api/reader/TabFileType.java index e6f6933758d..5e60501cc01 100644 --- a/api/src/org/labkey/api/reader/TabFileType.java +++ b/api/src/org/labkey/api/reader/TabFileType.java @@ -17,7 +17,6 @@ import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; import org.labkey.api.util.FileType; import org.labkey.api.util.StringUtilsLabKey; diff --git a/api/src/org/labkey/api/reader/TabLoader.java b/api/src/org/labkey/api/reader/TabLoader.java index a072081ce51..e1778222be9 100644 --- a/api/src/org/labkey/api/reader/TabLoader.java +++ b/api/src/org/labkey/api/reader/TabLoader.java @@ -19,7 +19,8 @@ import org.apache.commons.io.input.CharSequenceReader; import org.apache.commons.lang3.StringEscapeUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -69,7 +70,7 @@ public class TabLoader extends DataLoader public static final FileType TSV_FILE_TYPE = new TabFileType(Arrays.asList(".tsv", ".txt"), ".tsv", "text/tab-separated-values"); public static final FileType CSV_FILE_TYPE = new TabFileType(Collections.singletonList(".csv"), ".csv", "text/comma-separated-values"); - private static final Logger _log = Logger.getLogger(TabLoader.class); + private static final Logger _log = LogManager.getLogger(TabLoader.class); public static class TsvFactory extends AbstractDataLoaderFactory { diff --git a/api/src/org/labkey/api/reader/XMLStreamReaderWrapper.java b/api/src/org/labkey/api/reader/XMLStreamReaderWrapper.java index 6e7a540f756..94f4d3ee0d4 100644 --- a/api/src/org/labkey/api/reader/XMLStreamReaderWrapper.java +++ b/api/src/org/labkey/api/reader/XMLStreamReaderWrapper.java @@ -16,11 +16,11 @@ package org.labkey.api.reader; -import javax.xml.stream.XMLStreamReader; -import javax.xml.stream.XMLStreamException; -import javax.xml.stream.Location; -import javax.xml.namespace.QName; import javax.xml.namespace.NamespaceContext; +import javax.xml.namespace.QName; +import javax.xml.stream.Location; +import javax.xml.stream.XMLStreamException; +import javax.xml.stream.XMLStreamReader; /** * User: arauch diff --git a/api/src/org/labkey/api/reports/ExternalScriptEngine.java b/api/src/org/labkey/api/reports/ExternalScriptEngine.java index fddd511b4b9..61da3ca84ef 100644 --- a/api/src/org/labkey/api/reports/ExternalScriptEngine.java +++ b/api/src/org/labkey/api/reports/ExternalScriptEngine.java @@ -20,13 +20,25 @@ import org.labkey.api.miniprofiler.CustomTiming; import org.labkey.api.miniprofiler.MiniProfiler; import org.labkey.api.reader.Readers; +import org.labkey.api.reports.report.r.ParamReplacementSvc; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.FileUtil; -import org.labkey.api.reports.report.r.ParamReplacementSvc; import org.labkey.api.util.URIUtil; -import javax.script.*; -import java.io.*; +import javax.script.AbstractScriptEngine; +import javax.script.Bindings; +import javax.script.ScriptContext; +import javax.script.ScriptEngineFactory; +import javax.script.ScriptException; +import javax.script.SimpleBindings; +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; +import java.io.Reader; +import java.io.Writer; import java.util.ArrayList; import java.util.List; import java.util.Map; diff --git a/api/src/org/labkey/api/reports/RConnectionHolder.java b/api/src/org/labkey/api/reports/RConnectionHolder.java index b72daeaad49..c5f6288daa6 100644 --- a/api/src/org/labkey/api/reports/RConnectionHolder.java +++ b/api/src/org/labkey/api/reports/RConnectionHolder.java @@ -15,10 +15,11 @@ */ package org.labkey.api.reports; +import org.rosuda.REngine.Rserve.RConnection; + import javax.script.ScriptException; import javax.servlet.http.HttpSessionBindingEvent; import javax.servlet.http.HttpSessionBindingListener; -import org.rosuda.REngine.Rserve.RConnection; import java.util.HashSet; // diff --git a/api/src/org/labkey/api/reports/RDockerScriptEngine.java b/api/src/org/labkey/api/reports/RDockerScriptEngine.java index e167eafd867..5789510c97a 100644 --- a/api/src/org/labkey/api/reports/RDockerScriptEngine.java +++ b/api/src/org/labkey/api/reports/RDockerScriptEngine.java @@ -16,7 +16,8 @@ package org.labkey.api.reports; import org.apache.commons.io.FilenameUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.docker.DockerService; @@ -40,7 +41,7 @@ */ public class RDockerScriptEngine extends RScriptEngine { - private static final Logger LOG = Logger.getLogger(RDockerScriptEngine.class); + private static final Logger LOG = LogManager.getLogger(RDockerScriptEngine.class); private static DockerService _ds; private final String _remoteWorkingDir; diff --git a/api/src/org/labkey/api/reports/ReportService.java b/api/src/org/labkey/api/reports/ReportService.java index f96fedfcaa5..23d2d9395c4 100644 --- a/api/src/org/labkey/api/reports/ReportService.java +++ b/api/src/org/labkey/api/reports/ReportService.java @@ -16,7 +16,7 @@ package org.labkey.api.reports; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; diff --git a/api/src/org/labkey/api/reports/RserveScriptEngine.java b/api/src/org/labkey/api/reports/RserveScriptEngine.java index 874013870a6..9417cafe01f 100644 --- a/api/src/org/labkey/api/reports/RserveScriptEngine.java +++ b/api/src/org/labkey/api/reports/RserveScriptEngine.java @@ -16,7 +16,8 @@ package org.labkey.api.reports; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.file.PathMapper; import org.labkey.api.reports.report.RReport; import org.labkey.api.util.FileUtil; @@ -38,7 +39,7 @@ public class RserveScriptEngine extends RScriptEngine { - private static final Logger LOG = Logger.getLogger(RserveScriptEngine.class); + private static final Logger LOG = LogManager.getLogger(RserveScriptEngine.class); private String localHostIP = "127.0.0.1"; private String localHostName = "localhost"; diff --git a/api/src/org/labkey/api/reports/model/ReportPropsManager.java b/api/src/org/labkey/api/reports/model/ReportPropsManager.java index 9daeb78d8cc..cd535d89f19 100644 --- a/api/src/org/labkey/api/reports/model/ReportPropsManager.java +++ b/api/src/org/labkey/api/reports/model/ReportPropsManager.java @@ -15,7 +15,8 @@ */ package org.labkey.api.reports.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; @@ -54,7 +55,7 @@ */ public class ReportPropsManager extends ContainerManager.AbstractContainerListener { - private static final Logger _log = Logger.getLogger(ReportPropsManager.class); + private static final Logger _log = LogManager.getLogger(ReportPropsManager.class); private static final String PROPERTIES_DOMAIN = "Report Properties"; private static final String NAMESPACE_PREFIX = "ReportProperties"; private static final String TYPE_PROPERTIES = "Properties"; diff --git a/api/src/org/labkey/api/reports/report/ChartReportDescriptor.java b/api/src/org/labkey/api/reports/report/ChartReportDescriptor.java index 10f628d21a8..f4c21be1837 100644 --- a/api/src/org/labkey/api/reports/report/ChartReportDescriptor.java +++ b/api/src/org/labkey/api/reports/report/ChartReportDescriptor.java @@ -17,8 +17,6 @@ package org.labkey.api.reports.report; import org.apache.commons.lang3.math.NumberUtils; -import org.labkey.api.view.ViewContext; -import org.labkey.api.visualization.GenericChartReport; import java.util.Arrays; import java.util.List; diff --git a/api/src/org/labkey/api/reports/report/DbReportIdentifier.java b/api/src/org/labkey/api/reports/report/DbReportIdentifier.java index 8896f9b7db0..8f517a10efd 100644 --- a/api/src/org/labkey/api/reports/report/DbReportIdentifier.java +++ b/api/src/org/labkey/api/reports/report/DbReportIdentifier.java @@ -15,7 +15,8 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.reports.Report; @@ -37,7 +38,7 @@ public class DbReportIdentifier extends AbstractReportIdentifier { protected static final String PREFIX = "db:"; - private static Logger LOG = Logger.getLogger(DbReportIdentifier.class); + private static Logger LOG = LogManager.getLogger(DbReportIdentifier.class); private final int _id; diff --git a/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java b/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java index 526f6e88c8b..191a8faaa42 100644 --- a/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java +++ b/api/src/org/labkey/api/reports/report/ExternalScriptEngineReport.java @@ -20,7 +20,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.attachments.AttachmentParent; import org.labkey.api.collections.CaseInsensitiveHashSet; -import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.query.QueryService.NamedParameterNotProvided; diff --git a/api/src/org/labkey/api/reports/report/JavaScriptReport.java b/api/src/org/labkey/api/reports/report/JavaScriptReport.java index ee5cf25a20a..98494f8ab04 100644 --- a/api/src/org/labkey/api/reports/report/JavaScriptReport.java +++ b/api/src/org/labkey/api/reports/report/JavaScriptReport.java @@ -22,7 +22,12 @@ import org.labkey.api.query.QueryView; import org.labkey.api.reports.LabkeyScriptEngineManager; import org.labkey.api.services.ServiceRegistry; -import org.labkey.api.view.*; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.JspTemplate; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NotFoundException; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartView; import org.labkey.api.view.template.ClientDependency; import javax.script.ScriptEngine; diff --git a/api/src/org/labkey/api/reports/report/ModuleQueryRReportDescriptor.java b/api/src/org/labkey/api/reports/report/ModuleQueryRReportDescriptor.java index f336d6dd051..56e9d6f5f29 100644 --- a/api/src/org/labkey/api/reports/report/ModuleQueryRReportDescriptor.java +++ b/api/src/org/labkey/api/reports/report/ModuleQueryRReportDescriptor.java @@ -20,10 +20,10 @@ import org.labkey.api.util.Path; import org.labkey.api.view.template.ClientDependency; +import java.util.HashMap; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.Map; -import java.util.HashMap; /* * User: Dave diff --git a/api/src/org/labkey/api/reports/report/ModuleQueryReportResource.java b/api/src/org/labkey/api/reports/report/ModuleQueryReportResource.java index b13d92681e6..619ed67b695 100644 --- a/api/src/org/labkey/api/reports/report/ModuleQueryReportResource.java +++ b/api/src/org/labkey/api/reports/report/ModuleQueryReportResource.java @@ -15,7 +15,7 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.labkey.api.resource.Resource; import org.labkey.api.util.Pair; @@ -71,7 +71,7 @@ protected ReportDescriptorType loadMetaData() } catch(IOException | XmlException e) { - Logger.getLogger(ModuleQueryReportResource.class).warn("Unable to load query report metadata from file " + _sourceFile.getPath(), e); + LogManager.getLogger(ModuleQueryReportResource.class).warn("Unable to load query report metadata from file " + _sourceFile.getPath(), e); } return d; diff --git a/api/src/org/labkey/api/reports/report/ModuleRReportResource.java b/api/src/org/labkey/api/reports/report/ModuleRReportResource.java index a622086662b..9f9fba3a0d2 100644 --- a/api/src/org/labkey/api/reports/report/ModuleRReportResource.java +++ b/api/src/org/labkey/api/reports/report/ModuleRReportResource.java @@ -15,7 +15,7 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.labkey.api.reports.RScriptEngine; import org.labkey.api.resource.Resource; @@ -95,7 +95,7 @@ protected ReportDescriptorType loadMetaData() } catch (XmlException e) { - Logger.getLogger(ModuleRReportResource.class).warn("Unable to load R report metadata from file " + LogManager.getLogger(ModuleRReportResource.class).warn("Unable to load R report metadata from file " + _sourceFile.getPath(), e); } } diff --git a/api/src/org/labkey/api/reports/report/ModuleReportDependenciesResource.java b/api/src/org/labkey/api/reports/report/ModuleReportDependenciesResource.java index 715baf10808..ebe511116c7 100644 --- a/api/src/org/labkey/api/reports/report/ModuleReportDependenciesResource.java +++ b/api/src/org/labkey/api/reports/report/ModuleReportDependenciesResource.java @@ -15,7 +15,7 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.labkey.api.resource.Resource; import org.labkey.api.view.template.ClientDependency; @@ -67,7 +67,7 @@ protected ReportDescriptorType loadMetaData() } catch(XmlException e) { - Logger.getLogger(ModuleReportDependenciesResource.class).warn("Unable to load report metadata from file " + LogManager.getLogger(ModuleReportDependenciesResource.class).warn("Unable to load report metadata from file " + _metaDataFile.getPath(), e); } } diff --git a/api/src/org/labkey/api/reports/report/ModuleReportIdentifier.java b/api/src/org/labkey/api/reports/report/ModuleReportIdentifier.java index 1442c8743a6..44493385c63 100644 --- a/api/src/org/labkey/api/reports/report/ModuleReportIdentifier.java +++ b/api/src/org/labkey/api/reports/report/ModuleReportIdentifier.java @@ -15,10 +15,10 @@ */ package org.labkey.api.reports.report; -import org.labkey.api.reports.Report; -import org.labkey.api.reports.ReportService; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleLoader; +import org.labkey.api.reports.Report; +import org.labkey.api.reports.ReportService; import org.labkey.api.util.Path; import org.labkey.api.writer.ContainerUser; diff --git a/api/src/org/labkey/api/reports/report/ModuleReportResource.java b/api/src/org/labkey/api/reports/report/ModuleReportResource.java index 0fd40cc2b14..8e9ea319b3b 100644 --- a/api/src/org/labkey/api/reports/report/ModuleReportResource.java +++ b/api/src/org/labkey/api/reports/report/ModuleReportResource.java @@ -15,7 +15,7 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.labkey.api.data.ContainerManager; import org.labkey.api.resource.Resource; @@ -60,7 +60,7 @@ public void loadScript() } catch(IOException e) { - Logger.getLogger(ModuleReportResource.class).warn("Unable to load report script from source file " + _sourceFile.getPath(), e); + LogManager.getLogger(ModuleReportResource.class).warn("Unable to load report script from source file " + _sourceFile.getPath(), e); } } @@ -85,17 +85,17 @@ protected ReportDescriptorType loadMetaData() } catch (ParseException e) { - Logger.getLogger(ModuleReportResource.class).warn("Unable to parse moduleReportCreatedDate \"" + createdDateStr + "\" from file " + _sourceFile.getPath(), e); + LogManager.getLogger(ModuleReportResource.class).warn("Unable to parse moduleReportCreatedDate \"" + createdDateStr + "\" from file " + _sourceFile.getPath(), e); } } } catch(IOException e) { - Logger.getLogger(ModuleReportResource.class).warn("Unable to load report metadata from file " + _metaDataFile.getPath(), e); + LogManager.getLogger(ModuleReportResource.class).warn("Unable to load report metadata from file " + _metaDataFile.getPath(), e); } catch(XmlException e) { - Logger.getLogger(ModuleReportResource.class).warn("Unable to load query report metadata from file " + _sourceFile.getPath(), e); + LogManager.getLogger(ModuleReportResource.class).warn("Unable to load query report metadata from file " + _sourceFile.getPath(), e); } } return d; diff --git a/api/src/org/labkey/api/reports/report/RReportJob.java b/api/src/org/labkey/api/reports/report/RReportJob.java index c2879cd2bc2..b111ed31e77 100644 --- a/api/src/org/labkey/api/reports/report/RReportJob.java +++ b/api/src/org/labkey/api/reports/report/RReportJob.java @@ -18,7 +18,8 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; @@ -51,7 +52,7 @@ */ public class RReportJob extends PipelineJob implements Serializable { - private static final Logger _log = Logger.getLogger(RReportJob.class); + private static final Logger _log = LogManager.getLogger(RReportJob.class); private static final ThreadLocal _jobIdentifier = new ThreadLocal<>(); public static final String PROCESSING_STATUS = "Processing"; diff --git a/api/src/org/labkey/api/reports/report/RedirectReport.java b/api/src/org/labkey/api/reports/report/RedirectReport.java index 68f1946f542..27380ca5ade 100644 --- a/api/src/org/labkey/api/reports/report/RedirectReport.java +++ b/api/src/org/labkey/api/reports/report/RedirectReport.java @@ -15,7 +15,8 @@ */ package org.labkey.api.reports.report; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.settings.AppProps; @@ -34,7 +35,7 @@ */ public abstract class RedirectReport extends AbstractReport { - private static final Logger LOG = Logger.getLogger(RedirectReport.class); + private static final Logger LOG = LogManager.getLogger(RedirectReport.class); public static final String REDIRECT_URL = ReportDescriptor.Prop.redirectUrl.name(); public static final String TARGET = "target"; diff --git a/api/src/org/labkey/api/reports/report/ScriptEngineReport.java b/api/src/org/labkey/api/reports/report/ScriptEngineReport.java index a9fed7171b8..79e3bcf8911 100644 --- a/api/src/org/labkey/api/reports/report/ScriptEngineReport.java +++ b/api/src/org/labkey/api/reports/report/ScriptEngineReport.java @@ -17,7 +17,8 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportContext; @@ -111,7 +112,7 @@ public abstract class ScriptEngineReport extends ScriptReport implements Report. public static final String SUBSTITUTION_MAP = "substitutionMap.txt"; public static final String CONSOLE_OUTPUT = "console.txt"; - private static Logger _log = Logger.getLogger(ScriptEngineReport.class); + private static Logger _log = LogManager.getLogger(ScriptEngineReport.class); static { diff --git a/api/src/org/labkey/api/reports/report/r/AbstractParamReplacement.java b/api/src/org/labkey/api/reports/report/r/AbstractParamReplacement.java index 27fec768fce..b62c8d4e9e7 100644 --- a/api/src/org/labkey/api/reports/report/r/AbstractParamReplacement.java +++ b/api/src/org/labkey/api/reports/report/r/AbstractParamReplacement.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.reports.Report; -import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.thumbnail.Thumbnail; import org.labkey.api.view.ViewContext; diff --git a/api/src/org/labkey/api/reports/report/r/ParamReplacement.java b/api/src/org/labkey/api/reports/report/r/ParamReplacement.java index 58a4b6fa773..c1a56c9a704 100644 --- a/api/src/org/labkey/api/reports/report/r/ParamReplacement.java +++ b/api/src/org/labkey/api/reports/report/r/ParamReplacement.java @@ -17,15 +17,14 @@ package org.labkey.api.reports.report.r; import org.jetbrains.annotations.Nullable; +import org.labkey.api.reports.Report; import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.thumbnail.Thumbnail; import org.labkey.api.view.HttpView; import org.labkey.api.view.ViewContext; -import org.labkey.api.reports.Report; import java.io.File; import java.io.IOException; -import java.util.Collection; import java.util.List; import java.util.Map; diff --git a/api/src/org/labkey/api/reports/report/r/ParamReplacementSvc.java b/api/src/org/labkey/api/reports/report/r/ParamReplacementSvc.java index e7d9467a07b..02f52e079a5 100644 --- a/api/src/org/labkey/api/reports/report/r/ParamReplacementSvc.java +++ b/api/src/org/labkey/api/reports/report/r/ParamReplacementSvc.java @@ -17,7 +17,8 @@ package org.labkey.api.reports.report.r; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.reader.Readers; import org.labkey.api.reports.Report; @@ -26,7 +27,9 @@ import org.labkey.api.util.PageFlowUtil; import org.labkey.api.writer.PrintWriters; -import java.io.*; +import java.io.BufferedReader; +import java.io.File; +import java.io.PrintWriter; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -47,7 +50,7 @@ */ public class ParamReplacementSvc { - private static final Logger _log = Logger.getLogger(ParamReplacementSvc.class); + private static final Logger _log = LogManager.getLogger(ParamReplacementSvc.class); private static final ParamReplacementSvc _instance = new ParamReplacementSvc(); private static final Map _outputSubstitutions = new HashMap<>(); diff --git a/api/src/org/labkey/api/reports/report/r/view/ConsoleOutput.java b/api/src/org/labkey/api/reports/report/r/view/ConsoleOutput.java index 58970daad5f..e0f0d626bc5 100644 --- a/api/src/org/labkey/api/reports/report/r/view/ConsoleOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/ConsoleOutput.java @@ -16,10 +16,10 @@ package org.labkey.api.reports.report.r.view; +import org.labkey.api.reports.Report; +import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.reports.report.r.AbstractParamReplacement; -import org.labkey.api.reports.report.RReport; -import org.labkey.api.reports.Report; import org.labkey.api.view.HttpView; import org.labkey.api.view.ViewContext; diff --git a/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java b/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java index 6ccdf1e6036..c82051199a9 100644 --- a/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java +++ b/api/src/org/labkey/api/reports/report/r/view/DownloadOutputView.java @@ -16,20 +16,14 @@ package org.labkey.api.reports.report.r.view; -import org.labkey.api.attachments.Attachment; -import org.labkey.api.attachments.AttachmentFile; import org.labkey.api.attachments.AttachmentParent; -import org.labkey.api.attachments.AttachmentService; -import org.labkey.api.attachments.FileAttachmentFile; import org.labkey.api.reports.report.ReportUrls; import org.labkey.api.reports.report.r.ParamReplacement; import org.labkey.api.util.GUID; import org.labkey.api.util.PageFlowUtil; import java.io.File; -import java.io.IOException; import java.io.PrintWriter; -import java.util.Collections; /** * User: Karl Lum diff --git a/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java b/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java index a1d5e2f172d..0dd90b5b276 100644 --- a/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java +++ b/api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java @@ -21,7 +21,6 @@ import org.labkey.api.util.FileUtil; import java.io.File; -import java.io.IOException; /** * User: Dax Hawkins diff --git a/api/src/org/labkey/api/reports/report/r/view/FileOutput.java b/api/src/org/labkey/api/reports/report/r/view/FileOutput.java index 96d246ca365..80801b5e86c 100644 --- a/api/src/org/labkey/api/reports/report/r/view/FileOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/FileOutput.java @@ -18,7 +18,6 @@ import org.labkey.api.attachments.AttachmentParent; import org.labkey.api.reports.report.ScriptOutput; -import org.labkey.api.reports.report.r.AbstractParamReplacement; import org.labkey.api.reports.report.r.ParamReplacement; import org.labkey.api.view.HtmlView; import org.labkey.api.view.HttpView; diff --git a/api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java b/api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java index 91065bc0caf..a5c6846a0ff 100644 --- a/api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/HtmlOutput.java @@ -16,13 +16,13 @@ package org.labkey.api.reports.report.r.view; +import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.reports.report.r.AbstractParamReplacement; import org.labkey.api.reports.report.r.ParamReplacement; -import org.labkey.api.reports.report.RReport; +import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.HttpView; import org.labkey.api.view.ViewContext; -import org.labkey.api.util.PageFlowUtil; import java.io.File; import java.io.PrintWriter; diff --git a/api/src/org/labkey/api/reports/report/r/view/KnitrOutput.java b/api/src/org/labkey/api/reports/report/r/view/KnitrOutput.java index e51539bfb8f..c2d5ae10439 100644 --- a/api/src/org/labkey/api/reports/report/r/view/KnitrOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/KnitrOutput.java @@ -27,10 +27,8 @@ import org.labkey.api.view.ViewContext; import java.io.File; -import java.io.IOException; import java.io.PrintWriter; import java.net.URI; -import java.util.regex.Pattern; /** * User: dax diff --git a/api/src/org/labkey/api/reports/report/r/view/PostscriptOutput.java b/api/src/org/labkey/api/reports/report/r/view/PostscriptOutput.java index 70ec3993bc7..1393429eb04 100644 --- a/api/src/org/labkey/api/reports/report/r/view/PostscriptOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/PostscriptOutput.java @@ -18,7 +18,6 @@ import org.labkey.api.attachments.AttachmentParent; import org.labkey.api.reports.report.ScriptOutput; -import org.labkey.api.reports.report.r.AbstractParamReplacement; import org.labkey.api.reports.report.r.ParamReplacement; import org.labkey.api.view.HtmlView; import org.labkey.api.view.HttpView; diff --git a/api/src/org/labkey/api/reports/report/r/view/ROutputView.java b/api/src/org/labkey/api/reports/report/r/view/ROutputView.java index 6f3596a5479..f4ebe6cf6bd 100644 --- a/api/src/org/labkey/api/reports/report/r/view/ROutputView.java +++ b/api/src/org/labkey/api/reports/report/r/view/ROutputView.java @@ -16,7 +16,8 @@ package org.labkey.api.reports.report.r.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.reports.ReportService; import org.labkey.api.reports.report.RReportDescriptor; import org.labkey.api.reports.report.ScriptEngineReport; @@ -49,7 +50,7 @@ public class ROutputView extends HttpView private boolean _isRemote = false; private List _files = new ArrayList<>(); private Map _properties; - protected static Logger LOG = Logger.getLogger(ROutputView.class); + protected static Logger LOG = LogManager.getLogger(ROutputView.class); private static boolean ALLOW_REMOTE_FILESIZE_BYPASS = false; public ROutputView(ParamReplacement param) diff --git a/api/src/org/labkey/api/reports/report/r/view/SvgOutput.java b/api/src/org/labkey/api/reports/report/r/view/SvgOutput.java index ad1285b5048..d5fef6929d0 100644 --- a/api/src/org/labkey/api/reports/report/r/view/SvgOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/SvgOutput.java @@ -16,7 +16,7 @@ package org.labkey.api.reports.report.r.view; import org.apache.batik.transcoder.TranscoderException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.attachments.DocumentConversionService; import org.labkey.api.reader.Readers; import org.labkey.api.thumbnail.Thumbnail; @@ -66,7 +66,7 @@ public Thumbnail renderThumbnail(ViewContext context) throws IOException } catch (TranscoderException e) { - Logger.getLogger(SvgOutput.class).error("Couldn't generate thumbnail", e); + LogManager.getLogger(SvgOutput.class).error("Couldn't generate thumbnail", e); } } } diff --git a/api/src/org/labkey/api/reports/report/r/view/TextOutput.java b/api/src/org/labkey/api/reports/report/r/view/TextOutput.java index 330621f9371..4e43f7c383a 100644 --- a/api/src/org/labkey/api/reports/report/r/view/TextOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/TextOutput.java @@ -16,13 +16,13 @@ package org.labkey.api.reports.report.r.view; +import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.reports.report.r.AbstractParamReplacement; import org.labkey.api.reports.report.r.ParamReplacement; -import org.labkey.api.reports.report.RReport; +import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.HttpView; import org.labkey.api.view.ViewContext; -import org.labkey.api.util.PageFlowUtil; import java.io.File; import java.io.PrintWriter; diff --git a/api/src/org/labkey/api/reports/report/r/view/TsvOutput.java b/api/src/org/labkey/api/reports/report/r/view/TsvOutput.java index 2ab347a6278..9920bf2836d 100644 --- a/api/src/org/labkey/api/reports/report/r/view/TsvOutput.java +++ b/api/src/org/labkey/api/reports/report/r/view/TsvOutput.java @@ -17,6 +17,8 @@ package org.labkey.api.reports.report.r.view; import org.apache.commons.beanutils.ConvertUtils; +import org.labkey.api.reader.ColumnDescriptor; +import org.labkey.api.reader.TabLoader; import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.ScriptOutput; import org.labkey.api.reports.report.r.AbstractParamReplacement; @@ -24,11 +26,8 @@ import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.HttpView; import org.labkey.api.view.ViewContext; -import org.labkey.api.reader.TabLoader; -import org.labkey.api.reader.ColumnDescriptor; import java.io.File; -import java.io.IOException; import java.io.PrintWriter; import java.util.ArrayList; import java.util.HashMap; diff --git a/api/src/org/labkey/api/reports/report/view/RunReportView.java b/api/src/org/labkey/api/reports/report/view/RunReportView.java index d654e3a136b..8e3accf7f2e 100644 --- a/api/src/org/labkey/api/reports/report/view/RunReportView.java +++ b/api/src/org/labkey/api/reports/report/view/RunReportView.java @@ -21,7 +21,10 @@ import org.labkey.api.reports.Report; import org.labkey.api.reports.report.ReportDescriptor; import org.labkey.api.util.URLHelper; -import org.labkey.api.view.*; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.TabStripView; import org.springframework.validation.BindException; import java.io.PrintWriter; diff --git a/api/src/org/labkey/api/reports/report/view/ajaxScriptReportDesigner.jsp b/api/src/org/labkey/api/reports/report/view/ajaxScriptReportDesigner.jsp index d5c11a263ec..d1fe26e788b 100644 --- a/api/src/org/labkey/api/reports/report/view/ajaxScriptReportDesigner.jsp +++ b/api/src/org/labkey/api/reports/report/view/ajaxScriptReportDesigner.jsp @@ -32,6 +32,7 @@ <%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.security.roles.ProjectAdminRole" %> <%@ page import="org.labkey.api.study.StudyService" %> +<%@ page import="org.labkey.api.util.HtmlString" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.util.Pair" %> <%@ page import="org.labkey.api.util.UniqueID" %> @@ -42,12 +43,11 @@ <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="java.util.ArrayList" %> <%@ page import="java.util.HashMap" %> -<%@ page import="java.util.LinkedList" %> <%@ page import="static java.lang.Boolean.TRUE" %> +<%@ page import="java.util.LinkedList" %> <%@ page import="java.util.List" %> <%@ page import="java.util.ListIterator" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.util.HtmlString" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%! diff --git a/api/src/org/labkey/api/reports/report/view/renderQueryReport.jsp b/api/src/org/labkey/api/reports/report/view/renderQueryReport.jsp index b1f9a968688..8d1345848e9 100644 --- a/api/src/org/labkey/api/reports/report/view/renderQueryReport.jsp +++ b/api/src/org/labkey/api/reports/report/view/renderQueryReport.jsp @@ -26,7 +26,6 @@ <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.springframework.validation.BindException" %> <%@ page import="org.springframework.validation.ObjectError" %> -<%@ page import="java.util.List" %> <%@ page extends="org.labkey.api.jsp.JspBase"%> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%! diff --git a/api/src/org/labkey/api/search/SearchService.java b/api/src/org/labkey/api/search/SearchService.java index ef7dda2e2ec..eb5aab16e1d 100644 --- a/api/src/org/labkey/api/search/SearchService.java +++ b/api/src/org/labkey/api/search/SearchService.java @@ -16,7 +16,8 @@ package org.labkey.api.search; import org.apache.commons.collections4.ListUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -67,8 +68,8 @@ public interface SearchService { // create logger for package which can be set via logger-manage.view - Logger _packageLogger = Logger.getLogger(SearchService.class.getPackage().getName()); - Logger _log = Logger.getLogger(SearchService.class); + Logger _packageLogger = LogManager.getLogger(SearchService.class.getPackage().getName()); + Logger _log = LogManager.getLogger(SearchService.class); long DEFAULT_FILE_SIZE_LIMIT = 100L; // 100 MB diff --git a/api/src/org/labkey/api/security/ActionNames.java b/api/src/org/labkey/api/security/ActionNames.java index 06af8db665c..0afdb880409 100644 --- a/api/src/org/labkey/api/security/ActionNames.java +++ b/api/src/org/labkey/api/security/ActionNames.java @@ -16,9 +16,9 @@ package org.labkey.api.security; -import java.lang.annotation.Target; import java.lang.annotation.ElementType; import java.lang.annotation.Retention; +import java.lang.annotation.Target; /** * Specify comma-separated names for an action. Once this annotation is added to an action, it replaces the diff --git a/api/src/org/labkey/api/security/ApiKeyManager.java b/api/src/org/labkey/api/security/ApiKeyManager.java index f02c173f03b..743d05e48f7 100644 --- a/api/src/org/labkey/api/security/ApiKeyManager.java +++ b/api/src/org/labkey/api/security/ApiKeyManager.java @@ -15,7 +15,7 @@ */ package org.labkey.api.security; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; diff --git a/api/src/org/labkey/api/security/AuthenticatedRequest.java b/api/src/org/labkey/api/security/AuthenticatedRequest.java index 0234f07f951..cfad2b55741 100644 --- a/api/src/org/labkey/api/security/AuthenticatedRequest.java +++ b/api/src/org/labkey/api/security/AuthenticatedRequest.java @@ -17,7 +17,8 @@ package org.labkey.api.security; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheManager; @@ -60,7 +61,7 @@ */ public class AuthenticatedRequest extends HttpServletRequestWrapper implements AutoCloseable { - private static final Logger _log = Logger.getLogger(AuthenticatedRequest.class); + private static final Logger _log = LogManager.getLogger(AuthenticatedRequest.class); private final User _user; private boolean _loggedIn; diff --git a/api/src/org/labkey/api/security/AuthenticatedResponse.java b/api/src/org/labkey/api/security/AuthenticatedResponse.java index 029035567bf..a64d79b6df3 100644 --- a/api/src/org/labkey/api/security/AuthenticatedResponse.java +++ b/api/src/org/labkey/api/security/AuthenticatedResponse.java @@ -18,10 +18,10 @@ import org.labkey.api.util.PageFlowUtil; -import javax.servlet.http.HttpServletResponseWrapper; import javax.servlet.http.HttpServletResponse; -import java.io.PrintWriter; +import javax.servlet.http.HttpServletResponseWrapper; import java.io.IOException; +import java.io.PrintWriter; import java.io.Writer; import java.util.Locale; diff --git a/api/src/org/labkey/api/security/AuthenticationManager.java b/api/src/org/labkey/api/security/AuthenticationManager.java index b66ba2c0a6d..f4ff7a6bc55 100644 --- a/api/src/org/labkey/api/security/AuthenticationManager.java +++ b/api/src/org/labkey/api/security/AuthenticationManager.java @@ -17,7 +17,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -112,7 +113,7 @@ public class AuthenticationManager { public static final String ALL_DOMAINS = "*"; - private static final Logger _log = Logger.getLogger(AuthenticationManager.class); + private static final Logger _log = LogManager.getLogger(AuthenticationManager.class); // All registered authentication providers (DbLogin, LDAP, SSO, etc.) private static final List _allProviders = new CopyOnWriteArrayList<>(); diff --git a/api/src/org/labkey/api/security/AuthenticationProviderCache.java b/api/src/org/labkey/api/security/AuthenticationProviderCache.java index 3cbe4814af7..5a1256abf2b 100644 --- a/api/src/org/labkey/api/security/AuthenticationProviderCache.java +++ b/api/src/org/labkey/api/security/AuthenticationProviderCache.java @@ -25,7 +25,6 @@ import java.util.Collections; import java.util.LinkedHashMap; import java.util.LinkedHashSet; -import java.util.List; import java.util.Set; /** diff --git a/api/src/org/labkey/api/security/ConfigurationSettings.java b/api/src/org/labkey/api/security/ConfigurationSettings.java index c8910803ec3..2c14db58c06 100644 --- a/api/src/org/labkey/api/security/ConfigurationSettings.java +++ b/api/src/org/labkey/api/security/ConfigurationSettings.java @@ -1,7 +1,8 @@ package org.labkey.api.security; import org.apache.commons.codec.binary.Base64; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONObject; import org.labkey.api.data.AES; import org.labkey.api.settings.AppProps; @@ -10,7 +11,7 @@ public class ConfigurationSettings { - private static final Logger LOG = Logger.getLogger(ConfigurationSettings.class); + private static final Logger LOG = LogManager.getLogger(ConfigurationSettings.class); private final Map _standardSettings; private final Map _properties; diff --git a/api/src/org/labkey/api/security/ContextualRoles.java b/api/src/org/labkey/api/security/ContextualRoles.java index 47a516dc521..8265e3f2543 100644 --- a/api/src/org/labkey/api/security/ContextualRoles.java +++ b/api/src/org/labkey/api/security/ContextualRoles.java @@ -18,9 +18,9 @@ import org.labkey.api.security.roles.HasContextualRoles; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Annotation to add additional contextual roles during permission checking. diff --git a/api/src/org/labkey/api/security/GroupManager.java b/api/src/org/labkey/api/security/GroupManager.java index 8f90e97a9ca..4b290604973 100644 --- a/api/src/org/labkey/api/security/GroupManager.java +++ b/api/src/org/labkey/api/security/GroupManager.java @@ -16,7 +16,8 @@ package org.labkey.api.security; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -75,7 +76,7 @@ */ public class GroupManager { - private static final Logger _log = Logger.getLogger(GroupManager.class); + private static final Logger _log = LogManager.getLogger(GroupManager.class); private static final CoreSchema _core = CoreSchema.getInstance(); private static final int[] EMPTY_INT_ARRAY = new int[0]; diff --git a/api/src/org/labkey/api/security/IgnoresTermsOfUse.java b/api/src/org/labkey/api/security/IgnoresTermsOfUse.java index a9e584da1a6..a62e719fe13 100644 --- a/api/src/org/labkey/api/security/IgnoresTermsOfUse.java +++ b/api/src/org/labkey/api/security/IgnoresTermsOfUse.java @@ -16,9 +16,9 @@ package org.labkey.api.security; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Marker for actions that should not ensure that the user has accepted any terms of use diff --git a/api/src/org/labkey/api/security/MemberType.java b/api/src/org/labkey/api/security/MemberType.java index 943528c8dd4..8f28d349df0 100644 --- a/api/src/org/labkey/api/security/MemberType.java +++ b/api/src/org/labkey/api/security/MemberType.java @@ -17,8 +17,6 @@ import org.jetbrains.annotations.Nullable; -import java.lang.*; - /** * User: adam * Date: 11/12/12 diff --git a/api/src/org/labkey/api/security/MutableSecurityPolicy.java b/api/src/org/labkey/api/security/MutableSecurityPolicy.java index 1fa7af2103d..f6000d02063 100644 --- a/api/src/org/labkey/api/security/MutableSecurityPolicy.java +++ b/api/src/org/labkey/api/security/MutableSecurityPolicy.java @@ -18,14 +18,18 @@ import org.apache.commons.beanutils.ConversionException; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.json.JSONArray; import org.labkey.api.data.ContainerManager; +import org.labkey.api.security.roles.NoPermissionsRole; import org.labkey.api.security.roles.Role; import org.labkey.api.security.roles.RoleManager; -import org.labkey.api.security.roles.NoPermissionsRole; import org.labkey.api.util.DateUtil; -import org.json.JSONArray; -import java.util.*; +import java.util.ArrayList; +import java.util.Date; +import java.util.Iterator; +import java.util.List; +import java.util.Map; /* * User: Dave diff --git a/api/src/org/labkey/api/security/RequiresLogin.java b/api/src/org/labkey/api/security/RequiresLogin.java index f48a82ea438..39fea5eb7a8 100644 --- a/api/src/org/labkey/api/security/RequiresLogin.java +++ b/api/src/org/labkey/api/security/RequiresLogin.java @@ -16,9 +16,9 @@ package org.labkey.api.security; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Indicates that a user must be authenticated (not a guest), but does not require any particular permission. diff --git a/api/src/org/labkey/api/security/RequiresNoPermission.java b/api/src/org/labkey/api/security/RequiresNoPermission.java index 5c12c933a14..77d640cb657 100644 --- a/api/src/org/labkey/api/security/RequiresNoPermission.java +++ b/api/src/org/labkey/api/security/RequiresNoPermission.java @@ -16,9 +16,9 @@ package org.labkey.api.security; +import java.lang.annotation.ElementType; import java.lang.annotation.Retention; import java.lang.annotation.Target; -import java.lang.annotation.ElementType; /** * Indicates that an action does not require any kind of authentication or permission to invoke. Use with extreme diff --git a/api/src/org/labkey/api/security/SecurityLogger.java b/api/src/org/labkey/api/security/SecurityLogger.java index dee2ebb3beb..7b044a00a26 100644 --- a/api/src/org/labkey/api/security/SecurityLogger.java +++ b/api/src/org/labkey/api/security/SecurityLogger.java @@ -16,8 +16,9 @@ package org.labkey.api.security; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; -import org.apache.log4j.Priority; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; import org.jetbrains.annotations.Nullable; import java.util.ArrayList; @@ -30,9 +31,9 @@ * Date: 2013-02-01 */ -public class SecurityLogger extends Logger +public class SecurityLogger extends org.apache.logging.log4j.core.Logger { - private static final Logger _log = Logger.getLogger(SecurityManager.class); + private static final Logger _log = LogManager.getLogger(SecurityManager.class); static SecurityLogger instance = new SecurityLogger("SecurityLogger"); @@ -102,7 +103,7 @@ public static boolean outdent() private SecurityLogger(String name) { - super(name); + super((LoggerContext) LogManager.getContext(), name, _log.getMessageFactory()); } @@ -210,12 +211,6 @@ public boolean isDebugEnabled() return _log.isDebugEnabled(); } - @Override - public boolean isEnabledFor(Priority level) - { - return _log.isEnabledFor(level); - } - @Override public void warn(Object message) { diff --git a/api/src/org/labkey/api/security/SecurityManager.java b/api/src/org/labkey/api/security/SecurityManager.java index 7aba63ea08f..e371ef7b779 100644 --- a/api/src/org/labkey/api/security/SecurityManager.java +++ b/api/src/org/labkey/api/security/SecurityManager.java @@ -20,8 +20,9 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -135,7 +136,7 @@ public class SecurityManager { - private static final Logger _log = Logger.getLogger(SecurityManager.class); + private static final Logger _log = LogManager.getLogger(SecurityManager.class); private static final CoreSchema core = CoreSchema.getInstance(); private static final List VIEW_FACTORIES = new CopyOnWriteArrayList<>(); private static final List TERMS_OF_USE_PROVIDERS = new CopyOnWriteArrayList<>(); diff --git a/api/src/org/labkey/api/security/SecurityMessage.java b/api/src/org/labkey/api/security/SecurityMessage.java index 01758736cea..f1dbea0d025 100644 --- a/api/src/org/labkey/api/security/SecurityMessage.java +++ b/api/src/org/labkey/api/security/SecurityMessage.java @@ -16,10 +16,10 @@ package org.labkey.api.security; +import org.labkey.api.data.Container; import org.labkey.api.settings.LookAndFeelProperties; import org.labkey.api.util.MailHelper; import org.labkey.api.util.emailTemplate.EmailTemplate; -import org.labkey.api.data.Container; import javax.mail.Address; import javax.mail.internet.MimeMessage; diff --git a/api/src/org/labkey/api/security/SecurityPolicy.java b/api/src/org/labkey/api/security/SecurityPolicy.java index ceec295ff5e..21b5e8a1bab 100644 --- a/api/src/org/labkey/api/security/SecurityPolicy.java +++ b/api/src/org/labkey/api/security/SecurityPolicy.java @@ -15,7 +15,8 @@ */ package org.labkey.api.security; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.CacheManager; @@ -55,7 +56,7 @@ */ public class SecurityPolicy implements HasPermission { - private static final Logger LOG = Logger.getLogger(SecurityPolicy.class); + private static final Logger LOG = LogManager.getLogger(SecurityPolicy.class); protected final SortedSet _assignments = new TreeSet<>(); protected final String _resourceId; diff --git a/api/src/org/labkey/api/security/SecurityPolicyManager.java b/api/src/org/labkey/api/security/SecurityPolicyManager.java index 61b04716569..63126ad71b3 100644 --- a/api/src/org/labkey/api/security/SecurityPolicyManager.java +++ b/api/src/org/labkey/api/security/SecurityPolicyManager.java @@ -15,7 +15,8 @@ */ package org.labkey.api.security; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportContext; @@ -62,7 +63,7 @@ */ public class SecurityPolicyManager { - private static final Logger logger = Logger.getLogger(SecurityPolicyManager.class); + private static final Logger logger = LogManager.getLogger(SecurityPolicyManager.class); private static final CoreSchema core = CoreSchema.getInstance(); private static final Cache CACHE = new DatabaseCache<>(core.getSchema().getScope(), CacheManager.UNLIMITED, "SecurityPolicies"); diff --git a/api/src/org/labkey/api/security/UserManager.java b/api/src/org/labkey/api/security/UserManager.java index b09d6ee91a0..a84408fec0d 100644 --- a/api/src/org/labkey/api/security/UserManager.java +++ b/api/src/org/labkey/api/security/UserManager.java @@ -17,7 +17,8 @@ package org.labkey.api.security; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; @@ -83,7 +84,7 @@ public class UserManager { - private static final Logger LOG = Logger.getLogger(UserManager.class); + private static final Logger LOG = LogManager.getLogger(UserManager.class); private static final CoreSchema CORE = CoreSchema.getInstance(); // NOTE: This static map will slowly grow, since user IDs & timestamps are added and never removed. It's a trivial amount of data, though. diff --git a/api/src/org/labkey/api/security/UserPrincipal.java b/api/src/org/labkey/api/security/UserPrincipal.java index 13694fb4128..2dc89f192f3 100644 --- a/api/src/org/labkey/api/security/UserPrincipal.java +++ b/api/src/org/labkey/api/security/UserPrincipal.java @@ -22,8 +22,8 @@ import org.labkey.api.data.Parameter; import org.labkey.api.security.roles.Role; -import java.security.Principal; import java.io.Serializable; +import java.security.Principal; import java.util.Set; /** diff --git a/api/src/org/labkey/api/security/ValidEmail.java b/api/src/org/labkey/api/security/ValidEmail.java index 355b1313a57..95eacd562c2 100644 --- a/api/src/org/labkey/api/security/ValidEmail.java +++ b/api/src/org/labkey/api/security/ValidEmail.java @@ -17,7 +17,8 @@ package org.labkey.api.security; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.data.ColumnInfo; @@ -45,7 +46,7 @@ */ public class ValidEmail { - private static final Logger LOG = Logger.getLogger(ValidEmail.class); + private static final Logger LOG = LogManager.getLogger(ValidEmail.class); private final InternetAddress _internetAddress; diff --git a/api/src/org/labkey/api/security/impersonation/GroupImpersonationContextFactory.java b/api/src/org/labkey/api/security/impersonation/GroupImpersonationContextFactory.java index 323eb7248cb..6ce49702471 100644 --- a/api/src/org/labkey/api/security/impersonation/GroupImpersonationContextFactory.java +++ b/api/src/org/labkey/api/security/impersonation/GroupImpersonationContextFactory.java @@ -38,7 +38,6 @@ import java.util.Collection; import java.util.LinkedList; import java.util.List; -import java.util.Map; import java.util.Set; /** diff --git a/api/src/org/labkey/api/security/impersonation/RoleImpersonationContextFactory.java b/api/src/org/labkey/api/security/impersonation/RoleImpersonationContextFactory.java index 35afb2045e2..c81cea29a5d 100644 --- a/api/src/org/labkey/api/security/impersonation/RoleImpersonationContextFactory.java +++ b/api/src/org/labkey/api/security/impersonation/RoleImpersonationContextFactory.java @@ -39,7 +39,6 @@ import java.util.Collections; import java.util.HashSet; import java.util.LinkedList; -import java.util.Map; import java.util.Set; /** diff --git a/api/src/org/labkey/api/security/roles/AbstractModuleScopedRole.java b/api/src/org/labkey/api/security/roles/AbstractModuleScopedRole.java index 2daacf8b73f..094a437801d 100644 --- a/api/src/org/labkey/api/security/roles/AbstractModuleScopedRole.java +++ b/api/src/org/labkey/api/security/roles/AbstractModuleScopedRole.java @@ -17,7 +17,6 @@ import org.labkey.api.data.Container; import org.labkey.api.module.Module; -import org.labkey.api.module.ModuleLoader; import org.labkey.api.security.SecurableResource; import org.labkey.api.security.SecurityPolicy; import org.labkey.api.security.permissions.Permission; diff --git a/api/src/org/labkey/api/security/roles/ApplicationAdminRole.java b/api/src/org/labkey/api/security/roles/ApplicationAdminRole.java index 0bda022bc4c..56476e0f37c 100644 --- a/api/src/org/labkey/api/security/roles/ApplicationAdminRole.java +++ b/api/src/org/labkey/api/security/roles/ApplicationAdminRole.java @@ -17,7 +17,11 @@ import org.labkey.api.security.Group; import org.labkey.api.security.SecurityManager; -import org.labkey.api.security.permissions.*; +import org.labkey.api.security.permissions.ApplicationAdminPermission; +import org.labkey.api.security.permissions.EnableRestrictedModules; +import org.labkey.api.security.permissions.Permission; +import org.labkey.api.security.permissions.TroubleShooterPermission; +import org.labkey.api.security.permissions.UserManagementPermission; import java.util.Arrays; import java.util.Collection; diff --git a/api/src/org/labkey/api/security/roles/AuthorRole.java b/api/src/org/labkey/api/security/roles/AuthorRole.java index 2e6788db044..40005c141fa 100644 --- a/api/src/org/labkey/api/security/roles/AuthorRole.java +++ b/api/src/org/labkey/api/security/roles/AuthorRole.java @@ -19,8 +19,8 @@ import org.labkey.api.reports.permissions.ShareReportPermission; import org.labkey.api.security.SecurableResource; import org.labkey.api.security.SecurityPolicy; -import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.InsertPermission; +import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.ReadSomePermission; /* diff --git a/api/src/org/labkey/api/security/roles/OwnerRole.java b/api/src/org/labkey/api/security/roles/OwnerRole.java index 6415b20a231..b71070fb9e4 100644 --- a/api/src/org/labkey/api/security/roles/OwnerRole.java +++ b/api/src/org/labkey/api/security/roles/OwnerRole.java @@ -15,10 +15,10 @@ */ package org.labkey.api.security.roles; -import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.security.permissions.DeletePermission; +import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.ReadSomePermission; +import org.labkey.api.security.permissions.UpdatePermission; /* * User: Dave diff --git a/api/src/org/labkey/api/security/roles/Role.java b/api/src/org/labkey/api/security/roles/Role.java index c163db63bb9..5e0c7cc981d 100644 --- a/api/src/org/labkey/api/security/roles/Role.java +++ b/api/src/org/labkey/api/security/roles/Role.java @@ -15,13 +15,13 @@ */ package org.labkey.api.security.roles; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Parameter; import org.labkey.api.module.Module; import org.labkey.api.security.SecurableResource; import org.labkey.api.security.SecurityPolicy; -import org.labkey.api.security.permissions.Permission; import org.labkey.api.security.UserPrincipal; -import org.jetbrains.annotations.NotNull; +import org.labkey.api.security.permissions.Permission; import java.util.Collection; import java.util.Collections; diff --git a/api/src/org/labkey/api/security/roles/RoleConverter.java b/api/src/org/labkey/api/security/roles/RoleConverter.java index 5884c5e63b0..6c8bb0e0336 100644 --- a/api/src/org/labkey/api/security/roles/RoleConverter.java +++ b/api/src/org/labkey/api/security/roles/RoleConverter.java @@ -16,7 +16,8 @@ package org.labkey.api.security.roles; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; /* * User: Dave @@ -25,7 +26,7 @@ */ public class RoleConverter implements Converter { - private static final Logger _log = Logger.getLogger(RoleConverter.class); + private static final Logger _log = LogManager.getLogger(RoleConverter.class); @Override public Object convert(Class type, Object value) diff --git a/api/src/org/labkey/api/security/roles/RoleManager.java b/api/src/org/labkey/api/security/roles/RoleManager.java index 27e2a15e647..d9e8ecedd9d 100644 --- a/api/src/org/labkey/api/security/roles/RoleManager.java +++ b/api/src/org/labkey/api/security/roles/RoleManager.java @@ -16,7 +16,7 @@ package org.labkey.api.security.roles; import org.apache.commons.collections4.CollectionUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.junit.Assert; import org.labkey.api.data.ContainerManager; @@ -97,7 +97,7 @@ public static Role getRole(String name) { Role role = _nameToRoleMap.get(name); if (null == role) - Logger.getLogger(RoleManager.class).warn("Could not resolve the role " + name + "! The role may no longer exist, or may not yet be registered."); + LogManager.getLogger(RoleManager.class).warn("Could not resolve the role " + name + "! The role may no longer exist, or may not yet be registered."); return role; } @@ -105,7 +105,7 @@ public static Role getRole(Class clazz) { Role role = _classToRoleMap.get(clazz); if (null == role) - Logger.getLogger(RoleManager.class).warn("Could not resolve the role " + clazz.getName() + "! Did you forget to register the role with RoleManager.register()?"); + LogManager.getLogger(RoleManager.class).warn("Could not resolve the role " + clazz.getName() + "! Did you forget to register the role with RoleManager.register()?"); return role; } @@ -119,7 +119,7 @@ public static Permission getPermission(Class clazz) { Permission perm = (Permission) _classToRoleMap.get(clazz); if (null == perm) - Logger.getLogger(RoleManager.class).warn("Could not resolve the permission " + clazz.getName() + "! If this is not part of a role, you must register it separately with RoleManager.register()."); + LogManager.getLogger(RoleManager.class).warn("Could not resolve the permission " + clazz.getName() + "! If this is not part of a role, you must register it separately with RoleManager.register()."); return perm; } @@ -127,7 +127,7 @@ public static Permission getPermission(String uniqueName) { Permission perm = (Permission) _nameToRoleMap.get(uniqueName); if (null == perm) - Logger.getLogger(RoleManager.class).warn("Could not resolve the permission " + uniqueName + "! The permission may no longer exist, or may not yet be registered."); + LogManager.getLogger(RoleManager.class).warn("Could not resolve the permission " + uniqueName + "! The permission may no longer exist, or may not yet be registered."); return perm; } @@ -170,7 +170,7 @@ public static void registerRole(Role role, boolean addPermissionsToAdminRoles) } catch (InstantiationException | IllegalAccessException e) { - Logger.getLogger(RoleManager.class).error("Exception while instantiating permission " + permClass, e); + LogManager.getLogger(RoleManager.class).error("Exception while instantiating permission " + permClass, e); } } diff --git a/api/src/org/labkey/api/security/roles/SiteAdminRole.java b/api/src/org/labkey/api/security/roles/SiteAdminRole.java index 126b5ec9243..a1ad1da1159 100644 --- a/api/src/org/labkey/api/security/roles/SiteAdminRole.java +++ b/api/src/org/labkey/api/security/roles/SiteAdminRole.java @@ -15,7 +15,16 @@ */ package org.labkey.api.security.roles; -import org.labkey.api.security.permissions.*; +import org.labkey.api.security.permissions.AdminOperationsPermission; +import org.labkey.api.security.permissions.AnalystPermission; +import org.labkey.api.security.permissions.BrowserDeveloperPermission; +import org.labkey.api.security.permissions.CanUseSendMessageApiPermission; +import org.labkey.api.security.permissions.EditModuleResourcesPermission; +import org.labkey.api.security.permissions.Permission; +import org.labkey.api.security.permissions.PlatformDeveloperPermission; +import org.labkey.api.security.permissions.SiteAdminPermission; +import org.labkey.api.security.permissions.TrustedPermission; +import org.labkey.api.security.permissions.UploadFileBasedModulePermission; import org.labkey.api.settings.AppProps; import java.util.Arrays; diff --git a/api/src/org/labkey/api/settings/LookAndFeelProperties.java b/api/src/org/labkey/api/settings/LookAndFeelProperties.java index 349180d2d88..00d5a6f2835 100644 --- a/api/src/org/labkey/api/settings/LookAndFeelProperties.java +++ b/api/src/org/labkey/api/settings/LookAndFeelProperties.java @@ -15,7 +15,7 @@ */ package org.labkey.api.settings; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -158,7 +158,7 @@ public String getSystemEmailAddress() //initial login will be used as the default value. During setup user will be prompted to change. String systemEmailAddress = lookupStringValue(SYSTEM_EMAIL_ADDRESS_PROP, ""); if (systemEmailAddress.isEmpty()) - Logger.getLogger(this.getClass()).error(String.format("System Email Address became unset somehow. Visit '%s/admin-projectSettings.view' to fix it", + LogManager.getLogger(this.getClass()).error(String.format("System Email Address became unset somehow. Visit '%s/admin-projectSettings.view' to fix it", _settingsContainer.getTitle().isEmpty() ? "" : _settingsContainer.getPath())); return systemEmailAddress; } diff --git a/api/src/org/labkey/api/settings/WriteableLookAndFeelProperties.java b/api/src/org/labkey/api/settings/WriteableLookAndFeelProperties.java index 5d7ffa7eae2..45c3de53e45 100644 --- a/api/src/org/labkey/api/settings/WriteableLookAndFeelProperties.java +++ b/api/src/org/labkey/api/settings/WriteableLookAndFeelProperties.java @@ -23,9 +23,24 @@ import org.labkey.api.security.ValidEmail; import org.labkey.api.util.FolderDisplayMode; import org.labkey.api.view.ActionURL; + import java.util.Collection; -import static org.labkey.api.settings.LookAndFeelProperties.*; +import static org.labkey.api.settings.LookAndFeelProperties.COMPANY_NAME_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.CUSTOM_LOGIN_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.CUSTOM_WELCOME_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.DATE_PARSING_MODE; +import static org.labkey.api.settings.LookAndFeelProperties.DISCUSSION_ENABLED_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.FOLDER_DISPLAY_MODE; +import static org.labkey.api.settings.LookAndFeelProperties.HELP_MENU_ENABLED_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.LOGO_HREF_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.NAVIGATION_BAR_WIDTH; +import static org.labkey.api.settings.LookAndFeelProperties.REPORT_A_PROBLEM_PATH_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.SUPPORT_EMAIL; +import static org.labkey.api.settings.LookAndFeelProperties.SYSTEM_DESCRIPTION_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.SYSTEM_EMAIL_ADDRESS_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.SYSTEM_SHORT_NAME_PROP; +import static org.labkey.api.settings.LookAndFeelProperties.THEME_NAME_PROP; /** * User: adam diff --git a/api/src/org/labkey/api/study/SpecimenChangeListener.java b/api/src/org/labkey/api/study/SpecimenChangeListener.java index 8b6b1ec6690..1d6a4e2960c 100644 --- a/api/src/org/labkey/api/study/SpecimenChangeListener.java +++ b/api/src/org/labkey/api/study/SpecimenChangeListener.java @@ -1,21 +1,21 @@ -/* - * Copyright (c) 2014 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2014 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.security.User; diff --git a/api/src/org/labkey/api/study/SpecimenImportStrategy.java b/api/src/org/labkey/api/study/SpecimenImportStrategy.java index bfea9e2e03d..d405fd5cef5 100644 --- a/api/src/org/labkey/api/study/SpecimenImportStrategy.java +++ b/api/src/org/labkey/api/study/SpecimenImportStrategy.java @@ -17,6 +17,7 @@ package org.labkey.api.study; import org.labkey.api.data.Filter; + import java.io.Closeable; import java.util.Map; diff --git a/api/src/org/labkey/api/study/StudyEntity.java b/api/src/org/labkey/api/study/StudyEntity.java index ea66910e16e..3d349aa58f4 100644 --- a/api/src/org/labkey/api/study/StudyEntity.java +++ b/api/src/org/labkey/api/study/StudyEntity.java @@ -17,9 +17,9 @@ package org.labkey.api.study; import org.labkey.api.data.Container; -import org.labkey.api.security.SecurityPolicy; -import org.labkey.api.security.SecurableResource; import org.labkey.api.security.MutableSecurityPolicy; +import org.labkey.api.security.SecurableResource; +import org.labkey.api.security.SecurityPolicy; import org.labkey.api.security.User; /** diff --git a/api/src/org/labkey/api/study/actions/ParticipantVisitResolverChooser.java b/api/src/org/labkey/api/study/actions/ParticipantVisitResolverChooser.java index 13893d40507..5ece5715a9b 100644 --- a/api/src/org/labkey/api/study/actions/ParticipantVisitResolverChooser.java +++ b/api/src/org/labkey/api/study/actions/ParticipantVisitResolverChooser.java @@ -16,16 +16,16 @@ package org.labkey.api.study.actions; -import org.labkey.api.data.SimpleDisplayColumn; -import org.labkey.api.data.RenderContext; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.TableViewForm; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.study.assay.*; import org.labkey.api.gwt.client.DefaultValueType; +import org.labkey.api.study.assay.ParticipantVisitResolverType; +import org.labkey.api.util.PageFlowUtil; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; import java.util.List; /** diff --git a/api/src/org/labkey/api/study/actions/StudyPickerColumn.java b/api/src/org/labkey/api/study/actions/StudyPickerColumn.java index 026b4f42c6a..454ec266e37 100644 --- a/api/src/org/labkey/api/study/actions/StudyPickerColumn.java +++ b/api/src/org/labkey/api/study/actions/StudyPickerColumn.java @@ -16,6 +16,7 @@ package org.labkey.api.study.actions; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AbstractAssayProvider; import org.labkey.api.assay.actions.UploadWizardAction; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; @@ -24,7 +25,6 @@ import org.labkey.api.gwt.client.DefaultValueType; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.study.Study; -import org.labkey.api.assay.AbstractAssayProvider; import org.labkey.api.study.assay.AssayPublishService; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.element.Option; diff --git a/api/src/org/labkey/api/study/assay/AbstractParticipantVisitResolver.java b/api/src/org/labkey/api/study/assay/AbstractParticipantVisitResolver.java index 53df82d0c45..371876f9181 100644 --- a/api/src/org/labkey/api/study/assay/AbstractParticipantVisitResolver.java +++ b/api/src/org/labkey/api/study/assay/AbstractParticipantVisitResolver.java @@ -16,18 +16,16 @@ package org.labkey.api.study.assay; +import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; import org.labkey.api.security.User; import org.labkey.api.study.ParticipantVisit; -import org.jetbrains.annotations.NotNull; -import org.labkey.api.study.assay.ParticipantVisitImpl; -import org.labkey.api.study.assay.ParticipantVisitResolver; import java.util.Date; -import java.util.Map; import java.util.HashMap; +import java.util.Map; /** * User: brittp diff --git a/api/src/org/labkey/api/study/assay/ParticipantVisitResolver.java b/api/src/org/labkey/api/study/assay/ParticipantVisitResolver.java index f52ef1a865a..5968f222368 100644 --- a/api/src/org/labkey/api/study/assay/ParticipantVisitResolver.java +++ b/api/src/org/labkey/api/study/assay/ParticipantVisitResolver.java @@ -16,10 +16,10 @@ package org.labkey.api.study.assay; +import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; import org.labkey.api.study.ParticipantVisit; -import org.jetbrains.annotations.NotNull; import java.util.Date; diff --git a/api/src/org/labkey/api/study/assay/StudyContainerFilter.java b/api/src/org/labkey/api/study/assay/StudyContainerFilter.java index 23f2e6103de..61184b8f5b4 100644 --- a/api/src/org/labkey/api/study/assay/StudyContainerFilter.java +++ b/api/src/org/labkey/api/study/assay/StudyContainerFilter.java @@ -16,7 +16,6 @@ package org.labkey.api.study.assay; import org.labkey.api.assay.AssaySchema; -import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.study.Study; diff --git a/api/src/org/labkey/api/study/assay/StudyParticipantVisitResolverType.java b/api/src/org/labkey/api/study/assay/StudyParticipantVisitResolverType.java index 54f00674d92..6c8ae4d2efc 100644 --- a/api/src/org/labkey/api/study/assay/StudyParticipantVisitResolverType.java +++ b/api/src/org/labkey/api/study/assay/StudyParticipantVisitResolverType.java @@ -17,16 +17,16 @@ package org.labkey.api.study.assay; import org.labkey.api.assay.AssayRunUploadContext; -import org.labkey.api.view.InsertView; -import org.labkey.api.exp.api.ExpData; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.data.Container; import org.labkey.api.data.RenderContext; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpRun; import org.labkey.api.security.User; +import org.labkey.api.view.InsertView; -import java.util.Map; import java.util.Collection; +import java.util.Map; /** * User: jeckels diff --git a/api/src/org/labkey/api/study/assay/ThawListFileResolver.java b/api/src/org/labkey/api/study/assay/ThawListFileResolver.java index 5970afff8e1..b96c3cc2537 100644 --- a/api/src/org/labkey/api/study/assay/ThawListFileResolver.java +++ b/api/src/org/labkey/api/study/assay/ThawListFileResolver.java @@ -16,10 +16,10 @@ package org.labkey.api.study.assay; +import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; import org.labkey.api.study.ParticipantVisit; -import org.labkey.api.data.Container; -import org.jetbrains.annotations.NotNull; import java.util.Date; import java.util.Map; diff --git a/api/src/org/labkey/api/study/security/SecurityEscalationAuditProvider.java b/api/src/org/labkey/api/study/security/SecurityEscalationAuditProvider.java index 0bf7b83d9f6..19aeb29e8a5 100644 --- a/api/src/org/labkey/api/study/security/SecurityEscalationAuditProvider.java +++ b/api/src/org/labkey/api/study/security/SecurityEscalationAuditProvider.java @@ -15,7 +15,8 @@ */ package org.labkey.api.study.security; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.audit.AbstractAuditTypeProvider; import org.labkey.api.audit.AuditTypeEvent; import org.labkey.api.audit.AuditTypeProvider; @@ -50,7 +51,7 @@ */ public abstract class SecurityEscalationAuditProvider extends AbstractAuditTypeProvider implements AuditTypeProvider { - private static Logger _log = Logger.getLogger(SecurityEscalationAuditProvider.class); + private static Logger _log = LogManager.getLogger(SecurityEscalationAuditProvider.class); /** * A name for the event to log as. This shouldn't have any spaces, and uniquely diff --git a/api/src/org/labkey/api/survey/SurveyUrls.java b/api/src/org/labkey/api/survey/SurveyUrls.java index d67e59895b1..1a22cc8ee5a 100644 --- a/api/src/org/labkey/api/survey/SurveyUrls.java +++ b/api/src/org/labkey/api/survey/SurveyUrls.java @@ -15,10 +15,8 @@ */ package org.labkey.api.survey; -import org.jetbrains.annotations.Nullable; import org.labkey.api.action.UrlProvider; import org.labkey.api.data.Container; -import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; /** diff --git a/api/src/org/labkey/api/survey/model/SurveyDesign.java b/api/src/org/labkey/api/survey/model/SurveyDesign.java index da054867c9a..90eb0cea0ad 100644 --- a/api/src/org/labkey/api/survey/model/SurveyDesign.java +++ b/api/src/org/labkey/api/survey/model/SurveyDesign.java @@ -19,9 +19,6 @@ import org.labkey.api.data.Entity; import org.labkey.api.security.User; -import java.util.LinkedHashSet; -import java.util.Set; - /** * User: klum * Date: 12/11/12 diff --git a/api/src/org/labkey/api/thumbnail/ImageStreamThumbnailProvider.java b/api/src/org/labkey/api/thumbnail/ImageStreamThumbnailProvider.java index 6010e5c0271..964bf97b165 100644 --- a/api/src/org/labkey/api/thumbnail/ImageStreamThumbnailProvider.java +++ b/api/src/org/labkey/api/thumbnail/ImageStreamThumbnailProvider.java @@ -16,7 +16,8 @@ package org.labkey.api.thumbnail; import org.apache.batik.transcoder.TranscoderException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentType; @@ -40,7 +41,7 @@ */ public class ImageStreamThumbnailProvider implements ThumbnailProvider { - private static final Logger LOG = Logger.getLogger(ImageStreamThumbnailProvider.class); + private static final Logger LOG = LogManager.getLogger(ImageStreamThumbnailProvider.class); private final ThumbnailProvider _provider; private final @Nullable String _contentType; diff --git a/api/src/org/labkey/api/util/Button.java b/api/src/org/labkey/api/util/Button.java index d3c832b2c20..7e65c62a124 100644 --- a/api/src/org/labkey/api/util/Button.java +++ b/api/src/org/labkey/api/util/Button.java @@ -25,10 +25,17 @@ import java.util.Collections; import java.util.Map; +import static org.labkey.api.util.DOM.A; import static org.labkey.api.util.DOM.Attribute; -import static org.labkey.api.util.DOM.*; -import static org.labkey.api.util.DOM.LK.*; -import static org.labkey.api.util.DOM.Attribute.*; +import static org.labkey.api.util.DOM.Attribute.onclick; +import static org.labkey.api.util.DOM.Attribute.tabindex; +import static org.labkey.api.util.DOM.Attribute.title; +import static org.labkey.api.util.DOM.Attribute.type; +import static org.labkey.api.util.DOM.INPUT; +import static org.labkey.api.util.DOM.LK.FA; +import static org.labkey.api.util.DOM.SPAN; +import static org.labkey.api.util.DOM.at; +import static org.labkey.api.util.DOM.createHtmlFragment; /** diff --git a/api/src/org/labkey/api/util/CPUTimer.java b/api/src/org/labkey/api/util/CPUTimer.java index 1778baa693b..7d04dfcabc9 100644 --- a/api/src/org/labkey/api/util/CPUTimer.java +++ b/api/src/org/labkey/api/util/CPUTimer.java @@ -15,16 +15,21 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; -import java.util.*; +import java.util.Arrays; +import java.util.Comparator; +import java.util.Date; +import java.util.Set; +import java.util.WeakHashMap; /** * Lightweight utility to capture how much time is spent doing specifically instrumented actions. */ public class CPUTimer { - private static final Logger _log = Logger.getLogger(CPUTimer.class); + private static final Logger _log = LogManager.getLogger(CPUTimer.class); // diff --git a/api/src/org/labkey/api/util/CheckedInputStream.java b/api/src/org/labkey/api/util/CheckedInputStream.java index f4a6d305ddb..523732a62c3 100644 --- a/api/src/org/labkey/api/util/CheckedInputStream.java +++ b/api/src/org/labkey/api/util/CheckedInputStream.java @@ -15,7 +15,7 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.miniprofiler.MiniProfiler; @@ -52,7 +52,7 @@ protected void finalize() throws Throwable { if (!_closed) { - Logger.getLogger(CheckedInputStream.class).error("InputStream was not closed. Creation stacktrace:" + ExceptionUtil.renderStackTrace(_creationStackTrace)); + LogManager.getLogger(CheckedInputStream.class).error("InputStream was not closed. Creation stacktrace:" + ExceptionUtil.renderStackTrace(_creationStackTrace)); super.close(); } diff --git a/api/src/org/labkey/api/util/ContextListener.java b/api/src/org/labkey/api/util/ContextListener.java index f8330751607..b6d6de3526c 100644 --- a/api/src/org/labkey/api/util/ContextListener.java +++ b/api/src/org/labkey/api/util/ContextListener.java @@ -16,7 +16,10 @@ package org.labkey.api.util; import org.apache.commons.logging.LogFactory; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.NullConfiguration; import org.labkey.api.cache.CacheManager; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleLoader; @@ -50,8 +53,8 @@ public class ContextListener implements ServletContextListener System.setProperty(LOG_HOME_PROPERTY_NAME, System.getProperty("catalina.base") + "/logs"); } - // NOTE: this line of code with Logger.getLogger() has to happen after System.setProperty(LOG_HOME_PROPERTY_NAME) - private static final Logger _log = Logger.getLogger(ContextListener.class); + // NOTE: this line of code with LogManager.getLogger() has to happen after System.setProperty(LOG_HOME_PROPERTY_NAME) + private static final Logger _log = LogManager.getLogger(ContextListener.class); private static final List _shutdownListeners = new CopyOnWriteArrayList<>(); private static final List _startupListeners = new CopyOnWriteArrayList<>(); private static final ContextLoaderListener _springContextListener = new ContextLoaderListener(); @@ -74,8 +77,8 @@ public void contextDestroyed(ServletContextEvent servletContextEvent) ViewServlet.setShuttingDown(1000); getSpringContextListener().contextDestroyed(servletContextEvent); CacheManager.shutdown(); // Don't use a listener... we want this shutdown late - org.apache.log4j.LogManager.shutdown(); - org.apache.log4j.LogManager.resetConfiguration(); + LogManager.shutdown(); + LoggerContext.getContext(true).setConfiguration(new NullConfiguration()); org.apache.commons.beanutils.PropertyUtils.clearDescriptors(); org.apache.commons.beanutils.ConvertUtils.deregister(); java.beans.Introspector.flushCaches(); diff --git a/api/src/org/labkey/api/util/CountLimiter.java b/api/src/org/labkey/api/util/CountLimiter.java index fd4ea1985a5..7ec8408477d 100644 --- a/api/src/org/labkey/api/util/CountLimiter.java +++ b/api/src/org/labkey/api/util/CountLimiter.java @@ -15,7 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import java.util.ArrayList; import java.util.concurrent.TimeUnit; @@ -27,7 +28,7 @@ */ public class CountLimiter { - static final Logger _log = Logger.getLogger(CountLimiter.class); + static final Logger _log = LogManager.getLogger(CountLimiter.class); final String _name; boolean useSystem = false; // for small intervals or testing diff --git a/api/src/org/labkey/api/util/DOM.java b/api/src/org/labkey/api/util/DOM.java index d351ef16efe..e474bad952e 100644 --- a/api/src/org/labkey/api/util/DOM.java +++ b/api/src/org/labkey/api/util/DOM.java @@ -4,7 +4,8 @@ import com.google.common.collect.Iterators; import org.apache.commons.lang3.NotImplementedException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.action.LabKeyError; import org.labkey.api.action.SpringActionController; @@ -818,7 +819,7 @@ public static Renderable ERRORS(List z) catch (NoSuchMessageException nsme) { ExceptionUtil.logExceptionToMothership(context.getRequest(), nsme); - Logger log = Logger.getLogger(ErrorsTag.class); + Logger log = LogManager.getLogger(ErrorsTag.class); log.error("Failed to find a message: " + error, nsme); return createHtmlFragment("Unknown error: " + error, BR()); } diff --git a/api/src/org/labkey/api/util/DOMUtil.java b/api/src/org/labkey/api/util/DOMUtil.java index 326f202b0b4..eb0f0466129 100644 --- a/api/src/org/labkey/api/util/DOMUtil.java +++ b/api/src/org/labkey/api/util/DOMUtil.java @@ -15,13 +15,13 @@ */ package org.labkey.api.util; +import org.w3c.dom.NamedNodeMap; import org.w3c.dom.Node; import org.w3c.dom.NodeList; -import org.w3c.dom.NamedNodeMap; -import java.util.List; import java.util.ArrayList; import java.util.Collections; +import java.util.List; /* * User: Dave diff --git a/api/src/org/labkey/api/util/DateUtil.java b/api/src/org/labkey/api/util/DateUtil.java index 9f3f3d72ae7..bd8a5b4bdf9 100644 --- a/api/src/org/labkey/api/util/DateUtil.java +++ b/api/src/org/labkey/api/util/DateUtil.java @@ -19,7 +19,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.time.DateUtils; import org.apache.commons.lang3.time.FastDateFormat; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.jfree.util.StringUtils; @@ -59,7 +60,7 @@ private DateUtil() { } - private static final Logger LOG = Logger.getLogger(DateUtil.class); + private static final Logger LOG = LogManager.getLogger(DateUtil.class); private static final Map tzCache = new ConcurrentHashMap<>(); private static final Locale _localeDefault = Locale.getDefault(); private static final TimeZone _timezoneDefault = TimeZone.getDefault(); diff --git a/api/src/org/labkey/api/util/DebugInfoDumper.java b/api/src/org/labkey/api/util/DebugInfoDumper.java index dd21cc56157..d8bf0b645d5 100644 --- a/api/src/org/labkey/api/util/DebugInfoDumper.java +++ b/api/src/org/labkey/api/util/DebugInfoDumper.java @@ -16,7 +16,8 @@ package org.labkey.api.util; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.ConnectionWrapper; import org.labkey.api.data.DbScope; import org.labkey.api.files.FileSystemDirectoryListener; @@ -50,7 +51,7 @@ */ public class DebugInfoDumper { - private static final Logger LOG = Logger.getLogger(DebugInfoDumper.class); + private static final Logger LOG = LogManager.getLogger(DebugInfoDumper.class); private final File _threadDumpFile; private final File _heapDumpFile; @@ -229,22 +230,22 @@ public static File dumpHeap() throws Exception } /** - * Writes the current set of thread stacks once to the supplied logger. - */ - public static synchronized void dumpThreads(Logger log) + * Writes the thread dump into threads.txt + * */ + public static synchronized void dumpThreads(LoggerWriter logWriter) { - log.debug("*********************************************"); - log.debug("Starting thread dump - " + LocalDateTime.now().toString()); + logWriter.debug("*********************************************"); + logWriter.debug("Starting thread dump - " + LocalDateTime.now().toString()); long used = ManagementFactory.getMemoryMXBean().getHeapMemoryUsage().getUsed(); long max = ManagementFactory.getMemoryMXBean().getHeapMemoryUsage().getMax(); - log.debug("Heap usage at " + DecimalFormat.getPercentInstance().format(((double)used / (double)max)) + " - " + + logWriter.debug("Heap usage at " + DecimalFormat.getPercentInstance().format(((double)used / (double)max)) + " - " + FileUtils.byteCountToDisplaySize(used) + " from a max of " + FileUtils.byteCountToDisplaySize(max) + " (" + DecimalFormat.getInstance().format(used) + " / " + DecimalFormat.getInstance().format(max) + " bytes)"); - log.debug("*********************************************"); + logWriter.debug("*********************************************"); Map threads = Thread.getAllStackTraces(); for (Map.Entry threadEntry : threads.entrySet()) { - log.debug(""); + logWriter.debug(""); Thread thread = threadEntry.getKey(); StringBuilder threadInfo = new StringBuilder(thread.getName()); threadInfo.append(" ("); @@ -257,39 +258,47 @@ public static synchronized void dumpThreads(Logger log) threadInfo.append(", Database Connection SPIDs = "); threadInfo.append(spids); } - log.debug(threadInfo); + logWriter.debug(threadInfo.toString()); String uri = ViewServlet.getRequestURL(thread); if (null != uri) - log.debug(uri); + logWriter.debug(uri); for (StackTraceElement stackTraceElement : threadEntry.getValue()) { - log.debug("\t" + stackTraceElement.toString()); + logWriter.debug("\t" + stackTraceElement.toString()); } if (ConnectionWrapper.getProbableLeakCount() > 0) { - ConnectionWrapper.dumpLeaksForThread(thread, log); + ConnectionWrapper.dumpLeaksForThread(thread, logWriter); } } - log.debug("*********************************************"); - log.debug("Completed thread dump"); - log.debug("*********************************************"); + logWriter.debug("*********************************************"); + logWriter.debug("Completed thread dump"); + logWriter.debug("*********************************************"); for (DbScope dbScope : DbScope.getDbScopes()) { - dbScope.logCurrentConnectionState(log); + dbScope.logCurrentConnectionState(logWriter); } if (ConnectionWrapper.getActiveConnectionCount() > 0) { - log.debug("*********************************************"); - log.debug("Start dump of all open connections"); - log.debug("*********************************************"); - ConnectionWrapper.dumpOpenConnections(log); - log.debug("*********************************************"); - log.debug("Completed dump of all open connections"); - log.debug("*********************************************"); + logWriter.debug("*********************************************"); + logWriter.debug("Start dump of all open connections"); + logWriter.debug("*********************************************"); + ConnectionWrapper.dumpOpenConnections(logWriter); + logWriter.debug("*********************************************"); + logWriter.debug("Completed dump of all open connections"); + logWriter.debug("*********************************************"); } } + + /** + * Writes the current set of thread stacks once to the supplied logger. + */ + public static synchronized void dumpThreads(Logger log) + { + dumpThreads(new SimpleLoggerWriter(log)); + } } diff --git a/api/src/org/labkey/api/util/DomTestCase.java b/api/src/org/labkey/api/util/DomTestCase.java index b75441f702b..64af8410c09 100644 --- a/api/src/org/labkey/api/util/DomTestCase.java +++ b/api/src/org/labkey/api/util/DomTestCase.java @@ -5,8 +5,23 @@ import java.util.Arrays; -import static org.labkey.api.util.DOM.*; -import static org.labkey.api.util.DOM.Attribute.*; +import static org.labkey.api.util.DOM.Attribute.id; +import static org.labkey.api.util.DOM.Attribute.method; +import static org.labkey.api.util.DOM.Attribute.onclick; +import static org.labkey.api.util.DOM.Attribute.selected; +import static org.labkey.api.util.DOM.DIV; +import static org.labkey.api.util.DOM.Element; +import static org.labkey.api.util.DOM.H1; +import static org.labkey.api.util.DOM.H2; +import static org.labkey.api.util.DOM.LK; +import static org.labkey.api.util.DOM.OPTION; +import static org.labkey.api.util.DOM.SELECT; +import static org.labkey.api.util.DOM.SPAN; +import static org.labkey.api.util.DOM.at; +import static org.labkey.api.util.DOM.cl; +import static org.labkey.api.util.DOM.createHtml; +import static org.labkey.api.util.DOM.createHtmlFragment; +import static org.labkey.api.util.DOM.id; public class DomTestCase extends Assert diff --git a/api/src/org/labkey/api/util/ExceptionUtil.java b/api/src/org/labkey/api/util/ExceptionUtil.java index 67350f9bd2c..981ff6f44d0 100644 --- a/api/src/org/labkey/api/util/ExceptionUtil.java +++ b/api/src/org/labkey/api/util/ExceptionUtil.java @@ -17,7 +17,9 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -93,7 +95,7 @@ public class ExceptionUtil public static final String REQUEST_EXCEPTION_ATTRIBUTE = ExceptionUtil.class.getName() + "$exception"; private static final JobRunner JOB_RUNNER = new JobRunner("Mothership Reporting", 1); - private static final Logger LOG = Logger.getLogger(ExceptionUtil.class); + private static final Logger LOG = LogManager.getLogger(ExceptionUtil.class); // Allow 10 report submissions to mothership per minute private static final RateLimiter _reportingRateLimiter = new RateLimiter("exception reporting", 10, TimeUnit.MINUTES); @@ -1023,7 +1025,7 @@ ExceptionResponse handleIt(final User user, Exception ex, @Nullable String messa return null; }; SearchService dummySearch = (SearchService) Proxy.newProxyInstance(this.getClass().getClassLoader(), new Class[]{SearchService.class}, h); - Logger dummyLog = new Logger("mock logger") + Logger dummyLog = new org.apache.logging.log4j.core.Logger((LoggerContext) LogManager.getContext(), "mock logger", LogManager.getLogger("mock logger").getMessageFactory()) { @Override public void debug(Object message) @@ -1038,9 +1040,9 @@ public void error(Object message) { } @Override - public void error(Object message, Throwable t) + public void error(String message, Throwable t) { - res.addHeader("Logger.error", null!=message?String.valueOf(message):null!=t?t.getMessage():""); + res.addHeader("Logger.error", null!=message? message :null!=t?t.getMessage():""); } @Override public void fatal(Object message) diff --git a/api/src/org/labkey/api/util/FileLoggerWriter.java b/api/src/org/labkey/api/util/FileLoggerWriter.java new file mode 100644 index 00000000000..1bc8bce4cef --- /dev/null +++ b/api/src/org/labkey/api/util/FileLoggerWriter.java @@ -0,0 +1,151 @@ +package org.labkey.api.util; + +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; + +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; + +/** + * This loggerWriter will log the contents in a file. + * */ +public class FileLoggerWriter implements LoggerWriter, AutoCloseable +{ + private final String LINE_SEP = System.getProperty("line.separator"); + private static Logger LOG = LogManager.getLogger(FileLoggerWriter.class); + + private File _file; + private BufferedWriter _writer; + + public FileLoggerWriter(File file) + { + _file = file; + // Make sure that we try to mount the drive (if needed) before using the file + NetworkDrive.exists(_file); + try + { + _writer = new BufferedWriter(new FileWriter(_file, true)); + } + catch (IOException e) + { + LOG.error("Failed opening the file - " + _file.getName() , e); + } + + } + + @Override + public void close() + { + try + { + _writer.close(); + } + catch (IOException e) + { + LOG.error("Unable to close the file - " + _file.getName(), e); + } + } + + private boolean isFilePresent() + { + return _file != null; + } + + @Override + public void write(String message, @Nullable Throwable t) + { + if (isFilePresent()) + { + try + { + _writer.write(message); + _writer.write(LINE_SEP); + + if (null != t) + { + StackTraceElement[] stackTraceElements = t.getStackTrace(); + if (stackTraceElements != null) + { + for (StackTraceElement stackTraceElement : stackTraceElements) + { + _writer.write(stackTraceElement.toString()); + _writer.write(LINE_SEP); + } + } + } + } + catch (IOException e) + { + LOG.error("Failed appending to file - " + _file.getName(), e); + } + } + else + { + LOG.error("File not provided to write logs."); + } + + } + + @Override + public void debug(String message) + { + write(message, null); + } + + @Override + public void debug(String message, Throwable t) + { + write(message, t); + } + + @Override + public void error(String message) + { + write(message, null); + } + + @Override + public void error(String message, Throwable t) + { + write(message, t); + } + + @Override + public void info(String message) + { + write(message, null); + } + + @Override + public void info(String message, Throwable t) + { + write(message, t); + } + + @Override + public void fatal(String message) + { + write(message, null); + } + + @Override + public void fatal(String message, Throwable t) + { + write(message, t); + } + + @Override + public void trace(String message) + { + write(message, null); + } + + @Override + public void trace(String message, Throwable t) + { + write(message, t); + } +} diff --git a/api/src/org/labkey/api/util/FileNameUniquifier.java b/api/src/org/labkey/api/util/FileNameUniquifier.java index be0a83f53b1..7d7b57de280 100644 --- a/api/src/org/labkey/api/util/FileNameUniquifier.java +++ b/api/src/org/labkey/api/util/FileNameUniquifier.java @@ -16,8 +16,8 @@ package org.labkey.api.util; -import java.util.Set; import java.util.HashSet; +import java.util.Set; /** * Uniquify filenames by inserting _n immediately before the extension when another file of the same name is diff --git a/api/src/org/labkey/api/util/FileStream.java b/api/src/org/labkey/api/util/FileStream.java index 1342d034d69..edd0acf3897 100644 --- a/api/src/org/labkey/api/util/FileStream.java +++ b/api/src/org/labkey/api/util/FileStream.java @@ -19,7 +19,15 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import java.io.*; +import java.io.BufferedInputStream; +import java.io.BufferedOutputStream; +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; import java.util.Date; /** diff --git a/api/src/org/labkey/api/util/FileUtil.java b/api/src/org/labkey/api/util/FileUtil.java index cae0499586e..d6d52f7d934 100644 --- a/api/src/org/labkey/api/util/FileUtil.java +++ b/api/src/org/labkey/api/util/FileUtil.java @@ -19,7 +19,8 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -63,7 +64,7 @@ */ public class FileUtil { - private static final Logger LOG = Logger.getLogger(FileUtil.class); + private static final Logger LOG = LogManager.getLogger(FileUtil.class); private static File _tempDir = null; diff --git a/api/src/org/labkey/api/util/HTMLContentExtractor.java b/api/src/org/labkey/api/util/HTMLContentExtractor.java index 70c875b20db..cbcad566fe7 100644 --- a/api/src/org/labkey/api/util/HTMLContentExtractor.java +++ b/api/src/org/labkey/api/util/HTMLContentExtractor.java @@ -16,13 +16,13 @@ package org.labkey.api.util; -import javax.swing.text.html.HTMLEditorKit; +import javax.swing.text.MutableAttributeSet; import javax.swing.text.html.HTML; +import javax.swing.text.html.HTMLEditorKit; import javax.swing.text.html.parser.ParserDelegator; -import javax.swing.text.MutableAttributeSet; +import java.io.IOException; import java.io.Reader; import java.io.StringReader; -import java.io.IOException; public abstract class HTMLContentExtractor extends HTMLEditorKit.ParserCallback { diff --git a/api/src/org/labkey/api/util/HeartBeat.java b/api/src/org/labkey/api/util/HeartBeat.java index 02b19b5053b..d1061d2e322 100644 --- a/api/src/org/labkey/api/util/HeartBeat.java +++ b/api/src/org/labkey/api/util/HeartBeat.java @@ -15,7 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; /** * HeatBeatThread is faster than using System.currentTimeMillis() for @@ -47,7 +48,7 @@ public static long currentTimeMillis() // IMPL // - private static final Logger _log = Logger.getLogger(HeartBeat.class); + private static final Logger _log = LogManager.getLogger(HeartBeat.class); public static volatile int counter = 0; // covers more than 60yrs uptime public static volatile long currentTimeMillis = System.currentTimeMillis(); diff --git a/api/src/org/labkey/api/util/HttpUtil.java b/api/src/org/labkey/api/util/HttpUtil.java index 6d902b5c4b8..ed278c68627 100644 --- a/api/src/org/labkey/api/util/HttpUtil.java +++ b/api/src/org/labkey/api/util/HttpUtil.java @@ -26,7 +26,8 @@ import org.apache.http.impl.client.ContentEncodingHttpClient; import org.apache.http.protocol.BasicHttpContext; import org.apache.http.protocol.ExecutionContext; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.BaseApiAction; import org.labkey.api.miniprofiler.CustomTiming; import org.labkey.api.miniprofiler.MiniProfiler; @@ -53,7 +54,7 @@ */ public class HttpUtil { - private static final Logger LOG = Logger.getLogger(HttpUtil.class); + private static final Logger LOG = LogManager.getLogger(HttpUtil.class); private static final Pattern _metaRefreshRegex = Pattern.compile("", Pattern.CASE_INSENSITIVE | Pattern.MULTILINE); diff --git a/api/src/org/labkey/api/util/HttpsUtil.java b/api/src/org/labkey/api/util/HttpsUtil.java index 1eebfcdaa70..6666578c0b0 100644 --- a/api/src/org/labkey/api/util/HttpsUtil.java +++ b/api/src/org/labkey/api/util/HttpsUtil.java @@ -16,7 +16,8 @@ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.settings.AppProps; @@ -41,7 +42,7 @@ */ public class HttpsUtil { - private static final Logger LOG = Logger.getLogger(HttpsUtil.class); + private static final Logger LOG = LogManager.getLogger(HttpsUtil.class); private static final HostnameVerifier _hostnameVerifier = (urlHostName, session) -> true; private static SSLSocketFactory _socketFactory; diff --git a/api/src/org/labkey/api/util/IdentifierString.java b/api/src/org/labkey/api/util/IdentifierString.java index 5b937e258f7..5702579d3d8 100644 --- a/api/src/org/labkey/api/util/IdentifierString.java +++ b/api/src/org/labkey/api/util/IdentifierString.java @@ -16,8 +16,6 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.labkey.api.data.Container; -import org.apache.commons.beanutils.ConversionException; import java.util.regex.Pattern; diff --git a/api/src/org/labkey/api/util/ImageUtil.java b/api/src/org/labkey/api/util/ImageUtil.java index 76e6cb5f740..411dbdd5921 100644 --- a/api/src/org/labkey/api/util/ImageUtil.java +++ b/api/src/org/labkey/api/util/ImageUtil.java @@ -17,8 +17,8 @@ import net.coobird.thumbnailator.Thumbnails; import org.apache.commons.lang3.BooleanUtils; -import org.apache.log4j.Logger; -import org.apache.log4j.Priority; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.thumbnail.Thumbnail; @@ -53,47 +53,47 @@ */ public class ImageUtil { - private static Logger LOG = Logger.getLogger(ImageUtil.class); + private static Logger LOG = LogManager.getLogger(ImageUtil.class); static { XRLog.setLoggerImpl(new XRLogger() { - Priority toPriority(Level level) + org.apache.logging.log4j.Level toPriority(Level level) { int l = level.intValue(); if (l == Level.SEVERE.intValue()) - return org.apache.log4j.Level.ERROR; + return org.apache.logging.log4j.Level.ERROR; if (l == Level.WARNING.intValue()) - return org.apache.log4j.Level.WARN; + return org.apache.logging.log4j.Level.WARN; if (l == Level.INFO.intValue()) - return org.apache.log4j.Level.INFO; + return org.apache.logging.log4j.Level.INFO; if (l == Level.CONFIG.intValue()) - return org.apache.log4j.Level.INFO; + return org.apache.logging.log4j.Level.INFO; if (l == Level.FINE.intValue()) - return org.apache.log4j.Level.DEBUG; + return org.apache.logging.log4j.Level.DEBUG; if (l == Level.FINER.intValue()) - return org.apache.log4j.Level.DEBUG; + return org.apache.logging.log4j.Level.DEBUG; if (l == Level.FINEST.intValue()) - return org.apache.log4j.Level.TRACE; + return org.apache.logging.log4j.Level.TRACE; if (l == Level.ALL.intValue()) - return org.apache.log4j.Level.ALL; + return org.apache.logging.log4j.Level.ALL; if (l == Level.OFF.intValue()) - return org.apache.log4j.Level.OFF; - return org.apache.log4j.Level.DEBUG; + return org.apache.logging.log4j.Level.OFF; + return org.apache.logging.log4j.Level.DEBUG; } @Override public void log(String where, Level level, String msg) { - LOG.log(where, toPriority(level), msg, null); + LOG.log(toPriority(level), msg); } @Override public void log(String where, Level level, String msg, Throwable t) { - LOG.log(where, toPriority(level), msg, t); + LOG.log(toPriority(level), msg, t); } @Override diff --git a/api/src/org/labkey/api/util/Job.java b/api/src/org/labkey/api/util/Job.java index fb78cd50bf5..7f9806d5d0b 100644 --- a/api/src/org/labkey/api/util/Job.java +++ b/api/src/org/labkey/api/util/Job.java @@ -19,7 +19,6 @@ import java.util.concurrent.ExecutionException; import java.util.concurrent.Future; import java.util.concurrent.TimeUnit; -import java.util.concurrent.TimeoutException; /** * User: jeckels diff --git a/api/src/org/labkey/api/util/JobRunner.java b/api/src/org/labkey/api/util/JobRunner.java index d05370fb49b..16249b89c6e 100644 --- a/api/src/org/labkey/api/util/JobRunner.java +++ b/api/src/org/labkey/api/util/JobRunner.java @@ -16,11 +16,17 @@ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.DbScope; import java.util.HashMap; -import java.util.concurrent.*; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.Executor; +import java.util.concurrent.Future; +import java.util.concurrent.ScheduledThreadPoolExecutor; +import java.util.concurrent.ThreadFactory; +import java.util.concurrent.TimeUnit; import java.util.concurrent.atomic.AtomicInteger; /** @@ -40,7 +46,7 @@ */ public class JobRunner implements Executor { - static final Logger _log = Logger.getLogger(JobRunner.class); + static final Logger _log = LogManager.getLogger(JobRunner.class); private static final JobRunner _defaultJobRunner = new JobRunner("Default", 1); diff --git a/api/src/org/labkey/api/util/Link.java b/api/src/org/labkey/api/util/Link.java index 09c99870c1f..00f8c81d083 100644 --- a/api/src/org/labkey/api/util/Link.java +++ b/api/src/org/labkey/api/util/Link.java @@ -24,8 +24,10 @@ import java.util.Collections; import static org.labkey.api.util.DOM.A; +import static org.labkey.api.util.DOM.Attribute.href; +import static org.labkey.api.util.DOM.Attribute.onclick; +import static org.labkey.api.util.DOM.Attribute.target; import static org.labkey.api.util.DOM.at; -import static org.labkey.api.util.DOM.Attribute.*; public class Link extends DisplayElement implements HasHtmlString { diff --git a/api/src/org/labkey/api/util/LogOutputStream.java b/api/src/org/labkey/api/util/LogOutputStream.java index 819ac638f3c..dbb3ebb61c5 100644 --- a/api/src/org/labkey/api/util/LogOutputStream.java +++ b/api/src/org/labkey/api/util/LogOutputStream.java @@ -15,12 +15,11 @@ */ package org.labkey.api.util; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import java.io.ByteArrayOutputStream; -import java.io.IOException; /** * User: adam diff --git a/api/src/org/labkey/api/util/LogPrintWriter.java b/api/src/org/labkey/api/util/LogPrintWriter.java index 58e88508baa..c4fa841b7fc 100644 --- a/api/src/org/labkey/api/util/LogPrintWriter.java +++ b/api/src/org/labkey/api/util/LogPrintWriter.java @@ -15,8 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; import java.io.PrintWriter; diff --git a/api/src/org/labkey/api/util/LoggerWriter.java b/api/src/org/labkey/api/util/LoggerWriter.java new file mode 100644 index 00000000000..4f0f776fd56 --- /dev/null +++ b/api/src/org/labkey/api/util/LoggerWriter.java @@ -0,0 +1,36 @@ +package org.labkey.api.util; + +import org.jetbrains.annotations.Nullable; + +/** + * This is the helper class to provide a custom logger writer which can be + * used to route log messages to a different location than the logger. ex - to a file. + * + * User : ankurj + * Date : Jul 23, 2020 + * */ + +public interface LoggerWriter +{ + void write(String message, @Nullable Throwable t); + + void debug(String message); + + void debug(String message, Throwable t); + + void error(String message); + + void error(String message, Throwable t); + + void info(String message); + + void info(String message, Throwable t); + + void fatal(String message); + + void fatal(String message, Throwable t); + + void trace(String message); + + void trace(String message, Throwable t); +} diff --git a/api/src/org/labkey/api/util/MXBeanAppender.java b/api/src/org/labkey/api/util/MXBeanAppender.java deleted file mode 100644 index ea61a228e33..00000000000 --- a/api/src/org/labkey/api/util/MXBeanAppender.java +++ /dev/null @@ -1,146 +0,0 @@ -/* - * Copyright (c) 2012-2013 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.api.util; - -import org.apache.log4j.Level; -import org.apache.log4j.spi.LoggingEvent; -import org.labkey.api.mbean.ErrorsMXBean; -import org.labkey.api.mbean.LabKeyManagement; - -import javax.management.DynamicMBean; -import javax.management.StandardMBean; -import java.util.Date; -import java.util.LinkedList; -import java.util.concurrent.TimeUnit; - -/** - * User: matthewb - * Date: 2012-02-28 - * Time: 4:10 PM - */ -public class MXBeanAppender extends org.apache.log4j.AppenderSkeleton implements ErrorsMXBean -{ - private static class _Error implements Error - { - final LoggingEvent _event; - _Error(LoggingEvent e) - { - _event = e; - } - - @Override - public Date getTime() - { - return new Date(_event.getTimeStamp()); - } - - @Override - public String getMessage() - { - return String.valueOf(_event.getMessage()); - } - - @Override - public String getThreadName() - { - return _event.getThreadName(); - } - - @Override - public String getLevel() - { - return _event.getLevel().toString(); - } - - @Override - public String getLoggerName() - { - return _event.getLoggerName(); - } - } - - LinkedList<_Error> _events = new LinkedList<>(); - - public MXBeanAppender() - { - DynamicMBean mbean = new StandardMBean(this, ErrorsMXBean.class, true); - LabKeyManagement.register(mbean, "Errors", "recent"); - } - - @Override - protected synchronized void append(LoggingEvent loggingEvent) - { - if (loggingEvent.getLevel().toInt() == Level.DEBUG.toInt()) - return; - clean(); - _events.addFirst(new _Error(loggingEvent)); - } - - private synchronized void clean() - { - long yesterday = HeartBeat.currentTimeMillis() - TimeUnit.DAYS.toMillis(1); - while (_events.size() > 100 || !_events.isEmpty() && _events.getLast()._event.getTimeStamp() < yesterday) - _events.removeLast(); - } - - - @Override - public synchronized void close() - { - _events.clear(); - } - - - @Override - public boolean requiresLayout() - { - return false; - } - - - /* ErrorsMXBean */ - - @Override - public synchronized Error[] getErrors() - { - clean(); - return _events.toArray(new _Error[_events.size()]); - } - - @Override - public synchronized Date getTime() - { - return _events.isEmpty() ? null : _events.getFirst().getTime(); - } - - @Override - public synchronized String getMessage() - { - return _events.isEmpty() ? null : _events.getFirst().getMessage(); - } - - @Override - public synchronized String getLevel() - { - return _events.isEmpty() ? null : _events.getFirst().getLevel(); - } - - @Override - public synchronized void clear() - { - _events.clear(); - } -} diff --git a/api/src/org/labkey/api/util/MailHelper.java b/api/src/org/labkey/api/util/MailHelper.java index 108912e3d99..d780c2ae806 100644 --- a/api/src/org/labkey/api/util/MailHelper.java +++ b/api/src/org/labkey/api/util/MailHelper.java @@ -16,8 +16,9 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.provider.MessageAuditProvider; @@ -69,7 +70,7 @@ */ public class MailHelper { - private static Logger _log = Logger.getLogger(MailHelper.class); + private static Logger _log = LogManager.getLogger(MailHelper.class); private static Session _session = null; public static final String MESSAGE_AUDIT_EVENT = "MessageAuditEvent"; diff --git a/api/src/org/labkey/api/util/MemoryUsageLogger.java b/api/src/org/labkey/api/util/MemoryUsageLogger.java index f0af08bc544..34028dfd49d 100644 --- a/api/src/org/labkey/api/util/MemoryUsageLogger.java +++ b/api/src/org/labkey/api/util/MemoryUsageLogger.java @@ -15,7 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.settings.AppProps; import java.lang.management.ManagementFactory; @@ -29,7 +30,7 @@ */ public class MemoryUsageLogger implements Runnable { - private static final Logger LOG = Logger.getLogger(MemTracker.class); + private static final Logger LOG = LogManager.getLogger(MemTracker.class); private static final Object LOGGER_LOCK_OBJECT = new Object(); diff --git a/api/src/org/labkey/api/util/MimeMap.java b/api/src/org/labkey/api/util/MimeMap.java index 7279b7910d2..7c7cb4aafdc 100644 --- a/api/src/org/labkey/api/util/MimeMap.java +++ b/api/src/org/labkey/api/util/MimeMap.java @@ -17,7 +17,7 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -145,7 +145,7 @@ public int hashCode() } catch (Exception e) { - Logger.getLogger(MimeMap.class).error("unexpected error", e); + LogManager.getLogger(MimeMap.class).error("unexpected error", e); } } diff --git a/api/src/org/labkey/api/util/NetworkDrive.java b/api/src/org/labkey/api/util/NetworkDrive.java index aef7b03d68a..1f33394925a 100644 --- a/api/src/org/labkey/api/util/NetworkDrive.java +++ b/api/src/org/labkey/api/util/NetworkDrive.java @@ -16,7 +16,8 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.PipelineJobService; import java.io.File; @@ -111,7 +112,7 @@ public void unmount(char driveChar) p.waitFor(); } - private static Logger _log = Logger.getLogger(NetworkDrive.class); + private static Logger _log = LogManager.getLogger(NetworkDrive.class); /** * @return whether the file exists, mounting the drive if needed diff --git a/api/src/org/labkey/api/util/PageFlowUtil.java b/api/src/org/labkey/api/util/PageFlowUtil.java index 4837ef4e297..4ac5885af49 100644 --- a/api/src/org/labkey/api/util/PageFlowUtil.java +++ b/api/src/org/labkey/api/util/PageFlowUtil.java @@ -18,7 +18,8 @@ import org.apache.commons.codec.binary.Base64; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.tika.detect.DefaultDetector; import org.apache.tika.io.TikaInputStream; import org.apache.tika.metadata.Metadata; @@ -161,7 +162,7 @@ private enum TransformFormat xml } - private static final Logger _log = Logger.getLogger(PageFlowUtil.class); + private static final Logger _log = LogManager.getLogger(PageFlowUtil.class); private static final String _newline = System.getProperty("line.separator"); private static final Pattern urlPatternStart = Pattern.compile("((http|https|ftp|mailto)://\\S+).*"); diff --git a/api/src/org/labkey/api/util/PossiblyGZIPpedFileInputStreamFactory.java b/api/src/org/labkey/api/util/PossiblyGZIPpedFileInputStreamFactory.java index a9a0c19e439..f43864a88dc 100644 --- a/api/src/org/labkey/api/util/PossiblyGZIPpedFileInputStreamFactory.java +++ b/api/src/org/labkey/api/util/PossiblyGZIPpedFileInputStreamFactory.java @@ -15,7 +15,10 @@ */ package org.labkey.api.util; -import java.io.*; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.InputStream; import java.util.zip.GZIPInputStream; diff --git a/api/src/org/labkey/api/util/RateLimiter.java b/api/src/org/labkey/api/util/RateLimiter.java index 1ef154b1397..19d6bc094f0 100644 --- a/api/src/org/labkey/api/util/RateLimiter.java +++ b/api/src/org/labkey/api/util/RateLimiter.java @@ -15,7 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import java.util.ArrayList; @@ -31,7 +32,7 @@ public class RateLimiter { - static final Logger _log = Logger.getLogger(RateLimiter.class); + static final Logger _log = LogManager.getLogger(RateLimiter.class); final String _name; final Rate _target; diff --git a/api/src/org/labkey/api/util/ResponseHelper.java b/api/src/org/labkey/api/util/ResponseHelper.java index 9695a763f12..bb6deb9b45b 100644 --- a/api/src/org/labkey/api/util/ResponseHelper.java +++ b/api/src/org/labkey/api/util/ResponseHelper.java @@ -22,7 +22,6 @@ import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import javax.servlet.http.HttpServletResponseWrapper; import java.io.IOException; import java.time.Duration; import java.util.StringTokenizer; diff --git a/api/src/org/labkey/api/util/ResultSetUtil.java b/api/src/org/labkey/api/util/ResultSetUtil.java index ebc28adc78a..1da8b7d2f84 100644 --- a/api/src/org/labkey/api/util/ResultSetUtil.java +++ b/api/src/org/labkey/api/util/ResultSetUtil.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; @@ -42,7 +43,7 @@ public class ResultSetUtil { - private static final Logger _log = Logger.getLogger(ResultSetUtil.class); + private static final Logger _log = LogManager.getLogger(ResultSetUtil.class); public static final boolean STRICT_CHECKING = false; // If true, throws when ResultSets are closed more than once. Clean up ResultSet closing for #34406. private ResultSetUtil() diff --git a/api/src/org/labkey/api/util/ReturnURLString.java b/api/src/org/labkey/api/util/ReturnURLString.java index 5627cc39e55..a113900d6a8 100644 --- a/api/src/org/labkey/api/util/ReturnURLString.java +++ b/api/src/org/labkey/api/util/ReturnURLString.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ConvertHelper; @@ -25,8 +26,6 @@ import org.labkey.api.view.ViewServlet; import java.net.URISyntaxException; -import java.net.URLEncoder; -import java.nio.charset.Charset; import java.util.Arrays; import java.util.List; import java.util.Objects; @@ -41,7 +40,7 @@ */ public class ReturnURLString { - private static final Logger LOG = Logger.getLogger(ReturnURLString.class); + private static final Logger LOG = LogManager.getLogger(ReturnURLString.class); private final @Nullable URLHelper _url; diff --git a/api/src/org/labkey/api/util/SafeFileAppender.java b/api/src/org/labkey/api/util/SafeFileAppender.java deleted file mode 100644 index 994c681f017..00000000000 --- a/api/src/org/labkey/api/util/SafeFileAppender.java +++ /dev/null @@ -1,85 +0,0 @@ -/* - * Copyright (c) 2008-2019 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -package org.labkey.api.util; - -import org.apache.log4j.AppenderSkeleton; -import org.apache.log4j.Layout; -import org.apache.log4j.Logger; -import org.apache.log4j.spi.LoggingEvent; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; - -/** - * Custom Log4J appender that opens the log file and closes it for each logging operation, thus ensuring - * that the file does not stay locked. - * Created: Oct 18, 2005 - * @author bmaclean - */ -public class SafeFileAppender extends AppenderSkeleton -{ - private static Logger _log = Logger.getLogger(SafeFileAppender.class); - - private File _file; - - public SafeFileAppender(File file) - { - _file = file; - - // Make sure that we try to mount the drive (if needed) before using the file - NetworkDrive.exists(_file); - } - - @Override - public void append(LoggingEvent loggingEvent) - { - try (BufferedWriter writer = new BufferedWriter(new FileWriter(_file, true))) - { - writer.write(getLayout().format(loggingEvent)); - String[] exceptionStrings = loggingEvent.getThrowableStrRep(); - if (exceptionStrings != null) - { - for (String exceptionString : exceptionStrings) - { - writer.write(exceptionString); - writer.write(Layout.LINE_SEP); - } - } - } - catch (IOException e) - { - File parentFile = _file.getParentFile(); - if (parentFile != null && !NetworkDrive.exists(parentFile) && parentFile.mkdirs()) - append(loggingEvent); - else - _log.error("Failed appending to file.", e); - } - } - - @Override - public void close() - { - // Nothing to do, since nothing stays open. - } - - @Override - public boolean requiresLayout() - { - return true; - } -} diff --git a/api/src/org/labkey/api/util/SessionAppender.java b/api/src/org/labkey/api/util/SessionAppender.java index 11ba2eb387b..1ff714cbab4 100644 --- a/api/src/org/labkey/api/util/SessionAppender.java +++ b/api/src/org/labkey/api/util/SessionAppender.java @@ -15,24 +15,48 @@ */ package org.labkey.api.util; -import org.apache.log4j.spi.LoggingEvent; +import org.apache.logging.log4j.core.Appender; +import org.apache.logging.log4j.core.Core; +import org.apache.logging.log4j.core.Filter; +import org.apache.logging.log4j.core.Layout; +import org.apache.logging.log4j.core.LogEvent; +import org.apache.logging.log4j.core.appender.AbstractAppender; +import org.apache.logging.log4j.core.config.Property; +import org.apache.logging.log4j.core.config.plugins.Plugin; +import org.apache.logging.log4j.core.config.plugins.PluginAttribute; +import org.apache.logging.log4j.core.config.plugins.PluginElement; +import org.apache.logging.log4j.core.config.plugins.PluginFactory; import org.jetbrains.annotations.NotNull; import org.springframework.util.ConcurrentReferenceHashMap; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpSession; import java.io.Serializable; -import java.util.LinkedList; -import java.util.List; +import java.util.Collections; import java.util.Map; +import java.util.WeakHashMap; /** * User: matthewb * Date: Aug 18, 2009 * Time: 2:18:21 PM */ -public class SessionAppender extends org.apache.log4j.AppenderSkeleton +@Plugin(name = "SessionAppender", category = Core.CATEGORY_NAME, elementType = Appender.ELEMENT_TYPE, printObject = true) +public class SessionAppender extends AbstractAppender { + @PluginFactory + public static SessionAppender createAppender(@PluginAttribute("name") String name, + @PluginElement("Layout") Layout layout, + @PluginElement("Filter") final Filter filter) + { + return new SessionAppender(name, filter, layout, false, null); + } + + protected SessionAppender(String name, Filter filter, Layout layout, boolean ignoreExceptions, Property[] properties) + { + super(name, filter, layout, ignoreExceptions, properties); + } + static class AppenderInfo implements Serializable { AppenderInfo(String key, boolean on) @@ -43,7 +67,18 @@ static class AppenderInfo implements Serializable final String key; boolean on; - final List list = new LinkedList<>(); + final Map eventIdMap = new ConcurrentReferenceHashMap<>(16, ConcurrentReferenceHashMap.ReferenceType.WEAK) + { + @Override + public String put(LogEvent key, String value) + { + // Safeguard against runaway size. ConcurrentReferenceHashMap does not have removeEldestEntry so have + // to randomly remove an entry + if (size() > 1000) + remove(0); + return super.put(key, value); + } + }; int eventId=0; } @@ -74,42 +109,26 @@ public static String getAppendingInfoKey(HttpServletRequest request) } @Override - protected void append(LoggingEvent event) + public void append(LogEvent event) { AppenderInfo info = localInfo.get(); if (null == info || !info.on) return; - synchronized (info.list) + synchronized (info.eventIdMap) { - event.setProperty("eventId", String.valueOf(++info.eventId)); - info.list.add(event); - if (info.list.size() > 1000) - info.list.remove(0); + info.eventIdMap.put(event, String.valueOf(++info.eventId)); } } - @Override - public void close() - { - } - - - @Override - public boolean requiresLayout() - { - return false; - } - - - public static LoggingEvent[] getLoggingEvents(HttpServletRequest request) + public static Map getLoggingEvents(HttpServletRequest request) { AppenderInfo info = _getLoggingForSession(request); if (null == info) - return new LoggingEvent[0]; - synchronized (info.list) + return Collections.emptyMap(); + synchronized (info.eventIdMap) { - return info.list.toArray(new LoggingEvent[info.list.size()]); + return info.eventIdMap; } } diff --git a/api/src/org/labkey/api/util/SimpleLoggerWriter.java b/api/src/org/labkey/api/util/SimpleLoggerWriter.java new file mode 100644 index 00000000000..6cf4a0a0207 --- /dev/null +++ b/api/src/org/labkey/api/util/SimpleLoggerWriter.java @@ -0,0 +1,82 @@ +package org.labkey.api.util; + +import org.apache.logging.log4j.Logger; + +/** + * Simple implementation of LoggerWriter that uses the regular logger. + * */ +public class SimpleLoggerWriter implements LoggerWriter +{ + private Logger _log; + + public SimpleLoggerWriter(Logger log) + { + _log = log; + } + + @Override + public void write(String message, Throwable t) + { + + } + + @Override + public void debug(String message) + { + _log.debug(message); + } + + @Override + public void debug(String message, Throwable t) + { + _log.debug(message, t); + } + + @Override + public void error(String message) + { + _log.error(message); + } + + @Override + public void error(String message, Throwable t) + { + _log.error(message, t); + } + + @Override + public void info(String message) + { + _log.info(message); + } + + @Override + public void info(String message, Throwable t) + { + _log.info(message, t); + } + + @Override + public void fatal(String message) + { + _log.fatal(message); + } + + @Override + public void fatal(String message, Throwable t) + { + _log.fatal(message, t); + } + + @Override + public void trace(String message) + { + _log.trace(message); + } + + @Override + public void trace(String message, Throwable t) + { + _log.trace(message, t); + } +} diff --git a/api/src/org/labkey/api/util/StringExpressionFactory.java b/api/src/org/labkey/api/util/StringExpressionFactory.java index 7e8028534a7..edea31e0d88 100644 --- a/api/src/org/labkey/api/util/StringExpressionFactory.java +++ b/api/src/org/labkey/api/util/StringExpressionFactory.java @@ -16,7 +16,8 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -36,7 +37,6 @@ import org.labkey.api.view.ActionURL; import org.labkey.data.xml.StringExpressionType; -import javax.servlet.ServletException; import java.io.IOException; import java.io.Writer; import java.net.URISyntaxException; @@ -68,7 +68,7 @@ */ public class StringExpressionFactory { - private static final Logger LOG = Logger.getLogger(StringExpressionFactory.class); + private static final Logger LOG = LogManager.getLogger(StringExpressionFactory.class); private static final Cache templates = CacheManager.getCache(5000, CacheManager.DAY, "StringExpression templates"); private static final Cache templatesUrl = CacheManager.getCache(10000, CacheManager.DAY, "StringExpression template URLs"); diff --git a/api/src/org/labkey/api/util/StringSubstitution.java b/api/src/org/labkey/api/util/StringSubstitution.java index 9b97598276a..28e49f0e581 100644 --- a/api/src/org/labkey/api/util/StringSubstitution.java +++ b/api/src/org/labkey/api/util/StringSubstitution.java @@ -15,9 +15,9 @@ */ package org.labkey.api.util; -import java.util.regex.Pattern; -import java.util.regex.Matcher; import java.util.regex.MatchResult; +import java.util.regex.Matcher; +import java.util.regex.Pattern; /** * StringSubstitution runs regular expression string substitution diff --git a/api/src/org/labkey/api/util/SystemMaintenance.java b/api/src/org/labkey/api/util/SystemMaintenance.java index 845e8321939..1d25f88cb5a 100644 --- a/api/src/org/labkey/api/util/SystemMaintenance.java +++ b/api/src/org/labkey/api/util/SystemMaintenance.java @@ -17,7 +17,7 @@ package org.labkey.api.util; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.PropertyManager; diff --git a/api/src/org/labkey/api/util/SystemMaintenanceJob.java b/api/src/org/labkey/api/util/SystemMaintenanceJob.java index 0358294c08a..6e7a0a2b41b 100644 --- a/api/src/org/labkey/api/util/SystemMaintenanceJob.java +++ b/api/src/org/labkey/api/util/SystemMaintenanceJob.java @@ -15,7 +15,8 @@ */ package org.labkey.api.util; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -38,7 +39,7 @@ */ public class SystemMaintenanceJob implements org.quartz.Job, Callable { - private static final Logger LOG = Logger.getLogger(SystemMaintenanceJob.class); + private static final Logger LOG = LogManager.getLogger(SystemMaintenanceJob.class); private final @Nullable String _taskName; private final @Nullable User _user; diff --git a/api/src/org/labkey/api/util/URLHelper.java b/api/src/org/labkey/api/util/URLHelper.java index 7d15f31e9e3..cc07016042b 100644 --- a/api/src/org/labkey/api/util/URLHelper.java +++ b/api/src/org/labkey/api/util/URLHelper.java @@ -22,7 +22,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.data.CompareType; @@ -60,7 +61,7 @@ */ public class URLHelper implements Cloneable, Serializable, HasHtmlString { - private static final Logger LOG = Logger.getLogger(URLHelper.class); + private static final Logger LOG = LogManager.getLogger(URLHelper.class); protected String _scheme = "http"; protected String _host = null; diff --git a/api/src/org/labkey/api/util/XmlBeansUtil.java b/api/src/org/labkey/api/util/XmlBeansUtil.java index fdaff08d94b..f04da63e0c5 100644 --- a/api/src/org/labkey/api/util/XmlBeansUtil.java +++ b/api/src/org/labkey/api/util/XmlBeansUtil.java @@ -15,7 +15,12 @@ */ package org.labkey.api.util; -import org.apache.xmlbeans.*; +import org.apache.xmlbeans.XmlCursor; +import org.apache.xmlbeans.XmlError; +import org.apache.xmlbeans.XmlException; +import org.apache.xmlbeans.XmlObject; +import org.apache.xmlbeans.XmlOptions; +import org.apache.xmlbeans.XmlTokenSource; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.portal.ProjectUrls; diff --git a/api/src/org/labkey/api/util/emailTemplate/EmailTemplate.java b/api/src/org/labkey/api/util/emailTemplate/EmailTemplate.java index 97864f38d3e..aac02812b41 100644 --- a/api/src/org/labkey/api/util/emailTemplate/EmailTemplate.java +++ b/api/src/org/labkey/api/util/emailTemplate/EmailTemplate.java @@ -16,7 +16,8 @@ package org.labkey.api.util.emailTemplate; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -51,7 +52,7 @@ */ public abstract class EmailTemplate { - private static final Logger LOG = Logger.getLogger(EmailTemplate.class); + private static final Logger LOG = LogManager.getLogger(EmailTemplate.class); /** Pattern for recognizing substitution syntax, which is of the form ^TOKEN^ */ private static final Pattern SCRIPT_PATTERN = Pattern.compile("\\^(.*?)\\^"); private static final List REPLACEMENT_PARAMS = new ArrayList<>(); diff --git a/api/src/org/labkey/api/util/emailTemplate/EmailTemplateService.java b/api/src/org/labkey/api/util/emailTemplate/EmailTemplateService.java index f37ca0a188f..313d0074797 100644 --- a/api/src/org/labkey/api/util/emailTemplate/EmailTemplateService.java +++ b/api/src/org/labkey/api/util/emailTemplate/EmailTemplateService.java @@ -16,7 +16,8 @@ package org.labkey.api.util.emailTemplate; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.PropertyManager; @@ -37,7 +38,7 @@ */ public class EmailTemplateService { - static Logger _log = Logger.getLogger(EmailTemplateService.class); + static Logger _log = LogManager.getLogger(EmailTemplateService.class); private static final String EMAIL_TEMPLATE_PROPERTIES_MAP_NAME = "emailTemplateProperties"; private static final String MESSAGE_SUBJECT_PART = "subject"; diff --git a/api/src/org/labkey/api/view/AbstractView.java b/api/src/org/labkey/api/view/AbstractView.java index a9fffe36026..86ab5c8a965 100644 --- a/api/src/org/labkey/api/view/AbstractView.java +++ b/api/src/org/labkey/api/view/AbstractView.java @@ -20,7 +20,6 @@ import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import java.util.Map; /** * User: matthewb diff --git a/api/src/org/labkey/api/view/BaseWebPartFactory.java b/api/src/org/labkey/api/view/BaseWebPartFactory.java index d1fab573989..0d019c7969e 100644 --- a/api/src/org/labkey/api/view/BaseWebPartFactory.java +++ b/api/src/org/labkey/api/view/BaseWebPartFactory.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.PropertyUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; @@ -42,7 +43,7 @@ */ public abstract class BaseWebPartFactory implements WebPartFactory { - private static final Logger LOG = Logger.getLogger(Portal.class); + private static final Logger LOG = LogManager.getLogger(Portal.class); private static final Set defaultAllowableScopes = PageFlowUtil.set("folder"); private final boolean _editable; diff --git a/api/src/org/labkey/api/view/DataView.java b/api/src/org/labkey/api/view/DataView.java index 0e5c2c812a9..980ae5220d1 100644 --- a/api/src/org/labkey/api/view/DataView.java +++ b/api/src/org/labkey/api/view/DataView.java @@ -16,7 +16,8 @@ package org.labkey.api.view; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -58,7 +59,7 @@ public abstract class DataView extends WebPartView { private DataRegion _dataRegion = null; - private static final Logger _log = Logger.getLogger(DataView.class); + private static final Logger _log = LogManager.getLogger(DataView.class); // Call this constructor if you need to subclass the RenderContext public DataView(DataRegion dataRegion, RenderContext ctx) diff --git a/api/src/org/labkey/api/view/DefaultModelAndView.java b/api/src/org/labkey/api/view/DefaultModelAndView.java index 7b1a375c6d7..cf55c51238f 100644 --- a/api/src/org/labkey/api/view/DefaultModelAndView.java +++ b/api/src/org/labkey/api/view/DefaultModelAndView.java @@ -16,8 +16,8 @@ package org.labkey.api.view; -import org.springframework.web.servlet.View; import org.springframework.web.servlet.ModelAndView; +import org.springframework.web.servlet.View; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; diff --git a/api/src/org/labkey/api/view/GWTView.java b/api/src/org/labkey/api/view/GWTView.java index a9cdb7b8705..f7ea6c28d35 100644 --- a/api/src/org/labkey/api/view/GWTView.java +++ b/api/src/org/labkey/api/view/GWTView.java @@ -19,7 +19,11 @@ import com.google.gwt.core.client.EntryPoint; import org.labkey.api.compliance.ComplianceService; -import java.util.*; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; /** * Wrapper around a GWT (Google Web Toolkit) module that knows how to render into the overall HTML of the page. diff --git a/api/src/org/labkey/api/view/HttpView.java b/api/src/org/labkey/api/view/HttpView.java index 60e035f6f8a..90f3d5f3901 100644 --- a/api/src/org/labkey/api/view/HttpView.java +++ b/api/src/org/labkey/api/view/HttpView.java @@ -16,7 +16,7 @@ package org.labkey.api.view; import org.apache.commons.lang3.ObjectUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.HasViewContext; @@ -40,7 +40,6 @@ import java.io.PrintWriter; import java.io.Writer; import java.util.ArrayList; -import java.util.Collection; import java.util.HashMap; import java.util.LinkedHashSet; import java.util.List; @@ -143,7 +142,7 @@ public final void render(ModelBean model, HttpServletRequest request, HttpServle response.flushBuffer(); } if (!ExceptionUtil.isIgnorable(e)) - Logger.getLogger(HttpView.class).error("Exception while rendering view; creation stacktrace:" + ExceptionUtil.renderStackTrace(_creationStackTrace)); + LogManager.getLogger(HttpView.class).error("Exception while rendering view; creation stacktrace:" + ExceptionUtil.renderStackTrace(_creationStackTrace)); throw e; } finally @@ -428,7 +427,7 @@ public static HttpView viewFromString(String viewName) } catch (Exception x) { - Logger.getLogger(HttpView.class).error(x); + LogManager.getLogger(HttpView.class).error(x); } return null; } diff --git a/api/src/org/labkey/api/view/NavTreeCustomizer.java b/api/src/org/labkey/api/view/NavTreeCustomizer.java index 41215032bfd..5ffed592759 100644 --- a/api/src/org/labkey/api/view/NavTreeCustomizer.java +++ b/api/src/org/labkey/api/view/NavTreeCustomizer.java @@ -15,9 +15,6 @@ */ package org.labkey.api.view; -import org.labkey.api.data.Container; -import org.labkey.api.security.User; - import java.util.List; public interface NavTreeCustomizer diff --git a/api/src/org/labkey/api/view/NavTreeManager.java b/api/src/org/labkey/api/view/NavTreeManager.java index ed3b97640b2..5c98fe126aa 100644 --- a/api/src/org/labkey/api/view/NavTreeManager.java +++ b/api/src/org/labkey/api/view/NavTreeManager.java @@ -16,7 +16,8 @@ package org.labkey.api.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.Cache; @@ -38,7 +39,7 @@ */ public class NavTreeManager { - private static final Logger _log = Logger.getLogger(NavTreeManager.class); + private static final Logger _log = LogManager.getLogger(NavTreeManager.class); private static final String EXPAND_CONTAINERS_KEY = NavTreeManager.class.getName() + "/expandedContainers"; private static final String CACHE_PREFIX = NavTreeManager.class.getName() + "/"; private static final String NULL_MARKER = "__null marker representing the root__"; // ConcurrentHashMap does not support null keys diff --git a/api/src/org/labkey/api/view/PopupUserView.java b/api/src/org/labkey/api/view/PopupUserView.java index 7d09b3f0b7a..7cc16a3e1d3 100644 --- a/api/src/org/labkey/api/view/PopupUserView.java +++ b/api/src/org/labkey/api/view/PopupUserView.java @@ -20,7 +20,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.UserUrls; import org.labkey.api.security.impersonation.ImpersonationContext; -import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.settings.AppProps; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.template.PageConfig; diff --git a/api/src/org/labkey/api/view/Portal.java b/api/src/org/labkey/api/view/Portal.java index d1d3156dc67..d88c1bc2553 100644 --- a/api/src/org/labkey/api/view/Portal.java +++ b/api/src/org/labkey/api/view/Portal.java @@ -20,7 +20,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -91,8 +92,22 @@ import java.util.TreeMap; import java.util.stream.Collectors; -import static org.labkey.api.util.DOM.*; -import static org.labkey.api.util.DOM.Attribute.*; +import static org.labkey.api.util.DOM.Attribute.action; +import static org.labkey.api.util.DOM.Attribute.method; +import static org.labkey.api.util.DOM.Attribute.name; +import static org.labkey.api.util.DOM.Attribute.type; +import static org.labkey.api.util.DOM.Attribute.value; +import static org.labkey.api.util.DOM.DIV; +import static org.labkey.api.util.DOM.HR; +import static org.labkey.api.util.DOM.INPUT; +import static org.labkey.api.util.DOM.LK; +import static org.labkey.api.util.DOM.OPTION; +import static org.labkey.api.util.DOM.Renderable; +import static org.labkey.api.util.DOM.SELECT; +import static org.labkey.api.util.DOM.SPAN; +import static org.labkey.api.util.DOM.at; +import static org.labkey.api.util.DOM.cl; +import static org.labkey.api.util.DOM.createHtml; /** * Manages the configuration of portal pages, which can be configured by admins to show @@ -100,7 +115,7 @@ */ public class Portal implements ModuleChangeListener { - private static final Logger LOG = Logger.getLogger(Portal.class); + private static final Logger LOG = LogManager.getLogger(Portal.class); private static final WebPartBeanLoader FACTORY = new WebPartBeanLoader(); public static final String FOLDER_PORTAL_PAGE = "folder"; diff --git a/api/src/org/labkey/api/view/SimpleFolderTab.java b/api/src/org/labkey/api/view/SimpleFolderTab.java index 449d2831631..41397951fc4 100644 --- a/api/src/org/labkey/api/view/SimpleFolderTab.java +++ b/api/src/org/labkey/api/view/SimpleFolderTab.java @@ -16,7 +16,8 @@ package org.labkey.api.view; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -42,7 +43,7 @@ */ public class SimpleFolderTab extends FolderTab.PortalPage { - private static final Logger LOGGER = Logger.getLogger(SimpleFolderTab.class); + private static final Logger LOGGER = LogManager.getLogger(SimpleFolderTab.class); private List _requiredWebParts = new ArrayList<>(); private List _preferredWebParts = new ArrayList<>(); private List _selectors = new ArrayList<>(); diff --git a/api/src/org/labkey/api/view/SimpleTextDisplayElement.java b/api/src/org/labkey/api/view/SimpleTextDisplayElement.java index b666386f4e7..613a183dd79 100644 --- a/api/src/org/labkey/api/view/SimpleTextDisplayElement.java +++ b/api/src/org/labkey/api/view/SimpleTextDisplayElement.java @@ -19,8 +19,8 @@ import org.labkey.api.data.RenderContext; import org.labkey.api.util.PageFlowUtil; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * Just renders the text directly into the page, HTML-encoding as needed. diff --git a/api/src/org/labkey/api/view/SimpleWebPartFactory.java b/api/src/org/labkey/api/view/SimpleWebPartFactory.java index b98ddb30296..ce68db89e99 100644 --- a/api/src/org/labkey/api/view/SimpleWebPartFactory.java +++ b/api/src/org/labkey/api/view/SimpleWebPartFactory.java @@ -16,10 +16,10 @@ package org.labkey.api.view; import org.jetbrains.annotations.NotNull; +import org.labkey.api.action.BaseViewAction; import org.labkey.api.util.UnexpectedException; -import org.springframework.web.servlet.ModelAndView; import org.springframework.validation.BindException; -import org.labkey.api.action.BaseViewAction; +import org.springframework.web.servlet.ModelAndView; import java.lang.reflect.Constructor; diff --git a/api/src/org/labkey/api/view/TabStripView.java b/api/src/org/labkey/api/view/TabStripView.java index 495bfa56f96..2a15f7f44bb 100644 --- a/api/src/org/labkey/api/view/TabStripView.java +++ b/api/src/org/labkey/api/view/TabStripView.java @@ -18,15 +18,12 @@ import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.Container; import org.labkey.api.util.URLHelper; import org.labkey.api.view.template.ClientDependency; import org.springframework.web.servlet.ModelAndView; import java.util.LinkedHashSet; import java.util.List; -import java.util.function.Function; -import java.util.function.Predicate; /** * User: Karl Lum diff --git a/api/src/org/labkey/api/view/UnauthorizedException.java b/api/src/org/labkey/api/view/UnauthorizedException.java index 09352d5cc1e..636e61c5979 100644 --- a/api/src/org/labkey/api/view/UnauthorizedException.java +++ b/api/src/org/labkey/api/view/UnauthorizedException.java @@ -18,8 +18,6 @@ import org.apache.commons.lang3.StringUtils; import org.labkey.api.util.SkipMothershipLogging; -import javax.servlet.http.HttpServletResponse; - /** * Signals to the HTTP client that the request is not authorized, via a 401 status code. */ diff --git a/api/src/org/labkey/api/view/UpdateView.java b/api/src/org/labkey/api/view/UpdateView.java index 3d26d9e1e19..b3d5a494889 100644 --- a/api/src/org/labkey/api/view/UpdateView.java +++ b/api/src/org/labkey/api/view/UpdateView.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataRegion; import org.labkey.api.data.RenderContext; @@ -30,7 +31,7 @@ */ public class UpdateView extends DataView { - private static Logger _log = Logger.getLogger(UpdateView.class); + private static Logger _log = LogManager.getLogger(UpdateView.class); public UpdateView(DataRegion dataRegion, TableViewForm form, BindException errors) { diff --git a/api/src/org/labkey/api/view/ViewServlet.java b/api/src/org/labkey/api/view/ViewServlet.java index e80e797a8a1..12a8bc3ac8d 100644 --- a/api/src/org/labkey/api/view/ViewServlet.java +++ b/api/src/org/labkey/api/view/ViewServlet.java @@ -16,7 +16,8 @@ package org.labkey.api.view; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; @@ -79,7 +80,7 @@ */ public class ViewServlet extends HttpServlet { - private static final Logger _log = Logger.getLogger(ViewServlet.class); + private static final Logger _log = LogManager.getLogger(ViewServlet.class); public static final String ORIGINAL_URL_STRING = "LABKEY.OriginalURL"; // String public static final String ORIGINAL_URL_URLHELPER = "LABKEY.OriginalURLHelper"; // URLHelper diff --git a/api/src/org/labkey/api/view/WebPartCache.java b/api/src/org/labkey/api/view/WebPartCache.java index 3af17b0fe54..032a1cac86b 100644 --- a/api/src/org/labkey/api/view/WebPartCache.java +++ b/api/src/org/labkey/api/view/WebPartCache.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheLoader; @@ -48,7 +49,7 @@ */ public class WebPartCache { - private static final Logger LOG = Logger.getLogger(WebPartCache.class); + private static final Logger LOG = LogManager.getLogger(WebPartCache.class); private static final Cache> CACHE = CacheManager.getStringKeyCache(10000, CacheManager.DAY, "Webparts"); static public Portal.PortalPage getPortalPage(@NotNull Container c, @NotNull String pageId) diff --git a/api/src/org/labkey/api/view/WebPartView.java b/api/src/org/labkey/api/view/WebPartView.java index bf416de0b91..aaae219f1f7 100644 --- a/api/src/org/labkey/api/view/WebPartView.java +++ b/api/src/org/labkey/api/view/WebPartView.java @@ -16,7 +16,8 @@ package org.labkey.api.view; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.action.ApiJsonWriter; import org.labkey.api.action.ApiResponse; @@ -83,7 +84,7 @@ public WebPartFrame getFrame(ViewContext context, FrameConfig config) private final boolean _devMode = AppProps.getInstance().isDevMode(); protected String _debugViewDescription = null; - private static final Logger LOG = Logger.getLogger(WebPartView.class); + private static final Logger LOG = LogManager.getLogger(WebPartView.class); @Override @@ -374,12 +375,12 @@ protected final void renderInternal(ModelBean model, HttpServletRequest request, } catch (RedirectException x) { - Logger.getLogger(WebPartView.class).warn("Shouldn't throw redirect during renderView()", x); + LogManager.getLogger(WebPartView.class).warn("Shouldn't throw redirect during renderView()", x); throw x; } catch (UnauthorizedException x) { - Logger.getLogger(WebPartView.class).warn("Shouldn't throw unauthorized during renderView()", x); + LogManager.getLogger(WebPartView.class).warn("Shouldn't throw unauthorized during renderView()", x); errorHtml = ExceptionUtil.getUnauthorizedMessage(getViewContext()); } catch (NotFoundException x) @@ -398,7 +399,7 @@ protected final void renderInternal(ModelBean model, HttpServletRequest request, if (!ExceptionUtil.isIgnorable(exceptionToRender)) { - Logger log = Logger.getLogger(WebPartView.class); + Logger log = LogManager.getLogger(WebPartView.class); ActionURL url = getViewContext().getActionURL(); log.error("renderView() exception in " + getClass().getName() + (null != url ? " while responding to " + getViewContext().getActionURL().getLocalURIString() : ""), exceptionToRender); log.error("View creation stacktrace:" + ExceptionUtil.renderStackTrace(_creationStackTrace)); diff --git a/api/src/org/labkey/api/view/menu/ContainerMenu.java b/api/src/org/labkey/api/view/menu/ContainerMenu.java index 91ab767e138..76805fb94ee 100644 --- a/api/src/org/labkey/api/view/menu/ContainerMenu.java +++ b/api/src/org/labkey/api/view/menu/ContainerMenu.java @@ -16,11 +16,11 @@ package org.labkey.api.view.menu; -import org.labkey.api.view.ViewContext; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerManager; import org.labkey.api.view.NavTree; import org.labkey.api.view.NavTreeManager; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.Container; +import org.labkey.api.view.ViewContext; import java.util.Set; diff --git a/api/src/org/labkey/api/view/menu/ProjectAdminMenu.java b/api/src/org/labkey/api/view/menu/ProjectAdminMenu.java index e1db9138137..9eaa5e227bc 100644 --- a/api/src/org/labkey/api/view/menu/ProjectAdminMenu.java +++ b/api/src/org/labkey/api/view/menu/ProjectAdminMenu.java @@ -18,7 +18,6 @@ import org.labkey.api.admin.AdminUrls; import org.labkey.api.data.Container; -import org.labkey.api.security.SecurityUrls; import org.labkey.api.security.User; import org.labkey.api.security.UserUrls; import org.labkey.api.security.permissions.AdminPermission; diff --git a/api/src/org/labkey/api/view/menu/ProjectsMenu.java b/api/src/org/labkey/api/view/menu/ProjectsMenu.java index 992acbb036f..ed6c7341805 100644 --- a/api/src/org/labkey/api/view/menu/ProjectsMenu.java +++ b/api/src/org/labkey/api/view/menu/ProjectsMenu.java @@ -16,11 +16,11 @@ package org.labkey.api.view.menu; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.ActionURL; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.Container; import java.util.Collections; import java.util.List; diff --git a/api/src/org/labkey/api/view/template/ClientDependency.java b/api/src/org/labkey/api/view/template/ClientDependency.java index da538a17173..875737d6562 100644 --- a/api/src/org/labkey/api/view/template/ClientDependency.java +++ b/api/src/org/labkey/api/view/template/ClientDependency.java @@ -16,7 +16,8 @@ package org.labkey.api.view.template; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.Cache; @@ -63,7 +64,7 @@ */ public abstract class ClientDependency { - private static final Logger LOG = Logger.getLogger(ClientDependency.class); + private static final Logger LOG = LogManager.getLogger(ClientDependency.class); static final Cache, ClientDependency> CACHE = CacheManager.getBlockingCache(10000, CacheManager.MONTH, "Client dependencies", new ClientDependencyCacheLoader()); static diff --git a/api/src/org/labkey/api/view/template/ClientDependencyCacheLoader.java b/api/src/org/labkey/api/view/template/ClientDependencyCacheLoader.java index 64d83532d6d..74472f31c8a 100644 --- a/api/src/org/labkey/api/view/template/ClientDependencyCacheLoader.java +++ b/api/src/org/labkey/api/view/template/ClientDependencyCacheLoader.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view.template; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.CacheLoader; @@ -41,7 +42,7 @@ public class ClientDependencyCacheLoader implements CacheLoader, ClientDependency> { - private static final Logger LOG = Logger.getLogger(ClientDependencyCacheLoader.class); + private static final Logger LOG = LogManager.getLogger(ClientDependencyCacheLoader.class); private static final Set EXISTING_LISTENERS = new ConcurrentHashSet<>(); public ClientDependencyCacheLoader() diff --git a/api/src/org/labkey/api/view/template/ExternalClientDependency.java b/api/src/org/labkey/api/view/template/ExternalClientDependency.java index 56bd2e0e737..6a51fb1725d 100644 --- a/api/src/org/labkey/api/view/template/ExternalClientDependency.java +++ b/api/src/org/labkey/api/view/template/ExternalClientDependency.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view.template; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.clientLibrary.xml.ModeTypeEnum; /** @@ -23,7 +24,7 @@ */ public class ExternalClientDependency extends ClientDependency { - private static final Logger _log = Logger.getLogger(ExternalClientDependency.class); + private static final Logger _log = LogManager.getLogger(ExternalClientDependency.class); private final String _uri; diff --git a/api/src/org/labkey/api/view/template/FilePathClientDependency.java b/api/src/org/labkey/api/view/template/FilePathClientDependency.java index 42f7fb486e3..584c60bfc80 100644 --- a/api/src/org/labkey/api/view/template/FilePathClientDependency.java +++ b/api/src/org/labkey/api/view/template/FilePathClientDependency.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view.template; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.util.Path; import org.labkey.clientLibrary.xml.ModeTypeEnum; @@ -25,7 +26,7 @@ */ public class FilePathClientDependency extends ClientDependency { - private static final Logger _log = Logger.getLogger(FilePathClientDependency.class); + private static final Logger _log = LogManager.getLogger(FilePathClientDependency.class); protected final Path _filePath; diff --git a/api/src/org/labkey/api/view/template/LibClientDependency.java b/api/src/org/labkey/api/view/template/LibClientDependency.java index 77bd27a07b1..da86d263d4a 100644 --- a/api/src/org/labkey/api/view/template/LibClientDependency.java +++ b/api/src/org/labkey/api/view/template/LibClientDependency.java @@ -15,7 +15,8 @@ */ package org.labkey.api.view.template; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlOptions; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; @@ -37,7 +38,7 @@ */ public class LibClientDependency extends FilePathClientDependency { - private static final Logger _log = Logger.getLogger(LibClientDependency.class); + private static final Logger _log = LogManager.getLogger(LibClientDependency.class); private final Resource _resource; private final List> _suppliers = new LinkedList<>(); diff --git a/api/src/org/labkey/api/visualization/TimeChartReport.java b/api/src/org/labkey/api/visualization/TimeChartReport.java index 73b0645777c..97d95cc5913 100644 --- a/api/src/org/labkey/api/visualization/TimeChartReport.java +++ b/api/src/org/labkey/api/visualization/TimeChartReport.java @@ -21,8 +21,6 @@ import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewContext; -import java.io.IOException; - /* * User: brittp * Date: Jan 28, 2011 diff --git a/api/src/org/labkey/api/webdav/AbstractWebdavResourceCollection.java b/api/src/org/labkey/api/webdav/AbstractWebdavResourceCollection.java index 126a7ad4121..36de918d72a 100644 --- a/api/src/org/labkey/api/webdav/AbstractWebdavResourceCollection.java +++ b/api/src/org/labkey/api/webdav/AbstractWebdavResourceCollection.java @@ -20,7 +20,6 @@ import org.labkey.api.util.FileStream; import org.labkey.api.util.Path; -import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.Collection; diff --git a/api/src/org/labkey/api/webdav/WebdavResource.java b/api/src/org/labkey/api/webdav/WebdavResource.java index f2c982bf9b1..cfd080c36c8 100644 --- a/api/src/org/labkey/api/webdav/WebdavResource.java +++ b/api/src/org/labkey/api/webdav/WebdavResource.java @@ -24,7 +24,6 @@ import org.labkey.api.view.ViewContext; import org.labkey.api.writer.ContainerUser; -import javax.validation.constraints.Null; import java.io.File; import java.io.IOException; import java.io.InputStream; diff --git a/api/src/org/labkey/api/websocket/BrowserEndpoint.java b/api/src/org/labkey/api/websocket/BrowserEndpoint.java index 11e3ea1058c..514bfdb995f 100644 --- a/api/src/org/labkey/api/websocket/BrowserEndpoint.java +++ b/api/src/org/labkey/api/websocket/BrowserEndpoint.java @@ -15,7 +15,8 @@ */ package org.labkey.api.websocket; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.security.SecurityManager; import org.labkey.api.security.User; @@ -49,7 +50,7 @@ public abstract class BrowserEndpoint { - static Logger LOG = Logger.getLogger(BrowserEndpoint.class); + static Logger LOG = LogManager.getLogger(BrowserEndpoint.class); protected Session browserSession; ServerEndpoint serverEndpoint = null; diff --git a/api/src/org/labkey/api/wiki/MacroProvider.java b/api/src/org/labkey/api/wiki/MacroProvider.java index 3d482bcdb97..a25f57f444d 100644 --- a/api/src/org/labkey/api/wiki/MacroProvider.java +++ b/api/src/org/labkey/api/wiki/MacroProvider.java @@ -16,8 +16,8 @@ package org.labkey.api.wiki; -import org.labkey.api.view.ViewContext; import org.labkey.api.view.HttpView; +import org.labkey.api.view.ViewContext; import java.util.Map; diff --git a/api/src/org/labkey/api/wiki/WikiRendererDisplayColumn.java b/api/src/org/labkey/api/wiki/WikiRendererDisplayColumn.java index 49aff2597e2..208914aab2c 100644 --- a/api/src/org/labkey/api/wiki/WikiRendererDisplayColumn.java +++ b/api/src/org/labkey/api/wiki/WikiRendererDisplayColumn.java @@ -15,7 +15,8 @@ */ package org.labkey.api.wiki; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataColumn; @@ -35,7 +36,7 @@ public class WikiRendererDisplayColumn extends DataColumn @NotNull private String _renderTypeColumnName; private WikiRendererType _defaultRenderer = WikiRendererType.TEXT_WITH_LINKS; - private static final Logger _log = Logger.getLogger(WikiRendererDisplayColumn.class); + private static final Logger _log = LogManager.getLogger(WikiRendererDisplayColumn.class); public WikiRendererDisplayColumn(ColumnInfo contentColumn, @NotNull String renderTypeColumnName, WikiRendererType defaultRenderer) { diff --git a/api/src/org/labkey/api/writer/ContainerUser.java b/api/src/org/labkey/api/writer/ContainerUser.java index 3c621d774b7..7091baf6eab 100644 --- a/api/src/org/labkey/api/writer/ContainerUser.java +++ b/api/src/org/labkey/api/writer/ContainerUser.java @@ -16,8 +16,8 @@ package org.labkey.api.writer; -import org.labkey.api.security.User; import org.labkey.api.data.Container; +import org.labkey.api.security.User; /* * User: adam diff --git a/api/src/org/labkey/api/writer/FileSystemFile.java b/api/src/org/labkey/api/writer/FileSystemFile.java index be2e555af4e..18d1a225246 100644 --- a/api/src/org/labkey/api/writer/FileSystemFile.java +++ b/api/src/org/labkey/api/writer/FileSystemFile.java @@ -27,7 +27,6 @@ import java.io.BufferedInputStream; import java.io.File; import java.io.FileInputStream; -import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; diff --git a/api/src/org/labkey/api/writer/MemoryVirtualFile.java b/api/src/org/labkey/api/writer/MemoryVirtualFile.java index 7c6b5f778f0..9b20bf85ad0 100644 --- a/api/src/org/labkey/api/writer/MemoryVirtualFile.java +++ b/api/src/org/labkey/api/writer/MemoryVirtualFile.java @@ -25,7 +25,6 @@ import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; import java.io.File; -import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; import java.io.PrintWriter; diff --git a/api/src/org/labkey/api/writer/ZipFile.java b/api/src/org/labkey/api/writer/ZipFile.java index afe0a83e93a..e70aa6f94fd 100644 --- a/api/src/org/labkey/api/writer/ZipFile.java +++ b/api/src/org/labkey/api/writer/ZipFile.java @@ -26,7 +26,6 @@ import javax.servlet.http.HttpServletResponse; import java.io.BufferedOutputStream; import java.io.File; -import java.io.FileNotFoundException; import java.io.IOException; import java.io.InputStream; import java.io.OutputStream; diff --git a/api/src/org/labkey/api/writer/ZipUtil.java b/api/src/org/labkey/api/writer/ZipUtil.java index e0b7cba9aaa..6314916c949 100644 --- a/api/src/org/labkey/api/writer/ZipUtil.java +++ b/api/src/org/labkey/api/writer/ZipUtil.java @@ -15,7 +15,7 @@ */ package org.labkey.api.writer; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.util.CheckedInputStream; import org.labkey.api.util.FileUtil; diff --git a/api/webapp/WEB-INF/applicationContext.xml b/api/webapp/WEB-INF/applicationContext.xml index 43c508842ef..a2ceed1f136 100644 --- a/api/webapp/WEB-INF/applicationContext.xml +++ b/api/webapp/WEB-INF/applicationContext.xml @@ -1,12 +1,8 @@ + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd"> diff --git a/assay/api-src/org/labkey/api/assay/DefaultAssaySaveHandler.java b/assay/api-src/org/labkey/api/assay/DefaultAssaySaveHandler.java index f6774dbc346..9b5a64fafdb 100644 --- a/assay/api-src/org/labkey/api/assay/DefaultAssaySaveHandler.java +++ b/assay/api-src/org/labkey/api/assay/DefaultAssaySaveHandler.java @@ -16,7 +16,8 @@ package org.labkey.api.assay; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -56,7 +57,7 @@ */ public class DefaultAssaySaveHandler extends DefaultExperimentSaveHandler implements AssaySaveHandler { - protected static final Logger LOG = Logger.getLogger(DefaultAssaySaveHandler.class); + protected static final Logger LOG = LogManager.getLogger(DefaultAssaySaveHandler.class); protected AssayProvider _provider; @Override diff --git a/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java b/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java index 1db50202364..d5106e7f5e2 100644 --- a/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java +++ b/assay/api-src/org/labkey/api/assay/dilution/DilutionDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.api.assay.dilution; import org.apache.commons.lang3.EnumUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.nab.NabSpecimen; @@ -76,7 +77,7 @@ */ public abstract class DilutionDataHandler extends AbstractExperimentDataHandler { - public static final Logger LOG = Logger.getLogger(DilutionDataHandler.class); + public static final Logger LOG = LogManager.getLogger(DilutionDataHandler.class); public static final String NAB_PROPERTY_LSID_PREFIX = "NabProperty"; diff --git a/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java b/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java index 4eef268a64b..3e2c1061f8b 100644 --- a/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java +++ b/assay/api-src/org/labkey/api/assay/matrix/AbstractMatrixDataHandler.java @@ -16,7 +16,8 @@ package org.labkey.api.assay.matrix; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; import org.labkey.api.data.SQLFragment; @@ -55,7 +56,7 @@ public abstract class AbstractMatrixDataHandler extends AbstractExperimentDataHa protected final String _dbSchemaName; protected final String _dataTableName; - private static final Logger LOG = Logger.getLogger(AbstractMatrixDataHandler.class); + private static final Logger LOG = LogManager.getLogger(AbstractMatrixDataHandler.class); private static boolean autoCreateSamples = true; // CONSIDER: move this flag to the assay design public AbstractMatrixDataHandler(String idColName, String dbSchemaName, String dataTableName) diff --git a/assay/api-src/org/labkey/api/assay/nab/RenderAssayBean.java b/assay/api-src/org/labkey/api/assay/nab/RenderAssayBean.java index b304a1a0e88..540169743c2 100644 --- a/assay/api-src/org/labkey/api/assay/nab/RenderAssayBean.java +++ b/assay/api-src/org/labkey/api/assay/nab/RenderAssayBean.java @@ -15,7 +15,8 @@ */ package org.labkey.api.assay.nab; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.announcements.DiscussionService; import org.labkey.api.assay.dilution.DilutionAssayProvider; @@ -73,7 +74,7 @@ */ public class RenderAssayBean extends RenderAssayForm { - private static final Logger LOG = Logger.getLogger(RenderAssayBean.class); + private static final Logger LOG = LogManager.getLogger(RenderAssayBean.class); private ViewContext _context; private DilutionAssayRun _assay; private boolean _printView; diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java b/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java index 4d6d2fc7c05..56aefdd5070 100644 --- a/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java +++ b/assay/api-src/org/labkey/api/assay/plate/PlateUtils.java @@ -16,7 +16,8 @@ package org.labkey.api.assay.plate; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.RowMap; import org.labkey.api.query.ValidationException; @@ -32,7 +33,7 @@ */ public class PlateUtils { - public static final Logger LOG = Logger.getLogger(PlateUtils.class); + public static final Logger LOG = LogManager.getLogger(PlateUtils.class); private static final int START_ROW = 6; //0 based, row 7 in the workshet private static final int START_COL = 0; diff --git a/assay/src/org/labkey/api/assay/nab/view/runDetails.jsp b/assay/src/org/labkey/api/assay/nab/view/runDetails.jsp index 84fb5c3965d..05ed41ba462 100644 --- a/assay/src/org/labkey/api/assay/nab/view/runDetails.jsp +++ b/assay/src/org/labkey/api/assay/nab/view/runDetails.jsp @@ -18,10 +18,10 @@ <%@ page import="org.labkey.api.assay.dilution.DilutionAssayRun" %> <%@ page import="org.labkey.api.assay.nab.RenderAssayBean" %> <%@ page import="org.labkey.api.security.permissions.InsertPermission" %> +<%@ page import="org.labkey.api.settings.LookAndFeelProperties" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.api.settings.LookAndFeelProperties" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/assay/src/org/labkey/api/assay/nab/view/runGraph.jsp b/assay/src/org/labkey/api/assay/nab/view/runGraph.jsp index 130a1376272..b99342d7856 100644 --- a/assay/src/org/labkey/api/assay/nab/view/runGraph.jsp +++ b/assay/src/org/labkey/api/assay/nab/view/runGraph.jsp @@ -16,10 +16,10 @@ */ %> <%@ page import="org.labkey.api.assay.nab.RenderAssayBean" %> +<%@ page import="org.labkey.api.assay.nab.view.RunDetailOptions" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.assay.nab.view.RunDetailOptions" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/assay/src/org/labkey/api/assay/nab/view/runNotes.jsp b/assay/src/org/labkey/api/assay/nab/view/runNotes.jsp index 38b98063387..0f327b0ee1e 100644 --- a/assay/src/org/labkey/api/assay/nab/view/runNotes.jsp +++ b/assay/src/org/labkey/api/assay/nab/view/runNotes.jsp @@ -16,9 +16,9 @@ */ %> <%@ page import="org.labkey.api.assay.dilution.DilutionAssayRun" %> +<%@ page import="org.labkey.api.assay.nab.NabUrls" %> <%@ page import="org.labkey.api.assay.nab.RenderAssayBean" %> <%@ page import="org.labkey.api.data.Container" %> -<%@ page import="org.labkey.api.assay.nab.NabUrls" %> <%@ page import="org.labkey.api.query.QueryView" %> <%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.security.permissions.DeletePermission" %> diff --git a/assay/src/org/labkey/api/assay/nab/view/runProperties.jsp b/assay/src/org/labkey/api/assay/nab/view/runProperties.jsp index 83ad45fa4f9..5189c525c2b 100644 --- a/assay/src/org/labkey/api/assay/nab/view/runProperties.jsp +++ b/assay/src/org/labkey/api/assay/nab/view/runProperties.jsp @@ -15,12 +15,12 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.assay.nab.RenderAssayBean" %> +<%@ page import="org.labkey.api.util.Pair" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.util.Pair" %> -<%@ page import="java.util.Map" %> <%@ page import="java.util.Iterator" %> -<%@ page import="org.labkey.api.assay.nab.RenderAssayBean" %> +<%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/assay/src/org/labkey/assay/AssayContainerListener.java b/assay/src/org/labkey/assay/AssayContainerListener.java index 8897d092f7c..3875dc8b12e 100644 --- a/assay/src/org/labkey/assay/AssayContainerListener.java +++ b/assay/src/org/labkey/assay/AssayContainerListener.java @@ -17,23 +17,19 @@ package org.labkey.assay; import org.jetbrains.annotations.NotNull; -import org.labkey.assay.plate.PlateManager; -import org.labkey.assay.query.AssayDbSchema; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerManager.ContainerListener; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Table; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayService; +import org.labkey.assay.plate.PlateManager; +import java.beans.PropertyChangeEvent; import java.util.ArrayList; -import java.util.Collections; import java.util.Collection; - -import java.beans.PropertyChangeEvent; +import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; diff --git a/assay/src/org/labkey/assay/AssayDocumentProvider.java b/assay/src/org/labkey/assay/AssayDocumentProvider.java index 40726230b94..1163df96f78 100644 --- a/assay/src/org/labkey/assay/AssayDocumentProvider.java +++ b/assay/src/org/labkey/assay/AssayDocumentProvider.java @@ -4,13 +4,13 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.search.SearchService; import org.labkey.api.search.SearchService.DocumentProvider; import org.labkey.api.search.SearchService.IndexTask; -import org.labkey.api.assay.AssayService; import org.labkey.api.security.User; import java.util.Date; diff --git a/assay/src/org/labkey/assay/AssayImportServiceImpl.java b/assay/src/org/labkey/assay/AssayImportServiceImpl.java index 7fdccc500da..9c9f4c79796 100644 --- a/assay/src/org/labkey/assay/AssayImportServiceImpl.java +++ b/assay/src/org/labkey/assay/AssayImportServiceImpl.java @@ -18,6 +18,9 @@ import gwt.client.org.labkey.assay.designer.client.AssayImporterService; import org.apache.commons.lang3.StringUtils; import org.labkey.api.assay.AssayDomainService; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.exp.ChangePropertyDescriptorException; @@ -40,14 +43,11 @@ import org.labkey.api.iterator.CloseableIterator; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.DataLoader; -import org.labkey.assay.actions.ImportAction; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewContext; +import org.labkey.assay.actions.ImportAction; import javax.servlet.http.HttpSession; import java.io.File; diff --git a/assay/src/org/labkey/assay/AssayListPortalView.java b/assay/src/org/labkey/assay/AssayListPortalView.java index 97a1efd1704..70aa99624dd 100644 --- a/assay/src/org/labkey/assay/AssayListPortalView.java +++ b/assay/src/org/labkey/assay/AssayListPortalView.java @@ -16,11 +16,11 @@ package org.labkey.assay; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.data.ActionButton; import org.labkey.api.data.ButtonBar; import org.labkey.api.query.QuerySettings; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; diff --git a/assay/src/org/labkey/assay/AssayListQueryView.java b/assay/src/org/labkey/assay/AssayListQueryView.java index 2382cde6083..1480a8d8d52 100644 --- a/assay/src/org/labkey/assay/AssayListQueryView.java +++ b/assay/src/org/labkey/assay/AssayListQueryView.java @@ -16,6 +16,8 @@ package org.labkey.assay; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.data.ActionButton; import org.labkey.api.data.ButtonBar; import org.labkey.api.data.Container; @@ -23,8 +25,6 @@ import org.labkey.api.data.Sort; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; diff --git a/assay/src/org/labkey/assay/AssayModule.java b/assay/src/org/labkey/assay/AssayModule.java index 52af331d6ba..3dd694352f9 100644 --- a/assay/src/org/labkey/assay/AssayModule.java +++ b/assay/src/org/labkey/assay/AssayModule.java @@ -26,8 +26,8 @@ import org.labkey.api.assay.AssayService; import org.labkey.api.assay.AssayUrls; import org.labkey.api.assay.TsvDataHandler; -import org.labkey.api.assay.plate.PlateMetadataDataHandler; import org.labkey.api.assay.plate.AssayPlateMetadataService; +import org.labkey.api.assay.plate.PlateMetadataDataHandler; import org.labkey.api.assay.plate.PlateService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -56,8 +56,8 @@ import org.labkey.api.view.WebPartFactory; import org.labkey.assay.pipeline.AssayImportRunTask; import org.labkey.assay.plate.AssayPlateDataDomainKind; -import org.labkey.assay.plate.PlateManager; import org.labkey.assay.plate.AssayPlateMetadataServiceImpl; +import org.labkey.assay.plate.PlateManager; import org.labkey.assay.plate.TsvPlateTypeHandler; import org.labkey.assay.plate.query.PlateSchema; import org.labkey.assay.query.AssayDbSchema; diff --git a/assay/src/org/labkey/assay/DefaultAssayDomainKind.java b/assay/src/org/labkey/assay/DefaultAssayDomainKind.java index d486bb079f5..476b51b1b92 100644 --- a/assay/src/org/labkey/assay/DefaultAssayDomainKind.java +++ b/assay/src/org/labkey/assay/DefaultAssayDomainKind.java @@ -15,8 +15,8 @@ */ package org.labkey.assay; -import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.assay.AssayDomainKind; +import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.property.Domain; import java.util.Set; diff --git a/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java b/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java index 0b1b1002a29..d0255c571e0 100644 --- a/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java +++ b/assay/src/org/labkey/assay/FileBasedModuleDataHandler.java @@ -15,7 +15,8 @@ */ package org.labkey.assay; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.Container; import org.labkey.api.exp.XarContext; import org.labkey.api.exp.api.AbstractExperimentDataHandler; @@ -25,7 +26,6 @@ import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; diff --git a/assay/src/org/labkey/assay/ModuleAssayCache.java b/assay/src/org/labkey/assay/ModuleAssayCache.java index d7c98c9268c..d17b655ec18 100644 --- a/assay/src/org/labkey/assay/ModuleAssayCache.java +++ b/assay/src/org/labkey/assay/ModuleAssayCache.java @@ -1,6 +1,7 @@ package org.labkey.assay; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.assay.AssayProvider; @@ -24,7 +25,7 @@ public class ModuleAssayCache { private static final ModuleAssayCache INSTANCE = new ModuleAssayCache(); - private static final Logger LOG = Logger.getLogger(ModuleAssayCache.class); + private static final Logger LOG = LogManager.getLogger(ModuleAssayCache.class); private static final ModuleResourceCache> PROVIDER_CACHE = ModuleResourceCaches.create("Module assay providers", new ModuleAssayCacheHandler(), ResourceRootProvider.getAssayProviders(Path.rootPath)); private static final Object PROVIDER_LOCK = new Object(); diff --git a/assay/src/org/labkey/assay/ModuleAssayCacheHandler.java b/assay/src/org/labkey/assay/ModuleAssayCacheHandler.java index 3758557b5c6..b513d19cddd 100644 --- a/assay/src/org/labkey/assay/ModuleAssayCacheHandler.java +++ b/assay/src/org/labkey/assay/ModuleAssayCacheHandler.java @@ -18,7 +18,6 @@ import org.apache.xmlbeans.XmlException; import org.jetbrains.annotations.Nullable; -import org.labkey.api.files.FileSystemDirectoryListener; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleResourceCacheHandler; import org.labkey.api.module.ModuleResourceCacheListener; diff --git a/assay/src/org/labkey/assay/ModuleAssayProvider.java b/assay/src/org/labkey/assay/ModuleAssayProvider.java index 51b277ee6ae..b688b30b49f 100644 --- a/assay/src/org/labkey/assay/ModuleAssayProvider.java +++ b/assay/src/org/labkey/assay/ModuleAssayProvider.java @@ -16,7 +16,8 @@ package org.labkey.assay; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; @@ -24,6 +25,15 @@ import org.fhcrc.cpas.exp.xml.PropertyDescriptorType; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayDataType; +import org.labkey.api.assay.AssayPipelineProvider; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssaySaveHandler; +import org.labkey.api.assay.AssayTableMetadata; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.TsvDataHandler; +import org.labkey.api.assay.actions.AssayRunUploadForm; +import org.labkey.api.assay.actions.UploadWizardAction; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpDataRunInput; @@ -46,15 +56,6 @@ import org.labkey.api.security.User; import org.labkey.api.services.ServiceRegistry; import org.labkey.api.study.TimepointType; -import org.labkey.api.assay.actions.AssayRunUploadForm; -import org.labkey.api.assay.actions.UploadWizardAction; -import org.labkey.api.assay.AssayDataType; -import org.labkey.api.assay.AssayPipelineProvider; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssaySaveHandler; -import org.labkey.api.assay.AssayTableMetadata; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.TsvDataHandler; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.FileType; import org.labkey.api.util.PageFlowUtil; @@ -91,7 +92,7 @@ */ public class ModuleAssayProvider extends TsvAssayProvider { - private static final Logger LOG = Logger.getLogger(ModuleAssayProvider.class); + private static final Logger LOG = LogManager.getLogger(ModuleAssayProvider.class); private static final String DOMAINS_DIR_NAME = "domains"; public static class ModuleAssayException extends RuntimeException diff --git a/assay/src/org/labkey/assay/PlateBasedAssaySampleTypeDomainKind.java b/assay/src/org/labkey/assay/PlateBasedAssaySampleTypeDomainKind.java index ce32680dc02..3743f8d3630 100644 --- a/assay/src/org/labkey/assay/PlateBasedAssaySampleTypeDomainKind.java +++ b/assay/src/org/labkey/assay/PlateBasedAssaySampleTypeDomainKind.java @@ -17,18 +17,18 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.json.JSONObject; +import org.labkey.api.assay.AssayDomainKind; +import org.labkey.api.assay.plate.AbstractPlateBasedAssayProvider; import org.labkey.api.data.Container; import org.labkey.api.exp.Lsid; -import org.labkey.api.assay.AssayDomainKind; import org.labkey.api.exp.TemplateInfo; -import org.json.JSONObject; import org.labkey.api.exp.api.SampleTypeDomainKindProperties; import org.labkey.api.exp.property.Domain; import org.labkey.api.gwt.client.model.GWTDomain; import org.labkey.api.gwt.client.model.GWTPropertyDescriptor; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; -import org.labkey.api.assay.plate.AbstractPlateBasedAssayProvider; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; import org.labkey.api.writer.ContainerUser; diff --git a/assay/src/org/labkey/assay/PlateController.java b/assay/src/org/labkey/assay/PlateController.java index b076925bad1..e35ebbbabf7 100644 --- a/assay/src/org/labkey/assay/PlateController.java +++ b/assay/src/org/labkey/assay/PlateController.java @@ -16,7 +16,8 @@ package org.labkey.assay; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.FormHandlerAction; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.GWTServiceAction; @@ -66,7 +67,7 @@ public class PlateController extends SpringActionController { private static final SpringActionController.DefaultActionResolver _actionResolver = new DefaultActionResolver(PlateController.class); - private static final Logger _log = Logger.getLogger(PlateController.class); + private static final Logger _log = LogManager.getLogger(PlateController.class); public PlateController() { diff --git a/assay/src/org/labkey/assay/TextAreaDataCollector.java b/assay/src/org/labkey/assay/TextAreaDataCollector.java index 7c0d43d8594..6676bad5ecd 100644 --- a/assay/src/org/labkey/assay/TextAreaDataCollector.java +++ b/assay/src/org/labkey/assay/TextAreaDataCollector.java @@ -17,11 +17,11 @@ package org.labkey.assay; import org.jetbrains.annotations.NotNull; -import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.assay.AbstractTempDirDataCollector; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.exp.ExperimentException; +import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.view.HtmlView; import org.labkey.api.view.HttpView; diff --git a/assay/src/org/labkey/assay/TsvProviderSchema.java b/assay/src/org/labkey/assay/TsvProviderSchema.java index 7f98074c7de..0ab6c4bce87 100644 --- a/assay/src/org/labkey/assay/TsvProviderSchema.java +++ b/assay/src/org/labkey/assay/TsvProviderSchema.java @@ -2,7 +2,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AssayProviderSchema; -import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerForeignKey; diff --git a/assay/src/org/labkey/assay/actions/AssayBatchDetailsAction.java b/assay/src/org/labkey/assay/actions/AssayBatchDetailsAction.java index 0de95c55bc8..dd9cfecbe07 100644 --- a/assay/src/org/labkey/assay/actions/AssayBatchDetailsAction.java +++ b/assay/src/org/labkey/assay/actions/AssayBatchDetailsAction.java @@ -16,25 +16,25 @@ package org.labkey.assay.actions; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExpExperiment; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.view.NotFoundException; -import org.labkey.api.view.RedirectException; -import org.labkey.api.view.ViewContext; -import org.labkey.api.view.NavTree; -import org.labkey.api.view.ActionURL; import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.Container; -import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.exp.api.ExpExperiment; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.springframework.web.servlet.ModelAndView; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.NavTree; +import org.labkey.api.view.NotFoundException; +import org.labkey.api.view.RedirectException; +import org.labkey.api.view.ViewContext; import org.springframework.validation.BindException; +import org.springframework.web.servlet.ModelAndView; /** * User: kevink diff --git a/assay/src/org/labkey/assay/actions/AssayBatchesAction.java b/assay/src/org/labkey/assay/actions/AssayBatchesAction.java index 95c10a0ab55..ced4403917d 100644 --- a/assay/src/org/labkey/assay/actions/AssayBatchesAction.java +++ b/assay/src/org/labkey/assay/actions/AssayBatchesAction.java @@ -18,15 +18,15 @@ import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.actions.AssayRunsAction; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.data.DataRegionSelection; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.actions.AssayRunsAction; -import org.labkey.api.assay.actions.BaseAssayAction; import org.labkey.api.util.HelpTopic; import org.labkey.api.view.NavTree; import org.labkey.api.view.ViewContext; -import org.labkey.api.data.DataRegionSelection; import org.labkey.assay.view.AssayBatchesView; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/assay/src/org/labkey/assay/actions/AssayResultsAction.java b/assay/src/org/labkey/assay/actions/AssayResultsAction.java index 38dd2145d79..7850fc6caf4 100644 --- a/assay/src/org/labkey/assay/actions/AssayResultsAction.java +++ b/assay/src/org/labkey/assay/actions/AssayResultsAction.java @@ -16,13 +16,13 @@ package org.labkey.assay.actions; +import org.labkey.api.assay.AssayResultsView; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.assay.actions.BaseAssayAction; import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.AssayResultsView; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.HelpTopic; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.NavTree; diff --git a/assay/src/org/labkey/assay/actions/BaseProtocolAPIAction.java b/assay/src/org/labkey/assay/actions/BaseProtocolAPIAction.java index 186e1ae8ba6..c3cf04b644f 100644 --- a/assay/src/org/labkey/assay/actions/BaseProtocolAPIAction.java +++ b/assay/src/org/labkey/assay/actions/BaseProtocolAPIAction.java @@ -20,6 +20,8 @@ import org.labkey.api.action.ApiResponse; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.exp.api.AssayJSONConverter; import org.labkey.api.exp.api.DefaultExperimentSaveHandler; @@ -27,8 +29,6 @@ import org.labkey.api.exp.api.ExperimentJSONConverter; import org.labkey.api.exp.api.ExperimentSaveHandler; import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.Pair; import org.labkey.api.view.NotFoundException; import org.springframework.validation.BindException; diff --git a/assay/src/org/labkey/assay/actions/DeleteAction.java b/assay/src/org/labkey/assay/actions/DeleteAction.java index e7606dbbf3c..2868cf2e10a 100644 --- a/assay/src/org/labkey/assay/actions/DeleteAction.java +++ b/assay/src/org/labkey/assay/actions/DeleteAction.java @@ -16,19 +16,19 @@ package org.labkey.assay.actions; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.permissions.*; import org.labkey.api.security.User; import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; +import org.labkey.api.security.permissions.ReadPermission; +import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.RedirectException; import org.labkey.api.view.UnauthorizedException; import org.labkey.api.view.ViewContext; -import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.security.DesignAssayPermission; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/assay/src/org/labkey/assay/actions/DeleteProtocolAction.java b/assay/src/org/labkey/assay/actions/DeleteProtocolAction.java index a895ddce243..e3e5c6fb4ae 100644 --- a/assay/src/org/labkey/assay/actions/DeleteProtocolAction.java +++ b/assay/src/org/labkey/assay/actions/DeleteProtocolAction.java @@ -16,11 +16,11 @@ package org.labkey.assay.actions; import org.labkey.api.action.MutatingApiAction; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.gwt.client.assay.model.GWTProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.view.NotFoundException; import org.labkey.api.view.UnauthorizedException; import org.labkey.assay.AssayManager; diff --git a/assay/src/org/labkey/assay/actions/GetAssayBatchAction.java b/assay/src/org/labkey/assay/actions/GetAssayBatchAction.java index 4656596e551..ff2df8cb927 100644 --- a/assay/src/org/labkey/assay/actions/GetAssayBatchAction.java +++ b/assay/src/org/labkey/assay/actions/GetAssayBatchAction.java @@ -17,12 +17,12 @@ import org.labkey.api.action.ApiResponse; import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.assay.DefaultAssaySaveHandler; import org.labkey.api.exp.api.AssayJSONConverter; import org.labkey.api.exp.api.ExpExperiment; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.DefaultAssaySaveHandler; import org.springframework.validation.BindException; /** diff --git a/assay/src/org/labkey/assay/actions/GetAssayBatchesAction.java b/assay/src/org/labkey/assay/actions/GetAssayBatchesAction.java index a90966a0171..a3a8c982077 100644 --- a/assay/src/org/labkey/assay/actions/GetAssayBatchesAction.java +++ b/assay/src/org/labkey/assay/actions/GetAssayBatchesAction.java @@ -18,12 +18,12 @@ import org.json.JSONArray; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.assay.DefaultAssaySaveHandler; import org.labkey.api.exp.api.AssayJSONConverter; import org.labkey.api.exp.api.ExpExperiment; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.DefaultAssaySaveHandler; import org.springframework.validation.BindException; import java.util.ArrayList; diff --git a/assay/src/org/labkey/assay/actions/GetAssayRunsAction.java b/assay/src/org/labkey/assay/actions/GetAssayRunsAction.java index 67a843f4f93..17e4d053eef 100644 --- a/assay/src/org/labkey/assay/actions/GetAssayRunsAction.java +++ b/assay/src/org/labkey/assay/actions/GetAssayRunsAction.java @@ -12,7 +12,6 @@ import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentJSONConverter; -import org.labkey.api.exp.api.ExperimentSaveHandler; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; diff --git a/assay/src/org/labkey/assay/actions/ImportAction.java b/assay/src/org/labkey/assay/actions/ImportAction.java index 5ebba795733..be6219a474d 100644 --- a/assay/src/org/labkey/assay/actions/ImportAction.java +++ b/assay/src/org/labkey/assay/actions/ImportAction.java @@ -16,16 +16,16 @@ package org.labkey.assay.actions; import org.apache.commons.lang3.StringUtils; -import org.labkey.api.data.Container; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.security.RequiresPermission; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; import org.labkey.api.assay.actions.BaseAssayAction; import org.labkey.api.assay.actions.DesignerAction; import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.assay.security.DesignAssayPermission; +import org.labkey.api.data.Container; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.security.RequiresPermission; import org.labkey.api.util.NetworkDrive; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NavTree; diff --git a/assay/src/org/labkey/assay/actions/ImportRunApiAction.java b/assay/src/org/labkey/assay/actions/ImportRunApiAction.java index 627c417b584..954f53a1e98 100644 --- a/assay/src/org/labkey/assay/actions/ImportRunApiAction.java +++ b/assay/src/org/labkey/assay/actions/ImportRunApiAction.java @@ -16,7 +16,8 @@ package org.labkey.assay.actions; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.action.ApiResponse; @@ -78,7 +79,7 @@ @ApiVersion(12.3) public class ImportRunApiAction extends MutatingApiAction { - static Logger LOG = Logger.getLogger(ImportRunApiAction.class); + static Logger LOG = LogManager.getLogger(ImportRunApiAction.class); @Override public ApiResponse execute(ImportRunApiForm form, BindException errors) throws Exception diff --git a/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java b/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java index bd891e8945f..e7c271bd3c9 100644 --- a/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java +++ b/assay/src/org/labkey/assay/actions/PipelineDataCollectorRedirectAction.java @@ -18,6 +18,9 @@ import org.labkey.api.action.LabKeyError; import org.labkey.api.action.SimpleErrorView; import org.labkey.api.action.SimpleViewAction; +import org.labkey.api.assay.AssayDataCollector; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.PipelineDataCollector; import org.labkey.api.data.Container; import org.labkey.api.data.DataRegionSelection; import org.labkey.api.exp.api.ExpData; @@ -27,9 +30,6 @@ import org.labkey.api.pipeline.PipelineService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.assay.AssayDataCollector; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.PipelineDataCollector; import org.labkey.api.util.NetworkDrive; import org.labkey.api.view.NavTree; import org.labkey.api.view.NotFoundException; diff --git a/assay/src/org/labkey/assay/actions/SaveAssayBatchAction.java b/assay/src/org/labkey/assay/actions/SaveAssayBatchAction.java index 81314fff064..1035292440e 100644 --- a/assay/src/org/labkey/assay/actions/SaveAssayBatchAction.java +++ b/assay/src/org/labkey/assay/actions/SaveAssayBatchAction.java @@ -20,6 +20,7 @@ import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiVersion; import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.assay.AssayProvider; import org.labkey.api.data.DbScope; import org.labkey.api.exp.api.AssayJSONConverter; import org.labkey.api.exp.api.ExpExperiment; @@ -28,7 +29,6 @@ import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.assay.AssayProvider; import org.springframework.validation.BindException; import java.util.ArrayList; diff --git a/assay/src/org/labkey/assay/actions/SaveAssayRunsAction.java b/assay/src/org/labkey/assay/actions/SaveAssayRunsAction.java index 322e60785c8..e103d769309 100644 --- a/assay/src/org/labkey/assay/actions/SaveAssayRunsAction.java +++ b/assay/src/org/labkey/assay/actions/SaveAssayRunsAction.java @@ -7,7 +7,6 @@ import org.labkey.api.assay.AssayProvider; import org.labkey.api.data.DbScope; import org.labkey.api.exp.api.AssayJSONConverter; -import org.labkey.api.exp.api.DefaultExperimentSaveHandler; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentJSONConverter; diff --git a/assay/src/org/labkey/assay/actions/SaveProtocolAction.java b/assay/src/org/labkey/assay/actions/SaveProtocolAction.java index 588dc74374d..b68643650b5 100644 --- a/assay/src/org/labkey/assay/actions/SaveProtocolAction.java +++ b/assay/src/org/labkey/assay/actions/SaveProtocolAction.java @@ -19,15 +19,15 @@ import org.labkey.api.action.Marshaller; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.assay.AssayDomainService; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.gwt.client.assay.model.GWTProtocol; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.view.NotFoundException; import org.labkey.api.view.UnauthorizedException; -import org.labkey.assay.AssayManager; import org.labkey.assay.AssayDomainServiceImpl; +import org.labkey.assay.AssayManager; import org.springframework.validation.BindException; @Marshal(Marshaller.Jackson) diff --git a/assay/src/org/labkey/assay/actions/ShowSelectedDataAction.java b/assay/src/org/labkey/assay/actions/ShowSelectedDataAction.java index eb9e36fbbfe..c47c4e8e52f 100644 --- a/assay/src/org/labkey/assay/actions/ShowSelectedDataAction.java +++ b/assay/src/org/labkey/assay/actions/ShowSelectedDataAction.java @@ -24,9 +24,7 @@ import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; -import org.springframework.validation.Errors; import java.util.Set; diff --git a/assay/src/org/labkey/assay/actions/ShowSelectedRunsAction.java b/assay/src/org/labkey/assay/actions/ShowSelectedRunsAction.java index 9553ab964dd..b4503057c41 100644 --- a/assay/src/org/labkey/assay/actions/ShowSelectedRunsAction.java +++ b/assay/src/org/labkey/assay/actions/ShowSelectedRunsAction.java @@ -16,12 +16,6 @@ package org.labkey.assay.actions; import org.labkey.api.action.SimpleRedirectAction; -import org.labkey.api.security.RequiresPermission; -import org.labkey.api.security.permissions.*; -import org.labkey.api.util.URLHelper; -import org.labkey.api.view.ActionURL; -import org.labkey.api.data.DataRegionSelection; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.assay.AssayUrls; import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.ContainerFilter; @@ -30,7 +24,6 @@ import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; -import org.springframework.validation.Errors; import java.util.Set; diff --git a/assay/src/org/labkey/assay/actions/TemplateAction.java b/assay/src/org/labkey/assay/actions/TemplateAction.java index 426e8f078bd..effcba956cd 100644 --- a/assay/src/org/labkey/assay/actions/TemplateAction.java +++ b/assay/src/org/labkey/assay/actions/TemplateAction.java @@ -16,6 +16,10 @@ package org.labkey.assay.actions; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.DataRegion; import org.labkey.api.data.DisplayColumn; @@ -28,10 +32,6 @@ import org.labkey.api.exp.property.Domain; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.view.NavTree; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/assay/src/org/labkey/assay/actions/TsvImportAction.java b/assay/src/org/labkey/assay/actions/TsvImportAction.java index d9ba0a18c6c..ee4722bc1b8 100644 --- a/assay/src/org/labkey/assay/actions/TsvImportAction.java +++ b/assay/src/org/labkey/assay/actions/TsvImportAction.java @@ -15,8 +15,8 @@ */ package org.labkey.assay.actions; -import org.labkey.api.security.RequiresPermission; import org.labkey.api.assay.security.DesignAssayPermission; +import org.labkey.api.security.RequiresPermission; import org.springframework.web.servlet.ModelAndView; import java.util.Map; diff --git a/assay/src/org/labkey/assay/pipeline/AssayImportRunTask.java b/assay/src/org/labkey/assay/pipeline/AssayImportRunTask.java index 7e2c7df059a..5df90444c9f 100644 --- a/assay/src/org/labkey/assay/pipeline/AssayImportRunTask.java +++ b/assay/src/org/labkey/assay/pipeline/AssayImportRunTask.java @@ -17,6 +17,11 @@ import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssayDataCollector; +import org.labkey.api.assay.AssayDataType; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayRunUploadContext; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.exp.ExperimentException; @@ -43,11 +48,6 @@ import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayDataCollector; -import org.labkey.api.assay.AssayDataType; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayRunUploadContext; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.NetworkDrive; diff --git a/assay/src/org/labkey/assay/plate/CurveFitFactory.java b/assay/src/org/labkey/assay/plate/CurveFitFactory.java index f9097c0ed77..b98dd55d15c 100644 --- a/assay/src/org/labkey/assay/plate/CurveFitFactory.java +++ b/assay/src/org/labkey/assay/plate/CurveFitFactory.java @@ -17,9 +17,9 @@ package org.labkey.assay.plate; import org.labkey.api.assay.dilution.DilutionCurve; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.statistics.FitFailedException; import org.labkey.api.data.statistics.StatsService; -import org.labkey.api.assay.plate.WellGroup; import java.util.Collections; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/EmptyCurveImpl.java b/assay/src/org/labkey/assay/plate/EmptyCurveImpl.java index a52cbc5a7dd..103fcb81646 100644 --- a/assay/src/org/labkey/assay/plate/EmptyCurveImpl.java +++ b/assay/src/org/labkey/assay/plate/EmptyCurveImpl.java @@ -15,11 +15,11 @@ */ package org.labkey.assay.plate; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.statistics.CurveFit; import org.labkey.api.data.statistics.DoublePoint; import org.labkey.api.data.statistics.FitFailedException; import org.labkey.api.data.statistics.StatsService; -import org.labkey.api.assay.plate.WellGroup; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/ParameterCurveImpl.java b/assay/src/org/labkey/assay/plate/ParameterCurveImpl.java index 843ca893215..5a630c5e459 100644 --- a/assay/src/org/labkey/assay/plate/ParameterCurveImpl.java +++ b/assay/src/org/labkey/assay/plate/ParameterCurveImpl.java @@ -16,11 +16,11 @@ package org.labkey.assay.plate; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.statistics.CurveFit; import org.labkey.api.data.statistics.DoublePoint; import org.labkey.api.data.statistics.FitFailedException; import org.labkey.api.data.statistics.StatsService; -import org.labkey.api.assay.plate.WellGroup; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java b/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java index 1730cce4c63..ea7fe6d5538 100644 --- a/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java +++ b/assay/src/org/labkey/assay/plate/PlateDataServiceImpl.java @@ -20,7 +20,8 @@ import gwt.client.org.labkey.plate.designer.client.model.GWTPlate; import gwt.client.org.labkey.plate.designer.client.model.GWTPosition; import gwt.client.org.labkey.plate.designer.client.model.GWTWellGroup; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.assay.plate.PlateService; import org.labkey.api.assay.plate.PlateTemplate; import org.labkey.api.assay.plate.PlateTypeHandler; @@ -29,15 +30,12 @@ import org.labkey.api.assay.plate.WellGroupTemplate; import org.labkey.api.gwt.server.BaseRemoteService; import org.labkey.api.query.ValidationException; -import org.labkey.api.util.Pair; import org.labkey.api.view.ViewContext; import java.sql.SQLException; import java.util.ArrayList; import java.util.Arrays; -import java.util.Collections; import java.util.HashMap; -import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; @@ -49,7 +47,7 @@ */ public class PlateDataServiceImpl extends BaseRemoteService implements PlateDataService { - private static final Logger LOG = Logger.getLogger(PlateDataServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(PlateDataServiceImpl.class); public PlateDataServiceImpl(ViewContext context) { diff --git a/assay/src/org/labkey/assay/plate/PlateImpl.java b/assay/src/org/labkey/assay/plate/PlateImpl.java index cbeccafe4df..31fa025cdfd 100644 --- a/assay/src/org/labkey/assay/plate/PlateImpl.java +++ b/assay/src/org/labkey/assay/plate/PlateImpl.java @@ -22,7 +22,6 @@ import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.assay.plate.WellGroupTemplate; import org.labkey.api.view.ActionURL; -import org.labkey.assay.PlateController; import java.util.List; import java.util.Map; diff --git a/assay/src/org/labkey/assay/plate/PlateManager.java b/assay/src/org/labkey/assay/plate/PlateManager.java index 149302dfc27..a27831e95a9 100644 --- a/assay/src/org/labkey/assay/plate/PlateManager.java +++ b/assay/src/org/labkey/assay/plate/PlateManager.java @@ -16,7 +16,8 @@ package org.labkey.assay.plate; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Test; @@ -53,7 +54,6 @@ import org.labkey.api.exp.OntologyObject; import org.labkey.api.exp.PropertyDescriptor; import org.labkey.api.exp.PropertyType; -import org.labkey.api.exp.api.ExpObject; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; @@ -67,7 +67,6 @@ import org.labkey.api.util.Pair; import org.labkey.api.util.TestContext; import org.labkey.api.view.ActionURL; -import org.labkey.assay.PlateController; import org.labkey.assay.TsvAssayProvider; import org.labkey.assay.query.AssayDbSchema; @@ -100,7 +99,7 @@ */ public class PlateManager implements PlateService { - private static final Logger LOG = Logger.getLogger(PlateManager.class); + private static final Logger LOG = LogManager.getLogger(PlateManager.class); private static final String LSID_CLASS_OBJECT_ID = "objectType"; private List _detailsLinkResolvers = new ArrayList<>(); diff --git a/assay/src/org/labkey/assay/plate/PolynomialCurveImpl.java b/assay/src/org/labkey/assay/plate/PolynomialCurveImpl.java index f5566b4c379..1fb49a62ef3 100644 --- a/assay/src/org/labkey/assay/plate/PolynomialCurveImpl.java +++ b/assay/src/org/labkey/assay/plate/PolynomialCurveImpl.java @@ -16,11 +16,11 @@ package org.labkey.assay.plate; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.statistics.CurveFit; import org.labkey.api.data.statistics.DoublePoint; import org.labkey.api.data.statistics.FitFailedException; import org.labkey.api.data.statistics.StatsService; -import org.labkey.api.assay.plate.WellGroup; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/PropertySetImpl.java b/assay/src/org/labkey/assay/plate/PropertySetImpl.java index 55c23ab763e..40c65f0552f 100644 --- a/assay/src/org/labkey/assay/plate/PropertySetImpl.java +++ b/assay/src/org/labkey/assay/plate/PropertySetImpl.java @@ -17,7 +17,6 @@ package org.labkey.assay.plate; import org.labkey.api.data.Container; -import org.labkey.api.exp.Identifiable; import org.labkey.api.study.PropertySet; import java.util.Collections; diff --git a/assay/src/org/labkey/assay/plate/WellGroupCurveImpl.java b/assay/src/org/labkey/assay/plate/WellGroupCurveImpl.java index ec772432c41..f9832e7d46d 100644 --- a/assay/src/org/labkey/assay/plate/WellGroupCurveImpl.java +++ b/assay/src/org/labkey/assay/plate/WellGroupCurveImpl.java @@ -17,14 +17,19 @@ package org.labkey.assay.plate; import org.labkey.api.assay.dilution.DilutionCurve; +import org.labkey.api.assay.plate.WellData; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.statistics.CurveFit; import org.labkey.api.data.statistics.DoublePoint; import org.labkey.api.data.statistics.FitFailedException; import org.labkey.api.data.statistics.StatsService; -import org.labkey.api.assay.plate.WellData; -import org.labkey.api.assay.plate.WellGroup; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; /** * User: brittp diff --git a/assay/src/org/labkey/assay/plate/WellGroupImpl.java b/assay/src/org/labkey/assay/plate/WellGroupImpl.java index 461a00739e5..58eab9602fb 100644 --- a/assay/src/org/labkey/assay/plate/WellGroupImpl.java +++ b/assay/src/org/labkey/assay/plate/WellGroupImpl.java @@ -31,7 +31,13 @@ import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.view.ActionURL; -import java.util.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; /** * User: brittp diff --git a/assay/src/org/labkey/assay/plate/query/PlateQueryView.java b/assay/src/org/labkey/assay/plate/query/PlateQueryView.java index 74a96685738..d9dffad1d77 100644 --- a/assay/src/org/labkey/assay/plate/query/PlateQueryView.java +++ b/assay/src/org/labkey/assay/plate/query/PlateQueryView.java @@ -18,11 +18,9 @@ import org.labkey.api.data.ActionButton; import org.labkey.api.data.Sort; -import org.labkey.api.query.QueryAction; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; import org.labkey.api.query.UserSchema; -import org.labkey.api.view.ActionURL; import java.io.IOException; import java.sql.SQLException; diff --git a/assay/src/org/labkey/assay/plate/query/PlateQueryViewImpl.java b/assay/src/org/labkey/assay/plate/query/PlateQueryViewImpl.java index bda094e7ed8..fd67f2e592f 100644 --- a/assay/src/org/labkey/assay/plate/query/PlateQueryViewImpl.java +++ b/assay/src/org/labkey/assay/plate/query/PlateQueryViewImpl.java @@ -16,17 +16,21 @@ package org.labkey.assay.plate.query; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; import org.labkey.api.query.QuerySettings; -import org.labkey.api.view.ViewContext; import org.labkey.api.view.DataView; -import org.labkey.api.data.*; +import org.labkey.api.view.ViewContext; -import java.util.List; -import java.util.Map; -import java.util.HashMap; import java.io.IOException; import java.sql.ResultSet; import java.sql.SQLException; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * User: brittp diff --git a/assay/src/org/labkey/assay/plate/query/PlateSchema.java b/assay/src/org/labkey/assay/plate/query/PlateSchema.java index 062ed3c40ea..e4328d978ed 100644 --- a/assay/src/org/labkey/assay/plate/query/PlateSchema.java +++ b/assay/src/org/labkey/assay/plate/query/PlateSchema.java @@ -17,7 +17,8 @@ package org.labkey.assay.plate.query; import org.jetbrains.annotations.NotNull; -import org.labkey.assay.query.AssayDbSchema; +import org.labkey.api.assay.plate.PlateService; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; @@ -26,8 +27,7 @@ import org.labkey.api.query.QuerySchema; import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; -import org.labkey.api.assay.plate.PlateService; -import org.labkey.api.assay.plate.WellGroup; +import org.labkey.assay.query.AssayDbSchema; import java.util.HashSet; import java.util.Set; diff --git a/assay/src/org/labkey/assay/plate/query/PlateTable.java b/assay/src/org/labkey/assay/plate/query/PlateTable.java index 2a37c1b62ba..704ae4acf78 100644 --- a/assay/src/org/labkey/assay/plate/query/PlateTable.java +++ b/assay/src/org/labkey/assay/plate/query/PlateTable.java @@ -16,7 +16,6 @@ package org.labkey.assay.plate.query; -import org.labkey.assay.query.AssayDbSchema; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; import org.labkey.api.data.ContainerFilter; @@ -28,6 +27,7 @@ import org.labkey.api.exp.PropertyType; import org.labkey.api.query.FieldKey; import org.labkey.api.query.PropertyForeignKey; +import org.labkey.assay.query.AssayDbSchema; import java.util.ArrayList; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/query/WellGroupTable.java b/assay/src/org/labkey/assay/plate/query/WellGroupTable.java index 2ee0ea17d58..c38ddd4e47e 100644 --- a/assay/src/org/labkey/assay/plate/query/WellGroupTable.java +++ b/assay/src/org/labkey/assay/plate/query/WellGroupTable.java @@ -16,7 +16,7 @@ package org.labkey.assay.plate.query; -import org.labkey.assay.query.AssayDbSchema; +import org.labkey.api.assay.plate.WellGroup; import org.labkey.api.data.CompareType; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.SimpleFilter; @@ -30,7 +30,7 @@ import org.labkey.api.query.FieldKey; import org.labkey.api.query.LookupForeignKey; import org.labkey.api.query.PropertyForeignKey; -import org.labkey.api.assay.plate.WellGroup; +import org.labkey.assay.query.AssayDbSchema; import java.util.ArrayList; import java.util.List; diff --git a/assay/src/org/labkey/assay/plate/view/plateTemplateList.jsp b/assay/src/org/labkey/assay/plate/view/plateTemplateList.jsp index 3567bed1d6f..6492b6a981f 100644 --- a/assay/src/org/labkey/assay/plate/view/plateTemplateList.jsp +++ b/assay/src/org/labkey/assay/plate/view/plateTemplateList.jsp @@ -25,18 +25,18 @@ <%@ page import="org.labkey.api.security.permissions.UpdatePermission" %> <%@ page import="org.labkey.api.util.Link" %> <%@ page import="org.labkey.api.util.Pair" %> +<%@ page import="org.labkey.api.util.element.Input" %> +<%@ page import="org.labkey.api.util.element.Option" %> +<%@ page import="org.labkey.api.util.element.Select" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.assay.PlateController" %> <%@ page import="org.labkey.assay.plate.PlateManager" %> +<%@ page import="java.util.ArrayList" %> <%@ page import="java.util.HashMap" %> <%@ page import="java.util.List" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.util.element.Input" %> -<%@ page import="org.labkey.api.util.element.Select" %> -<%@ page import="org.labkey.api.util.element.Option" %> -<%@ page import="java.util.ArrayList" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> diff --git a/assay/src/org/labkey/assay/query/AssayProviderTable.java b/assay/src/org/labkey/assay/query/AssayProviderTable.java index 1fc8455e1ab..0441415a7fd 100644 --- a/assay/src/org/labkey/assay/query/AssayProviderTable.java +++ b/assay/src/org/labkey/assay/query/AssayProviderTable.java @@ -16,13 +16,13 @@ package org.labkey.assay.query; import org.jetbrains.annotations.NotNull; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssaySchema; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.JdbcType; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.VirtualTable; import org.labkey.api.query.ExprColumn; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssaySchema; -import org.labkey.api.assay.AssayService; /** * User: kevink diff --git a/assay/src/org/labkey/assay/query/AssaySchemaImpl.java b/assay/src/org/labkey/assay/query/AssaySchemaImpl.java index 2ca0ebe66c0..019612ae556 100644 --- a/assay/src/org/labkey/assay/query/AssaySchemaImpl.java +++ b/assay/src/org/labkey/assay/query/AssaySchemaImpl.java @@ -22,6 +22,11 @@ import org.jmock.lib.legacy.ClassImposteriser; import org.junit.Assert; import org.junit.Test; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayProviderSchema; +import org.labkey.api.assay.AssaySchema; +import org.labkey.api.assay.AssayService; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -36,11 +41,6 @@ import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; import org.labkey.api.security.User; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayProviderSchema; -import org.labkey.api.assay.AssaySchema; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ViewContext; diff --git a/assay/src/org/labkey/assay/query/TypeDisplayColumn.java b/assay/src/org/labkey/assay/query/TypeDisplayColumn.java index 2a4ead32b4a..e07f6633a10 100644 --- a/assay/src/org/labkey/assay/query/TypeDisplayColumn.java +++ b/assay/src/org/labkey/assay/query/TypeDisplayColumn.java @@ -16,7 +16,12 @@ package org.labkey.assay.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; @@ -25,10 +30,6 @@ import org.labkey.api.exp.api.ExperimentUrls; import org.labkey.api.query.FieldKey; import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; -import org.labkey.api.assay.security.DesignAssayPermission; import org.labkey.api.util.PageFlowUtil; import java.io.IOException; @@ -41,7 +42,7 @@ */ public class TypeDisplayColumn extends DataColumn { - private static final Logger LOG = Logger.getLogger(TypeDisplayColumn.class); + private static final Logger LOG = LogManager.getLogger(TypeDisplayColumn.class); private static final FieldKey LSID_FIELD_KEY = new FieldKey(null, "LSID"); diff --git a/assay/src/org/labkey/assay/view/AssayBaseWebPartFactory.java b/assay/src/org/labkey/assay/view/AssayBaseWebPartFactory.java index b308e13e716..ff2dbf49e30 100644 --- a/assay/src/org/labkey/assay/view/AssayBaseWebPartFactory.java +++ b/assay/src/org/labkey/assay/view/AssayBaseWebPartFactory.java @@ -16,9 +16,17 @@ package org.labkey.assay.view; import org.jetbrains.annotations.NotNull; -import org.labkey.api.view.*; -import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.assay.actions.ProtocolIdForm; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.view.BaseWebPartFactory; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NotFoundException; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartFactory; +import org.labkey.api.view.WebPartView; public abstract class AssayBaseWebPartFactory extends BaseWebPartFactory { diff --git a/assay/src/org/labkey/assay/view/AssayBatchesWebPartFactory.java b/assay/src/org/labkey/assay/view/AssayBatchesWebPartFactory.java index d21c75ceb36..93646e88db9 100644 --- a/assay/src/org/labkey/assay/view/AssayBatchesWebPartFactory.java +++ b/assay/src/org/labkey/assay/view/AssayBatchesWebPartFactory.java @@ -16,9 +16,9 @@ package org.labkey.assay.view; -import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.assay.AssayProtocolSchema; import org.labkey.api.assay.AssayUrls; +import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.Portal; import org.labkey.api.view.ViewContext; diff --git a/assay/src/org/labkey/assay/view/AssayList2WebPartFactory.java b/assay/src/org/labkey/assay/view/AssayList2WebPartFactory.java index 917180a48b6..5477f96914b 100644 --- a/assay/src/org/labkey/assay/view/AssayList2WebPartFactory.java +++ b/assay/src/org/labkey/assay/view/AssayList2WebPartFactory.java @@ -16,7 +16,12 @@ package org.labkey.assay.view; import org.jetbrains.annotations.NotNull; -import org.labkey.api.view.*; +import org.labkey.api.view.AlwaysAvailableWebPartFactory; +import org.labkey.api.view.JspView; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartFactory; +import org.labkey.api.view.WebPartView; /** * User: Mark Igra diff --git a/assay/src/org/labkey/assay/view/AssayResultsWebPartFactory.java b/assay/src/org/labkey/assay/view/AssayResultsWebPartFactory.java index 45f86062d99..45cbca872f2 100644 --- a/assay/src/org/labkey/assay/view/AssayResultsWebPartFactory.java +++ b/assay/src/org/labkey/assay/view/AssayResultsWebPartFactory.java @@ -19,9 +19,11 @@ import org.labkey.api.assay.AssayProtocolSchema; import org.labkey.api.assay.AssayResultsView; import org.labkey.api.assay.AssayUrls; -import org.labkey.api.view.*; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartView; /** * User: kevink diff --git a/assay/src/org/labkey/assay/view/AssayRunsWebPartFactory.java b/assay/src/org/labkey/assay/view/AssayRunsWebPartFactory.java index 2b265546d44..f116de2c83c 100644 --- a/assay/src/org/labkey/assay/view/AssayRunsWebPartFactory.java +++ b/assay/src/org/labkey/assay/view/AssayRunsWebPartFactory.java @@ -17,12 +17,12 @@ package org.labkey.assay.view; import org.labkey.api.admin.ImportContext; -import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.assay.AssayProtocolSchema; import org.labkey.api.assay.AssayRunsView; import org.labkey.api.assay.AssayService; import org.labkey.api.assay.AssayUrls; +import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.Portal; import org.labkey.api.view.ViewContext; diff --git a/assay/src/org/labkey/assay/view/assayList2.jsp b/assay/src/org/labkey/assay/view/assayList2.jsp index e1fd7052506..2e894f9096b 100644 --- a/assay/src/org/labkey/assay/view/assayList2.jsp +++ b/assay/src/org/labkey/assay/view/assayList2.jsp @@ -15,13 +15,13 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.assay.AssayService" %> +<%@ page import="org.labkey.api.assay.AssayUrls" %> <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.data.ContainerFilter" %> <%@ page import="org.labkey.api.exp.api.ExpProtocol" %> <%@ page import="org.labkey.api.security.permissions.AdminPermission" %> <%@ page import="org.labkey.api.security.permissions.InsertPermission" %> -<%@ page import="org.labkey.api.assay.AssayService" %> -<%@ page import="org.labkey.api.assay.AssayUrls" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="java.util.List" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> diff --git a/assay/src/org/labkey/assay/view/assaySetup.jsp b/assay/src/org/labkey/assay/view/assaySetup.jsp index e78d427658b..260cddeda70 100644 --- a/assay/src/org/labkey/assay/view/assaySetup.jsp +++ b/assay/src/org/labkey/assay/view/assaySetup.jsp @@ -16,13 +16,13 @@ */ %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> +<%@ page import="org.labkey.api.assay.AssayService" %> +<%@ page import="org.labkey.api.assay.security.DesignAssayPermission" %> <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.pipeline.PipelineService" %> <%@ page import="org.labkey.api.pipeline.PipelineUrls" %> <%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.security.permissions.AdminOperationsPermission" %> -<%@ page import="org.labkey.api.assay.AssayService" %> -<%@ page import="org.labkey.api.assay.security.DesignAssayPermission" %> <%@ page import="org.labkey.api.util.HelpTopic" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> diff --git a/assay/src/org/labkey/assay/view/begin.jsp b/assay/src/org/labkey/assay/view/begin.jsp index f4ea2c86dc2..cc9ad264a4f 100644 --- a/assay/src/org/labkey/assay/view/begin.jsp +++ b/assay/src/org/labkey/assay/view/begin.jsp @@ -18,8 +18,8 @@ <%@ page import="org.json.JSONObject" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="org.labkey.assay.AssayController" %> +<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/assay/src/org/labkey/assay/view/chooseAssayType.jsp b/assay/src/org/labkey/assay/view/chooseAssayType.jsp index 4fad5e6a968..6a935a9683e 100644 --- a/assay/src/org/labkey/assay/view/chooseAssayType.jsp +++ b/assay/src/org/labkey/assay/view/chooseAssayType.jsp @@ -15,13 +15,13 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.assay.AssayProvider" %> +<%@ page import="org.labkey.api.assay.AssayService" %> +<%@ page import="org.labkey.api.assay.AssayUrls" %> <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.exp.api.ExperimentUrls" %> <%@ page import="org.labkey.api.files.FileContentService" %> <%@ page import="org.labkey.api.pipeline.PipelineUrls" %> -<%@ page import="org.labkey.api.assay.AssayProvider" %> -<%@ page import="org.labkey.api.assay.AssayService" %> -<%@ page import="org.labkey.api.assay.AssayUrls" %> <%@ page import="org.labkey.api.util.HelpTopic" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.util.Pair" %> diff --git a/assay/src/org/labkey/assay/view/customizeAssayDetailsWebPart.jsp b/assay/src/org/labkey/assay/view/customizeAssayDetailsWebPart.jsp index 59b5ac049a1..3ee209e4818 100644 --- a/assay/src/org/labkey/assay/view/customizeAssayDetailsWebPart.jsp +++ b/assay/src/org/labkey/assay/view/customizeAssayDetailsWebPart.jsp @@ -15,9 +15,9 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.exp.api.ExpProtocol" %> <%@ page import="org.labkey.api.assay.AssayProvider" %> <%@ page import="org.labkey.api.assay.AssayService" %> +<%@ page import="org.labkey.api.exp.api.ExpProtocol" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> diff --git a/assay/src/org/labkey/assay/view/dataUpload.jsp b/assay/src/org/labkey/assay/view/dataUpload.jsp index 3c3b8b37301..c0f0b82344b 100644 --- a/assay/src/org/labkey/assay/view/dataUpload.jsp +++ b/assay/src/org/labkey/assay/view/dataUpload.jsp @@ -15,10 +15,10 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.exp.ExperimentException"%> -<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> -<%@ page import="org.labkey.api.assay.AssayDataCollector" %> +<%@ page import="org.labkey.api.assay.AssayDataCollector"%> <%@ page import="org.labkey.api.assay.AssayProvider" %> +<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> +<%@ page import="org.labkey.api.exp.ExperimentException" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="java.io.File" %> diff --git a/assay/src/org/labkey/assay/view/moduleAssayListView.jsp b/assay/src/org/labkey/assay/view/moduleAssayListView.jsp index dbe4e3ba2ef..c7974fd4af2 100644 --- a/assay/src/org/labkey/assay/view/moduleAssayListView.jsp +++ b/assay/src/org/labkey/assay/view/moduleAssayListView.jsp @@ -18,8 +18,8 @@ <%@ page import="org.json.JSONObject" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="org.labkey.assay.AssayController" %> +<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/assay/src/org/labkey/assay/view/moduleAssayUpload.jsp b/assay/src/org/labkey/assay/view/moduleAssayUpload.jsp index 2dbf00c0df2..285f0b17ca8 100644 --- a/assay/src/org/labkey/assay/view/moduleAssayUpload.jsp +++ b/assay/src/org/labkey/assay/view/moduleAssayUpload.jsp @@ -16,19 +16,19 @@ */ %> <%@ page import="org.json.JSONObject"%> +<%@ page import="org.labkey.api.assay.AssayProvider" %> +<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> <%@ page import="org.labkey.api.exp.api.AssayJSONConverter" %> <%@ page import="org.labkey.api.exp.api.ExpExperiment" %> <%@ page import="org.labkey.api.exp.api.ExpProtocol" %> +<%@ page import="org.labkey.api.exp.api.ExperimentJSONConverter" %> <%@ page import="org.labkey.api.exp.api.ExperimentService" %> -<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> -<%@ page import="org.labkey.api.assay.AssayProvider" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.NotFoundException" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.assay.AssayController" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.exp.api.ExperimentJSONConverter" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/assay/src/org/labkey/assay/view/newUploadBatchProperties.jsp b/assay/src/org/labkey/assay/view/newUploadBatchProperties.jsp index 22b4598b413..bab7729dd57 100644 --- a/assay/src/org/labkey/assay/view/newUploadBatchProperties.jsp +++ b/assay/src/org/labkey/assay/view/newUploadBatchProperties.jsp @@ -15,9 +15,9 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.exp.property.DomainProperty" %> -<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> <%@ page import="org.labkey.api.assay.AssayProvider" %> +<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> +<%@ page import="org.labkey.api.exp.property.DomainProperty" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="java.util.Map" %> diff --git a/assay/src/org/labkey/assay/view/resultDetails.jsp b/assay/src/org/labkey/assay/view/resultDetails.jsp index 8f267967097..5dba8394c97 100644 --- a/assay/src/org/labkey/assay/view/resultDetails.jsp +++ b/assay/src/org/labkey/assay/view/resultDetails.jsp @@ -23,8 +23,8 @@ <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="org.labkey.assay.AssayController" %> +<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="java.util.Map" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/assay/src/org/labkey/assay/view/runDetails.jsp b/assay/src/org/labkey/assay/view/runDetails.jsp index 31e8cdc82a9..0e64b595b43 100644 --- a/assay/src/org/labkey/assay/view/runDetails.jsp +++ b/assay/src/org/labkey/assay/view/runDetails.jsp @@ -19,12 +19,12 @@ <%@ page import="org.labkey.api.exp.api.AssayJSONConverter" %> <%@ page import="org.labkey.api.exp.api.ExpProtocol" %> <%@ page import="org.labkey.api.exp.api.ExpRun" %> +<%@ page import="org.labkey.api.exp.api.ExperimentJSONConverter" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="org.labkey.assay.AssayController" %> +<%@ page import="org.labkey.assay.ModuleAssayProvider" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.exp.api.ExperimentJSONConverter" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/assay/src/org/labkey/assay/view/tsvDataDescription.jsp b/assay/src/org/labkey/assay/view/tsvDataDescription.jsp index 5db152cbc35..2f88de65937 100644 --- a/assay/src/org/labkey/assay/view/tsvDataDescription.jsp +++ b/assay/src/org/labkey/assay/view/tsvDataDescription.jsp @@ -15,15 +15,15 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.data.ColumnRenderProperties" %> -<%@ page import="org.labkey.api.exp.property.DomainProperty" %> -<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> -<%@ page import="org.labkey.assay.actions.TemplateAction" %> <%@ page import="org.labkey.api.assay.AssayProvider" %> <%@ page import="org.labkey.api.assay.AssayUrls" %> <%@ page import="org.labkey.api.assay.PipelineDataCollector" %> +<%@ page import="org.labkey.api.assay.actions.AssayRunUploadForm" %> +<%@ page import="org.labkey.api.data.ColumnRenderProperties" %> +<%@ page import="org.labkey.api.exp.property.DomainProperty" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> +<%@ page import="org.labkey.assay.actions.TemplateAction" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/audit/src/org/labkey/audit/AuditLogImpl.java b/audit/src/org/labkey/audit/AuditLogImpl.java index 78c43120a85..1347b319514 100644 --- a/audit/src/org/labkey/audit/AuditLogImpl.java +++ b/audit/src/org/labkey/audit/AuditLogImpl.java @@ -16,14 +16,13 @@ package org.labkey.audit; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DbScope; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; @@ -54,7 +53,7 @@ public class AuditLogImpl implements AuditLogService, StartupListener { private static final AuditLogImpl _instance = new AuditLogImpl(); - private static final Logger _log = Logger.getLogger(AuditLogImpl.class); + private static final Logger _log = org.apache.logging.log4j.LogManager.getLogger(AuditLogImpl.class); private Queue> _eventTypeQueue = new LinkedList<>(); private AtomicBoolean _logToDatabase = new AtomicBoolean(false); diff --git a/audit/src/org/labkey/audit/model/LogManager.java b/audit/src/org/labkey/audit/model/LogManager.java index 49f08a1f61b..26a206d4ecf 100644 --- a/audit/src/org/labkey/audit/model/LogManager.java +++ b/audit/src/org/labkey/audit/model/LogManager.java @@ -16,7 +16,7 @@ package org.labkey.audit.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; @@ -53,7 +53,7 @@ */ public class LogManager { - private static final Logger _log = Logger.getLogger(LogManager.class); + private static final Logger _log = org.apache.logging.log4j.LogManager.getLogger(LogManager.class); private static final LogManager _instance = new LogManager(); private static final int COMMENT_MAX = 500; private static final int STRING_KEY_MAX = 1000; @@ -76,7 +76,7 @@ public TableInfo getTinfoAuditLog() public K _insertEvent(User user, K type) { - Logger auditLogger = Logger.getLogger("org.labkey.audit.event." + type.getEventType().replaceAll(" ", "")); + Logger auditLogger = org.apache.logging.log4j.LogManager.getLogger("org.labkey.audit.event." + type.getEventType().replaceAll(" ", "")); auditLogger.info(type.getAuditLogMessage()); AuditTypeProvider provider = AuditLogService.get().getAuditProvider(type.getEventType()); diff --git a/audit/src/org/labkey/audit/query/AuditLogUpdateService.java b/audit/src/org/labkey/audit/query/AuditLogUpdateService.java index 94424f2e471..d528d2016d5 100644 --- a/audit/src/org/labkey/audit/query/AuditLogUpdateService.java +++ b/audit/src/org/labkey/audit/query/AuditLogUpdateService.java @@ -25,14 +25,10 @@ import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; import org.labkey.api.query.AbstractQueryUpdateService; -import org.labkey.api.query.DuplicateKeyException; import org.labkey.api.query.FieldKey; -import org.labkey.api.query.InvalidKeyException; -import org.labkey.api.query.QueryUpdateServiceException; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; -import java.sql.SQLException; import java.util.HashMap; import java.util.Map; diff --git a/bigiron/src/org/labkey/bigiron/mssql/BaseMicrosoftSqlServerDialect.java b/bigiron/src/org/labkey/bigiron/mssql/BaseMicrosoftSqlServerDialect.java index 5f71165ecf3..6f8778564d8 100644 --- a/bigiron/src/org/labkey/bigiron/mssql/BaseMicrosoftSqlServerDialect.java +++ b/bigiron/src/org/labkey/bigiron/mssql/BaseMicrosoftSqlServerDialect.java @@ -17,8 +17,9 @@ package org.labkey.bigiron.mssql; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -72,7 +73,7 @@ // Dialect specifics for Microsoft SQL Server abstract class BaseMicrosoftSqlServerDialect extends SqlDialect { - private static final Logger LOG = Logger.getLogger(BaseMicrosoftSqlServerDialect.class); + private static final Logger LOG = LogManager.getLogger(BaseMicrosoftSqlServerDialect.class); // SQLServer limits maximum index key size of 900 bytes private static final int MAX_INDEX_SIZE = 900; diff --git a/bigiron/src/org/labkey/bigiron/mssql/MicrosoftSqlServerDialectFactory.java b/bigiron/src/org/labkey/bigiron/mssql/MicrosoftSqlServerDialectFactory.java index bea8a24fe11..efd756ec434 100644 --- a/bigiron/src/org/labkey/bigiron/mssql/MicrosoftSqlServerDialectFactory.java +++ b/bigiron/src/org/labkey/bigiron/mssql/MicrosoftSqlServerDialectFactory.java @@ -16,7 +16,8 @@ package org.labkey.bigiron.mssql; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -47,7 +48,7 @@ */ public class MicrosoftSqlServerDialectFactory implements SqlDialectFactory { - private static final Logger LOG = Logger.getLogger(MicrosoftSqlServerDialectFactory.class); + private static final Logger LOG = LogManager.getLogger(MicrosoftSqlServerDialectFactory.class); public static final String PRODUCT_NAME = "Microsoft SQL Server"; private volatile TableResolver _tableResolver = new StandardTableResolver(); diff --git a/bigiron/src/org/labkey/bigiron/mysql/MySqlDialectFactory.java b/bigiron/src/org/labkey/bigiron/mysql/MySqlDialectFactory.java index 3468fb56b33..1590c79f29d 100644 --- a/bigiron/src/org/labkey/bigiron/mysql/MySqlDialectFactory.java +++ b/bigiron/src/org/labkey/bigiron/mysql/MySqlDialectFactory.java @@ -16,7 +16,8 @@ package org.labkey.bigiron.mysql; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.dialect.DatabaseNotSupportedException; import org.labkey.api.data.dialect.SqlDialect; @@ -35,7 +36,7 @@ */ public class MySqlDialectFactory implements SqlDialectFactory { - private static final Logger _log = Logger.getLogger(MySqlDialectFactory.class); + private static final Logger _log = LogManager.getLogger(MySqlDialectFactory.class); private String getProductName() { diff --git a/bigiron/src/org/labkey/bigiron/oracle/OracleDialectFactory.java b/bigiron/src/org/labkey/bigiron/oracle/OracleDialectFactory.java index 50113ec2cdd..55645d54fe8 100644 --- a/bigiron/src/org/labkey/bigiron/oracle/OracleDialectFactory.java +++ b/bigiron/src/org/labkey/bigiron/oracle/OracleDialectFactory.java @@ -16,7 +16,8 @@ package org.labkey.bigiron.oracle; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -44,7 +45,7 @@ */ public class OracleDialectFactory implements SqlDialectFactory { - private static final Logger _log = Logger.getLogger(OracleDialectFactory.class); + private static final Logger _log = LogManager.getLogger(OracleDialectFactory.class); private String getProductName() { diff --git a/bigiron/src/org/labkey/bigiron/oracle/OracleMetaDataConnectionPool.java b/bigiron/src/org/labkey/bigiron/oracle/OracleMetaDataConnectionPool.java index 900aa27c63c..aaf42ca75bb 100644 --- a/bigiron/src/org/labkey/bigiron/oracle/OracleMetaDataConnectionPool.java +++ b/bigiron/src/org/labkey/bigiron/oracle/OracleMetaDataConnectionPool.java @@ -17,7 +17,8 @@ import com.google.common.cache.Cache; import com.google.common.cache.CacheBuilder; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.ConnectionPool; import org.labkey.api.data.DbScope; import org.labkey.api.data.SqlSelector; @@ -34,7 +35,7 @@ public class OracleMetaDataConnectionPool extends ConnectionPool private int _openCursorsMax; private final DbScope _dbScope; private final int _openCursorTarget; - private static final Logger LOG = Logger.getLogger(OracleMetaDataConnectionPool.class); + private static final Logger LOG = LogManager.getLogger(OracleMetaDataConnectionPool.class); public OracleMetaDataConnectionPool(DbScope scope) { diff --git a/core/api-src/org/labkey/api/admin/HealthCheckRegistry.java b/core/api-src/org/labkey/api/admin/HealthCheckRegistry.java index df129354828..ebad58fb98f 100644 --- a/core/api-src/org/labkey/api/admin/HealthCheckRegistry.java +++ b/core/api-src/org/labkey/api/admin/HealthCheckRegistry.java @@ -1,21 +1,22 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import java.util.Collection; @@ -32,7 +33,7 @@ */ public class HealthCheckRegistry { - private static final Logger LOG = Logger.getLogger(HealthCheckRegistry.class); + private static final Logger LOG = LogManager.getLogger(HealthCheckRegistry.class); public static final String DEFAULT_CATEGORY = "default"; public static final String TRIAL_INSTANCES_CATEGORY = "trial"; diff --git a/core/api-src/org/labkey/api/admin/TableXmlUtils.java b/core/api-src/org/labkey/api/admin/TableXmlUtils.java index 6d7c07c2122..326d2f08d79 100644 --- a/core/api-src/org/labkey/api/admin/TableXmlUtils.java +++ b/core/api-src/org/labkey/api/admin/TableXmlUtils.java @@ -15,7 +15,8 @@ */ package org.labkey.api.admin; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.admin.sitevalidation.SiteValidationResult; import org.labkey.api.admin.sitevalidation.SiteValidationResultList; import org.labkey.api.data.DbSchema; @@ -38,7 +39,7 @@ */ public class TableXmlUtils { - private static final Logger _log = Logger.getLogger(TableXmlUtils.class); + private static final Logger _log = LogManager.getLogger(TableXmlUtils.class); // Careful: don't use DbSchema.get(), schema.getTable(), or schema.getTables() -- we don't want schema.xml applied // and we don't want to cache these TableInfos (because schema.xml hasn't been applied). @@ -516,7 +517,7 @@ private static void compareTableDocuments(TablesDocument dbTablesDoc, catch (Exception e) { rlOut.addError("ERROR: Exception in compare: ").append(e.getMessage()); - Logger.getLogger(TableXmlUtils.class).warn(e); + LogManager.getLogger(TableXmlUtils.class).warn(e); } } diff --git a/core/api-src/org/labkey/api/products/ProductRegistry.java b/core/api-src/org/labkey/api/products/ProductRegistry.java index b54a2a94ae9..4bf57590c35 100644 --- a/core/api-src/org/labkey/api/products/ProductRegistry.java +++ b/core/api-src/org/labkey/api/products/ProductRegistry.java @@ -15,7 +15,8 @@ */ package org.labkey.api.products; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.AfterClass; @@ -40,7 +41,7 @@ public class ProductRegistry { - private static final Logger _logger = Logger.getLogger(ProductRegistry.class); + private static final Logger _logger = LogManager.getLogger(ProductRegistry.class); private static final Map _productMap = new ConcurrentCaseInsensitiveSortedMap<>(); private static final Map _moduleProviderMap = new ConcurrentHashMap<>(); private static final Map _sectionMap = new ConcurrentCaseInsensitiveSortedMap<>(); diff --git a/core/resources/scripts/console.js b/core/resources/scripts/console.js index a2325a8df89..f288dfc3f2f 100644 --- a/core/resources/scripts/console.js +++ b/core/resources/scripts/console.js @@ -4,9 +4,9 @@ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 */ -var Logger = org.apache.log4j.Logger; +var LogManager = org.apache.logging.log4j.LogManager; -var logger = Logger.getLogger(org.labkey.api.script.ScriptService.Console); +var logger = LogManager.getLogger(org.labkey.api.script.ScriptService.Console); function formatPart(o) { diff --git a/core/src/org/labkey/core/CoreContainerListener.java b/core/src/org/labkey/core/CoreContainerListener.java index 78b24e6e353..ebd9d1265df 100644 --- a/core/src/org/labkey/core/CoreContainerListener.java +++ b/core/src/org/labkey/core/CoreContainerListener.java @@ -15,7 +15,8 @@ */ package org.labkey.core; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; @@ -44,7 +45,7 @@ */ public class CoreContainerListener implements ContainerManager.ContainerListener { - private static final Logger _log = Logger.getLogger(CoreContainerListener.class); + private static final Logger _log = LogManager.getLogger(CoreContainerListener.class); @Override public void containerCreated(Container c, User user) diff --git a/core/src/org/labkey/core/CoreController.java b/core/src/org/labkey/core/CoreController.java index 30ff0b6685d..3ea03ec1515 100644 --- a/core/src/org/labkey/core/CoreController.java +++ b/core/src/org/labkey/core/CoreController.java @@ -19,7 +19,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.fileupload.disk.DiskFileItem; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.json.JSONArray; @@ -28,6 +29,7 @@ import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.ApiUsageException; +import org.labkey.api.action.BaseApiAction; import org.labkey.api.action.ExportAction; import org.labkey.api.action.FormApiAction; import org.labkey.api.action.MutatingApiAction; @@ -208,7 +210,7 @@ public class CoreController extends SpringActionController { private static final Map _customStylesheetCache = new ConcurrentHashMap<>(); - private static final Logger _log = Logger.getLogger(CoreController.class); + private static final Logger _log = LogManager.getLogger(CoreController.class); private static ActionResolver _actionResolver = new DefaultActionResolver(CoreController.class); private static final PropertyStore _normalStore = PropertyManager.getNormalStore(); @@ -2638,4 +2640,89 @@ public ApiResponse execute(TransformWikiForm form, BindException errors) return response; } } + + @RequiresNoPermission + public class TestLoggerAction extends BaseApiAction + { + private String[] nouns = { "LabKey", "Beaker", "Lab", "San Diego", "Seattle", + "Server", "Java", "Science", "Maths" }; + + private String[] verbs = { "kept", "developed", "made", + "found", "coined" }; + + private String[] phrases = { "tech is cool", + "computers and corn", + "One or two things that money can't buy", + "that's true about home grown tomatoes", + "drove my chevy to the levy but the levy was dry", + "them good old boys were drinking whiskey and rye", + "we're waxing down out surf boards, we can't wait for June", + "tell the teacher we are surfing", + "it's a 59,60,61,62,63,64,65,66,67,68,69 automobile..", + "beers and horn" }; + + private Logger log = LogManager.getLogger(TestLoggerAction.class); + + void randomSentence() + { + for (int i=0; i<50; i++) + { + randomSimpleSentence(); + + if (Math.random() > 0.5) + { + log.info(" and "); + randomSimpleSentence(); + } + } + } + + void randomSimpleSentence() + { + if (Math.random() > 0.5) + { + log.info("the Bus Is Outta Control! "); + randomNounPhrase(); + } + else + log.info("these pretzels are making me thirsty"); + } + + void randomNounPhrase() + { + int n = (int)(Math.random()*nouns.length); + log.info(phrases[n]); + + if (Math.random() > 0.5) + { + int m = (int)(Math.random()*phrases.length); + log.info(" " + nouns[m]); + } + else + { + int v = (int) (Math.random() * verbs.length); + log.info(" that " + verbs[v] + " "); + } + + } + + + @Override + protected ModelAndView handleGet() + { + Runnable testThread = this::randomSentence; + + for (int i=0; i < 4000; i++) + { + (new Thread(testThread)).start(); + } + return null; + } + + @Override + public Object execute(Object o, BindException errors) throws Exception + { + return null; + } + } } diff --git a/core/src/org/labkey/core/CoreModule.java b/core/src/org/labkey/core/CoreModule.java index f5ae6cefdec..deccc2c95a1 100644 --- a/core/src/org/labkey/core/CoreModule.java +++ b/core/src/org/labkey/core/CoreModule.java @@ -17,9 +17,11 @@ import com.google.common.collect.Sets; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Appender; -import org.apache.log4j.Logger; -import org.apache.log4j.RollingFileAppender; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.core.Appender; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.appender.RollingFileAppender; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.AdminConsoleService; @@ -260,7 +262,7 @@ */ public class CoreModule extends SpringModule implements SearchService.DocumentProvider { - private static final Logger LOG = Logger.getLogger(CoreModule.class); + private static final Logger LOG = LogManager.getLogger(CoreModule.class); static { @@ -826,18 +828,10 @@ public void shutdownPre() { } - Logger logger = Logger.getLogger(ActionsTsvWriter.class); + Logger logger = LogManager.getLogger(ActionsTsvWriter.class); if (null != logger) { - LOG.info("Starting to log statistics for actions prior to web application shut down"); - Appender appender = logger.getAppender("ACTION_STATS"); - - if (appender instanceof RollingFileAppender) - ((RollingFileAppender)appender).rollOver(); - else - Logger.getLogger(CoreModule.class).warn("Could not rollover the action stats tsv file--there was no appender named ACTION_STATS, or it is not a RollingFileAppender."); - StringBuilder buf = new StringBuilder(); try (TSVWriter writer = new ActionsTsvWriter()) @@ -846,7 +840,7 @@ public void shutdownPre() } catch (IOException e) { - Logger.getLogger(CoreModule.class).error("Exception exporting action stats", e); + LogManager.getLogger(CoreModule.class).error("Exception exporting action stats", e); } logger.info(buf.toString()); diff --git a/core/src/org/labkey/core/CoreUpgradeCode.java b/core/src/org/labkey/core/CoreUpgradeCode.java index 34f89ff175c..01d1f71f9dc 100644 --- a/core/src/org/labkey/core/CoreUpgradeCode.java +++ b/core/src/org/labkey/core/CoreUpgradeCode.java @@ -15,7 +15,10 @@ */ package org.labkey.core; -import org.apache.log4j.Logger; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.SystemUtils; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.CoreSchema; @@ -67,7 +70,7 @@ */ public class CoreUpgradeCode implements UpgradeCode { - private static final Logger LOG = Logger.getLogger(CoreUpgradeCode.class); + private static final Logger LOG = LogManager.getLogger(CoreUpgradeCode.class); // We don't call ContainerManager.getRoot() during upgrade code since the container table may not yet match // ContainerManager's assumptions. For example, older installations don't have a description column until diff --git a/core/src/org/labkey/core/admin/AbstractFileSiteSettingsAction.java b/core/src/org/labkey/core/admin/AbstractFileSiteSettingsAction.java index 887af98b9cc..a70dcfba4aa 100644 --- a/core/src/org/labkey/core/admin/AbstractFileSiteSettingsAction.java +++ b/core/src/org/labkey/core/admin/AbstractFileSiteSettingsAction.java @@ -16,7 +16,8 @@ package org.labkey.core.admin; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.SpringActionController; import org.labkey.api.attachments.Attachment; @@ -54,7 +55,7 @@ */ public abstract class AbstractFileSiteSettingsAction extends FormViewAction { - private static Logger _log = Logger.getLogger(FilesSiteSettingsAction.class); + private static Logger _log = LogManager.getLogger(FilesSiteSettingsAction.class); protected FileContentService _svc = FileContentService.get(); public AbstractFileSiteSettingsAction(Class commandClass) diff --git a/core/src/org/labkey/core/admin/ActionsView.java b/core/src/org/labkey/core/admin/ActionsView.java index f46e1f607c4..947b1585fb9 100644 --- a/core/src/org/labkey/core/admin/ActionsView.java +++ b/core/src/org/labkey/core/admin/ActionsView.java @@ -19,11 +19,11 @@ import org.labkey.api.action.ActionType; import org.labkey.api.action.SpringActionController; import org.labkey.api.admin.ActionsHelper; +import org.labkey.api.data.ContainerManager; import org.labkey.api.util.Formats; import org.labkey.api.util.PageFlowUtil; -import org.labkey.api.view.HttpView; import org.labkey.api.view.ActionURL; -import org.labkey.api.data.ContainerManager; +import org.labkey.api.view.HttpView; import java.io.PrintWriter; import java.util.Map; diff --git a/core/src/org/labkey/core/admin/AdminController.java b/core/src/org/labkey/core/admin/AdminController.java index 16f49d84dce..476854a6822 100644 --- a/core/src/org/labkey/core/admin/AdminController.java +++ b/core/src/org/labkey/core/admin/AdminController.java @@ -22,9 +22,10 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; -import org.apache.log4j.spi.LoggingEvent; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LogEvent; import org.apache.xmlbeans.XmlOptions; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -282,9 +283,9 @@ public class AdminController extends SpringActionController FileListAction.class ); - private static final Logger LOG = Logger.getLogger(AdminController.class); + private static final Logger LOG = LogManager.getLogger(AdminController.class); @SuppressWarnings("LoggerInitializedWithForeignClass") - private static final Logger CLIENT_LOG = Logger.getLogger(LogAction.class); + private static final Logger CLIENT_LOG = LogManager.getLogger(LogAction.class); private static final String HEAP_MEMORY_KEY = "Total Heap Memory"; private static long _errorMark = 0; @@ -4321,7 +4322,7 @@ public boolean handlePost(ExportFolderForm form, BindException errors) throws Ex FolderWriterImpl writer = new FolderWriterImpl(); FolderExportContext ctx = new FolderExportContext(getUser(), container, PageFlowUtil.set(form.getTypes()), form.getFormat(), form.isIncludeSubfolders(), form.getExportPhiLevel(), form.isShiftDates(), - form.isAlternateIds(), form.isMaskClinic(), new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class))); + form.isAlternateIds(), form.isMaskClinic(), new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class))); switch(form.getLocation()) { @@ -4566,7 +4567,7 @@ public boolean handlePost(ImportFolderForm form, BindException errors) throws Ex // the source template folder so that the zip file can be passed to the pipeline processes. FolderExportContext ctx = new FolderExportContext(getUser(), sourceContainer, getRegisteredFolderWritersForImplicitExport(sourceContainer), "new", false, - PHI.NotPHI, false, false, false, new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class))); + PHI.NotPHI, false, false, false, new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class))); FolderWriterImpl writer = new FolderWriterImpl(); String zipFileName = FileUtil.makeFileNameWithTimestamp(sourceContainer.getName(), "folder.zip"); try (ZipFile zip = new ZipFile(pipelineUnzipDir, zipFileName)) @@ -6759,7 +6760,7 @@ else if (!sourceContainer.hasEnableRestrictedModules(getUser()) && sourceContain FolderExportContext exportCtx = new FolderExportContext(getUser(), sourceContainer, PageFlowUtil.set(form.getTemplateWriterTypes()), "new", form.getTemplateIncludeSubfolders(), PHI.NotPHI, false, false, false, - new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class))); + new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class))); c = ContainerManager.createContainerFromTemplate(parent, folderName, folderTitle, sourceContainer, getUser(), exportCtx); } @@ -7627,17 +7628,18 @@ public ApiResponse execute(Object o, BindException errors) eventId = Integer.parseInt(s); } catch (NumberFormatException x) {} - LoggingEvent[] events = SessionAppender.getLoggingEvents(getViewContext().getRequest()); - ArrayList> list = new ArrayList<>(events.length); - for (LoggingEvent e : events) + Map events = SessionAppender.getLoggingEvents(getViewContext().getRequest()); + ArrayList> list = new ArrayList<>(events.size()); + for (Map.Entry entry : events.entrySet()) { - if (eventId==0 || eventId m = new HashMap<>(); - m.put("eventId", e.getProperty("eventId")); + m.put("eventId", entry.getValue()); m.put("level", e.getLevel().toString()); - m.put("message", e.getMessage()); - m.put("timestamp", new Date(e.getTimeStamp())); + m.put("message", e.getMessage().getFormattedMessage()); + m.put("timestamp", new Date(e.getTimeMillis())); list.add(m); } } @@ -7753,10 +7755,10 @@ public boolean handlePost(LoggingForm form, BindException errors) if (form.logging != on) { if (!form.logging) - Logger.getLogger(AdminController.class).info("turn session logging OFF"); + LogManager.getLogger(AdminController.class).info("turn session logging OFF"); SessionAppender.setLoggingForSession(getViewContext().getRequest(), form.logging); if (form.logging) - Logger.getLogger(AdminController.class).info("turn session logging ON"); + LogManager.getLogger(AdminController.class).info("turn session logging ON"); } return true; } diff --git a/core/src/org/labkey/core/admin/CopyFileRootPipelineJob.java b/core/src/org/labkey/core/admin/CopyFileRootPipelineJob.java index 1e6a385cebb..6c12ce2052b 100644 --- a/core/src/org/labkey/core/admin/CopyFileRootPipelineJob.java +++ b/core/src/org/labkey/core/admin/CopyFileRootPipelineJob.java @@ -19,7 +19,8 @@ import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.junit.Test; import org.labkey.api.data.Container; @@ -492,7 +493,7 @@ public List compareJobs(PipelineJob job2) public static class TestCase extends PipelineJob.TestSerialization { - private static Logger LOG = Logger.getLogger(CopyFileRootPipelineJob.class); + private static Logger LOG = LogManager.getLogger(CopyFileRootPipelineJob.class); @Test public void testSerialize() diff --git a/core/src/org/labkey/core/admin/addNewExternalRedirectHost.jsp b/core/src/org/labkey/core/admin/addNewExternalRedirectHost.jsp index c90b4aad41d..c375ceaed50 100644 --- a/core/src/org/labkey/core/admin/addNewExternalRedirectHost.jsp +++ b/core/src/org/labkey/core/admin/addNewExternalRedirectHost.jsp @@ -1,6 +1,6 @@ +<%@ page import="org.labkey.api.admin.AdminUrls" %> <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.security.permissions.AdminOperationsPermission" %> -<%@ page import="org.labkey.api.admin.AdminUrls" %> <% /* * Copyright (c) 2019 LabKey Corporation diff --git a/core/src/org/labkey/core/admin/importer/FolderTypeImporterFactory.java b/core/src/org/labkey/core/admin/importer/FolderTypeImporterFactory.java index 5e85620c9fc..b2d671307ae 100644 --- a/core/src/org/labkey/core/admin/importer/FolderTypeImporterFactory.java +++ b/core/src/org/labkey/core/admin/importer/FolderTypeImporterFactory.java @@ -17,8 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.data.Container; diff --git a/core/src/org/labkey/core/admin/importer/ModulePropertiesImporterFactory.java b/core/src/org/labkey/core/admin/importer/ModulePropertiesImporterFactory.java index d2a6d6189f3..24fd0b1fc31 100644 --- a/core/src/org/labkey/core/admin/importer/ModulePropertiesImporterFactory.java +++ b/core/src/org/labkey/core/admin/importer/ModulePropertiesImporterFactory.java @@ -17,8 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.module.Module; diff --git a/core/src/org/labkey/core/admin/importer/PageImporterFactory.java b/core/src/org/labkey/core/admin/importer/PageImporterFactory.java index 4f9a1806ea4..dba600145f8 100644 --- a/core/src/org/labkey/core/admin/importer/PageImporterFactory.java +++ b/core/src/org/labkey/core/admin/importer/PageImporterFactory.java @@ -18,10 +18,9 @@ import org.apache.commons.lang3.StringUtils; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.admin.InvalidFileException; diff --git a/core/src/org/labkey/core/admin/importer/SearchSettingsImporterFactory.java b/core/src/org/labkey/core/admin/importer/SearchSettingsImporterFactory.java index 650f4e5351c..db364d30924 100644 --- a/core/src/org/labkey/core/admin/importer/SearchSettingsImporterFactory.java +++ b/core/src/org/labkey/core/admin/importer/SearchSettingsImporterFactory.java @@ -17,8 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.data.Container; diff --git a/core/src/org/labkey/core/admin/importer/SecurityGroupImporterFactory.java b/core/src/org/labkey/core/admin/importer/SecurityGroupImporterFactory.java index 8ae7ec36f08..801ed571c9a 100644 --- a/core/src/org/labkey/core/admin/importer/SecurityGroupImporterFactory.java +++ b/core/src/org/labkey/core/admin/importer/SecurityGroupImporterFactory.java @@ -18,13 +18,13 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobWarning; -import org.labkey.api.security.*; +import org.labkey.api.security.GroupManager; import org.labkey.api.security.SecurityManager; import org.labkey.api.writer.VirtualFile; import org.labkey.folder.xml.FolderDocument; diff --git a/core/src/org/labkey/core/admin/logger/LoggerController.java b/core/src/org/labkey/core/admin/logger/LoggerController.java index 4f300cbb716..008ad46a00b 100644 --- a/core/src/org/labkey/core/admin/logger/LoggerController.java +++ b/core/src/org/labkey/core/admin/logger/LoggerController.java @@ -16,11 +16,13 @@ package org.labkey.core.admin.logger; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Category; -import org.apache.log4j.Level; -import org.apache.log4j.LogManager; -import org.apache.log4j.Logger; -import org.apache.log4j.xml.DOMConfigurator; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.Configuration; +import org.apache.logging.log4j.core.config.Configurator; +import org.apache.logging.log4j.core.config.LoggerConfig; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.Marshal; import org.labkey.api.action.Marshaller; @@ -46,10 +48,11 @@ import org.springframework.validation.Errors; import org.springframework.web.servlet.ModelAndView; -import java.net.URL; -import java.util.ArrayList; +import java.net.URISyntaxException; import java.util.Collection; -import java.util.Enumeration; +import java.util.HashSet; +import java.util.Objects; +import java.util.Set; /** * User: kevink @@ -60,7 +63,7 @@ public class LoggerController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(LoggerController.class); - private static final Logger LOG = Logger.getLogger(LoggerController.class); + private static final Logger LOG = LogManager.getLogger(LoggerController.class); public static void registerAdminConsoleLinks() { @@ -81,17 +84,30 @@ public static class LoggerLevel private String level; private boolean inherited; + public static LoggerLevel fromLoggerConfig(LoggerConfig log) + { + LoggerConfig parent = log.getParent(); + String parentName = parent != null ? parent.getName() : ""; + + return getLoggerLevel(parentName, log.getLevel(), log.getName()); + } + public static LoggerLevel fromLogger(Logger log) { - Category parent = log.getParent(); - Level level = log.getLevel(); - Level effectiveLevel = log.getEffectiveLevel(); + Logger parent = ((org.apache.logging.log4j.core.Logger) log).getParent(); + String parentName = parent != null ? parent.getName() : null; + return getLoggerLevel(parentName, log.getLevel(), log.getName()); + } + + private static LoggerLevel getLoggerLevel(String parent, Level level, String name) + { LoggerLevel loggerLevel = new LoggerLevel(); - loggerLevel.setName(log.getName()); - loggerLevel.setParent(parent != null ? parent.getName() : null); - loggerLevel.setLevel(level != null ? level.toString() : effectiveLevel.toString()); - loggerLevel.setInherited(level == null); + loggerLevel.setName(name); + loggerLevel.setParent(parent); + loggerLevel.setLevel(level.toString()); + boolean inherited = parent != null && !parent.equalsIgnoreCase(name); + loggerLevel.setInherited(inherited); return loggerLevel; } @@ -134,6 +150,24 @@ public void setInherited(boolean inherited) { this.inherited = inherited; } + + @Override + public boolean equals(Object o) + { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + LoggerLevel that = (LoggerLevel) o; + return inherited == that.inherited && + name.equals(that.name) && + Objects.equals(parent, that.parent) && + level.equals(that.level); + } + + @Override + public int hashCode() + { + return Objects.hash(name, parent, level, inherited); + } } public static class ListFilter @@ -179,38 +213,53 @@ public class ListAction extends ReadOnlyApiAction @Override public SimpleResponse> execute(ListFilter filter, BindException errors) { - Level filterLevel = filter.getLevel() != null ? Level.toLevel(filter.getLevel()) : null; + Set loggers = new HashSet<>(); + LoggerContext loggerContext = (LoggerContext) LogManager.getContext(false); + Configuration configuration = loggerContext.getConfiguration(); - Collection loggers = new ArrayList<>(); - Enumeration currentLoggers = (Enumeration) LogManager.getCurrentLoggers(); - while (currentLoggers.hasMoreElements()) + Collection currentLoggers = loggerContext.getLoggers(); + Collection loggerConfigs = configuration.getLoggers().values(); + + for (LoggerConfig currentLogger: loggerConfigs) { - Logger log = currentLoggers.nextElement(); - if (!filter.isInherited() && log.getLevel() == null) + if (filterCheck(filter, currentLogger.getLevel(), currentLogger.getName())) continue; - if (filterLevel != null && !(filterLevel.equals(log.getLevel()) || filterLevel.equals(log.getEffectiveLevel()))) - continue; + loggers.add(LoggerLevel.fromLoggerConfig(currentLogger)); + } - if (filter.getContains() != null && !StringUtils.containsIgnoreCase(log.getName(), filter.getContains())) + for (Logger currentLogger: currentLoggers) + { + if (filterCheck(filter, currentLogger.getLevel(), currentLogger.getName())) continue; - loggers.add(LoggerLevel.fromLogger(log)); + loggers.add(LoggerLevel.fromLogger(currentLogger)); } return success(loggers); } + + private boolean filterCheck(ListFilter filter, Level level, String loggerName) + { + Level filterLevel = filter.getLevel() != null ? Level.toLevel(filter.getLevel()) : null; + + if (!filter.isInherited() && level == null) + return true; + + if (filterLevel != null && !(filterLevel.equals(level))) + return true; + + return filter.getContains() != null && !StringUtils.containsIgnoreCase(loggerName, filter.getContains()); + } } @RequiresPermission(AdminOperationsPermission.class) public class ResetAction extends MutatingApiAction { @Override - public SimpleResponse execute(Object o, BindException errors) + public SimpleResponse execute(Object o, BindException errors) throws URISyntaxException { - LogManager.resetConfiguration(); - URL url = getClass().getResource("/log4j.xml"); - DOMConfigurator.configure(url); + ((org.apache.logging.log4j.core.LoggerContext) LogManager.getContext(false)).reconfigure(); return success(); } } @@ -228,7 +277,7 @@ public SimpleResponse execute(LoggerLevel loggerLevel, BindExceptio // Update the logger level if (loggerLevel.level != null && (logger.getLevel() == null || !loggerLevel.level.equals(logger.getLevel().toString()))) { - logger.setLevel(Level.toLevel(loggerLevel.level)); + Configurator.setLevel(logger.getName(), Level.toLevel(loggerLevel.level)); } return success(LoggerLevel.fromLogger(logger)); diff --git a/core/src/org/labkey/core/admin/manageConcepts.jsp b/core/src/org/labkey/core/admin/manageConcepts.jsp index 3444d7f8a4a..0050954d51b 100644 --- a/core/src/org/labkey/core/admin/manageConcepts.jsp +++ b/core/src/org/labkey/core/admin/manageConcepts.jsp @@ -18,7 +18,6 @@ <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ page import="org.labkey.api.exp.property.Lookup" %> <%@ page import="org.labkey.api.settings.ConceptURIProperties" %> -<%@ page import="org.labkey.api.util.URLHelper" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.api.view.template.FrameFactoryClassic" %> <%@ page import="java.util.Map" %> diff --git a/core/src/org/labkey/core/admin/mapNetworkDrive.jsp b/core/src/org/labkey/core/admin/mapNetworkDrive.jsp index 67cff7d62be..a7cd1736e40 100644 --- a/core/src/org/labkey/core/admin/mapNetworkDrive.jsp +++ b/core/src/org/labkey/core/admin/mapNetworkDrive.jsp @@ -16,12 +16,12 @@ */ %> <%@ page import="org.labkey.api.security.permissions.AdminOperationsPermission" %> +<%@ page import="org.labkey.api.settings.NetworkDriveProps" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.core.admin.AdminController" %> <%@ page import="org.labkey.core.admin.FilesSiteSettingsAction" %> -<%@ page import="org.labkey.api.settings.NetworkDriveProps" %> <%@ page extends="org.labkey.api.jsp.FormPage" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> diff --git a/core/src/org/labkey/core/admin/miniprofiler/MiniProfilerController.java b/core/src/org/labkey/core/admin/miniprofiler/MiniProfilerController.java index 33facb2882b..52f69e49531 100644 --- a/core/src/org/labkey/core/admin/miniprofiler/MiniProfilerController.java +++ b/core/src/org/labkey/core/admin/miniprofiler/MiniProfilerController.java @@ -16,7 +16,8 @@ package org.labkey.core.admin.miniprofiler; import com.fasterxml.jackson.annotation.JsonIgnoreProperties; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.FormHandlerAction; import org.labkey.api.action.FormViewAction; import org.labkey.api.action.IgnoresAllocationTracking; @@ -58,7 +59,7 @@ public class MiniProfilerController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(MiniProfilerController.class); - private static final Logger LOG = Logger.getLogger(MiniProfilerController.class); + private static final Logger LOG = LogManager.getLogger(MiniProfilerController.class); public MiniProfilerController() { diff --git a/core/src/org/labkey/core/admin/properties.jsp b/core/src/org/labkey/core/admin/properties.jsp index a5975192540..66643815b8b 100644 --- a/core/src/org/labkey/core/admin/properties.jsp +++ b/core/src/org/labkey/core/admin/properties.jsp @@ -16,10 +16,10 @@ */ %> <%@ page import="org.labkey.api.collections.CaseInsensitiveTreeMap" %> +<%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView> me = (JspView>) HttpView.currentView(); diff --git a/core/src/org/labkey/core/admin/reorderFolders.jsp b/core/src/org/labkey/core/admin/reorderFolders.jsp index 2ec8d71da9e..84ce22b18a1 100644 --- a/core/src/org/labkey/core/admin/reorderFolders.jsp +++ b/core/src/org/labkey/core/admin/reorderFolders.jsp @@ -15,13 +15,13 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.admin.AdminUrls" %> +<%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.api.view.ViewContext" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.data.Container" %> -<%@ page import="java.util.List" %> -<%@ page import="org.labkey.api.admin.AdminUrls" %> +<%@ page import="org.labkey.api.view.ViewContext" %> <%@ page import="org.labkey.core.admin.AdminController" %> +<%@ page import="java.util.List" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/core/src/org/labkey/core/admin/testNetworkDrive.jsp b/core/src/org/labkey/core/admin/testNetworkDrive.jsp index bf9d792a71b..456fc7c8c36 100644 --- a/core/src/org/labkey/core/admin/testNetworkDrive.jsp +++ b/core/src/org/labkey/core/admin/testNetworkDrive.jsp @@ -16,8 +16,8 @@ */ %> <%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.core.admin.TestNetworkDriveBean" %> <%@ page import="org.labkey.api.view.JspView" %> +<%@ page import="org.labkey.core.admin.TestNetworkDriveBean" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% diff --git a/core/src/org/labkey/core/admin/usageMetrics/UsageMetricsServiceImpl.java b/core/src/org/labkey/core/admin/usageMetrics/UsageMetricsServiceImpl.java index 28a0ff9d588..28ad53ff8c1 100644 --- a/core/src/org/labkey/core/admin/usageMetrics/UsageMetricsServiceImpl.java +++ b/core/src/org/labkey/core/admin/usageMetrics/UsageMetricsServiceImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.core.admin.usageMetrics; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.ConcurrentHashSet; import org.labkey.api.usageMetrics.UsageMetricsProvider; @@ -36,7 +37,7 @@ */ public class UsageMetricsServiceImpl implements UsageMetricsService { - private static Logger LOG = Logger.getLogger(UsageMetricsServiceImpl.class); + private static Logger LOG = LogManager.getLogger(UsageMetricsServiceImpl.class); private final Map>> moduleUsageReports = new ConcurrentHashMap<>(); diff --git a/core/src/org/labkey/core/admin/writer/FolderTypeWriterFactory.java b/core/src/org/labkey/core/admin/writer/FolderTypeWriterFactory.java index 8ad17d930e1..232d95a525c 100644 --- a/core/src/org/labkey/core/admin/writer/FolderTypeWriterFactory.java +++ b/core/src/org/labkey/core/admin/writer/FolderTypeWriterFactory.java @@ -16,9 +16,9 @@ package org.labkey.core.admin.writer; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.module.Module; diff --git a/core/src/org/labkey/core/admin/writer/ModulePropertiesWriterFactory.java b/core/src/org/labkey/core/admin/writer/ModulePropertiesWriterFactory.java index afc2b9fb0c1..8a765dd90d2 100644 --- a/core/src/org/labkey/core/admin/writer/ModulePropertiesWriterFactory.java +++ b/core/src/org/labkey/core/admin/writer/ModulePropertiesWriterFactory.java @@ -17,9 +17,9 @@ import org.apache.commons.lang3.StringUtils; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.module.Module; diff --git a/core/src/org/labkey/core/admin/writer/SearchSettingsWriterFactory.java b/core/src/org/labkey/core/admin/writer/SearchSettingsWriterFactory.java index 9239750c58d..a155c045181 100644 --- a/core/src/org/labkey/core/admin/writer/SearchSettingsWriterFactory.java +++ b/core/src/org/labkey/core/admin/writer/SearchSettingsWriterFactory.java @@ -16,9 +16,9 @@ package org.labkey.core.admin.writer; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.writer.VirtualFile; diff --git a/core/src/org/labkey/core/analytics/AnalyticsServiceImpl.java b/core/src/org/labkey/core/analytics/AnalyticsServiceImpl.java index 46fbd32404d..9509652f6a6 100644 --- a/core/src/org/labkey/core/analytics/AnalyticsServiceImpl.java +++ b/core/src/org/labkey/core/analytics/AnalyticsServiceImpl.java @@ -16,7 +16,8 @@ package org.labkey.core.analytics; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.analytics.AnalyticsService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -243,7 +244,7 @@ static public void populateSettingsWithStartupProps() } catch (IllegalArgumentException ex) { - Logger.getLogger(AnalyticsServiceImpl.class).warn("error handling startup property", ex); + LogManager.getLogger(AnalyticsServiceImpl.class).warn("error handling startup property", ex); } }); properties.save(); diff --git a/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java b/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java index 556c41db517..d8606dd4193 100644 --- a/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java +++ b/core/src/org/labkey/core/dialect/PostgreSqlDialectFactory.java @@ -17,7 +17,8 @@ package org.labkey.core.dialect; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -46,7 +47,7 @@ */ public class PostgreSqlDialectFactory implements SqlDialectFactory { - private static final Logger _log = Logger.getLogger(PostgreSqlDialectFactory.class); + private static final Logger _log = LogManager.getLogger(PostgreSqlDialectFactory.class); @Override public @Nullable SqlDialect createFromDriverClassName(String driverClassName) diff --git a/core/src/org/labkey/core/junit/JunitController.java b/core/src/org/labkey/core/junit/JunitController.java index ec282e7ed5f..3a9d7822510 100644 --- a/core/src/org/labkey/core/junit/JunitController.java +++ b/core/src/org/labkey/core/junit/JunitController.java @@ -19,7 +19,13 @@ import org.apache.commons.collections4.IteratorUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.FastDateFormat; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.Configuration; +import org.apache.logging.log4j.core.config.LoggerConfig; +import org.apache.logging.log4j.core.layout.PatternLayout; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONObject; @@ -345,9 +351,12 @@ private JunitRunnable(List testClasses, List re { _testClasses = testClasses; _results = results; - _appender = new StatusAppender(); - _log = Logger.getLogger(JunitRunnable.class); - _log.addAppender(_appender); + _appender = new StatusAppender("StatusAppender", null, PatternLayout.createDefaultLayout(), false, null); + _log = LogManager.getLogger(JunitRunnable.class); + LoggerContext loggerContext = (LoggerContext) LogManager.getContext(true); + Configuration configuration = loggerContext.getConfiguration(); + LoggerConfig loggerConfig = configuration.getLoggerConfig(_log.getName()); + loggerConfig.addAppender(_appender, Level.toLevel(_log.getLevel().toString()), null); TestContext.setTestContext(request, user); } diff --git a/core/src/org/labkey/core/junit/JunitRunner.java b/core/src/org/labkey/core/junit/JunitRunner.java index 6dee25e7d69..f53baebb5d0 100644 --- a/core/src/org/labkey/core/junit/JunitRunner.java +++ b/core/src/org/labkey/core/junit/JunitRunner.java @@ -17,7 +17,8 @@ package org.labkey.core.junit; import junit.framework.TestCase; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.junit.runner.Description; import org.junit.runner.JUnitCore; import org.junit.runner.Request; @@ -40,7 +41,7 @@ */ public class JunitRunner { - private static final Logger LOG = Logger.getLogger(JunitRunner.class); + private static final Logger LOG = LogManager.getLogger(JunitRunner.class); public static class RunnerResult { diff --git a/core/src/org/labkey/core/login/DbLoginAuthenticationProvider.java b/core/src/org/labkey/core/login/DbLoginAuthenticationProvider.java index 8df93b6b512..f2a1e801a91 100644 --- a/core/src/org/labkey/core/login/DbLoginAuthenticationProvider.java +++ b/core/src/org/labkey/core/login/DbLoginAuthenticationProvider.java @@ -15,7 +15,8 @@ */ package org.labkey.core.login; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -154,7 +155,7 @@ public boolean test(HttpServletRequest httpServletRequest) int c = _count.incrementAndGet(); if (c % 10 == 0) - Logger.getLogger(DbLoginAuthenticationProvider.class).info(c + " requests"); + LogManager.getLogger(DbLoginAuthenticationProvider.class).info(c + " requests"); return c % 100 != 0; } diff --git a/core/src/org/labkey/core/login/LoginController.java b/core/src/org/labkey/core/login/LoginController.java index 7093b0c5c5d..2cde46c9e04 100644 --- a/core/src/org/labkey/core/login/LoginController.java +++ b/core/src/org/labkey/core/login/LoginController.java @@ -17,7 +17,8 @@ package org.labkey.core.login; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -145,7 +146,7 @@ */ public class LoginController extends SpringActionController { - private static final Logger _log = Logger.getLogger(LoginController.class); + private static final Logger _log = LogManager.getLogger(LoginController.class); private static final ActionResolver _actionResolver = new DefaultActionResolver(LoginController.class); public LoginController() diff --git a/core/src/org/labkey/core/login/PasswordRule.java b/core/src/org/labkey/core/login/PasswordRule.java index b116344f1f4..07e92194ad5 100644 --- a/core/src/org/labkey/core/login/PasswordRule.java +++ b/core/src/org/labkey/core/login/PasswordRule.java @@ -16,7 +16,8 @@ package org.labkey.core.login; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.security.SecurityManager; @@ -345,6 +346,6 @@ public static void testWeakPasswords() strong++; } - Logger.getLogger(PasswordRule.class).info("Total number: " + passwords.length + " Allowed by Weak: " + weak + " Allowed by Strong: " + strong); + LogManager.getLogger(PasswordRule.class).info("Total number: " + passwords.length + " Allowed by Weak: " + weak + " Allowed by Strong: " + strong); } } diff --git a/core/src/org/labkey/core/notification/EmailServiceImpl.java b/core/src/org/labkey/core/notification/EmailServiceImpl.java index 1f4a611f27f..6813be99ec0 100644 --- a/core/src/org/labkey/core/notification/EmailServiceImpl.java +++ b/core/src/org/labkey/core/notification/EmailServiceImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.core.notification; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Rule; @@ -72,7 +73,7 @@ */ public class EmailServiceImpl implements EmailService { - private static final Logger _log = Logger.getLogger(EmailService.class); + private static final Logger _log = LogManager.getLogger(EmailService.class); private static final String EMAIL_PREF_CATEGORY = "EmailService.emailPrefs"; @Override diff --git a/core/src/org/labkey/core/notification/NotificationEndpoint.java b/core/src/org/labkey/core/notification/NotificationEndpoint.java index d26d7f609da..3bdd81207d8 100644 --- a/core/src/org/labkey/core/notification/NotificationEndpoint.java +++ b/core/src/org/labkey/core/notification/NotificationEndpoint.java @@ -17,7 +17,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.security.User; import org.labkey.api.util.MemTracker; @@ -45,7 +46,7 @@ @ServerEndpoint(value="/_websocket/notifications", configurator=NotificationEndpoint.Configurator.class) public class NotificationEndpoint extends Endpoint { - static final Logger LOG = Logger.getLogger(NotificationEndpoint.class); + static final Logger LOG = LogManager.getLogger(NotificationEndpoint.class); static final MultiValuedMap endpointsMap = new ArrayListValuedHashMap<>(); private Session session; diff --git a/core/src/org/labkey/core/portal/ProjectController.java b/core/src/org/labkey/core/portal/ProjectController.java index b468726cc5b..a2e2dc19378 100644 --- a/core/src/org/labkey/core/portal/ProjectController.java +++ b/core/src/org/labkey/core/portal/ProjectController.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.IteratorUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.Action; import org.labkey.api.action.ActionType; @@ -109,7 +110,7 @@ public class ProjectController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ProjectController.class); - private static final Logger _log = Logger.getLogger(ProjectController.class); + private static final Logger _log = LogManager.getLogger(ProjectController.class); public static class ProjectUrlsImpl implements ProjectUrls { diff --git a/core/src/org/labkey/core/portal/UtilController.java b/core/src/org/labkey/core/portal/UtilController.java index 645f6a5c274..cc4d3dbc496 100644 --- a/core/src/org/labkey/core/portal/UtilController.java +++ b/core/src/org/labkey/core/portal/UtilController.java @@ -15,7 +15,8 @@ */ package org.labkey.core.portal; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.SimpleViewAction; import org.labkey.api.action.SpringActionController; import org.labkey.api.security.RequiresPermission; @@ -41,7 +42,7 @@ public class UtilController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(UtilController.class); - private static final Logger _log = Logger.getLogger(ProjectController.class); + private static final Logger _log = LogManager.getLogger(ProjectController.class); public UtilController() { diff --git a/core/src/org/labkey/core/products/ProductController.java b/core/src/org/labkey/core/products/ProductController.java index d701fe77955..f38d7ebcab9 100644 --- a/core/src/org/labkey/core/products/ProductController.java +++ b/core/src/org/labkey/core/products/ProductController.java @@ -16,7 +16,8 @@ package org.labkey.core.products; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.Marshal; import org.labkey.api.action.Marshaller; import org.labkey.api.action.ReadOnlyApiAction; @@ -36,7 +37,7 @@ public class ProductController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ProductController.class); - private static final Logger _log = Logger.getLogger(ProductController.class); + private static final Logger _log = LogManager.getLogger(ProductController.class); public ProductController() { diff --git a/core/src/org/labkey/core/query/UsersTable.java b/core/src/org/labkey/core/query/UsersTable.java index 7e7bb2dcd5a..ec78581bb43 100644 --- a/core/src/org/labkey/core/query/UsersTable.java +++ b/core/src/org/labkey/core/query/UsersTable.java @@ -15,7 +15,8 @@ */ package org.labkey.core.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.SpringAttachmentFile; @@ -109,7 +110,7 @@ public class UsersTable extends SimpleUserSchema.SimpleTable FieldKey.fromParts("DisplayName"))); } - private final static Logger LOG = Logger.getLogger(UsersTable.class); + private final static Logger LOG = LogManager.getLogger(UsersTable.class); public UsersTable(UserSchema schema, TableInfo table) { diff --git a/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java b/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java index 674e32bfec8..f8c8e93e07a 100644 --- a/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java +++ b/core/src/org/labkey/core/reader/DataLoaderServiceImpl.java @@ -19,7 +19,8 @@ import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -52,7 +53,7 @@ */ public class DataLoaderServiceImpl implements DataLoaderService { - private static final Logger _log = Logger.getLogger(DataLoaderService.class); + private static final Logger _log = LogManager.getLogger(DataLoaderService.class); private Map _fileTypeToFactory; private MultiValuedMap _extensionToFactory; diff --git a/core/src/org/labkey/core/reports/ScriptEngineManagerImpl.java b/core/src/org/labkey/core/reports/ScriptEngineManagerImpl.java index 3c69a56c75e..5a9560ca527 100644 --- a/core/src/org/labkey/core/reports/ScriptEngineManagerImpl.java +++ b/core/src/org/labkey/core/reports/ScriptEngineManagerImpl.java @@ -20,7 +20,8 @@ import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -79,7 +80,7 @@ */ public class ScriptEngineManagerImpl extends ScriptEngineManager implements LabkeyScriptEngineManager { - private static final Logger LOG = Logger.getLogger(ScriptEngineManagerImpl.class); + private static final Logger LOG = LogManager.getLogger(ScriptEngineManagerImpl.class); public static final String SCRIPT_ENGINE_MAP = "ExternalScriptEngineMap"; private static final String ENGINE_DEF_MAP_PREFIX = "ScriptEngineDefinition_"; diff --git a/core/src/org/labkey/core/thumbnail/ThumbnailServiceImpl.java b/core/src/org/labkey/core/thumbnail/ThumbnailServiceImpl.java index c7d4af0a48d..d5b2480e7ac 100644 --- a/core/src/org/labkey/core/thumbnail/ThumbnailServiceImpl.java +++ b/core/src/org/labkey/core/thumbnail/ThumbnailServiceImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.core.thumbnail; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentFile; import org.labkey.api.attachments.AttachmentService; @@ -43,7 +44,7 @@ */ public class ThumbnailServiceImpl implements ThumbnailService { - private static final Logger LOG = Logger.getLogger(ThumbnailServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(ThumbnailServiceImpl.class); private static final BlockingQueue QUEUE = new LinkedBlockingQueue<>(1000); private static final ThumbnailGeneratingThread THREAD = new ThumbnailGeneratingThread(); diff --git a/core/src/org/labkey/core/user/DeactivateUsersBean.java b/core/src/org/labkey/core/user/DeactivateUsersBean.java index f0f152f08e9..7ea188e05aa 100644 --- a/core/src/org/labkey/core/user/DeactivateUsersBean.java +++ b/core/src/org/labkey/core/user/DeactivateUsersBean.java @@ -18,7 +18,9 @@ import org.labkey.api.security.User; import org.labkey.api.view.ActionURL; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; /* * User: Dave diff --git a/core/src/org/labkey/core/user/DeleteUsersBean.java b/core/src/org/labkey/core/user/DeleteUsersBean.java index 12fbe65b099..99072994687 100644 --- a/core/src/org/labkey/core/user/DeleteUsersBean.java +++ b/core/src/org/labkey/core/user/DeleteUsersBean.java @@ -18,9 +18,9 @@ import org.labkey.api.security.User; import org.labkey.api.view.ActionURL; -import java.util.List; import java.util.ArrayList; import java.util.Collections; +import java.util.List; /* * User: Dave diff --git a/core/src/org/labkey/core/user/toggleInactive.jsp b/core/src/org/labkey/core/user/toggleInactive.jsp index e794e2d9b1d..6442c29e3a7 100644 --- a/core/src/org/labkey/core/user/toggleInactive.jsp +++ b/core/src/org/labkey/core/user/toggleInactive.jsp @@ -15,10 +15,10 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.view.HttpView" %> +<%@ page import="org.labkey.api.security.AuthenticationManager" %> <%@ page import="org.labkey.api.view.ActionURL" %> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.core.user.UserController" %> -<%@ page import="org.labkey.api.security.AuthenticationManager" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% String inactiveCaption; diff --git a/core/src/org/labkey/core/user/toggleShowAll.jsp b/core/src/org/labkey/core/user/toggleShowAll.jsp index 28a1585e9e3..f88820f2c18 100644 --- a/core/src/org/labkey/core/user/toggleShowAll.jsp +++ b/core/src/org/labkey/core/user/toggleShowAll.jsp @@ -15,8 +15,8 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.ActionURL" %> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.core.security.SecurityController" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/core/src/org/labkey/core/vcs/VcsServiceImpl.java b/core/src/org/labkey/core/vcs/VcsServiceImpl.java index 4d017ef7d88..a19e7761c2c 100644 --- a/core/src/org/labkey/core/vcs/VcsServiceImpl.java +++ b/core/src/org/labkey/core/vcs/VcsServiceImpl.java @@ -1,6 +1,7 @@ package org.labkey.core.vcs; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.vcs.Vcs; import org.labkey.api.vcs.VcsService; @@ -10,7 +11,7 @@ public class VcsServiceImpl implements VcsService { - private static final Logger LOG = Logger.getLogger(VcsServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(VcsServiceImpl.class); @Override public @Nullable Vcs getVcs(File directory) diff --git a/core/src/org/labkey/core/view/template/bootstrap/PageTemplate.java b/core/src/org/labkey/core/view/template/bootstrap/PageTemplate.java index d07a5f9fc97..d1ef22b8770 100644 --- a/core/src/org/labkey/core/view/template/bootstrap/PageTemplate.java +++ b/core/src/org/labkey/core/view/template/bootstrap/PageTemplate.java @@ -17,7 +17,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.module.FolderType; @@ -28,7 +29,6 @@ import org.labkey.api.settings.FooterProperties; import org.labkey.api.settings.TemplateProperties; import org.labkey.api.view.ActionURL; -import org.labkey.api.view.HtmlView; import org.labkey.api.view.HttpView; import org.labkey.api.view.JspView; import org.labkey.api.view.NavTree; @@ -211,7 +211,7 @@ public static class NavigationModel private final ViewContext _context; private final List _menus; - private static final Logger LOG = Logger.getLogger(NavigationModel.class); + private static final Logger LOG = LogManager.getLogger(NavigationModel.class); private NavigationModel(ViewContext context, PageConfig page) { diff --git a/core/src/org/labkey/core/view/template/bootstrap/dialog.jsp b/core/src/org/labkey/core/view/template/bootstrap/dialog.jsp index 70a214264fe..e89528ff6d8 100644 --- a/core/src/org/labkey/core/view/template/bootstrap/dialog.jsp +++ b/core/src/org/labkey/core/view/template/bootstrap/dialog.jsp @@ -19,7 +19,6 @@ <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.PageConfig" %> -<%@ page import="org.labkey.core.view.template.bootstrap.PageTemplate" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/core/src/org/labkey/core/view/template/bootstrap/wizard.jsp b/core/src/org/labkey/core/view/template/bootstrap/wizard.jsp index 040064185f6..83ac18facbd 100644 --- a/core/src/org/labkey/core/view/template/bootstrap/wizard.jsp +++ b/core/src/org/labkey/core/view/template/bootstrap/wizard.jsp @@ -18,8 +18,8 @@ <%@ page buffer="none" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.view.template.PageConfig" %> <%@ page import="org.labkey.api.view.NavTree" %> +<%@ page import="org.labkey.api.view.template.PageConfig" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/core/src/org/labkey/core/webdav/DavController.java b/core/src/org/labkey/core/webdav/DavController.java index 55d9e62882f..3b36df64844 100644 --- a/core/src/org/labkey/core/webdav/DavController.java +++ b/core/src/org/labkey/core/webdav/DavController.java @@ -24,8 +24,9 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.FastDateFormat; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -189,7 +190,7 @@ */ public class DavController extends SpringActionController { - private static final Logger _log = Logger.getLogger(DavController.class); + private static final Logger _log = LogManager.getLogger(DavController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(DavController.class); public static final String name = "_dav_"; @@ -687,7 +688,7 @@ public ModelAndView handleRequest(HttpServletRequest request, HttpServletRespons clearLastError(); long start=0; - if (_log.isEnabledFor(Level.DEBUG)) + if (_log.isEnabled(Level.DEBUG)) { long modified = getRequest().getDateHeader("If-Modified-Since"); boolean isBasicAuthentication = SecurityManager.isBasicAuthentication(getRequest()); diff --git a/core/src/org/labkey/core/webdav/WebdavServlet.java b/core/src/org/labkey/core/webdav/WebdavServlet.java index e31c2ad7975..1c14ed9f9de 100644 --- a/core/src/org/labkey/core/webdav/WebdavServlet.java +++ b/core/src/org/labkey/core/webdav/WebdavServlet.java @@ -24,7 +24,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.http.HttpStatus; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.miniprofiler.RequestInfo; import org.labkey.api.settings.AppProps; import org.labkey.api.util.MemTracker; @@ -50,7 +51,7 @@ public class WebdavServlet extends HttpServlet { - Logger _log = Logger.getLogger(WebdavServlet.class); + Logger _log = LogManager.getLogger(WebdavServlet.class); @Override protected void service(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException @@ -117,7 +118,7 @@ protected void service(HttpServletRequest request, HttpServletResponse response) catch (URISyntaxException e) { } - Logger.getRootLogger().error("Improper welcome URL: " + AppProps.getInstance().getSiteWelcomePageUrlString()); + LogManager.getRootLogger().error("Improper welcome URL: " + AppProps.getInstance().getSiteWelcomePageUrlString()); try {response.reset();}catch(IllegalStateException x){/*pass*/} } diff --git a/core/src/org/labkey/core/wiki/HtmlRenderer.java b/core/src/org/labkey/core/wiki/HtmlRenderer.java index 83492956845..8d2c7046d0e 100644 --- a/core/src/org/labkey/core/wiki/HtmlRenderer.java +++ b/core/src/org/labkey/core/wiki/HtmlRenderer.java @@ -17,7 +17,6 @@ package org.labkey.core.wiki; import org.apache.commons.lang3.StringUtils; - import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.Attachment; @@ -25,14 +24,23 @@ import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.TidyUtil; import org.labkey.api.view.template.ClientDependency; -import org.labkey.api.wiki.WikiRenderer; import org.labkey.api.wiki.FormattedHtml; +import org.labkey.api.wiki.WikiRenderer; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashSet; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/core/src/org/labkey/core/wiki/RadeoxMacroProxy.java b/core/src/org/labkey/core/wiki/RadeoxMacroProxy.java index 21e70bff20c..9d4b2d84f0b 100644 --- a/core/src/org/labkey/core/wiki/RadeoxMacroProxy.java +++ b/core/src/org/labkey/core/wiki/RadeoxMacroProxy.java @@ -16,14 +16,18 @@ package org.labkey.core.wiki; +import org.labkey.api.view.HttpView; +import org.labkey.api.wiki.MacroProvider; import org.radeox.macro.BaseMacro; import org.radeox.macro.parameter.MacroParameter; -import org.labkey.api.wiki.MacroProvider; -import org.labkey.api.view.HttpView; -import java.io.Writer; import java.io.IOException; -import java.util.*; +import java.io.Writer; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.Map; +import java.util.Set; /** * User: Mark Igra diff --git a/core/src/org/labkey/core/wiki/RadeoxRenderer.java b/core/src/org/labkey/core/wiki/RadeoxRenderer.java index 841892598d8..60d6fd2cde3 100644 --- a/core/src/org/labkey/core/wiki/RadeoxRenderer.java +++ b/core/src/org/labkey/core/wiki/RadeoxRenderer.java @@ -16,7 +16,8 @@ package org.labkey.core.wiki; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Before; @@ -646,7 +647,7 @@ public void handleMatch(StringBuffer buffer, MatchResult result, FilterContext c */ public static class LinkTestFilter extends LocaleRegexTokenFilter { - private static final Logger log = Logger.getLogger(org.radeox.filter.LinkTestFilter.class); + private static final Logger log = LogManager.getLogger(org.radeox.filter.LinkTestFilter.class); private MessageFormat urlFormatter; diff --git a/core/src/org/labkey/core/wiki/WebPartSubstitutionHandler.java b/core/src/org/labkey/core/wiki/WebPartSubstitutionHandler.java index 93527b2d634..1c6af5bcc7f 100644 --- a/core/src/org/labkey/core/wiki/WebPartSubstitutionHandler.java +++ b/core/src/org/labkey/core/wiki/WebPartSubstitutionHandler.java @@ -16,7 +16,8 @@ package org.labkey.core.wiki; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.settings.AppProps; @@ -44,7 +45,7 @@ */ public class WebPartSubstitutionHandler implements HtmlRenderer.SubstitutionHandler { - private static final Logger LOG = Logger.getLogger(WebPartSubstitutionHandler.class); + private static final Logger LOG = LogManager.getLogger(WebPartSubstitutionHandler.class); private static final ThreadLocal>> _paramsStack = ThreadLocal.withInitial(Stack::new); diff --git a/experiment/src/org/labkey/experiment/ChooseExperimentTypeBean.java b/experiment/src/org/labkey/experiment/ChooseExperimentTypeBean.java index 4f0786f3950..8fbbd07de05 100644 --- a/experiment/src/org/labkey/experiment/ChooseExperimentTypeBean.java +++ b/experiment/src/org/labkey/experiment/ChooseExperimentTypeBean.java @@ -16,10 +16,10 @@ package org.labkey.experiment; +import org.labkey.api.exp.ExperimentRunType; import org.labkey.api.exp.Handler; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.view.ActionURL; -import org.labkey.api.exp.ExperimentRunType; import java.util.List; import java.util.Set; diff --git a/experiment/src/org/labkey/experiment/CustomPropertyRenderer.java b/experiment/src/org/labkey/experiment/CustomPropertyRenderer.java index b51884e7802..ef8c0779dcd 100644 --- a/experiment/src/org/labkey/experiment/CustomPropertyRenderer.java +++ b/experiment/src/org/labkey/experiment/CustomPropertyRenderer.java @@ -18,7 +18,6 @@ import org.labkey.api.data.Container; import org.labkey.api.exp.ObjectProperty; -import org.labkey.api.view.ViewContext; import java.util.List; diff --git a/experiment/src/org/labkey/experiment/DataURLRelativizer.java b/experiment/src/org/labkey/experiment/DataURLRelativizer.java index 4e35ea48881..b17986bc9ca 100644 --- a/experiment/src/org/labkey/experiment/DataURLRelativizer.java +++ b/experiment/src/org/labkey/experiment/DataURLRelativizer.java @@ -20,8 +20,8 @@ import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.security.User; -import org.labkey.api.view.ActionURL; import org.labkey.api.util.FileUtil; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; import java.io.IOException; diff --git a/experiment/src/org/labkey/experiment/ExperimentRunDisplayColumn.java b/experiment/src/org/labkey/experiment/ExperimentRunDisplayColumn.java index 81e62c8a14e..aefeb6f2323 100644 --- a/experiment/src/org/labkey/experiment/ExperimentRunDisplayColumn.java +++ b/experiment/src/org/labkey/experiment/ExperimentRunDisplayColumn.java @@ -15,14 +15,14 @@ */ package org.labkey.experiment; -import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.RenderContext; -import org.labkey.api.view.ActionURL; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/ExperimentRunGraph.java b/experiment/src/org/labkey/experiment/ExperimentRunGraph.java index 55545e2a0fb..0d1fc51c64d 100644 --- a/experiment/src/org/labkey/experiment/ExperimentRunGraph.java +++ b/experiment/src/org/labkey/experiment/ExperimentRunGraph.java @@ -15,15 +15,16 @@ */ package org.labkey.experiment; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRunItem; import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExpRunItem; import org.labkey.api.settings.AppProps; import org.labkey.api.util.ConfigurationException; import org.labkey.api.util.DotRunner; @@ -64,7 +65,7 @@ public class ExperimentRunGraph { private static File baseDirectory; - private static Logger _log = Logger.getLogger(ExperimentRunGraph.class); + private static Logger _log = LogManager.getLogger(ExperimentRunGraph.class); private static int MAX_WIDTH_SMALL_FONT = 8; private static int MAX_WIDTH_BIG_FONT = 3; private static int MAX_SIBLINGS = 5; diff --git a/experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java b/experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java index bf93f507273..cbcfd70e84a 100644 --- a/experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java +++ b/experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java @@ -16,7 +16,8 @@ package org.labkey.experiment; import com.google.common.collect.Sets; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.DbSchema; @@ -68,7 +69,7 @@ */ public class ExperimentUpgradeCode implements UpgradeCode { - private static final Logger LOG = Logger.getLogger(ExperimentUpgradeCode.class); + private static final Logger LOG = LogManager.getLogger(ExperimentUpgradeCode.class); /** * Called from multiple experiment upgrade scripts, @@ -89,7 +90,7 @@ public static void rebuildAllEdges(ModuleContext context) private static void materializeSampleType(ExpSampleTypeImpl st) { - Logger log = Logger.getLogger(ExperimentUpgradeCode.class); + Logger log = LogManager.getLogger(ExperimentUpgradeCode.class); Domain domain = st.getDomain(); DomainKind kind = null; try diff --git a/experiment/src/org/labkey/experiment/ExternalDocsURLCustomPropertyRenderer.java b/experiment/src/org/labkey/experiment/ExternalDocsURLCustomPropertyRenderer.java index 000e2d2faf4..08ca390af45 100644 --- a/experiment/src/org/labkey/experiment/ExternalDocsURLCustomPropertyRenderer.java +++ b/experiment/src/org/labkey/experiment/ExternalDocsURLCustomPropertyRenderer.java @@ -17,14 +17,14 @@ package org.labkey.experiment; import org.labkey.api.data.Container; -import org.labkey.api.view.ActionURL; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.exp.ObjectProperty; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.util.List; -import java.net.URL; import java.net.MalformedURLException; +import java.net.URL; +import java.util.List; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/FileLinkFileListener.java b/experiment/src/org/labkey/experiment/FileLinkFileListener.java index 6bf504e63f6..7c5a48b9459 100644 --- a/experiment/src/org/labkey/experiment/FileLinkFileListener.java +++ b/experiment/src/org/labkey/experiment/FileLinkFileListener.java @@ -15,7 +15,8 @@ */ package org.labkey.experiment; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -47,7 +48,7 @@ */ public class FileLinkFileListener implements FileListener { - private static final Logger LOG = Logger.getLogger(FileLinkFileListener.class); + private static final Logger LOG = LogManager.getLogger(FileLinkFileListener.class); @Override public String getSourceName() diff --git a/experiment/src/org/labkey/experiment/LineageGraphDisplayColumn.java b/experiment/src/org/labkey/experiment/LineageGraphDisplayColumn.java index f3e93103bef..7e321050d8d 100644 --- a/experiment/src/org/labkey/experiment/LineageGraphDisplayColumn.java +++ b/experiment/src/org/labkey/experiment/LineageGraphDisplayColumn.java @@ -15,14 +15,18 @@ */ package org.labkey.experiment; -import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExpMaterial; +import org.labkey.api.exp.api.ExpObject; +import org.labkey.api.exp.api.ExpProtocolApplication; +import org.labkey.api.exp.api.ExpRun; import org.labkey.api.view.ActionURL; -import org.labkey.api.exp.api.*; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/ProtocolApplicationDisplayColumn.java b/experiment/src/org/labkey/experiment/ProtocolApplicationDisplayColumn.java index aef1595ddad..7ccdefcc556 100644 --- a/experiment/src/org/labkey/experiment/ProtocolApplicationDisplayColumn.java +++ b/experiment/src/org/labkey/experiment/ProtocolApplicationDisplayColumn.java @@ -15,14 +15,14 @@ */ package org.labkey.experiment; -import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.exp.api.ExpProtocolApplication; import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/ProtocolApplications.jsp b/experiment/src/org/labkey/experiment/ProtocolApplications.jsp index 04c597207e1..b57fd84eb36 100644 --- a/experiment/src/org/labkey/experiment/ProtocolApplications.jsp +++ b/experiment/src/org/labkey/experiment/ProtocolApplications.jsp @@ -19,6 +19,7 @@ <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.exp.ExperimentDataHandler" %> <%@ page import="org.labkey.api.exp.Identifiable" %> +<%@ page import="org.labkey.api.exp.LsidManager" %> <%@ page import="org.labkey.api.exp.api.ExpData" %> <%@ page import="org.labkey.api.exp.api.ExpDataProtocolInput" %> <%@ page import="org.labkey.api.exp.api.ExpDataRunInput" %> @@ -42,7 +43,6 @@ <%@ page import="java.util.Map" %> <%@ page import="java.util.Objects" %> <%@ page import="java.util.Set" %> -<%@ page import="org.labkey.api.exp.LsidManager" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/experiment/src/org/labkey/experiment/ProtocolDetails.jsp b/experiment/src/org/labkey/experiment/ProtocolDetails.jsp index 7f20457713d..feb2cb36fad 100644 --- a/experiment/src/org/labkey/experiment/ProtocolDetails.jsp +++ b/experiment/src/org/labkey/experiment/ProtocolDetails.jsp @@ -15,9 +15,9 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.view.HttpView"%> +<%@ page import="org.labkey.api.exp.api.ExpProtocol"%> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.exp.api.ExpProtocol" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/experiment/src/org/labkey/experiment/ProtocolDisplayColumn.java b/experiment/src/org/labkey/experiment/ProtocolDisplayColumn.java index 35ebb99f003..c01f4dfb6fb 100644 --- a/experiment/src/org/labkey/experiment/ProtocolDisplayColumn.java +++ b/experiment/src/org/labkey/experiment/ProtocolDisplayColumn.java @@ -15,14 +15,14 @@ */ package org.labkey.experiment; -import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.RenderContext; -import org.labkey.api.view.ActionURL; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.exp.api.ExpProtocol; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/ProtocolWebPart.java b/experiment/src/org/labkey/experiment/ProtocolWebPart.java index 5b62afba629..d8ef9112309 100644 --- a/experiment/src/org/labkey/experiment/ProtocolWebPart.java +++ b/experiment/src/org/labkey/experiment/ProtocolWebPart.java @@ -17,35 +17,20 @@ import org.labkey.api.data.ActionButton; import org.labkey.api.data.ButtonBar; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.DataRegion; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.query.ExpProtocolTable; import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; -import org.labkey.api.query.FilteredTable; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; -import org.labkey.api.view.GridView; import org.labkey.api.view.ViewContext; -import org.labkey.experiment.api.ExperimentServiceImpl; import org.labkey.experiment.controllers.exp.ExperimentController; -import org.springframework.validation.BindException; - -import java.io.PrintWriter; -import java.util.Collections; -import java.util.List; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/RunGroupWebPart.java b/experiment/src/org/labkey/experiment/RunGroupWebPart.java index 205269540a2..fe796473fa4 100644 --- a/experiment/src/org/labkey/experiment/RunGroupWebPart.java +++ b/experiment/src/org/labkey/experiment/RunGroupWebPart.java @@ -15,12 +15,18 @@ */ package org.labkey.experiment; -import org.labkey.api.view.*; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.TableInfo; import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.data.*; -import org.labkey.api.security.permissions.InsertPermission; -import org.labkey.api.query.QueryView; import org.labkey.api.query.QuerySettings; +import org.labkey.api.query.QueryView; +import org.labkey.api.security.permissions.InsertPermission; +import org.labkey.api.view.DataView; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; import org.labkey.experiment.controllers.exp.ExperimentController; /** diff --git a/experiment/src/org/labkey/experiment/SampleTypeDisplayColumn.java b/experiment/src/org/labkey/experiment/SampleTypeDisplayColumn.java index cc6d0d4a8e8..5db419af986 100644 --- a/experiment/src/org/labkey/experiment/SampleTypeDisplayColumn.java +++ b/experiment/src/org/labkey/experiment/SampleTypeDisplayColumn.java @@ -16,16 +16,16 @@ package org.labkey.experiment; -import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.exp.api.ExpMaterial; import org.labkey.api.exp.api.ExpSampleType; -import org.labkey.api.view.ActionURL; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/XarExportPipelineJob.java b/experiment/src/org/labkey/experiment/XarExportPipelineJob.java index 39c1e938756..f73f03d2265 100644 --- a/experiment/src/org/labkey/experiment/XarExportPipelineJob.java +++ b/experiment/src/org/labkey/experiment/XarExportPipelineJob.java @@ -18,16 +18,16 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import org.labkey.api.exp.ExperimentException; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.experiment.pipeline.ExperimentPipelineProvider; -import org.labkey.api.exp.ExperimentException; import org.labkey.experiment.xar.XarExportSelection; -import java.io.FileOutputStream; import java.io.File; +import java.io.FileOutputStream; import java.io.IOException; /** diff --git a/experiment/src/org/labkey/experiment/XarExporter.java b/experiment/src/org/labkey/experiment/XarExporter.java index e39752aaf26..1f5454babef 100644 --- a/experiment/src/org/labkey/experiment/XarExporter.java +++ b/experiment/src/org/labkey/experiment/XarExporter.java @@ -17,7 +17,7 @@ package org.labkey.experiment; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlCursor; import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlOptions; diff --git a/experiment/src/org/labkey/experiment/XarReader.java b/experiment/src/org/labkey/experiment/XarReader.java index dbab96857e5..d8cc553a5e8 100644 --- a/experiment/src/org/labkey/experiment/XarReader.java +++ b/experiment/src/org/labkey/experiment/XarReader.java @@ -78,28 +78,7 @@ import org.labkey.api.util.FileUtil; import org.labkey.api.util.GUID; import org.labkey.api.util.Pair; -import org.labkey.experiment.api.Data; -import org.labkey.experiment.api.DataInput; -import org.labkey.experiment.api.ExpDataImpl; -import org.labkey.experiment.api.ExpExperimentImpl; -import org.labkey.experiment.api.ExpMaterialImpl; -import org.labkey.experiment.api.ExpProtocolApplicationImpl; -import org.labkey.experiment.api.ExpProtocolImpl; -import org.labkey.experiment.api.ExpRunImpl; -import org.labkey.experiment.api.ExpSampleTypeImpl; -import org.labkey.experiment.api.Experiment; -import org.labkey.experiment.api.ExperimentRun; -import org.labkey.experiment.api.ExperimentServiceImpl; -import org.labkey.experiment.api.IdentifiableEntity; -import org.labkey.experiment.api.Material; -import org.labkey.experiment.api.MaterialInput; -import org.labkey.experiment.api.Protocol; -import org.labkey.experiment.api.ProtocolAction; -import org.labkey.experiment.api.ProtocolActionPredecessor; -import org.labkey.experiment.api.ProtocolActionStepDetail; -import org.labkey.experiment.api.ProtocolApplication; -import org.labkey.experiment.api.RunItem; -import org.labkey.experiment.api.SampleTypeServiceImpl; +import org.labkey.experiment.api.*; import org.labkey.experiment.api.property.DomainImpl; import org.labkey.experiment.pipeline.MoveRunsPipelineJob; import org.labkey.experiment.xar.AbstractXarImporter; diff --git a/experiment/src/org/labkey/experiment/api/AbstractRunItemImpl.java b/experiment/src/org/labkey/experiment/api/AbstractRunItemImpl.java index d6fa1280438..5ea2b5aaed4 100644 --- a/experiment/src/org/labkey/experiment/api/AbstractRunItemImpl.java +++ b/experiment/src/org/labkey/experiment/api/AbstractRunItemImpl.java @@ -24,8 +24,8 @@ import org.labkey.api.data.TableSelector; import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpProtocolApplication; -import org.labkey.api.exp.api.ExpRunItem; import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExpRunItem; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; diff --git a/experiment/src/org/labkey/experiment/api/CountOfUniqueValueTableCustomizer.java b/experiment/src/org/labkey/experiment/api/CountOfUniqueValueTableCustomizer.java index e204a6b2ecf..f1cf8b33442 100644 --- a/experiment/src/org/labkey/experiment/api/CountOfUniqueValueTableCustomizer.java +++ b/experiment/src/org/labkey/experiment/api/CountOfUniqueValueTableCustomizer.java @@ -16,13 +16,13 @@ package org.labkey.experiment.api; import org.apache.commons.collections4.MultiValuedMap; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.CounterDefinition; import org.labkey.api.data.TableCustomizer; import org.labkey.api.data.TableInfo; -import org.apache.log4j.Logger; - import java.lang.reflect.InvocationTargetException; import java.util.Collection; import java.util.Collections; @@ -56,7 +56,7 @@ */ public class CountOfUniqueValueTableCustomizer implements TableCustomizer { - private static final Logger _log = Logger.getLogger(CountOfUniqueValueTableCustomizer.class); + private static final Logger _log = LogManager.getLogger(CountOfUniqueValueTableCustomizer.class); private final CounterDefinition _counterDefinition; diff --git a/experiment/src/org/labkey/experiment/api/Data.java b/experiment/src/org/labkey/experiment/api/Data.java index dca4e0bfe14..689a26e8be7 100644 --- a/experiment/src/org/labkey/experiment/api/Data.java +++ b/experiment/src/org/labkey/experiment/api/Data.java @@ -19,7 +19,6 @@ import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpObject; import org.labkey.api.util.FileUtil; -import org.labkey.api.util.URLHelper; import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; diff --git a/experiment/src/org/labkey/experiment/api/DataLinkColumn.java b/experiment/src/org/labkey/experiment/api/DataLinkColumn.java index 3dbe96cfebe..db2c3a9956b 100644 --- a/experiment/src/org/labkey/experiment/api/DataLinkColumn.java +++ b/experiment/src/org/labkey/experiment/api/DataLinkColumn.java @@ -15,18 +15,18 @@ */ package org.labkey.experiment.api; -import org.labkey.api.data.DataColumn; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.settings.AppProps; -import org.labkey.api.view.ActionURL; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; import org.labkey.experiment.controllers.exp.ExperimentController; -import java.io.Writer; import java.io.IOException; +import java.io.Writer; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java index d3d1927634d..778581fb353 100644 --- a/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpDataClassDataTableImpl.java @@ -16,7 +16,7 @@ package org.labkey.experiment.api; import org.apache.commons.beanutils.ConversionException; -import org.apache.log4j.Level; +import org.apache.logging.log4j.Level; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentFile; diff --git a/experiment/src/org/labkey/experiment/api/ExpDataClassTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataClassTableImpl.java index 5ba89fa2861..04690f8e705 100644 --- a/experiment/src/org/labkey/experiment/api/ExpDataClassTableImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpDataClassTableImpl.java @@ -21,8 +21,8 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.data.Container; import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerForeignKey; import org.labkey.api.data.JdbcType; diff --git a/experiment/src/org/labkey/experiment/api/ExpDataImpl.java b/experiment/src/org/labkey/experiment/api/ExpDataImpl.java index ca7c84fd72d..dc1d85890e5 100644 --- a/experiment/src/org/labkey/experiment/api/ExpDataImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpDataImpl.java @@ -18,7 +18,8 @@ import org.apache.commons.io.FilenameUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -95,7 +96,7 @@ public class ExpDataImpl extends AbstractRunItemImpl implements ExpData { - private static final Logger LOG = Logger.getLogger(ExpDataImpl.class); + private static final Logger LOG = LogManager.getLogger(ExpDataImpl.class); public static final SearchService.SearchCategory expDataCategory = new SearchService.SearchCategory("data", "ExpData"); diff --git a/experiment/src/org/labkey/experiment/api/ExpProtocolApplicationImpl.java b/experiment/src/org/labkey/experiment/api/ExpProtocolApplicationImpl.java index 7fb2024251e..2cf4832e666 100644 --- a/experiment/src/org/labkey/experiment/api/ExpProtocolApplicationImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpProtocolApplicationImpl.java @@ -24,7 +24,6 @@ import org.labkey.api.data.SqlExecutor; import org.labkey.api.data.Table; import org.labkey.api.data.dialect.SqlDialect; -import org.labkey.api.exp.ExperimentProtocolHandler; import org.labkey.api.exp.OntologyManager; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpDataProtocolInput; @@ -33,8 +32,6 @@ import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpProtocolApplication; import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ProtocolImplementation; import org.labkey.api.exp.api.ProvenanceService; import org.labkey.api.exp.query.ExpProtocolApplicationTable; import org.labkey.api.exp.query.ExpSchema; diff --git a/experiment/src/org/labkey/experiment/api/ExpProtocolImpl.java b/experiment/src/org/labkey/experiment/api/ExpProtocolImpl.java index 87fe38dc6e3..181183a9684 100644 --- a/experiment/src/org/labkey/experiment/api/ExpProtocolImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpProtocolImpl.java @@ -27,7 +27,6 @@ import org.labkey.api.data.TableSelector; import org.labkey.api.exp.ExperimentException; import org.labkey.api.exp.ExperimentProtocolHandler; -import org.labkey.api.exp.ExperimentRunType; import org.labkey.api.exp.ObjectProperty; import org.labkey.api.exp.ProtocolParameter; import org.labkey.api.exp.api.ExpDataProtocolInput; diff --git a/experiment/src/org/labkey/experiment/api/ExpProtocolTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpProtocolTableImpl.java index e5f3ebf7e41..5eb64647273 100644 --- a/experiment/src/org/labkey/experiment/api/ExpProtocolTableImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpProtocolTableImpl.java @@ -21,8 +21,8 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.TableSelector; diff --git a/experiment/src/org/labkey/experiment/api/ExpQCFlagTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpQCFlagTableImpl.java index 43cd22bc547..629b1ad63a4 100644 --- a/experiment/src/org/labkey/experiment/api/ExpQCFlagTableImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpQCFlagTableImpl.java @@ -17,7 +17,8 @@ package org.labkey.experiment.api; import org.apache.commons.beanutils.ConversionException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AssayFlagHandler; @@ -56,7 +57,7 @@ public class ExpQCFlagTableImpl extends ExpTableImpl implements ExpQCFlagTable { - private static final Logger LOG = Logger.getLogger(ExpQCFlagTableImpl.class); + private static final Logger LOG = LogManager.getLogger(ExpQCFlagTableImpl.class); private AssayProvider _provider; private ExpProtocol _assayProtocol; diff --git a/experiment/src/org/labkey/experiment/api/ExpRunGroupMapTableImpl.java b/experiment/src/org/labkey/experiment/api/ExpRunGroupMapTableImpl.java index 967e2be256a..daf15360d2b 100644 --- a/experiment/src/org/labkey/experiment/api/ExpRunGroupMapTableImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpRunGroupMapTableImpl.java @@ -18,7 +18,15 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ConvertHelper; +import org.labkey.api.data.MutableColumnInfo; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableSelector; import org.labkey.api.exp.query.ExpRunGroupMapTable; import org.labkey.api.query.AbstractQueryUpdateService; import org.labkey.api.query.FieldKey; diff --git a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java index c1277d8452d..4c76fa6c3e4 100644 --- a/experiment/src/org/labkey/experiment/api/ExpRunImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExpRunImpl.java @@ -17,13 +17,11 @@ package org.labkey.experiment.api; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AssayFileWriter; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.cache.DbCache; import org.labkey.api.cloud.CloudStoreService; import org.labkey.api.data.Container; @@ -58,7 +56,6 @@ import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryRowReference; -import org.labkey.api.query.SchemaKey; import org.labkey.api.security.User; import org.labkey.api.security.permissions.DeletePermission; import org.labkey.api.settings.AppProps; @@ -93,7 +90,7 @@ public class ExpRunImpl extends ExpIdentifiableEntityImpl impleme private List _dataOutputs = new ArrayList<>(); private ExpRunImpl _replacedByRun; private Integer _maxOutputActionSequence = null; - private static final Logger LOG = Logger.getLogger(ExpRunImpl.class); + private static final Logger LOG = LogManager.getLogger(ExpRunImpl.class); static public List fromRuns(List runs) { diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java index 95ad250245b..a3e68ceab3e 100644 --- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java +++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java @@ -23,7 +23,8 @@ import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.fhcrc.cpas.exp.xml.SimpleTypeNames; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -175,7 +176,7 @@ public class ExperimentServiceImpl implements ExperimentService { - private static final Logger LOG = Logger.getLogger(ExperimentServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(ExperimentServiceImpl.class); private Cache protocolCache; @@ -7096,7 +7097,7 @@ public void testRunInputProperties() throws Exception final User user = TestContext.get().getUser(); final Container c = JunitUtil.getTestContainer(); final ViewBackgroundInfo info = new ViewBackgroundInfo(c, user, null); - final Logger log = Logger.getLogger(ExperimentServiceImpl.class); + final Logger log = LogManager.getLogger(ExperimentServiceImpl.class); // assert no MaterialInput exp.object exist assertEquals(0L, countMaterialInputObjects(c)); diff --git a/experiment/src/org/labkey/experiment/api/ExperimentStressTest.java b/experiment/src/org/labkey/experiment/api/ExperimentStressTest.java index fa585c69d79..e3331ed545e 100644 --- a/experiment/src/org/labkey/experiment/api/ExperimentStressTest.java +++ b/experiment/src/org/labkey/experiment/api/ExperimentStressTest.java @@ -1,6 +1,7 @@ package org.labkey.experiment.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assume; import org.junit.Before; import org.junit.Test; @@ -29,7 +30,7 @@ public class ExperimentStressTest { - private static final Logger LOG = Logger.getLogger(ExperimentStressTest.class); + private static final Logger LOG = LogManager.getLogger(ExperimentStressTest.class); @Before public void setup() diff --git a/experiment/src/org/labkey/experiment/api/IdentifiableEntity.java b/experiment/src/org/labkey/experiment/api/IdentifiableEntity.java index 028e6fc6e87..89d90df944f 100644 --- a/experiment/src/org/labkey/experiment/api/IdentifiableEntity.java +++ b/experiment/src/org/labkey/experiment/api/IdentifiableEntity.java @@ -15,13 +15,11 @@ */ package org.labkey.experiment.api; -import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.exp.Identifiable; import org.labkey.api.exp.IdentifiableBase; import org.labkey.api.security.User; import org.labkey.api.util.GUID; -import org.labkey.api.util.URLHelper; import java.util.Date; import java.util.List; diff --git a/experiment/src/org/labkey/experiment/api/LineagePerfTest.java b/experiment/src/org/labkey/experiment/api/LineagePerfTest.java index 28ecef87d55..7e85b54b886 100644 --- a/experiment/src/org/labkey/experiment/api/LineagePerfTest.java +++ b/experiment/src/org/labkey/experiment/api/LineagePerfTest.java @@ -16,7 +16,8 @@ package org.labkey.experiment.api; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.junit.AfterClass; import org.junit.Assert; @@ -75,7 +76,7 @@ @TestTimeout(TestTimeout.DEFAULT * 10) public class LineagePerfTest extends Assert { - private static final Logger LOG = Logger.getLogger(LineagePerfTest.class); + private static final Logger LOG = LogManager.getLogger(LineagePerfTest.class); private static boolean _currentSetting; private static User _user; diff --git a/experiment/src/org/labkey/experiment/api/LineageTableInfo.java b/experiment/src/org/labkey/experiment/api/LineageTableInfo.java index 189ce2b4515..10c9bf68b96 100644 --- a/experiment/src/org/labkey/experiment/api/LineageTableInfo.java +++ b/experiment/src/org/labkey/experiment/api/LineageTableInfo.java @@ -17,6 +17,9 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ContainerForeignKey; @@ -39,9 +42,6 @@ import org.labkey.api.query.LookupForeignKey; import org.labkey.api.query.QueryForeignKey; import org.labkey.api.query.UserSchema; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; import org.labkey.api.util.StringExpression; /** diff --git a/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java b/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java index 7d5952f201c..e00535870a6 100644 --- a/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java +++ b/experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java @@ -21,14 +21,15 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AbstractAuditTypeProvider; +import org.labkey.api.audit.AuditHandler; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; import org.labkey.api.audit.DetailedAuditTypeEvent; -import org.labkey.api.audit.AuditHandler; import org.labkey.api.audit.SampleTimelineAuditEvent; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheManager; @@ -60,8 +61,8 @@ import org.labkey.api.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpSampleType; import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.SampleTypeService; import org.labkey.api.exp.api.SampleTypeDomainKindProperties; +import org.labkey.api.exp.api.SampleTypeService; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainKind; import org.labkey.api.exp.property.DomainProperty; @@ -122,7 +123,7 @@ public static SampleTypeServiceImpl get() return (SampleTypeServiceImpl) SampleTypeService.get(); } - private static final Logger LOG = Logger.getLogger(SampleTypeServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(SampleTypeServiceImpl.class); // SampleType -> Container cache private final Cache sampleTypeCache = CacheManager.getStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "SampleTypeToContainer"); diff --git a/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java b/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java index 80621c44142..5a20137679e 100644 --- a/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java +++ b/experiment/src/org/labkey/experiment/api/SampleTypeUpdateServiceDI.java @@ -17,8 +17,9 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.converters.IntegerConverter; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -76,7 +77,7 @@ */ public class SampleTypeUpdateServiceDI extends DefaultQueryUpdateService { - public static final Logger LOG = Logger.getLogger(SampleTypeUpdateServiceDI.class); + public static final Logger LOG = LogManager.getLogger(SampleTypeUpdateServiceDI.class); public enum Options { SkipDerivation diff --git a/experiment/src/org/labkey/experiment/api/UniqueValueCounterTestCase.java b/experiment/src/org/labkey/experiment/api/UniqueValueCounterTestCase.java index 4e260718f7c..37668b6281a 100644 --- a/experiment/src/org/labkey/experiment/api/UniqueValueCounterTestCase.java +++ b/experiment/src/org/labkey/experiment/api/UniqueValueCounterTestCase.java @@ -45,8 +45,8 @@ import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; import static org.junit.Assert.assertThat; +import static org.junit.Assert.assertTrue; public class UniqueValueCounterTestCase { diff --git a/experiment/src/org/labkey/experiment/api/property/LookupValidator.java b/experiment/src/org/labkey/experiment/api/property/LookupValidator.java index 65610ce53af..4f6fdb18985 100644 --- a/experiment/src/org/labkey/experiment/api/property/LookupValidator.java +++ b/experiment/src/org/labkey/experiment/api/property/LookupValidator.java @@ -17,11 +17,11 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.ColumnRenderProperties; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.ForeignKey; import org.labkey.api.data.JdbcType; -import org.labkey.api.data.ColumnRenderProperties; import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; import org.labkey.api.exp.PropertyDescriptor; diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java index e8f2bac7288..3dda75f2511 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java @@ -19,7 +19,8 @@ import au.com.bytecode.opencsv.CSVWriter; import org.apache.commons.collections4.iterators.ArrayIterator; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.poi.openxml4j.exceptions.InvalidFormatException; import org.apache.poi.ss.usermodel.Workbook; import org.jetbrains.annotations.NotNull; @@ -27,7 +28,25 @@ import org.json.JSONArray; import org.json.JSONException; import org.json.JSONObject; -import org.labkey.api.action.*; +import org.labkey.api.action.ApiJsonWriter; +import org.labkey.api.action.ApiResponse; +import org.labkey.api.action.ApiSimpleResponse; +import org.labkey.api.action.ApiUsageException; +import org.labkey.api.action.ExportAction; +import org.labkey.api.action.FormHandlerAction; +import org.labkey.api.action.FormViewAction; +import org.labkey.api.action.HasViewContext; +import org.labkey.api.action.LabKeyError; +import org.labkey.api.action.Marshal; +import org.labkey.api.action.Marshaller; +import org.labkey.api.action.MutatingApiAction; +import org.labkey.api.action.QueryViewAction; +import org.labkey.api.action.ReadOnlyApiAction; +import org.labkey.api.action.ReturnUrlForm; +import org.labkey.api.action.SimpleApiJsonForm; +import org.labkey.api.action.SimpleErrorView; +import org.labkey.api.action.SimpleViewAction; +import org.labkey.api.action.SpringActionController; import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.assay.AssayService; import org.labkey.api.assay.actions.UploadWizardAction; @@ -163,30 +182,7 @@ import org.labkey.api.view.ViewServlet; import org.labkey.api.view.WebPartView; import org.labkey.api.view.template.PageConfig; -import org.labkey.experiment.ChooseExperimentTypeBean; -import org.labkey.experiment.ConfirmDeleteView; -import org.labkey.experiment.CustomPropertiesView; -import org.labkey.experiment.DataClassWebPart; -import org.labkey.experiment.DerivedSamplePropertyHelper; -import org.labkey.experiment.DotGraph; -import org.labkey.experiment.ExpDataFileListener; -import org.labkey.experiment.ExperimentRunDisplayColumn; -import org.labkey.experiment.ExperimentRunGraph; -import org.labkey.experiment.LSIDRelativizer; -import org.labkey.experiment.LineageGraphDisplayColumn; -import org.labkey.experiment.MoveRunsBean; -import org.labkey.experiment.NoPipelineRootSetView; -import org.labkey.experiment.ParentChildView; -import org.labkey.experiment.ProtocolApplicationDisplayColumn; -import org.labkey.experiment.ProtocolDisplayColumn; -import org.labkey.experiment.ProtocolWebPart; -import org.labkey.experiment.RunGroupWebPart; -import org.labkey.experiment.SampleTypeDisplayColumn; -import org.labkey.experiment.SampleTypeWebPart; -import org.labkey.experiment.StandardAndCustomPropertiesView; -import org.labkey.experiment.XarExportPipelineJob; -import org.labkey.experiment.XarExportType; -import org.labkey.experiment.XarExporter; +import org.labkey.experiment.*; import org.labkey.experiment.api.DataClass; import org.labkey.experiment.api.DataClassDomainKind; import org.labkey.experiment.api.ExpDataClassAttachmentParent; @@ -277,7 +273,7 @@ */ public class ExperimentController extends SpringActionController { - private static final Logger _log = Logger.getLogger(ExperimentController.class); + private static final Logger _log = LogManager.getLogger(ExperimentController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ExperimentController.class); private static final String GUEST_DIRECTORY_NAME = "guest"; diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentForm.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentForm.java index 5df535d168b..f048f295b9d 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentForm.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentForm.java @@ -13,12 +13,12 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - + package org.labkey.experiment.controllers.exp; +import org.labkey.api.data.BeanViewForm; import org.labkey.experiment.api.Experiment; import org.labkey.experiment.api.ExperimentServiceImpl; -import org.labkey.api.data.BeanViewForm; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunForm.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunForm.java index a8e65de2973..6ecb7776cb7 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunForm.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunForm.java @@ -19,7 +19,6 @@ import org.labkey.api.view.NotFoundException; import org.labkey.experiment.api.ExpRunImpl; import org.labkey.experiment.api.ExperimentServiceImpl; -import org.springframework.web.servlet.ModelAndView; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunGroupsView.java b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunGroupsView.java index d1910cd23be..e6c4b3a3a31 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunGroupsView.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ExperimentRunGroupsView.java @@ -16,14 +16,23 @@ package org.labkey.experiment.controllers.exp; -import org.labkey.api.view.*; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.Container; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.TableInfo; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.query.ExpSchema; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; -import org.labkey.api.exp.query.ExpSchema; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.data.*; import org.labkey.api.security.User; import org.labkey.api.security.permissions.UpdatePermission; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.Collapsible; +import org.labkey.api.view.DataView; +import org.labkey.api.view.NavTreeManager; +import org.labkey.api.view.SimpleTextDisplayElement; +import org.labkey.api.view.VBox; import org.springframework.validation.BindException; /** diff --git a/experiment/src/org/labkey/experiment/controllers/exp/GraphMoreGrid.java b/experiment/src/org/labkey/experiment/controllers/exp/GraphMoreGrid.java index b665fa7b119..9ab7458b4e1 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/GraphMoreGrid.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/GraphMoreGrid.java @@ -16,7 +16,12 @@ package org.labkey.experiment.controllers.exp; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.TableInfo; import org.labkey.api.view.ActionURL; import org.labkey.api.view.GridView; import org.labkey.api.view.NotFoundException; diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ProtocolParametersView.java b/experiment/src/org/labkey/experiment/controllers/exp/ProtocolParametersView.java index 0de9d0557ca..5fe36715993 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ProtocolParametersView.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ProtocolParametersView.java @@ -16,11 +16,8 @@ package org.labkey.experiment.controllers.exp; -import org.labkey.api.view.JspView; import org.labkey.api.exp.api.ExpProtocol; -import org.labkey.api.exp.api.ExperimentService; - -import java.sql.SQLException; +import org.labkey.api.view.JspView; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/controllers/exp/ProtocolSuccessorPredecessorView.java b/experiment/src/org/labkey/experiment/controllers/exp/ProtocolSuccessorPredecessorView.java index 99a2435d7f8..6e934833a55 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/ProtocolSuccessorPredecessorView.java +++ b/experiment/src/org/labkey/experiment/controllers/exp/ProtocolSuccessorPredecessorView.java @@ -16,7 +16,6 @@ package org.labkey.experiment.controllers.exp; -import org.labkey.api.data.ButtonBar; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; diff --git a/experiment/src/org/labkey/experiment/controllers/exp/experimentRunGraphView.jsp b/experiment/src/org/labkey/experiment/controllers/exp/experimentRunGraphView.jsp index fe6246c16a5..97daa106703 100644 --- a/experiment/src/org/labkey/experiment/controllers/exp/experimentRunGraphView.jsp +++ b/experiment/src/org/labkey/experiment/controllers/exp/experimentRunGraphView.jsp @@ -15,19 +15,19 @@ * limitations under the License. */ %> +<%@ page import="org.apache.commons.io.IOUtils" %> +<%@ page import="org.labkey.api.exp.ExperimentException" %> +<%@ page import="org.labkey.api.reader.Readers" %> +<%@ page import="org.labkey.api.util.UniqueID" %> +<%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.ViewContext" %> -<%@ page import="org.labkey.api.exp.ExperimentException" %> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.experiment.ExperimentRunGraph" %> -<%@ page import="org.labkey.experiment.controllers.exp.ExperimentRunGraphModel" %> -<%@ page import="org.labkey.api.reader.Readers" %> -<%@ page import="org.apache.commons.io.IOUtils" %> <%@ page import="org.labkey.experiment.controllers.exp.ExperimentController" %> +<%@ page import="org.labkey.experiment.controllers.exp.ExperimentRunGraphModel" %> <%@ page import="java.io.IOException" %> <%@ page import="java.io.Reader" %> -<%@ page import="org.labkey.api.view.ActionURL" %> -<%@ page import="org.labkey.api.util.UniqueID" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/experiment/src/org/labkey/experiment/controllers/property/DomainForm.java b/experiment/src/org/labkey/experiment/controllers/property/DomainForm.java index 2456d7ed808..f5db9854c0c 100644 --- a/experiment/src/org/labkey/experiment/controllers/property/DomainForm.java +++ b/experiment/src/org/labkey/experiment/controllers/property/DomainForm.java @@ -25,9 +25,6 @@ import org.labkey.api.exp.property.PropertyService; import org.labkey.api.view.ViewForm; -import java.util.LinkedHashMap; -import java.util.Map; - public class DomainForm extends ViewForm { private Domain _domain; diff --git a/experiment/src/org/labkey/experiment/controllers/property/templateUpdate.jsp b/experiment/src/org/labkey/experiment/controllers/property/templateUpdate.jsp index 8aa42480d2d..4cb876edc0b 100644 --- a/experiment/src/org/labkey/experiment/controllers/property/templateUpdate.jsp +++ b/experiment/src/org/labkey/experiment/controllers/property/templateUpdate.jsp @@ -16,8 +16,8 @@ */ %> <%@ page import="org.labkey.api.view.HttpView" %> -<%@ page import="org.labkey.experiment.controllers.property.PropertyController" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> +<%@ page import="org.labkey.experiment.controllers.property.PropertyController" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/experiment/src/org/labkey/experiment/defaults/DefaultValueServiceImpl.java b/experiment/src/org/labkey/experiment/defaults/DefaultValueServiceImpl.java index 55ccc4aa3af..8c698804f63 100644 --- a/experiment/src/org/labkey/experiment/defaults/DefaultValueServiceImpl.java +++ b/experiment/src/org/labkey/experiment/defaults/DefaultValueServiceImpl.java @@ -16,7 +16,7 @@ package org.labkey.experiment.defaults; import org.apache.commons.beanutils.ConversionException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; @@ -158,7 +158,7 @@ private void replaceObject(Container container, Domain domain, String objectLSID } catch (ConversionException e) { - Logger.getLogger(DefaultValueServiceImpl.class).warn("Unable to convert default value '" + value + "' for property " + property.getName() + ", dropping it"); + LogManager.getLogger(DefaultValueServiceImpl.class).warn("Unable to convert default value '" + value + "' for property " + property.getName() + ", dropping it"); } } } diff --git a/experiment/src/org/labkey/experiment/pipeline/ExpGeneratorHelper.java b/experiment/src/org/labkey/experiment/pipeline/ExpGeneratorHelper.java index 629d994ad0a..259aeb594a3 100644 --- a/experiment/src/org/labkey/experiment/pipeline/ExpGeneratorHelper.java +++ b/experiment/src/org/labkey/experiment/pipeline/ExpGeneratorHelper.java @@ -15,7 +15,7 @@ */ package org.labkey.experiment.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.CompareType; @@ -59,7 +59,6 @@ import java.net.URI; import java.net.URISyntaxException; import java.util.ArrayList; -import java.util.Collection; import java.util.HashMap; import java.util.LinkedHashMap; import java.util.LinkedHashSet; diff --git a/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineJob.java b/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineJob.java index 0e6bf6ef927..b83b849f57d 100644 --- a/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineJob.java +++ b/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineJob.java @@ -18,18 +18,19 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.exp.CompressedXarSource; +import org.labkey.api.exp.FileXarSource; +import org.labkey.api.exp.XarSource; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.api.ExperimentUrls; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExpRun; -import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.exp.XarSource; -import org.labkey.api.exp.CompressedXarSource; -import org.labkey.api.exp.FileXarSource; -import org.labkey.api.util.PageFlowUtil; -import org.apache.log4j.Logger; import java.io.File; import java.io.IOException; @@ -42,7 +43,7 @@ */ public class ExperimentPipelineJob extends PipelineJob { - private static Logger _log = Logger.getLogger(ExperimentPipelineJob.class); + private static Logger _log = LogManager.getLogger(ExperimentPipelineJob.class); private static final Object _experimentLock = new Object(); diff --git a/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineProvider.java b/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineProvider.java index baed29aba52..c757ed5eb01 100644 --- a/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineProvider.java +++ b/experiment/src/org/labkey/experiment/pipeline/ExperimentPipelineProvider.java @@ -16,13 +16,13 @@ package org.labkey.experiment.pipeline; +import org.labkey.api.module.Module; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineDirectory; import org.labkey.api.pipeline.PipelineProvider; +import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ViewContext; -import org.labkey.api.module.Module; -import org.labkey.api.security.permissions.InsertPermission; import org.labkey.experiment.controllers.exp.ExperimentController; import java.io.File; diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsPipelineJob.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsPipelineJob.java index d70f8bf86dd..84982e06495 100644 --- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsPipelineJob.java +++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsPipelineJob.java @@ -18,13 +18,18 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.labkey.api.pipeline.*; +import org.labkey.api.data.Container; +import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.pipeline.LocalDirectory; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineJobService; +import org.labkey.api.pipeline.TaskId; +import org.labkey.api.pipeline.TaskPipeline; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewBackgroundInfo; -import org.labkey.api.data.Container; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExpRun; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java index 501a511a4cc..362df2d5a70 100644 --- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java +++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java @@ -15,42 +15,40 @@ */ package org.labkey.experiment.pipeline; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.xmlbeans.XmlException; +import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; +import org.fhcrc.cpas.exp.xml.ExperimentArchiveType; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; -import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobException; -import org.labkey.api.pipeline.RecordedActionSet; -import org.labkey.api.exp.api.ExperimentService; -import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.ExperimentDataHandler; -import org.labkey.api.exp.XarSource; import org.labkey.api.exp.ExperimentException; -import org.labkey.api.exp.XarFormatException; +import org.labkey.api.exp.XarSource; +import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.RecordedActionSet; import org.labkey.api.util.DateUtil; import org.labkey.api.util.FileUtil; import org.labkey.api.util.XmlBeansUtil; -import org.labkey.experiment.XarExporter; -import org.labkey.experiment.LSIDRelativizer; import org.labkey.experiment.DataURLRelativizer; +import org.labkey.experiment.LSIDRelativizer; +import org.labkey.experiment.XarExporter; import org.labkey.experiment.XarReader; import org.labkey.experiment.api.ExpRunImpl; import org.labkey.experiment.api.ExperimentServiceImpl; -import org.apache.log4j.Logger; -import org.apache.xmlbeans.XmlException; -import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; -import org.fhcrc.cpas.exp.xml.ExperimentArchiveType; -import java.net.URI; -import java.nio.file.Path; -import java.util.List; -import java.util.Map; -import java.util.HashMap; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.IOException; +import java.net.URI; +import java.nio.file.Path; import java.sql.BatchUpdateException; -import java.sql.SQLException; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * User: jeckels @@ -144,7 +142,7 @@ private void moveRun(MoveRunsPipelineJob job, ExpRunImpl experimentRun) throws E public static class MoveRunsXarSource extends XarSource { - private static final Logger _log = Logger.getLogger(MoveRunsXarSource.class); + private static final Logger _log = LogManager.getLogger(MoveRunsXarSource.class); private final String _xml; private File _logFile; diff --git a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTaskFactory.java b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTaskFactory.java index b13fbcb5c8c..c228c3005c9 100644 --- a/experiment/src/org/labkey/experiment/pipeline/MoveRunsTaskFactory.java +++ b/experiment/src/org/labkey/experiment/pipeline/MoveRunsTaskFactory.java @@ -15,13 +15,15 @@ */ package org.labkey.experiment.pipeline; -import org.labkey.api.pipeline.*; -import org.labkey.api.util.FileType; -import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.exp.api.ExpRun; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.pipeline.AbstractTaskFactory; +import org.labkey.api.pipeline.AbstractTaskFactorySettings; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.util.FileType; -import java.util.List; import java.util.Collections; +import java.util.List; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/pipeline/XarGeneratorSource.java b/experiment/src/org/labkey/experiment/pipeline/XarGeneratorSource.java index 49d3677cbb0..48887075b46 100644 --- a/experiment/src/org/labkey/experiment/pipeline/XarGeneratorSource.java +++ b/experiment/src/org/labkey/experiment/pipeline/XarGeneratorSource.java @@ -15,12 +15,10 @@ */ package org.labkey.experiment.pipeline; +import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; import org.labkey.api.exp.AbstractFileXarSource; import org.labkey.api.pipeline.PipelineJob; -import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; -import org.apache.xmlbeans.XmlException; -import java.io.IOException; import java.io.File; /* diff --git a/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java b/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java index 13ab9dc6a5c..f3d49efbc46 100644 --- a/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java +++ b/experiment/src/org/labkey/experiment/samples/UploadSamplesHelper.java @@ -17,7 +17,8 @@ package org.labkey.experiment.samples; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -81,7 +82,7 @@ public abstract class UploadSamplesHelper { - private static final Logger _log = Logger.getLogger(UploadSamplesHelper.class); + private static final Logger _log = LogManager.getLogger(UploadSamplesHelper.class); private static final String MATERIAL_LSID_SUFFIX = "ToBeReplaced"; diff --git a/experiment/src/org/labkey/experiment/samplesAndAnalytes.jsp b/experiment/src/org/labkey/experiment/samplesAndAnalytes.jsp index 62f333b3e2e..a0878df302d 100644 --- a/experiment/src/org/labkey/experiment/samplesAndAnalytes.jsp +++ b/experiment/src/org/labkey/experiment/samplesAndAnalytes.jsp @@ -18,12 +18,12 @@ <%@ page import="org.labkey.api.data.Container" %> <%@ page import="org.labkey.api.exp.api.ExpSampleType" %> <%@ page import="org.labkey.api.study.SamplesUrls" %> +<%@ page import="org.labkey.api.study.SpecimenService" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.experiment.api.ExpSampleTypeImpl" %> <%@ page import="org.labkey.experiment.api.SampleTypeServiceImpl" %> <%@ page import="org.labkey.experiment.controllers.exp.ExperimentController" %> <%@ page import="java.util.List" %> -<%@ page import="org.labkey.api.study.SpecimenService" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% Container proj = getContainer().getProject(); diff --git a/experiment/src/org/labkey/experiment/types/Concept.java b/experiment/src/org/labkey/experiment/types/Concept.java index 01055724c6b..4b9875087ab 100644 --- a/experiment/src/org/labkey/experiment/types/Concept.java +++ b/experiment/src/org/labkey/experiment/types/Concept.java @@ -17,8 +17,8 @@ package org.labkey.experiment.types; import org.apache.commons.lang3.StringUtils; -import org.labkey.api.exp.PropertyDescriptor; import org.labkey.api.data.ContainerManager; +import org.labkey.api.exp.PropertyDescriptor; import java.util.HashSet; diff --git a/experiment/src/org/labkey/experiment/types/importVocabulary.jsp b/experiment/src/org/labkey/experiment/types/importVocabulary.jsp index d2b7dc9c5ab..e0c6eb144cb 100644 --- a/experiment/src/org/labkey/experiment/types/importVocabulary.jsp +++ b/experiment/src/org/labkey/experiment/types/importVocabulary.jsp @@ -15,8 +15,8 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.experiment.types.TypesController" %> <%@ page import="org.labkey.api.view.HttpView" %> +<%@ page import="org.labkey.experiment.types.TypesController" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/experiment/src/org/labkey/experiment/xar/AbstractXarImporter.java b/experiment/src/org/labkey/experiment/xar/AbstractXarImporter.java index 7b808307f05..74b8b3e95bc 100644 --- a/experiment/src/org/labkey/experiment/xar/AbstractXarImporter.java +++ b/experiment/src/org/labkey/experiment/xar/AbstractXarImporter.java @@ -16,7 +16,7 @@ package org.labkey.experiment.xar; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.fhcrc.cpas.exp.xml.ExperimentArchiveType; import org.labkey.api.data.Container; import org.labkey.api.exp.XarContext; diff --git a/experiment/src/org/labkey/experiment/xar/AutoFileLSIDReplacer.java b/experiment/src/org/labkey/experiment/xar/AutoFileLSIDReplacer.java index 7f646baecd9..9ff1bf3041f 100644 --- a/experiment/src/org/labkey/experiment/xar/AutoFileLSIDReplacer.java +++ b/experiment/src/org/labkey/experiment/xar/AutoFileLSIDReplacer.java @@ -18,12 +18,12 @@ import org.apache.commons.codec.binary.Hex; import org.labkey.api.data.Container; +import org.labkey.api.exp.XarContext; import org.labkey.api.exp.XarFormatException; import org.labkey.api.exp.XarSource; -import org.labkey.api.exp.XarContext; -import org.labkey.api.exp.xar.Replacer; -import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.exp.api.ExpData; +import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.exp.xar.Replacer; import org.labkey.api.util.FileUtil; import org.labkey.api.util.PageFlowUtil; diff --git a/experiment/src/org/labkey/experiment/xar/FileResolver.java b/experiment/src/org/labkey/experiment/xar/FileResolver.java index 0e2face4215..86e0f0583ff 100644 --- a/experiment/src/org/labkey/experiment/xar/FileResolver.java +++ b/experiment/src/org/labkey/experiment/xar/FileResolver.java @@ -16,16 +16,22 @@ package org.labkey.experiment.xar; -import org.labkey.api.util.FileUtil; import org.labkey.api.exp.XarFormatException; import org.labkey.api.exp.xar.Replacer; +import org.labkey.api.util.FileUtil; import java.io.File; -import java.io.IOException; import java.io.FileFilter; -import java.util.*; -import java.util.regex.Pattern; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.regex.Matcher; +import java.util.regex.Pattern; /** * User: jeckels diff --git a/experiment/src/org/labkey/experiment/xar/FolderXarWriterFactory.java b/experiment/src/org/labkey/experiment/xar/FolderXarWriterFactory.java index d4da00afff7..c3c9711329c 100644 --- a/experiment/src/org/labkey/experiment/xar/FolderXarWriterFactory.java +++ b/experiment/src/org/labkey/experiment/xar/FolderXarWriterFactory.java @@ -17,9 +17,9 @@ import org.labkey.api.admin.AbstractFolderContext; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; diff --git a/filecontent/src/org/labkey/filecontent/FileContentModule.java b/filecontent/src/org/labkey/filecontent/FileContentModule.java index 259f4ff4055..c1c89c44aa7 100644 --- a/filecontent/src/org/labkey/filecontent/FileContentModule.java +++ b/filecontent/src/org/labkey/filecontent/FileContentModule.java @@ -43,7 +43,6 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; -import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.stream.Collectors; diff --git a/filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java b/filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java index 326c6f3bf92..13810cd80b6 100644 --- a/filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java +++ b/filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java @@ -19,7 +19,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -112,7 +113,7 @@ */ public class FileContentServiceImpl implements FileContentService { - private static final Logger _log = Logger.getLogger(FileContentServiceImpl.class); + private static final Logger _log = LogManager.getLogger(FileContentServiceImpl.class); private static final String UPLOAD_LOG = ".upload.log"; private static final FileContentServiceImpl INSTANCE = new FileContentServiceImpl(); diff --git a/filecontent/src/org/labkey/filecontent/FileImporter.java b/filecontent/src/org/labkey/filecontent/FileImporter.java index f2b4189cb72..a7e23048ea7 100644 --- a/filecontent/src/org/labkey/filecontent/FileImporter.java +++ b/filecontent/src/org/labkey/filecontent/FileImporter.java @@ -15,7 +15,7 @@ */ package org.labkey.filecontent; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; diff --git a/filecontent/src/org/labkey/filecontent/FilePropertiesDomainKind.java b/filecontent/src/org/labkey/filecontent/FilePropertiesDomainKind.java index 0d00cc50a11..45e48a07bbd 100644 --- a/filecontent/src/org/labkey/filecontent/FilePropertiesDomainKind.java +++ b/filecontent/src/org/labkey/filecontent/FilePropertiesDomainKind.java @@ -15,7 +15,6 @@ */ package org.labkey.filecontent; -import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.SQLFragment; import org.labkey.api.exp.Lsid; diff --git a/filecontent/src/org/labkey/filecontent/FileQueryUpdateService.java b/filecontent/src/org/labkey/filecontent/FileQueryUpdateService.java index 6b1d0382671..9545b64f6ce 100644 --- a/filecontent/src/org/labkey/filecontent/FileQueryUpdateService.java +++ b/filecontent/src/org/labkey/filecontent/FileQueryUpdateService.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.converters.IntegerConverter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -80,7 +81,7 @@ */ public class FileQueryUpdateService extends AbstractQueryUpdateService { - private static final Logger _log = Logger.getLogger(FileQueryUpdateService.class); + private static final Logger _log = LogManager.getLogger(FileQueryUpdateService.class); private Container _container; private Set _columns; private Domain _domain; diff --git a/filecontent/src/org/labkey/filecontent/FileSystemAttachmentParent.java b/filecontent/src/org/labkey/filecontent/FileSystemAttachmentParent.java index fcc964a0ed4..2af6008ef37 100644 --- a/filecontent/src/org/labkey/filecontent/FileSystemAttachmentParent.java +++ b/filecontent/src/org/labkey/filecontent/FileSystemAttachmentParent.java @@ -16,7 +16,8 @@ package org.labkey.filecontent; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.AttachmentDirectory; @@ -41,7 +42,7 @@ */ public class FileSystemAttachmentParent implements AttachmentDirectory { - private static final Logger LOG = Logger.getLogger(FileSystemAttachmentParent.class); + private static final Logger LOG = LogManager.getLogger(FileSystemAttachmentParent.class); private Container c; private String entityId; diff --git a/filecontent/src/org/labkey/filecontent/message/FileContentDigestProvider.java b/filecontent/src/org/labkey/filecontent/message/FileContentDigestProvider.java index d17f4463a6c..4048ae0294e 100644 --- a/filecontent/src/org/labkey/filecontent/message/FileContentDigestProvider.java +++ b/filecontent/src/org/labkey/filecontent/message/FileContentDigestProvider.java @@ -16,7 +16,8 @@ package org.labkey.filecontent.message; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; @@ -72,7 +73,7 @@ */ public class FileContentDigestProvider implements MessageDigest.Provider { - private static final Logger _log = Logger.getLogger(FileContentDigestProvider.class); + private static final Logger _log = LogManager.getLogger(FileContentDigestProvider.class); private final int _notificationOption; // the notification option to match : (short digest, daily digest) diff --git a/filecontent/src/org/labkey/filecontent/view/fileDigestNotify.jsp b/filecontent/src/org/labkey/filecontent/view/fileDigestNotify.jsp index ac326aff3af..a1e3f7c7bf6 100644 --- a/filecontent/src/org/labkey/filecontent/view/fileDigestNotify.jsp +++ b/filecontent/src/org/labkey/filecontent/view/fileDigestNotify.jsp @@ -15,6 +15,8 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.announcements.EmailOption" %> +<%@ page import="org.labkey.api.audit.provider.FileSystemAuditProvider" %> <%@ page import="org.labkey.api.files.FileUrls" %> <%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.util.DateUtil" %> @@ -27,8 +29,6 @@ <%@ page import="org.labkey.api.webdav.WebdavService" %> <%@ page import="java.util.List" %> <%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.audit.provider.FileSystemAuditProvider" %> -<%@ page import="org.labkey.api.announcements.EmailOption" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% diff --git a/internal/src/org/labkey/api/announcements/CommSchema.java b/internal/src/org/labkey/api/announcements/CommSchema.java index 43769b608c7..95f5763d374 100644 --- a/internal/src/org/labkey/api/announcements/CommSchema.java +++ b/internal/src/org/labkey/api/announcements/CommSchema.java @@ -17,8 +17,8 @@ import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; -import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.TableInfo; +import org.labkey.api.data.dialect.SqlDialect; /** * User: arauch diff --git a/internal/src/org/labkey/api/data/TableViewFormTestCase.java b/internal/src/org/labkey/api/data/TableViewFormTestCase.java index 9452e7e9545..a43de41adbb 100644 --- a/internal/src/org/labkey/api/data/TableViewFormTestCase.java +++ b/internal/src/org/labkey/api/data/TableViewFormTestCase.java @@ -32,7 +32,6 @@ import org.labkey.api.view.ViewContext; import org.springframework.validation.BindException; -import javax.servlet.ServletException; import java.sql.SQLException; import java.sql.Timestamp; import java.util.Date; diff --git a/internal/src/org/labkey/api/data/TransactionFilter.java b/internal/src/org/labkey/api/data/TransactionFilter.java index 10f310e65bb..93daf18f257 100644 --- a/internal/src/org/labkey/api/data/TransactionFilter.java +++ b/internal/src/org/labkey/api/data/TransactionFilter.java @@ -16,13 +16,13 @@ package org.labkey.api.data; -import java.io.IOException; import javax.servlet.Filter; import javax.servlet.FilterChain; import javax.servlet.FilterConfig; import javax.servlet.ServletException; import javax.servlet.ServletRequest; import javax.servlet.ServletResponse; +import java.io.IOException; public class TransactionFilter implements Filter { diff --git a/internal/src/org/labkey/api/exp/AbstractFileXarSource.java b/internal/src/org/labkey/api/exp/AbstractFileXarSource.java index 9bb078a5a69..5ff368fa092 100644 --- a/internal/src/org/labkey/api/exp/AbstractFileXarSource.java +++ b/internal/src/org/labkey/api/exp/AbstractFileXarSource.java @@ -16,19 +16,19 @@ package org.labkey.api.exp; +import org.apache.xmlbeans.XmlException; import org.fhcrc.cpas.exp.xml.ExperimentArchiveDocument; -import org.labkey.api.util.NetworkDrive; -import org.labkey.api.util.FileUtil; -import org.labkey.api.util.XmlBeansUtil; -import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.data.Container; +import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.security.User; -import org.apache.xmlbeans.XmlException; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.NetworkDrive; +import org.labkey.api.util.XmlBeansUtil; import javax.annotation.Nullable; -import java.io.IOException; -import java.io.FileInputStream; import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; import java.net.URI; import java.nio.file.Path; diff --git a/internal/src/org/labkey/api/exp/form/DeleteForm.java b/internal/src/org/labkey/api/exp/form/DeleteForm.java index 005578a5792..b06c1b9220c 100644 --- a/internal/src/org/labkey/api/exp/form/DeleteForm.java +++ b/internal/src/org/labkey/api/exp/form/DeleteForm.java @@ -15,8 +15,8 @@ */ package org.labkey.api.exp.form; -import org.labkey.api.data.DataRegionSelection; import org.labkey.api.assay.actions.ProtocolIdForm; +import org.labkey.api.data.DataRegionSelection; import java.util.Set; diff --git a/internal/src/org/labkey/api/exp/property/DomainTemplate.java b/internal/src/org/labkey/api/exp/property/DomainTemplate.java index 37357f058eb..499a833aeb1 100644 --- a/internal/src/org/labkey/api/exp/property/DomainTemplate.java +++ b/internal/src/org/labkey/api/exp/property/DomainTemplate.java @@ -15,7 +15,7 @@ */ package org.labkey.api.exp.property; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlCursor; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; @@ -102,21 +102,21 @@ public static DomainTemplate findTemplate(String moduleName, String groupName, S { if (moduleName == null || groupName == null || templateName == null) { - Logger.getLogger(DomainTemplate.class).warn("Module, group, and template name required to get domain template"); + LogManager.getLogger(DomainTemplate.class).warn("Module, group, and template name required to get domain template"); return null; } Module module = ModuleLoader.getInstance().getModule(moduleName); if (module == null) { - Logger.getLogger(DomainTemplate.class).warn("Module '" + moduleName + "' for domain template not found"); + LogManager.getLogger(DomainTemplate.class).warn("Module '" + moduleName + "' for domain template not found"); return null; } DomainTemplateGroup group = DomainTemplateGroup.get(module, groupName); if (group == null) { - Logger.getLogger(DomainTemplate.class).warn("Domain template group '" + groupName + "' not found in module '" + moduleName + "'"); + LogManager.getLogger(DomainTemplate.class).warn("Domain template group '" + groupName + "' not found in module '" + moduleName + "'"); return null; } diff --git a/internal/src/org/labkey/api/exp/property/DomainTemplateGroup.java b/internal/src/org/labkey/api/exp/property/DomainTemplateGroup.java index f5257f0992c..99e5f93b37a 100644 --- a/internal/src/org/labkey/api/exp/property/DomainTemplateGroup.java +++ b/internal/src/org/labkey/api/exp/property/DomainTemplateGroup.java @@ -15,7 +15,8 @@ */ package org.labkey.api.exp.property; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; import org.jetbrains.annotations.NotNull; @@ -65,7 +66,7 @@ */ public class DomainTemplateGroup { - static final Logger LOG = Logger.getLogger(DomainTemplateGroup.class); + static final Logger LOG = LogManager.getLogger(DomainTemplateGroup.class); private static final String DIR_NAME = "domain-templates"; private static final String SUFFIX = ".template.xml"; private static final ModuleResourceCache> CACHE = ModuleResourceCaches.create("Domain templates", new DomainTemplateGroupCacheHandler(), ResourceRootProvider.getStandard(new Path(DIR_NAME))); diff --git a/internal/src/org/labkey/api/exp/property/DomainUtil.java b/internal/src/org/labkey/api/exp/property/DomainUtil.java index 309fc1d29b2..fcc6b728028 100644 --- a/internal/src/org/labkey/api/exp/property/DomainUtil.java +++ b/internal/src/org/labkey/api/exp/property/DomainUtil.java @@ -19,7 +19,7 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AbstractAssayProvider; @@ -121,7 +121,7 @@ else if (AbstractAssayProvider.PARTICIPANT_VISIT_RESOLVER_PROPERTY_NAME.equalsIg } catch (Exception e) { - Logger.getLogger(DomainUtil.class).debug("Failed to parse JSON for default value. It may predate JSON encoding for thaw list.", e); + LogManager.getLogger(DomainUtil.class).debug("Failed to parse JSON for default value. It may predate JSON encoding for thaw list.", e); // And then fall through below to return defaultValue.toString(); } } diff --git a/internal/src/org/labkey/api/exp/property/SystemProperty.java b/internal/src/org/labkey/api/exp/property/SystemProperty.java index 3dae99fa979..f709f39eec3 100644 --- a/internal/src/org/labkey/api/exp/property/SystemProperty.java +++ b/internal/src/org/labkey/api/exp/property/SystemProperty.java @@ -16,7 +16,8 @@ package org.labkey.api.exp.property; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.ColumnRenderPropertiesImpl; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -36,7 +37,7 @@ public class SystemProperty { - static final private Logger _log = Logger.getLogger(SystemProperty.class); + static final private Logger _log = LogManager.getLogger(SystemProperty.class); static private Map _systemProperties = new LinkedHashMap<>(); static private boolean _registered = false; diff --git a/internal/src/org/labkey/api/gwt/server/BaseRemoteService.java b/internal/src/org/labkey/api/gwt/server/BaseRemoteService.java index 4ff91f6eb2f..2ea41cff399 100644 --- a/internal/src/org/labkey/api/gwt/server/BaseRemoteService.java +++ b/internal/src/org/labkey/api/gwt/server/BaseRemoteService.java @@ -17,23 +17,24 @@ package org.labkey.api.gwt.server; import com.google.gwt.user.server.rpc.RemoteServiceServlet; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; +import org.labkey.api.module.ModuleLoader; +import org.labkey.api.security.User; import org.labkey.api.settings.LookAndFeelProperties; +import org.labkey.api.util.ExceptionUtil; +import org.labkey.api.view.ActionURL; import org.labkey.api.view.UnauthorizedException; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.ActionURL; -import org.labkey.api.data.Container; -import org.labkey.api.security.User; -import org.labkey.api.util.ExceptionUtil; -import org.labkey.api.module.ModuleLoader; -import org.apache.log4j.Logger; import javax.servlet.ServletConfig; import javax.servlet.ServletContext; import javax.servlet.http.HttpServletResponse; +import java.io.IOException; import java.util.Enumeration; import java.util.Vector; -import java.io.IOException; /** * User: brittp @@ -42,7 +43,7 @@ */ public abstract class BaseRemoteService extends RemoteServiceServlet { - private static Logger _log = Logger.getLogger(BaseRemoteService.class); + private static Logger _log = LogManager.getLogger(BaseRemoteService.class); protected ViewContext _context; public BaseRemoteService(ViewContext context) diff --git a/internal/src/org/labkey/api/ldk/table/ContainerScopedTable.java b/internal/src/org/labkey/api/ldk/table/ContainerScopedTable.java index bae1c2f5f2e..7b51a7bb4aa 100644 --- a/internal/src/org/labkey/api/ldk/table/ContainerScopedTable.java +++ b/internal/src/org/labkey/api/ldk/table/ContainerScopedTable.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -65,7 +66,7 @@ public class ContainerScopedTable extends CustomP { private String _pseudoPk; private Set _realPKs = new HashSet<>(); - private static final Logger _log = Logger.getLogger(ContainerScopedTable.class); + private static final Logger _log = LogManager.getLogger(ContainerScopedTable.class); public ContainerScopedTable(SchemaType schema, TableInfo st, ContainerFilter cf, String newPk) { diff --git a/internal/src/org/labkey/api/ldk/table/SharedDataTable.java b/internal/src/org/labkey/api/ldk/table/SharedDataTable.java index e8473dab006..f47870f4ec7 100644 --- a/internal/src/org/labkey/api/ldk/table/SharedDataTable.java +++ b/internal/src/org/labkey/api/ldk/table/SharedDataTable.java @@ -15,7 +15,6 @@ */ package org.labkey.api.ldk.table; -import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.ContainerType; diff --git a/internal/src/org/labkey/api/message/digest/MessageDigest.java b/internal/src/org/labkey/api/message/digest/MessageDigest.java index 2abc79b7fca..1620cd8bdd8 100644 --- a/internal/src/org/labkey/api/message/digest/MessageDigest.java +++ b/internal/src/org/labkey/api/message/digest/MessageDigest.java @@ -15,7 +15,8 @@ */ package org.labkey.api.message.digest; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.PropertyManager; import org.labkey.api.util.ExceptionUtil; import org.quartz.Job; @@ -45,7 +46,7 @@ public abstract class MessageDigest private final List _providers = new CopyOnWriteArrayList<>(); - private static final Logger _log = Logger.getLogger(MessageDigest.class); + private static final Logger _log = LogManager.getLogger(MessageDigest.class); public interface Provider { diff --git a/internal/src/org/labkey/api/query/ExtendedTableDomainKind.java b/internal/src/org/labkey/api/query/ExtendedTableDomainKind.java index c318bf39bd3..eadb0f40f2f 100644 --- a/internal/src/org/labkey/api/query/ExtendedTableDomainKind.java +++ b/internal/src/org/labkey/api/query/ExtendedTableDomainKind.java @@ -15,12 +15,12 @@ */ package org.labkey.api.query; +import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.exp.ChangePropertyDescriptorException; import org.labkey.api.exp.Handler; import org.labkey.api.exp.Lsid; import org.labkey.api.exp.TemplateInfo; -import org.json.JSONObject; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.exp.property.DomainUtil; diff --git a/internal/src/org/labkey/api/query/PropertiesDisplayColumn.java b/internal/src/org/labkey/api/query/PropertiesDisplayColumn.java index 4aa910c7b95..4c64c588c57 100644 --- a/internal/src/org/labkey/api/query/PropertiesDisplayColumn.java +++ b/internal/src/org/labkey/api/query/PropertiesDisplayColumn.java @@ -21,9 +21,6 @@ import org.labkey.api.exp.OntologyManager; import org.labkey.api.exp.PropertyColumn; import org.labkey.api.exp.PropertyDescriptor; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.UserSchema; import org.labkey.api.security.UserPrincipal; import org.labkey.api.security.permissions.Permission; import org.labkey.api.security.permissions.ReadPermission; diff --git a/internal/src/org/labkey/api/query/ReexecutableRenderContext.java b/internal/src/org/labkey/api/query/ReexecutableRenderContext.java index 81ecd882c84..22605d4a06c 100644 --- a/internal/src/org/labkey/api/query/ReexecutableRenderContext.java +++ b/internal/src/org/labkey/api/query/ReexecutableRenderContext.java @@ -10,8 +10,6 @@ import org.labkey.api.data.SqlSelector; import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; -import org.labkey.api.query.FieldKey; -import org.labkey.api.query.QueryService; import org.labkey.api.util.Pair; import java.util.ArrayList; diff --git a/internal/src/org/labkey/api/query/SimpleUserSchema.java b/internal/src/org/labkey/api/query/SimpleUserSchema.java index 37d8835bd70..eadc4776251 100644 --- a/internal/src/org/labkey/api/query/SimpleUserSchema.java +++ b/internal/src/org/labkey/api/query/SimpleUserSchema.java @@ -17,7 +17,8 @@ package org.labkey.api.query; import com.google.common.collect.Iterables; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -73,7 +74,7 @@ */ public class SimpleUserSchema extends UserSchema { - private static final Logger _log = Logger.getLogger(SimpleUserSchema.class); + private static final Logger _log = LogManager.getLogger(SimpleUserSchema.class); // CaseInsensitiveTreeSet preserves case of the table names (from XML), unlike CaseInsensitiveHashSet private final Set _available = new CaseInsensitiveTreeSet(); diff --git a/internal/src/org/labkey/api/rss/RSSServiceImpl.java b/internal/src/org/labkey/api/rss/RSSServiceImpl.java index d457a6e85a3..3e4949db109 100644 --- a/internal/src/org/labkey/api/rss/RSSServiceImpl.java +++ b/internal/src/org/labkey/api/rss/RSSServiceImpl.java @@ -23,7 +23,7 @@ import com.rometools.rome.io.SyndFeedInput; import com.rometools.rome.io.SyndFeedOutput; import com.rometools.rome.io.XmlReader; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.TableInfo; @@ -86,7 +86,7 @@ public void aggregateFeeds(List feeds, User user, Writer writer) } catch (IOException e) { - Logger.getLogger(RSSService.class).error("Invalid RSS Feed: " + e.getMessage()); + LogManager.getLogger(RSSService.class).error("Invalid RSS Feed: " + e.getMessage()); } if (null != reader) @@ -100,7 +100,7 @@ public void aggregateFeeds(List feeds, User user, Writer writer) } catch (FeedException fe) { - Logger.getLogger(RSSService.class).error("Invalid Feed (FeedException): " + _feed.getFeedURL()); + LogManager.getLogger(RSSService.class).error("Invalid Feed (FeedException): " + _feed.getFeedURL()); } } } @@ -130,7 +130,7 @@ else if (o2 == null) } catch (Exception e) { - Logger.getLogger(RSSService.class).error("Error", e); + LogManager.getLogger(RSSService.class).error("Error", e); } } diff --git a/internal/src/org/labkey/api/script/ExternalScriptable.java b/internal/src/org/labkey/api/script/ExternalScriptable.java index 110b5b6ce46..56d4c8d6b5c 100644 --- a/internal/src/org/labkey/api/script/ExternalScriptable.java +++ b/internal/src/org/labkey/api/script/ExternalScriptable.java @@ -24,7 +24,13 @@ package org.labkey.api.script; -import org.mozilla.javascript.*; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.Function; +import org.mozilla.javascript.NativeJavaClass; +import org.mozilla.javascript.ScriptRuntime; +import org.mozilla.javascript.Scriptable; +import org.mozilla.javascript.ScriptableObject; +import org.mozilla.javascript.Wrapper; import javax.script.Bindings; import javax.script.ScriptContext; diff --git a/internal/src/org/labkey/api/script/RhinoCompiledScript.java b/internal/src/org/labkey/api/script/RhinoCompiledScript.java index 2de3494762e..79123314b18 100644 --- a/internal/src/org/labkey/api/script/RhinoCompiledScript.java +++ b/internal/src/org/labkey/api/script/RhinoCompiledScript.java @@ -26,9 +26,14 @@ package org.labkey.api.script; import com.sun.phobos.script.util.ExtendedScriptException; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.util.ExceptionUtil; -import org.mozilla.javascript.*; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.JavaScriptException; +import org.mozilla.javascript.RhinoException; +import org.mozilla.javascript.Script; +import org.mozilla.javascript.Scriptable; import javax.script.CompiledScript; import javax.script.ScriptContext; @@ -45,7 +50,7 @@ // kevink: Essentially the same as the original, with changes marked with kevink final class RhinoCompiledScript extends CompiledScript { - private final Logger _log = Logger.getLogger(RhinoCompiledScript.class); + private final Logger _log = LogManager.getLogger(RhinoCompiledScript.class); private RhinoScriptEngine engine; private Script script; diff --git a/internal/src/org/labkey/api/script/RhinoScriptEngine.java b/internal/src/org/labkey/api/script/RhinoScriptEngine.java index 237abe61696..872484b2d68 100644 --- a/internal/src/org/labkey/api/script/RhinoScriptEngine.java +++ b/internal/src/org/labkey/api/script/RhinoScriptEngine.java @@ -25,15 +25,42 @@ package org.labkey.api.script; import com.sun.phobos.script.javascript.RhinoScriptEngineFactory; -import com.sun.phobos.script.util.*; import com.sun.phobos.script.util.ExtendedScriptException; -import org.apache.log4j.Logger; +import com.sun.phobos.script.util.InterfaceImplementor; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.reports.LabKeyScriptEngine; import org.labkey.api.util.ExceptionUtil; -import org.mozilla.javascript.*; - -import javax.script.*; -import java.io.*; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.Function; +import org.mozilla.javascript.ImporterTopLevel; +import org.mozilla.javascript.JavaScriptException; +import org.mozilla.javascript.LazilyLoadedCtor; +import org.mozilla.javascript.RhinoException; +import org.mozilla.javascript.Script; +import org.mozilla.javascript.Scriptable; +import org.mozilla.javascript.ScriptableObject; +import org.mozilla.javascript.Synchronizer; +import org.mozilla.javascript.Undefined; +import org.mozilla.javascript.Wrapper; + +import javax.script.AbstractScriptEngine; +import javax.script.Bindings; +import javax.script.Compilable; +import javax.script.CompiledScript; +import javax.script.Invocable; +import javax.script.ScriptContext; +import javax.script.ScriptEngine; +import javax.script.ScriptEngineFactory; +import javax.script.ScriptException; +import javax.script.SimpleBindings; +import javax.script.SimpleScriptContext; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; +import java.io.StringReader; import java.lang.reflect.Method; import java.util.HashMap; import java.util.Map; @@ -58,7 +85,7 @@ // kevink: Essentially the same as the original, with changes marked with kevink public class RhinoScriptEngine extends AbstractScriptEngine implements LabKeyScriptEngine, Invocable, Compilable { - private final Logger _log = Logger.getLogger(RhinoScriptEngine.class); + private final Logger _log = LogManager.getLogger(RhinoScriptEngine.class); public static final boolean DEBUG = false; private static final String TOPLEVEL_SCRIPT_NAME = "META-INF/toplevel.js"; diff --git a/internal/src/org/labkey/api/script/RhinoService.java b/internal/src/org/labkey/api/script/RhinoService.java index caceaa87989..7df7facdc27 100644 --- a/internal/src/org/labkey/api/script/RhinoService.java +++ b/internal/src/org/labkey/api/script/RhinoService.java @@ -16,7 +16,8 @@ package org.labkey.api.script; import com.sun.phobos.script.javascript.RhinoScriptEngineFactory; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.junit.Assert; @@ -104,7 +105,7 @@ public final class RhinoService { - public static final Logger LOG = Logger.getLogger(ScriptService.Console.class); + public static final Logger LOG = LogManager.getLogger(ScriptService.Console.class); static final RhinoFactory RHINO_FACTORY = new RhinoFactory(); public static void register() @@ -847,7 +848,7 @@ public CompiledScript compile(Reader script) throws ScriptException */ class SandboxContextFactory extends ContextFactory { - private static final Logger log = Logger.getLogger(SandboxContextFactory.class); + private static final Logger log = LogManager.getLogger(SandboxContextFactory.class); static final ContextFactory SANDBOX = new SandboxContextFactory(); diff --git a/internal/src/org/labkey/api/script/ScriptUtils.java b/internal/src/org/labkey/api/script/ScriptUtils.java index 4ccb473208b..8e219da473b 100644 --- a/internal/src/org/labkey/api/script/ScriptUtils.java +++ b/internal/src/org/labkey/api/script/ScriptUtils.java @@ -18,7 +18,12 @@ import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.ValidationException; -import org.mozilla.javascript.*; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.ScriptRuntime; +import org.mozilla.javascript.Scriptable; +import org.mozilla.javascript.ScriptableObject; +import org.mozilla.javascript.Undefined; +import org.mozilla.javascript.UniqueTag; import java.util.ArrayList; import java.util.Date; diff --git a/internal/src/org/labkey/api/script/ScriptableErrors.java b/internal/src/org/labkey/api/script/ScriptableErrors.java index 6a75a03ff6c..b1a0f37a765 100644 --- a/internal/src/org/labkey/api/script/ScriptableErrors.java +++ b/internal/src/org/labkey/api/script/ScriptableErrors.java @@ -18,12 +18,12 @@ import org.labkey.api.query.ValidationException; import org.mozilla.javascript.BaseFunction; import org.mozilla.javascript.Context; +import org.mozilla.javascript.EvaluatorException; import org.mozilla.javascript.NativeJavaObject; import org.mozilla.javascript.ScriptRuntime; import org.mozilla.javascript.Scriptable; import org.mozilla.javascript.ScriptableObject; import org.mozilla.javascript.Wrapper; -import org.mozilla.javascript.EvaluatorException; import java.util.List; import java.util.Map; diff --git a/internal/src/org/labkey/api/script/ScriptableErrorsList.java b/internal/src/org/labkey/api/script/ScriptableErrorsList.java index 2b463a9b941..430a38d8b6d 100644 --- a/internal/src/org/labkey/api/script/ScriptableErrorsList.java +++ b/internal/src/org/labkey/api/script/ScriptableErrorsList.java @@ -20,9 +20,9 @@ import org.mozilla.javascript.BaseFunction; import org.mozilla.javascript.Context; import org.mozilla.javascript.EvaluatorException; +import org.mozilla.javascript.Scriptable; import org.mozilla.javascript.ScriptableObject; import org.mozilla.javascript.Wrapper; -import org.mozilla.javascript.Scriptable; import java.util.List; diff --git a/internal/src/org/labkey/api/script/ScriptableList.java b/internal/src/org/labkey/api/script/ScriptableList.java index 1477e156812..88eb8890499 100644 --- a/internal/src/org/labkey/api/script/ScriptableList.java +++ b/internal/src/org/labkey/api/script/ScriptableList.java @@ -16,11 +16,19 @@ package org.labkey.api.script; -import org.mozilla.javascript.*; +import org.mozilla.javascript.BaseFunction; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.EvaluatorException; +import org.mozilla.javascript.NativeJavaObject; +import org.mozilla.javascript.ScriptRuntime; +import org.mozilla.javascript.Scriptable; +import org.mozilla.javascript.ScriptableObject; +import org.mozilla.javascript.Undefined; +import org.mozilla.javascript.Wrapper; -import java.util.List; import java.util.ArrayList; import java.util.Collection; +import java.util.List; import java.util.Map; /** diff --git a/internal/src/org/labkey/api/script/ScriptableMap.java b/internal/src/org/labkey/api/script/ScriptableMap.java index 76d65911b45..a402390ab1e 100644 --- a/internal/src/org/labkey/api/script/ScriptableMap.java +++ b/internal/src/org/labkey/api/script/ScriptableMap.java @@ -16,10 +16,18 @@ package org.labkey.api.script; -import org.mozilla.javascript.*; +import org.mozilla.javascript.BaseFunction; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.EvaluatorException; +import org.mozilla.javascript.NativeJavaObject; +import org.mozilla.javascript.ScriptRuntime; +import org.mozilla.javascript.Scriptable; +import org.mozilla.javascript.ScriptableObject; +import org.mozilla.javascript.Undefined; +import org.mozilla.javascript.Wrapper; -import java.util.Map; import java.util.HashMap; +import java.util.Map; /** * ScriptableMap is a wrapper for java.util.Map instances that allows developers diff --git a/internal/src/org/labkey/api/script/TopLevel.java b/internal/src/org/labkey/api/script/TopLevel.java index ea2d120217d..9dea9de7621 100644 --- a/internal/src/org/labkey/api/script/TopLevel.java +++ b/internal/src/org/labkey/api/script/TopLevel.java @@ -1,22 +1,23 @@ -/* - * Copyright (c) 2011 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2011 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.script; -import org.mozilla.javascript.*; -import org.mozilla.javascript.tools.shell.Global; +import org.mozilla.javascript.Context; +import org.mozilla.javascript.ImporterTopLevel; +import org.mozilla.javascript.ScriptableObject; /** * User: kevink diff --git a/internal/src/org/labkey/api/security/BlacklistFilter.java b/internal/src/org/labkey/api/security/BlacklistFilter.java index 2a5a18c946c..b3e61298f01 100644 --- a/internal/src/org/labkey/api/security/BlacklistFilter.java +++ b/internal/src/org/labkey/api/security/BlacklistFilter.java @@ -17,8 +17,9 @@ import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheManager; import org.labkey.api.util.FileUtil; @@ -40,7 +41,7 @@ */ public class BlacklistFilter { - static Logger _log = Logger.getLogger(BlacklistFilter.class); + static Logger _log = LogManager.getLogger(BlacklistFilter.class); static Cache suspiciousMap = CacheManager.getStringKeyCache(1_000, CacheManager.HOUR, "suspicious cache"); diff --git a/internal/src/org/labkey/api/security/DummyAntiVirusService.java b/internal/src/org/labkey/api/security/DummyAntiVirusService.java index 2e9bfb1b8d9..4ed29638826 100644 --- a/internal/src/org/labkey/api/security/DummyAntiVirusService.java +++ b/internal/src/org/labkey/api/security/DummyAntiVirusService.java @@ -1,23 +1,24 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.security; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.audit.AuditLogService; @@ -37,7 +38,7 @@ public class DummyAntiVirusService implements AntiVirusService { - final static Logger LOG = Logger.getLogger(DummyAntiVirusService.class); + final static Logger LOG = LogManager.getLogger(DummyAntiVirusService.class); @Override public ScanResult scan(@NotNull File f, @Nullable String originalName, ViewBackgroundInfo info) diff --git a/internal/src/org/labkey/api/security/SecurityPointcutServiceImpl.java b/internal/src/org/labkey/api/security/SecurityPointcutServiceImpl.java index c4d34a76b83..c5b278ab5a2 100644 --- a/internal/src/org/labkey/api/security/SecurityPointcutServiceImpl.java +++ b/internal/src/org/labkey/api/security/SecurityPointcutServiceImpl.java @@ -1,24 +1,23 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2018 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.api.security; import org.labkey.api.module.Module; import org.labkey.api.settings.AppProps; import org.labkey.api.util.CSRFException; -import org.labkey.api.util.CSRFUtil; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.view.ViewServlet; diff --git a/internal/src/org/labkey/api/util/ContainerTree.java b/internal/src/org/labkey/api/util/ContainerTree.java index e92043df573..dc29550ae9f 100644 --- a/internal/src/org/labkey/api/util/ContainerTree.java +++ b/internal/src/org/labkey/api/util/ContainerTree.java @@ -16,7 +16,8 @@ package org.labkey.api.util; import org.apache.commons.collections4.MultiValuedMap; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -33,7 +34,7 @@ */ public class ContainerTree { - private static Logger _log = Logger.getLogger(ContainerTree.class); + private static Logger _log = LogManager.getLogger(ContainerTree.class); private Container _root; private User _user; diff --git a/internal/src/org/labkey/api/util/DiffMatchPatch.java b/internal/src/org/labkey/api/util/DiffMatchPatch.java index be6b34d507e..325b63dfbe9 100644 --- a/internal/src/org/labkey/api/util/DiffMatchPatch.java +++ b/internal/src/org/labkey/api/util/DiffMatchPatch.java @@ -20,8 +20,8 @@ package org.labkey.api.util; import java.io.UnsupportedEncodingException; -import java.net.URLEncoder; import java.net.URLDecoder; +import java.net.URLEncoder; import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; diff --git a/internal/src/org/labkey/api/util/HashHelpers.java b/internal/src/org/labkey/api/util/HashHelpers.java index 8e4895687e2..50c91eb34e9 100644 --- a/internal/src/org/labkey/api/util/HashHelpers.java +++ b/internal/src/org/labkey/api/util/HashHelpers.java @@ -15,11 +15,11 @@ */ package org.labkey.api.util; +import java.io.BufferedInputStream; import java.io.File; +import java.io.FileInputStream; import java.io.IOException; import java.io.InputStream; -import java.io.BufferedInputStream; -import java.io.FileInputStream; import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; diff --git a/internal/src/org/labkey/api/util/TextExtractor.java b/internal/src/org/labkey/api/util/TextExtractor.java index 71f6c0933e4..10d6c0ab7dd 100644 --- a/internal/src/org/labkey/api/util/TextExtractor.java +++ b/internal/src/org/labkey/api/util/TextExtractor.java @@ -17,9 +17,9 @@ import javax.swing.text.html.HTMLEditorKit; import javax.swing.text.html.parser.ParserDelegator; +import java.io.IOException; import java.io.Reader; import java.io.StringReader; -import java.io.IOException; /** * User: adam diff --git a/internal/src/org/labkey/api/view/FileServlet.java b/internal/src/org/labkey/api/view/FileServlet.java index 132545cb847..3dd30a29b65 100644 --- a/internal/src/org/labkey/api/view/FileServlet.java +++ b/internal/src/org/labkey/api/view/FileServlet.java @@ -16,17 +16,18 @@ package org.labkey.api.view; -import org.apache.log4j.Logger; import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.URLHelper; +import javax.servlet.RequestDispatcher; +import javax.servlet.ServletConfig; +import javax.servlet.ServletException; import javax.servlet.http.HttpServlet; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import javax.servlet.ServletException; -import javax.servlet.RequestDispatcher; -import javax.servlet.ServletConfig; import java.io.IOException; /** @@ -34,7 +35,7 @@ */ public class FileServlet extends HttpServlet { - static Logger _log = Logger.getLogger(FileServlet.class); + static Logger _log = LogManager.getLogger(FileServlet.class); private static final String PAGE_FLOW_ATTR = FileServlet.class.getName() + ".pageFlow"; @Override diff --git a/internal/src/org/labkey/api/view/SiteDownServlet.java b/internal/src/org/labkey/api/view/SiteDownServlet.java index c804a039802..7d7c757f4d3 100644 --- a/internal/src/org/labkey/api/view/SiteDownServlet.java +++ b/internal/src/org/labkey/api/view/SiteDownServlet.java @@ -16,11 +16,11 @@ package org.labkey.api.view; +import javax.servlet.ServletConfig; +import javax.servlet.ServletException; import javax.servlet.http.HttpServlet; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import javax.servlet.ServletException; -import javax.servlet.ServletConfig; import java.io.IOException; import java.io.Writer; diff --git a/internal/src/org/labkey/api/view/StaticContentCachingFilter.java b/internal/src/org/labkey/api/view/StaticContentCachingFilter.java index d1bfa27b148..9eb744e956b 100644 --- a/internal/src/org/labkey/api/view/StaticContentCachingFilter.java +++ b/internal/src/org/labkey/api/view/StaticContentCachingFilter.java @@ -17,10 +17,14 @@ package org.labkey.api.view; import org.labkey.api.settings.AppProps; -import org.labkey.api.util.HeartBeat; import org.labkey.api.util.ResponseHelper; -import javax.servlet.*; +import javax.servlet.Filter; +import javax.servlet.FilterChain; +import javax.servlet.FilterConfig; +import javax.servlet.ServletException; +import javax.servlet.ServletRequest; +import javax.servlet.ServletResponse; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import java.io.IOException; diff --git a/internal/src/org/labkey/api/view/ViewOutputStream.java b/internal/src/org/labkey/api/view/ViewOutputStream.java index 17c34d031ef..db28d7e8c71 100644 --- a/internal/src/org/labkey/api/view/ViewOutputStream.java +++ b/internal/src/org/labkey/api/view/ViewOutputStream.java @@ -15,10 +15,10 @@ */ package org.labkey.api.view; -import java.io.IOException; import javax.servlet.ServletOutputStream; import javax.servlet.http.HttpServletResponse; import javax.servlet.jsp.PageContext; +import java.io.IOException; public class ViewOutputStream extends ServletOutputStream diff --git a/internal/src/org/labkey/api/webdav/AbstractWebdavResolver.java b/internal/src/org/labkey/api/webdav/AbstractWebdavResolver.java index 8e2e259280b..f135c0468f8 100644 --- a/internal/src/org/labkey/api/webdav/AbstractWebdavResolver.java +++ b/internal/src/org/labkey/api/webdav/AbstractWebdavResolver.java @@ -29,7 +29,6 @@ import org.labkey.api.view.ViewContext; import java.beans.PropertyChangeEvent; -import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.Collection; diff --git a/internal/src/org/labkey/api/webdav/FileSystemResource.java b/internal/src/org/labkey/api/webdav/FileSystemResource.java index dd09ad03a3d..740d3c5c4a8 100644 --- a/internal/src/org/labkey/api/webdav/FileSystemResource.java +++ b/internal/src/org/labkey/api/webdav/FileSystemResource.java @@ -15,7 +15,8 @@ */ package org.labkey.api.webdav; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.attachments.Attachment; @@ -88,7 +89,7 @@ */ public class FileSystemResource extends AbstractWebdavResource { - private static final Logger _log = Logger.getLogger(FileSystemResource.class); + private static final Logger _log = LogManager.getLogger(FileSystemResource.class); public static final String URL_COL_PREFIX = "_labkeyurl_"; protected List _files; diff --git a/internal/src/org/labkey/api/webdav/ModuleStaticResolverImpl.java b/internal/src/org/labkey/api/webdav/ModuleStaticResolverImpl.java index a746a07f9d7..3688dd8d66a 100644 --- a/internal/src/org/labkey/api/webdav/ModuleStaticResolverImpl.java +++ b/internal/src/org/labkey/api/webdav/ModuleStaticResolverImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.api.webdav; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -72,7 +73,7 @@ public class ModuleStaticResolverImpl implements WebdavResolver, ModuleChangeLis ServiceRegistry.get().registerService(WebdavResolver.class, _instance); } - private static final Logger _log = Logger.getLogger(ModuleStaticResolverImpl.class); + private static final Logger _log = LogManager.getLogger(ModuleStaticResolverImpl.class); /** System property name for an extra directory of static content */ private static final String EXTRA_WEBAPP_DIR = "extrawebappdir"; diff --git a/internal/src/org/labkey/experiment/api/SampleTypeDomainKind.java b/internal/src/org/labkey/experiment/api/SampleTypeDomainKind.java index d5d918790a3..f24c492d7c9 100644 --- a/internal/src/org/labkey/experiment/api/SampleTypeDomainKind.java +++ b/internal/src/org/labkey/experiment/api/SampleTypeDomainKind.java @@ -18,7 +18,8 @@ import com.google.common.collect.Sets; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -38,8 +39,8 @@ import org.labkey.api.exp.api.ExpSampleType; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.exp.api.ExperimentUrls; -import org.labkey.api.exp.api.SampleTypeService; import org.labkey.api.exp.api.SampleTypeDomainKindProperties; +import org.labkey.api.exp.api.SampleTypeService; import org.labkey.api.exp.property.AbstractDomainKind; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.query.ExpSampleTypeTable; @@ -99,7 +100,7 @@ public class SampleTypeDomainKind extends AbstractDomainKind _issuesListDefProviders = new ConcurrentHashMap<>(); private final List _headerLinkProviders = new ArrayList<>(); diff --git a/issues/src/org/labkey/issue/query/IssueDefDomainKind.java b/issues/src/org/labkey/issue/query/IssueDefDomainKind.java index 79ce08010d0..f992131beaf 100644 --- a/issues/src/org/labkey/issue/query/IssueDefDomainKind.java +++ b/issues/src/org/labkey/issue/query/IssueDefDomainKind.java @@ -16,7 +16,6 @@ package org.labkey.issue.query; import com.google.common.collect.Sets; -import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.JdbcType; import org.labkey.api.data.PropertyStorageSpec; diff --git a/issues/src/org/labkey/issue/query/IssuesListDefTable.java b/issues/src/org/labkey/issue/query/IssuesListDefTable.java index 84bcd4c2a27..717a68b2bd8 100644 --- a/issues/src/org/labkey/issue/query/IssuesListDefTable.java +++ b/issues/src/org/labkey/issue/query/IssuesListDefTable.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -75,7 +76,7 @@ */ public class IssuesListDefTable extends FilteredTable { - private static final Logger LOG = Logger.getLogger(IssuesListDefTable.class); + private static final Logger LOG = LogManager.getLogger(IssuesListDefTable.class); private final static Set _AUTOPOPULATED_COLUMN_NAMES; static diff --git a/issues/src/org/labkey/issue/query/IssuesTable.java b/issues/src/org/labkey/issue/query/IssuesTable.java index ec16c1fc845..504fe1ee4fd 100644 --- a/issues/src/org/labkey/issue/query/IssuesTable.java +++ b/issues/src/org/labkey/issue/query/IssuesTable.java @@ -17,8 +17,9 @@ package org.labkey.issue.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -91,7 +92,7 @@ public class IssuesTable extends FilteredTable implements UpdateableTableInfo { - private static final Logger LOG = Logger.getLogger(IssuesTable.class); + private static final Logger LOG = LogManager.getLogger(IssuesTable.class); private Set> _allowablePermissions = new HashSet<>(); private IssueListDef _issueDef; diff --git a/issues/src/org/labkey/issue/view/IssuesWebPartFactory.java b/issues/src/org/labkey/issue/view/IssuesWebPartFactory.java index e4a973c5736..6f52afa1850 100644 --- a/issues/src/org/labkey/issue/view/IssuesWebPartFactory.java +++ b/issues/src/org/labkey/issue/view/IssuesWebPartFactory.java @@ -15,7 +15,6 @@ */ package org.labkey.issue.view; -import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.view.BaseWebPartFactory; diff --git a/issues/src/org/labkey/issue/view/RelatedIssuesView.java b/issues/src/org/labkey/issue/view/RelatedIssuesView.java index 6cf1bc682e0..2f10fb50c46 100644 --- a/issues/src/org/labkey/issue/view/RelatedIssuesView.java +++ b/issues/src/org/labkey/issue/view/RelatedIssuesView.java @@ -20,7 +20,6 @@ import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.ContainerFilterable; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.DataRegion; import org.labkey.api.data.SimpleFilter; diff --git a/issues/src/org/labkey/issue/view/SummaryWebPart.java b/issues/src/org/labkey/issue/view/SummaryWebPart.java index 1ef707b8a8c..5fb2f1164f7 100644 --- a/issues/src/org/labkey/issue/view/SummaryWebPart.java +++ b/issues/src/org/labkey/issue/view/SummaryWebPart.java @@ -26,7 +26,6 @@ import org.labkey.issue.model.IssueListDef; import org.labkey.issue.model.IssueManager; -import java.sql.SQLException; import java.util.Map; /** diff --git a/issues/src/org/labkey/issue/view/deleteIssueList.jsp b/issues/src/org/labkey/issue/view/deleteIssueList.jsp index 83d00aa3cf6..28f16d4fca7 100644 --- a/issues/src/org/labkey/issue/view/deleteIssueList.jsp +++ b/issues/src/org/labkey/issue/view/deleteIssueList.jsp @@ -15,15 +15,12 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.api.data.Container" %> +<%@ page import="org.labkey.api.query.QueryAction" %> +<%@ page import="org.labkey.api.query.QueryService"%> <%@ page import="org.labkey.api.view.ActionURL"%> <%@ page import="org.labkey.api.view.HttpView"%> -<%@ page import="org.labkey.api.view.JspView"%> -<%@ page import="org.labkey.api.view.ViewContext" %> -<%@ page import="org.labkey.issue.IssuesController" %> +<%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.issue.actions.DeleteIssueListAction" %> -<%@ page import="org.labkey.api.query.QueryService" %> -<%@ page import="org.labkey.api.query.QueryAction" %> <%@ page import="org.labkey.issue.query.IssuesQuerySchema" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> diff --git a/issues/src/org/labkey/issue/view/detailList.jsp b/issues/src/org/labkey/issue/view/detailList.jsp index 141eb94dce4..50331b4c9e4 100644 --- a/issues/src/org/labkey/issue/view/detailList.jsp +++ b/issues/src/org/labkey/issue/view/detailList.jsp @@ -41,7 +41,6 @@ <%@ page import="java.util.List" %> <%@ page import="java.util.Map" %> <%@ page import="java.util.Set" %> -<%@ page import="java.util.function.Function" %> <%@ page import="java.util.stream.Collectors" %> <%@ page import="java.util.stream.Stream" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> diff --git a/issues/src/org/labkey/issue/view/detailView.jsp b/issues/src/org/labkey/issue/view/detailView.jsp index 6df0782c2dd..3304cff67e0 100644 --- a/issues/src/org/labkey/issue/view/detailView.jsp +++ b/issues/src/org/labkey/issue/view/detailView.jsp @@ -20,7 +20,8 @@ <%@ page import="org.labkey.api.issues.IssueDetailHeaderLinkProvider" %> <%@ page import="org.labkey.api.issues.IssuesListDefService" %> <%@ page import="org.labkey.api.security.User"%> -<%@ page import="org.labkey.api.security.permissions.InsertPermission"%> +<%@ page import="org.labkey.api.security.UserManager"%> +<%@ page import="org.labkey.api.security.permissions.InsertPermission" %> <%@ page import="org.labkey.api.util.PageFlowUtil" %> <%@ page import="org.labkey.api.util.StringUtilsLabKey" %> <%@ page import="org.labkey.api.view.ActionURL" %> @@ -44,7 +45,6 @@ <%@ page import="java.util.Map" %> <%@ page import="java.util.stream.Collectors" %> <%@ page import="java.util.stream.Stream" %> -<%@ page import="org.labkey.api.security.UserManager" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/list/src/org/labkey/list/ListModule.java b/list/src/org/labkey/list/ListModule.java index 9e53bc2f524..db01055f01c 100644 --- a/list/src/org/labkey/list/ListModule.java +++ b/list/src/org/labkey/list/ListModule.java @@ -36,7 +36,6 @@ import org.labkey.api.security.permissions.PlatformDeveloperPermission; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.roles.RoleManager; -import org.labkey.api.settings.AdminConsole; import org.labkey.api.study.StudySerializationRegistry; import org.labkey.api.usageMetrics.UsageMetricsService; import org.labkey.api.util.PageFlowUtil; diff --git a/list/src/org/labkey/list/controllers/ListController.java b/list/src/org/labkey/list/controllers/ListController.java index d0ba8908d5a..c90265b7db9 100644 --- a/list/src/org/labkey/list/controllers/ListController.java +++ b/list/src/org/labkey/list/controllers/ListController.java @@ -18,7 +18,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -893,7 +893,7 @@ public void export(ListDefinitionForm form, HttpServletResponse response, BindEx } Container c = getContainer(); String datatype = ("lists"); - FolderExportContext ctx = new FolderExportContext(getUser(), c, PageFlowUtil.set(datatype), "List Export", new StaticLoggerGetter(Logger.getLogger(ListController.class))); + FolderExportContext ctx = new FolderExportContext(getUser(), c, PageFlowUtil.set(datatype), "List Export", new StaticLoggerGetter(LogManager.getLogger(ListController.class))); ctx.setListIds(IDs); ListWriter writer = new ListWriter(); diff --git a/list/src/org/labkey/list/model/FolderListImporter.java b/list/src/org/labkey/list/model/FolderListImporter.java index 4e9e7cc516f..67470584527 100644 --- a/list/src/org/labkey/list/model/FolderListImporter.java +++ b/list/src/org/labkey/list/model/FolderListImporter.java @@ -16,11 +16,11 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.pipeline.PipelineJob; diff --git a/list/src/org/labkey/list/model/FolderListWriter.java b/list/src/org/labkey/list/model/FolderListWriter.java index 09f1ae29ba3..3d634d2adf7 100644 --- a/list/src/org/labkey/list/model/FolderListWriter.java +++ b/list/src/org/labkey/list/model/FolderListWriter.java @@ -17,9 +17,9 @@ package org.labkey.list.model; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.exp.list.ListService; diff --git a/list/src/org/labkey/list/model/IntegerListDomainKind.java b/list/src/org/labkey/list/model/IntegerListDomainKind.java index 6c508ea8a18..af0f28a1035 100644 --- a/list/src/org/labkey/list/model/IntegerListDomainKind.java +++ b/list/src/org/labkey/list/model/IntegerListDomainKind.java @@ -19,9 +19,9 @@ import org.labkey.api.data.PropertyStorageSpec; import org.labkey.api.exp.list.ListDefinition; -import java.util.List; import java.util.Arrays; import java.util.Collection; +import java.util.List; /** * User: Nick diff --git a/list/src/org/labkey/list/model/ListDefinitionImpl.java b/list/src/org/labkey/list/model/ListDefinitionImpl.java index 0168fdb47f7..f49cf081874 100644 --- a/list/src/org/labkey/list/model/ListDefinitionImpl.java +++ b/list/src/org/labkey/list/model/ListDefinitionImpl.java @@ -16,7 +16,8 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -55,7 +56,6 @@ import org.labkey.list.controllers.ListController; import org.springframework.web.servlet.mvc.Controller; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; @@ -67,7 +67,7 @@ public class ListDefinitionImpl implements ListDefinition { - private static final Logger LOG = Logger.getLogger(ListDefinitionImpl.class); + private static final Logger LOG = LogManager.getLogger(ListDefinitionImpl.class); static public ListDefinitionImpl of(ListDef def) { diff --git a/list/src/org/labkey/list/model/ListImporter.java b/list/src/org/labkey/list/model/ListImporter.java index 863e37ec241..e3c3cd1f339 100644 --- a/list/src/org/labkey/list/model/ListImporter.java +++ b/list/src/org/labkey/list/model/ListImporter.java @@ -16,7 +16,7 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportException; diff --git a/list/src/org/labkey/list/model/ListItemImpl.java b/list/src/org/labkey/list/model/ListItemImpl.java index 7a0e48e9e97..b8eb65807df 100644 --- a/list/src/org/labkey/list/model/ListItemImpl.java +++ b/list/src/org/labkey/list/model/ListItemImpl.java @@ -16,7 +16,8 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.exp.ObjectProperty; import org.labkey.api.exp.OntologyManager; import org.labkey.api.exp.OntologyObject; @@ -35,7 +36,7 @@ public class ListItemImpl implements ListItem ListItm _itm; Map _properties; Map _oldProperties; - private static final Logger _log = Logger.getLogger(ListItemImpl.class); + private static final Logger _log = LogManager.getLogger(ListItemImpl.class); public ListItemImpl(ListDefinitionImpl list, ListItm item) { diff --git a/list/src/org/labkey/list/model/ListManager.java b/list/src/org/labkey/list/model/ListManager.java index 8874f786d70..fa11cb60563 100644 --- a/list/src/org/labkey/list/model/ListManager.java +++ b/list/src/org/labkey/list/model/ListManager.java @@ -19,7 +19,8 @@ import org.apache.commons.lang3.ObjectUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -88,7 +89,7 @@ public class ListManager implements SearchService.DocumentProvider { - private static final Logger LOG = Logger.getLogger(ListManager.class); + private static final Logger LOG = LogManager.getLogger(ListManager.class); private static final String LIST_SEQUENCE_NAME = "org.labkey.list.Lists"; private static final ListManager INSTANCE = new ListManager(); diff --git a/list/src/org/labkey/list/model/ListManagerSchema.java b/list/src/org/labkey/list/model/ListManagerSchema.java index 02607c69812..0b2eea34eea 100644 --- a/list/src/org/labkey/list/model/ListManagerSchema.java +++ b/list/src/org/labkey/list/model/ListManagerSchema.java @@ -24,9 +24,9 @@ import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.Sort; import org.labkey.api.data.RenderContext; import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.lists.permissions.DesignListPermission; @@ -38,7 +38,6 @@ import org.labkey.api.query.QueryView; import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; -import org.labkey.api.settings.AppProps; import org.labkey.api.util.Button; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; diff --git a/list/src/org/labkey/list/model/ListQuerySchema.java b/list/src/org/labkey/list/model/ListQuerySchema.java index a5318c14643..708debfdd88 100644 --- a/list/src/org/labkey/list/model/ListQuerySchema.java +++ b/list/src/org/labkey/list/model/ListQuerySchema.java @@ -16,7 +16,8 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -48,7 +49,7 @@ public class ListQuerySchema extends UserSchema { public static final String NAME = "lists"; public static final String DESCR = "Contains a data table for each defined list"; - private static final Logger LOG = Logger.getLogger(ListQuerySchema.class); + private static final Logger LOG = LogManager.getLogger(ListQuerySchema.class); public static void register(Module module) { diff --git a/list/src/org/labkey/list/model/ListServiceImpl.java b/list/src/org/labkey/list/model/ListServiceImpl.java index 7ac7b91d10d..35fb0eeccf5 100644 --- a/list/src/org/labkey/list/model/ListServiceImpl.java +++ b/list/src/org/labkey/list/model/ListServiceImpl.java @@ -16,7 +16,7 @@ package org.labkey.list.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportException; import org.labkey.api.admin.InvalidFileException; @@ -129,7 +129,7 @@ public void importListArchive(InputStream is, BindException errors, Container c, try { - li.processMany(new FileSystemFile(dir), c, user, errorList, Logger.getLogger(ListController.class)); + li.processMany(new FileSystemFile(dir), c, user, errorList, LogManager.getLogger(ListController.class)); for (String error : errorList) errors.reject(ERROR_MSG, error); diff --git a/list/src/org/labkey/list/model/ListTable.java b/list/src/org/labkey/list/model/ListTable.java index b5478f57064..76e12e274ae 100644 --- a/list/src/org/labkey/list/model/ListTable.java +++ b/list/src/org/labkey/list/model/ListTable.java @@ -17,7 +17,8 @@ package org.labkey.list.model; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -82,7 +83,7 @@ public class ListTable extends FilteredTable implements UpdateableTableInfo { private final ListDefinition _list; - private static final Logger LOG = Logger.getLogger(ListTable.class); + private static final Logger LOG = LogManager.getLogger(ListTable.class); private final boolean _allowMaxPhi; private final PHI _maxUserPhi; diff --git a/list/src/org/labkey/list/view/ListsWebPart.java b/list/src/org/labkey/list/view/ListsWebPart.java index 573d9bf887a..333731a119f 100644 --- a/list/src/org/labkey/list/view/ListsWebPart.java +++ b/list/src/org/labkey/list/view/ListsWebPart.java @@ -17,7 +17,6 @@ package org.labkey.list.view; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.Container; import org.labkey.api.exp.list.ListDefinition; import org.labkey.api.exp.list.ListService; import org.labkey.api.exp.list.ListUrls; @@ -26,12 +25,10 @@ import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.AlwaysAvailableWebPartFactory; import org.labkey.api.view.BaseWebPartFactory; -import org.labkey.api.view.HttpView; import org.labkey.api.view.JspView; import org.labkey.api.view.NavTree; import org.labkey.api.view.Portal; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.WebPartFactory; import org.labkey.api.view.WebPartView; import org.labkey.list.controllers.ListController; diff --git a/list/src/org/labkey/list/view/SingleListWebPartFactory.java b/list/src/org/labkey/list/view/SingleListWebPartFactory.java index 45e4ff28d03..f6e7524f4c9 100644 --- a/list/src/org/labkey/list/view/SingleListWebPartFactory.java +++ b/list/src/org/labkey/list/view/SingleListWebPartFactory.java @@ -21,7 +21,13 @@ import org.labkey.api.exp.list.ListDefinition; import org.labkey.api.exp.list.ListService; import org.labkey.api.query.QuerySettings; -import org.labkey.api.view.*; +import org.labkey.api.view.AlwaysAvailableWebPartFactory; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartView; import java.util.HashMap; import java.util.Map; diff --git a/list/src/org/labkey/list/view/deleteListDefinition.jsp b/list/src/org/labkey/list/view/deleteListDefinition.jsp index 223e17ccd79..91b0034f0d8 100644 --- a/list/src/org/labkey/list/view/deleteListDefinition.jsp +++ b/list/src/org/labkey/list/view/deleteListDefinition.jsp @@ -16,7 +16,6 @@ */ %> <%@ page import="org.labkey.api.exp.list.ListDefinition" %> -<%@ page import="org.labkey.list.controllers.ListController" %> <%@ page import="org.labkey.list.view.ListDefinitionForm" %> <%@ page import="java.util.Collection" %> <%@ page extends="org.labkey.api.jsp.FormPage" %> diff --git a/mothership/src/org/labkey/mothership/ExceptionStackTrace.java b/mothership/src/org/labkey/mothership/ExceptionStackTrace.java index 0bce0b53c1e..26df320bf6e 100644 --- a/mothership/src/org/labkey/mothership/ExceptionStackTrace.java +++ b/mothership/src/org/labkey/mothership/ExceptionStackTrace.java @@ -21,9 +21,9 @@ import org.labkey.api.security.User; import org.labkey.api.util.HashHelpers; -import java.io.StringReader; import java.io.BufferedReader; import java.io.IOException; +import java.io.StringReader; import java.util.Date; /** diff --git a/mothership/src/org/labkey/mothership/MetricJSONDisplayColumn.java b/mothership/src/org/labkey/mothership/MetricJSONDisplayColumn.java index f39597b3606..eb672fc97ea 100644 --- a/mothership/src/org/labkey/mothership/MetricJSONDisplayColumn.java +++ b/mothership/src/org/labkey/mothership/MetricJSONDisplayColumn.java @@ -20,7 +20,8 @@ import com.jayway.jsonpath.JsonPathException; import com.jayway.jsonpath.PathNotFoundException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; @@ -32,7 +33,7 @@ public class MetricJSONDisplayColumn extends DataColumn { - private static final Logger _log = Logger.getLogger(MetricJSONDisplayColumn.class); + private static final Logger _log = LogManager.getLogger(MetricJSONDisplayColumn.class); private String _jsonProp; diff --git a/mothership/src/org/labkey/mothership/MothershipController.java b/mothership/src/org/labkey/mothership/MothershipController.java index b7e0fa818d5..ba27677926e 100644 --- a/mothership/src/org/labkey/mothership/MothershipController.java +++ b/mothership/src/org/labkey/mothership/MothershipController.java @@ -19,11 +19,11 @@ import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.JsonPath; import com.jayway.jsonpath.JsonPathException; -import com.jayway.jsonpath.PathNotFoundException; import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.StringUtils; import org.apache.commons.validator.routines.InetAddressValidator; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jfree.chart.ChartColor; import org.jfree.chart.ChartFactory; @@ -37,7 +37,6 @@ import org.jfree.data.time.TimeSeries; import org.jfree.data.time.TimeSeriesCollection; import org.jfree.data.xy.XYDataset; -import org.json.JSONObject; import org.labkey.api.action.FormHandlerAction; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.action.ReturnUrlForm; @@ -58,8 +57,6 @@ import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; -import org.labkey.api.security.permissions.DeletePermission; -import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.util.DateUtil; @@ -73,7 +70,6 @@ import org.labkey.api.view.DetailsView; import org.labkey.api.view.GridView; import org.labkey.api.view.HtmlView; -import org.labkey.api.view.InsertView; import org.labkey.api.view.JspView; import org.labkey.api.view.NavTree; import org.labkey.api.view.NotFoundException; @@ -112,7 +108,7 @@ public class MothershipController extends SpringActionController { private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(MothershipController.class); - private static final Logger _log = Logger.getLogger(MothershipController.class); + private static final Logger _log = LogManager.getLogger(MothershipController.class); public MothershipController() { diff --git a/mothership/src/org/labkey/mothership/MothershipManager.java b/mothership/src/org/labkey/mothership/MothershipManager.java index 2e7a080f0bf..db786cfe753 100644 --- a/mothership/src/org/labkey/mothership/MothershipManager.java +++ b/mothership/src/org/labkey/mothership/MothershipManager.java @@ -19,7 +19,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectReader; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.CompareType; @@ -71,7 +72,7 @@ public class MothershipManager private static final String ISSUES_CONTAINER_PROP = "issuesContainer"; private static final ReentrantLock INSERT_EXCEPTION_LOCK = new ReentrantLock(); - private static final Logger log = Logger.getLogger(MothershipManager.class); + private static final Logger log = LogManager.getLogger(MothershipManager.class); public static MothershipManager get() { diff --git a/mothership/src/org/labkey/mothership/StackTraceDisplayColumn.java b/mothership/src/org/labkey/mothership/StackTraceDisplayColumn.java index 0ad3cddb5d5..2da5e714cb0 100644 --- a/mothership/src/org/labkey/mothership/StackTraceDisplayColumn.java +++ b/mothership/src/org/labkey/mothership/StackTraceDisplayColumn.java @@ -16,17 +16,17 @@ package org.labkey.mothership; -import org.labkey.api.data.DataColumn; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.DataColumn; import org.labkey.api.data.RenderContext; import org.labkey.api.util.PageFlowUtil; -import java.io.Writer; import java.io.IOException; -import java.io.StringReader; import java.io.LineNumberReader; -import java.util.List; +import java.io.StringReader; +import java.io.Writer; import java.util.ArrayList; +import java.util.List; /** * User: jeckels diff --git a/pipeline/src/org/labkey/pipeline/AbstractPipelineStartup.java b/pipeline/src/org/labkey/pipeline/AbstractPipelineStartup.java index 18d56ed942e..2152ce0b05d 100644 --- a/pipeline/src/org/labkey/pipeline/AbstractPipelineStartup.java +++ b/pipeline/src/org/labkey/pipeline/AbstractPipelineStartup.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleDependencySorter; @@ -48,14 +49,14 @@ */ public abstract class AbstractPipelineStartup { - private static final Logger _log = Logger.getLogger(AbstractPipelineStartup.class); + private static final Logger _log = LogManager.getLogger(AbstractPipelineStartup.class); /** * @return map from module name to BeanFactory */ - protected Map initContext(String log4JConfigPath, List moduleFiles, List moduleConfigFiles, List customConfigFiles, File webappDir, PipelineJobService.LocationType locationType) throws IOException + protected Map initContext(String name, String log4JConfigPath, List moduleFiles, List moduleConfigFiles, List customConfigFiles, File webappDir, PipelineJobService.LocationType locationType) throws IOException { - LoggerUtil.initLogging(log4JConfigPath); + LoggerUtil.initLogging(name, log4JConfigPath); //load the modules and sort them by dependencies ModuleLoader moduleLoader = new ModuleLoader(); diff --git a/pipeline/src/org/labkey/pipeline/PipelineController.java b/pipeline/src/org/labkey/pipeline/PipelineController.java index b64fc1b9ce8..72bb368e0f7 100644 --- a/pipeline/src/org/labkey/pipeline/PipelineController.java +++ b/pipeline/src/org/labkey/pipeline/PipelineController.java @@ -67,7 +67,6 @@ import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.SecurableResource; import org.labkey.api.security.SecurityManager; -import org.labkey.api.security.SecurityPolicy; import org.labkey.api.security.SecurityPolicyManager; import org.labkey.api.security.User; import org.labkey.api.security.UserManager; diff --git a/pipeline/src/org/labkey/pipeline/PipelineModule.java b/pipeline/src/org/labkey/pipeline/PipelineModule.java index 19cbc8d7c14..94245d53a17 100644 --- a/pipeline/src/org/labkey/pipeline/PipelineModule.java +++ b/pipeline/src/org/labkey/pipeline/PipelineModule.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.notification.NotificationService; import org.labkey.api.admin.sitevalidation.SiteValidationService; @@ -95,7 +96,7 @@ */ public class PipelineModule extends SpringModule implements ContainerManager.ContainerListener { - private static final Logger _log = Logger.getLogger(PipelineModule.class); + private static final Logger _log = LogManager.getLogger(PipelineModule.class); @Override public String getName() diff --git a/pipeline/src/org/labkey/pipeline/PipelineWebdavProvider.java b/pipeline/src/org/labkey/pipeline/PipelineWebdavProvider.java index 91295d44241..29c64ea2fec 100644 --- a/pipeline/src/org/labkey/pipeline/PipelineWebdavProvider.java +++ b/pipeline/src/org/labkey/pipeline/PipelineWebdavProvider.java @@ -33,7 +33,6 @@ import org.labkey.pipeline.api.PipelineServiceImpl; import java.io.File; -import java.net.URLEncoder; import java.util.ArrayList; import java.util.List; import java.util.Set; diff --git a/pipeline/src/org/labkey/pipeline/analysis/AnalysisController.java b/pipeline/src/org/labkey/pipeline/analysis/AnalysisController.java index 3f864eeec37..d3421a83ff4 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/AnalysisController.java +++ b/pipeline/src/org/labkey/pipeline/analysis/AnalysisController.java @@ -20,7 +20,8 @@ import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.io.input.ReaderInputStream; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.action.ApiResponse; @@ -86,7 +87,7 @@ */ public class AnalysisController extends SpringActionController { - private static final Logger LOG = Logger.getLogger(AnalysisController.class); + private static final Logger LOG = LogManager.getLogger(AnalysisController.class); private static final DefaultActionResolver _resolver = new DefaultActionResolver(AnalysisController.class); public AnalysisController() diff --git a/pipeline/src/org/labkey/pipeline/analysis/ConvertTaskFactory.java b/pipeline/src/org/labkey/pipeline/analysis/ConvertTaskFactory.java index c2d8b0e605c..819efc047d0 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/ConvertTaskFactory.java +++ b/pipeline/src/org/labkey/pipeline/analysis/ConvertTaskFactory.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.analysis; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.AbstractTaskFactory; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobService; @@ -43,7 +44,7 @@ */ public class ConvertTaskFactory extends AbstractTaskFactory { - private static final Logger LOG = Logger.getLogger(ConvertTaskFactory.class); + private static final Logger LOG = LogManager.getLogger(ConvertTaskFactory.class); private String _statusName = "CONVERSION"; private TaskId[] _commands; diff --git a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisJob.java b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisJob.java index 216506e2988..d79542cc699 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisJob.java +++ b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisJob.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.analysis; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.TaskId; @@ -41,7 +42,7 @@ public class FileAnalysisJob extends AbstractFileAnalysisJob private TaskId _taskPipelineId; private Map _variableMap; - private static final Logger LOG = Logger.getLogger(FileAnalysisJob.class); + private static final Logger LOG = LogManager.getLogger(FileAnalysisJob.class); // For serialization protected FileAnalysisJob() {} diff --git a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisPipelineProvider.java b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisPipelineProvider.java index 56353dc0b9e..513aa2ec1bf 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisPipelineProvider.java +++ b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisPipelineProvider.java @@ -15,25 +15,25 @@ */ package org.labkey.pipeline.analysis; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.data.Container; import org.labkey.api.exp.api.ExpData; import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; +import org.labkey.api.module.Module; +import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineActionConfig; import org.labkey.api.pipeline.PipelineDirectory; import org.labkey.api.pipeline.PipelineJobService; -import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.pipeline.PipelineStatusFile; import org.labkey.api.pipeline.file.AbstractFileAnalysisProvider; import org.labkey.api.pipeline.file.FileAnalysisTaskPipeline; import org.labkey.api.security.User; +import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.util.FileUtil; import org.labkey.api.util.NetworkDrive; import org.labkey.api.view.ViewContext; -import org.labkey.api.module.Module; -import org.labkey.api.security.permissions.InsertPermission; import java.io.File; import java.util.ArrayList; @@ -160,7 +160,7 @@ public void preDeleteStatusFile(User user, PipelineStatusFile sf) { if (FileUtil.deleteDir(analysisDir)) { - Logger.getLogger(FileAnalysisPipelineProvider.class).info(String.format("Job '%s' analysis directory no longer referenced by any runs and was moved to .deleted: %s", sf.getInfo(), analysisDir)); + LogManager.getLogger(FileAnalysisPipelineProvider.class).info(String.format("Job '%s' analysis directory no longer referenced by any runs and was moved to .deleted: %s", sf.getInfo(), analysisDir)); // Delete any ExpData remains for (ExpData data : children) @@ -175,7 +175,7 @@ public void preDeleteStatusFile(User user, PipelineStatusFile sf) { if (FileUtil.deleteDir(parent)) { - Logger.getLogger(FileAnalysisPipelineProvider.class).info(String.format("Job '%s' parent analysis directory no longer referenced by any runs and was moved to .deleted: %s", sf.getInfo(), parent)); + LogManager.getLogger(FileAnalysisPipelineProvider.class).info(String.format("Job '%s' parent analysis directory no longer referenced by any runs and was moved to .deleted: %s", sf.getInfo(), parent)); parent = parent.getParentFile(); contents = parent.list(); } @@ -183,7 +183,7 @@ public void preDeleteStatusFile(User user, PipelineStatusFile sf) } else { - Logger.getLogger(FileAnalysisPipelineProvider.class).warn(String.format("Failed to move job '%s' analysis directory to .deleted: %s", sf.getDescription(), analysisDir)); + LogManager.getLogger(FileAnalysisPipelineProvider.class).warn(String.format("Failed to move job '%s' analysis directory to .deleted: %s", sf.getDescription(), analysisDir)); } } } diff --git a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisProtocol.java b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisProtocol.java index af21f907abf..21449eb4734 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisProtocol.java +++ b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisProtocol.java @@ -17,7 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.pipeline.*; +import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.TaskId; import org.labkey.api.pipeline.file.AbstractFileAnalysisJob; import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocol; import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory; diff --git a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisTaskPipelineImpl.java b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisTaskPipelineImpl.java index 1d285d048ce..aca1b176b9e 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisTaskPipelineImpl.java +++ b/pipeline/src/org/labkey/pipeline/analysis/FileAnalysisTaskPipelineImpl.java @@ -15,7 +15,7 @@ */ package org.labkey.pipeline.analysis; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlObject; import org.apache.xmlbeans.XmlOptions; @@ -329,12 +329,12 @@ public static FileAnalysisTaskPipeline create(Module module, Resource pipelineCo } catch (XmlValidationException e) { - Logger.getLogger(PipelineJobServiceImpl.class).error(e); + LogManager.getLogger(PipelineJobServiceImpl.class).error(e); return null; } catch (XmlException |IOException e) { - Logger.getLogger(PipelineJobServiceImpl.class).error("Error loading task pipeline '" + pipelineConfig.getPath() + "':\n" + e.getMessage()); + LogManager.getLogger(PipelineJobServiceImpl.class).error("Error loading task pipeline '" + pipelineConfig.getPath() + "':\n" + e.getMessage()); return null; } diff --git a/pipeline/src/org/labkey/pipeline/analysis/internalListPipelines.jsp b/pipeline/src/org/labkey/pipeline/analysis/internalListPipelines.jsp index 4fe85fed1b2..8170f5912b2 100644 --- a/pipeline/src/org/labkey/pipeline/analysis/internalListPipelines.jsp +++ b/pipeline/src/org/labkey/pipeline/analysis/internalListPipelines.jsp @@ -16,12 +16,12 @@ */ %> <%@ page import="org.labkey.api.pipeline.PipelineJobService" %> -<%@ page import="org.labkey.api.pipeline.TaskPipeline" %> <%@ page import="org.labkey.api.pipeline.TaskId" %> -<%@ page import="java.util.Collection" %> +<%@ page import="org.labkey.api.pipeline.TaskPipeline" %> +<%@ page import="org.labkey.api.pipeline.file.FileAnalysisTaskPipeline" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.pipeline.analysis.AnalysisController" %> -<%@ page import="org.labkey.api.pipeline.file.FileAnalysisTaskPipeline" %> +<%@ page import="java.util.Collection" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/pipeline/src/org/labkey/pipeline/api/AbstractPipelineQueue.java b/pipeline/src/org/labkey/pipeline/api/AbstractPipelineQueue.java index 197fd939404..5b4b89e6c70 100644 --- a/pipeline/src/org/labkey/pipeline/api/AbstractPipelineQueue.java +++ b/pipeline/src/org/labkey/pipeline/api/AbstractPipelineQueue.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.admin.notification.Notification; import org.labkey.api.admin.notification.NotificationService; import org.labkey.api.data.ContainerManager; @@ -41,7 +42,7 @@ */ public abstract class AbstractPipelineQueue implements PipelineQueue { - private static final Logger LOG = Logger.getLogger(AbstractPipelineQueue.class); + private static final Logger LOG = LogManager.getLogger(AbstractPipelineQueue.class); @Override public void addJob(final PipelineJob job) throws PipelineValidationException diff --git a/pipeline/src/org/labkey/pipeline/api/AbstractWorkDirectory.java b/pipeline/src/org/labkey/pipeline/api/AbstractWorkDirectory.java index f4d08fb601b..b8f1bf3a643 100644 --- a/pipeline/src/org/labkey/pipeline/api/AbstractWorkDirectory.java +++ b/pipeline/src/org/labkey/pipeline/api/AbstractWorkDirectory.java @@ -18,14 +18,15 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.io.filefilter.FileFilterUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.RecordedAction; import org.labkey.api.pipeline.WorkDirFactory; import org.labkey.api.pipeline.WorkDirectory; import org.labkey.api.pipeline.cmd.TaskPath; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; -import org.labkey.api.assay.AssayFileWriter; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.NetworkDrive; @@ -50,7 +51,7 @@ */ public abstract class AbstractWorkDirectory implements WorkDirectory { - private static final Logger LOG = Logger.getLogger(AbstractWorkDirectory.class); + private static final Logger LOG = LogManager.getLogger(AbstractWorkDirectory.class); protected static final String WORK_DIR_SUFFIX = ".work"; protected static final FileType FT_WORK_DIR = new FileType(WORK_DIR_SUFFIX); diff --git a/pipeline/src/org/labkey/pipeline/api/ParamParserImpl.java b/pipeline/src/org/labkey/pipeline/api/ParamParserImpl.java index a377c7f1527..442dcf9841a 100644 --- a/pipeline/src/org/labkey/pipeline/api/ParamParserImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/ParamParserImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.ParamParser; import org.labkey.api.util.StringUtilsLabKey; import org.w3c.dom.Document; @@ -33,8 +34,19 @@ import javax.xml.transform.TransformerFactory; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; -import java.io.*; -import java.util.*; +import java.io.BufferedWriter; +import java.io.ByteArrayInputStream; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.StringWriter; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * InputParser is used to parse a set of name-value pair @@ -51,7 +63,7 @@ public class ParamParserImpl implements ParamParser { - private static Logger _log = Logger.getLogger(ParamParserImpl.class); + private static Logger _log = LogManager.getLogger(ParamParserImpl.class); private static String TAG_BIOML = "bioml"; private static String TAG_NOTE = "note"; diff --git a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java index eda87ce8614..17796695e14 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/PipeRootImpl.java @@ -17,7 +17,7 @@ package org.labkey.pipeline.api; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cloud.CloudStoreService; diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineEmailPreferences.java b/pipeline/src/org/labkey/pipeline/api/PipelineEmailPreferences.java index 76d8a1d7129..2a7b7f8e66f 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineEmailPreferences.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineEmailPreferences.java @@ -19,11 +19,11 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DbScope; import org.labkey.api.data.PropertyManager; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.TableSelector; @@ -49,7 +49,7 @@ public class PipelineEmailPreferences { private static final String PIPELINE_NOTIFICATION_TASKS = "PipelineNotificationTasks"; - private static final Logger _log = Logger.getLogger(PipelineEmailPreferences.class); + private static final Logger _log = LogManager.getLogger(PipelineEmailPreferences.class); public static final String PREF_NOTIFY_OWNER_ON_SUCCESS = "notifyOwnerOnSuccess"; public static final String PREF_NOTIFY_USERS_ON_SUCCESS = "notifyUsersOnSuccess"; diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineJobMarshaller.java b/pipeline/src/org/labkey/pipeline/api/PipelineJobMarshaller.java index 96f0be68321..a44e08d5a96 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineJobMarshaller.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineJobMarshaller.java @@ -21,7 +21,8 @@ import com.fasterxml.jackson.databind.annotation.JsonDeserialize; import com.fasterxml.jackson.databind.annotation.JsonSerialize; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Test; import org.labkey.api.collections.ArrayListMap; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -161,7 +162,7 @@ public Object deserializeFromJSON(String json, Class cls) } } - private static Logger LOG = Logger.getLogger(PipelineJobMarshaller.class); + private static Logger LOG = LogManager.getLogger(PipelineJobMarshaller.class); public static class TestCase extends PipelineJob.TestSerialization { diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineJobServiceImpl.java b/pipeline/src/org/labkey/pipeline/api/PipelineJobServiceImpl.java index bd1965e3674..45b403b1acb 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineJobServiceImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineJobServiceImpl.java @@ -16,7 +16,8 @@ package org.labkey.pipeline.api; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.SchemaType; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -91,7 +92,7 @@ public class PipelineJobServiceImpl implements PipelineJobService { public static final String MODULE_PIPELINE_DIR = "pipeline"; - private static final Logger LOG = Logger.getLogger(PipelineJobServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(PipelineJobServiceImpl.class); private static final String PIPELINE_TOOLS_ERROR = "Failed to locate %s. Use the site pipeline tools settings to specify where it can be found. (Currently '%s')"; private static final String INSTALLED_PIPELINE_TOOL_ERROR = "Failed to locate %s. Check tool install location defined in pipelineConfig.xml. (Currently '%s')"; private static final String MODULE_TASKS_DIR = "tasks"; diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineJobStoreImpl.java b/pipeline/src/org/labkey/pipeline/api/PipelineJobStoreImpl.java index c67fa514859..352e2a40ebe 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineJobStoreImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineJobStoreImpl.java @@ -17,7 +17,8 @@ package org.labkey.pipeline.api; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; @@ -39,7 +40,7 @@ */ public class PipelineJobStoreImpl extends PipelineJobMarshaller { - private static Logger _log = Logger.getLogger(PipelineJobStoreImpl.class); + private static Logger _log = LogManager.getLogger(PipelineJobStoreImpl.class); @Override public Object deserializeFromJSON(String json, Class cls) diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineManager.java b/pipeline/src/org/labkey/pipeline/api/PipelineManager.java index 9804b63be09..530de4cc202 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineManager.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineManager.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -106,7 +107,7 @@ */ public class PipelineManager { - private static final Logger _log = Logger.getLogger(PipelineManager.class); + private static final Logger _log = LogManager.getLogger(PipelineManager.class); private static final PipelineSchema pipeline = PipelineSchema.getInstance(); private static final BlockingCache CACHE = CacheManager.getBlockingStringKeyCache(CacheManager.UNLIMITED, CacheManager.DAY, "Pipeline roots", (key, argument) -> new TableSelector(pipeline.getTableInfoPipelineRoots(), (Filter)argument, null).getObject(PipelineRoot.class)); diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineQueueImpl.java b/pipeline/src/org/labkey/pipeline/api/PipelineQueueImpl.java index 31509c6eb93..6b33f39453a 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineQueueImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineQueueImpl.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.junit.Assert; import org.junit.Test; import org.labkey.api.data.ConnectionWrapper; @@ -47,7 +48,7 @@ */ public class PipelineQueueImpl extends AbstractPipelineQueue { - private static final Logger LOG = Logger.getLogger(PipelineQueueImpl.class); + private static final Logger LOG = LogManager.getLogger(PipelineQueueImpl.class); private static final int MAX_RUNNING_JOBS = 10; private final List _pending = new ArrayList<>(); diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineSchema.java b/pipeline/src/org/labkey/pipeline/api/PipelineSchema.java index ae165aaa687..559a03873ae 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineSchema.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineSchema.java @@ -17,8 +17,8 @@ import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbSchemaType; -import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.TableInfo; +import org.labkey.api.data.dialect.SqlDialect; /** */ diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineServiceImpl.java b/pipeline/src/org/labkey/pipeline/api/PipelineServiceImpl.java index 55f62b93289..b2774fed87c 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineServiceImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineServiceImpl.java @@ -19,14 +19,14 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Before; import org.junit.Test; import org.labkey.api.admin.ImportOptions; -import org.labkey.api.attachments.AttachmentDirectory; import org.labkey.api.audit.AuditLogService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -109,7 +109,7 @@ public class PipelineServiceImpl implements PipelineService { - private static final Logger LOG = Logger.getLogger(PipelineService.class); + private static final Logger LOG = LogManager.getLogger(PipelineService.class); private static final String PREF_LASTPROTOCOL = "lastprotocol"; private static final String PREF_LASTSEQUENCEDB = "lastsequencedb"; diff --git a/pipeline/src/org/labkey/pipeline/api/PipelineStatusManager.java b/pipeline/src/org/labkey/pipeline/api/PipelineStatusManager.java index f90f118fd31..31a9a468ace 100644 --- a/pipeline/src/org/labkey/pipeline/api/PipelineStatusManager.java +++ b/pipeline/src/org/labkey/pipeline/api/PipelineStatusManager.java @@ -16,7 +16,8 @@ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.CompareType; @@ -73,7 +74,7 @@ public class PipelineStatusManager public static final DbScope.TransactionKind TRANSACTION_KIND = () -> "PIPELINESTATUS"; private static PipelineSchema _schema = PipelineSchema.getInstance(); - private static final Logger LOG = Logger.getLogger(PipelineStatusManager.class); + private static final Logger LOG = LogManager.getLogger(PipelineStatusManager.class); public static TableInfo getTableInfo() { diff --git a/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java b/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java index 145ed800899..e1efd4fa912 100644 --- a/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java +++ b/pipeline/src/org/labkey/pipeline/api/ScriptTaskImpl.java @@ -16,8 +16,9 @@ package org.labkey.pipeline.api; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipeRoot; @@ -57,7 +58,7 @@ */ public class ScriptTaskImpl extends CommandTaskImpl { - public static final Logger LOG = Logger.getLogger(ScriptTaskImpl.class); + public static final Logger LOG = LogManager.getLogger(ScriptTaskImpl.class); private ScriptEngine _engine; diff --git a/pipeline/src/org/labkey/pipeline/api/SimpleTaskFactory.java b/pipeline/src/org/labkey/pipeline/api/SimpleTaskFactory.java index 824ccc82e15..9bb8f96f5bc 100644 --- a/pipeline/src/org/labkey/pipeline/api/SimpleTaskFactory.java +++ b/pipeline/src/org/labkey/pipeline/api/SimpleTaskFactory.java @@ -15,15 +15,13 @@ */ package org.labkey.pipeline.api; -import org.labkey.api.collections.CaseInsensitiveHashSet; -import org.labkey.api.assay.DefaultDataTransformer; -import org.labkey.pipeline.analysis.CommandTaskImpl; - import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; +import org.labkey.api.assay.DefaultDataTransformer; +import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleLoader; import org.labkey.api.pipeline.PipelineJob; @@ -41,6 +39,7 @@ import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.Path; +import org.labkey.pipeline.analysis.CommandTaskImpl; import org.labkey.pipeline.xml.DoubleInputType; import org.labkey.pipeline.xml.FileInputOutputType; import org.labkey.pipeline.xml.FileInputType; diff --git a/pipeline/src/org/labkey/pipeline/api/TaskFactoryCacheHandler.java b/pipeline/src/org/labkey/pipeline/api/TaskFactoryCacheHandler.java index 45736bed0bc..fa3d0bcbd18 100644 --- a/pipeline/src/org/labkey/pipeline/api/TaskFactoryCacheHandler.java +++ b/pipeline/src/org/labkey/pipeline/api/TaskFactoryCacheHandler.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; import org.jetbrains.annotations.Nullable; @@ -43,7 +44,7 @@ */ /* package */ class TaskFactoryCacheHandler implements ModuleResourceCacheHandler> { - private static final Logger LOG = Logger.getLogger(TaskFactoryCacheHandler.class); + private static final Logger LOG = LogManager.getLogger(TaskFactoryCacheHandler.class); private static final String TASK_CONFIG_EXTENSION = ".task.xml"; @Override diff --git a/pipeline/src/org/labkey/pipeline/api/TaskPipelineCacheHandler.java b/pipeline/src/org/labkey/pipeline/api/TaskPipelineCacheHandler.java index 4c9aee2abec..7811d8340eb 100644 --- a/pipeline/src/org/labkey/pipeline/api/TaskPipelineCacheHandler.java +++ b/pipeline/src/org/labkey/pipeline/api/TaskPipelineCacheHandler.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.api; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleResourceCacheHandler; @@ -41,7 +42,7 @@ */ /* package */ class TaskPipelineCacheHandler implements ModuleResourceCacheHandler> { - private static final Logger LOG = Logger.getLogger(TaskPipelineCacheHandler.class); + private static final Logger LOG = LogManager.getLogger(TaskPipelineCacheHandler.class); private static final String PIPELINE_CONFIG_EXTENSION = ".pipeline.xml"; @Override diff --git a/pipeline/src/org/labkey/pipeline/api/WorkDirectoryLocal.java b/pipeline/src/org/labkey/pipeline/api/WorkDirectoryLocal.java index 8a1ff057cae..33909993812 100644 --- a/pipeline/src/org/labkey/pipeline/api/WorkDirectoryLocal.java +++ b/pipeline/src/org/labkey/pipeline/api/WorkDirectoryLocal.java @@ -15,10 +15,10 @@ */ package org.labkey.pipeline.api; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.WorkDirFactory; import org.labkey.api.pipeline.WorkDirectory; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; -import org.apache.log4j.Logger; import java.io.File; import java.io.IOException; diff --git a/pipeline/src/org/labkey/pipeline/api/WorkDirectoryRemote.java b/pipeline/src/org/labkey/pipeline/api/WorkDirectoryRemote.java index ff8c783788a..57f51005324 100644 --- a/pipeline/src/org/labkey/pipeline/api/WorkDirectoryRemote.java +++ b/pipeline/src/org/labkey/pipeline/api/WorkDirectoryRemote.java @@ -16,7 +16,8 @@ package org.labkey.pipeline.api; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.WorkDirFactory; import org.labkey.api.pipeline.WorkDirectory; import org.labkey.api.pipeline.file.FileAnalysisJobSupport; @@ -46,7 +47,7 @@ */ public class WorkDirectoryRemote extends AbstractWorkDirectory { - private static Logger _systemLog = Logger.getLogger(WorkDirectoryRemote.class); + private static Logger _systemLog = LogManager.getLogger(WorkDirectoryRemote.class); private static final int FILE_LOCKS_DEFAULT = 5; diff --git a/pipeline/src/org/labkey/pipeline/cluster/ClusterStartup.java b/pipeline/src/org/labkey/pipeline/cluster/ClusterStartup.java index 358a998a89a..8c85267e29b 100644 --- a/pipeline/src/org/labkey/pipeline/cluster/ClusterStartup.java +++ b/pipeline/src/org/labkey/pipeline/cluster/ClusterStartup.java @@ -27,8 +27,6 @@ import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.reader.Readers; -import org.labkey.api.test.TestTimeout; -import org.labkey.api.test.TestWhen; import org.labkey.api.util.ContextListener; import org.labkey.api.util.FileUtil; import org.labkey.api.util.JunitUtil; @@ -65,7 +63,7 @@ public class ClusterStartup extends AbstractPipelineStartup */ public void run(List moduleFiles, List moduleConfigFiles, List customConfigFiles, File webappDir, String[] args) throws IOException, PipelineJobException { - Map factories = initContext("org/labkey/pipeline/mule/config/cluster.log4j.properties", moduleFiles, moduleConfigFiles, customConfigFiles, webappDir, PipelineJobService.LocationType.RemoteExecutionEngine); + Map factories = initContext("ClusterStartup", "org/labkey/pipeline/mule/config/cluster.log4j.properties", moduleFiles, moduleConfigFiles, customConfigFiles, webappDir, PipelineJobService.LocationType.RemoteExecutionEngine); // First arg is URI to serialized job's JSON file, based on the web server's file system if (args.length < 1) diff --git a/pipeline/src/org/labkey/pipeline/cluster/NoOpPipelineStatusWriter.java b/pipeline/src/org/labkey/pipeline/cluster/NoOpPipelineStatusWriter.java index 9627a6e8556..14f8d389439 100644 --- a/pipeline/src/org/labkey/pipeline/cluster/NoOpPipelineStatusWriter.java +++ b/pipeline/src/org/labkey/pipeline/cluster/NoOpPipelineStatusWriter.java @@ -15,8 +15,8 @@ */ package org.labkey.pipeline.cluster; -import org.labkey.api.pipeline.PipelineStatusFile; import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineStatusFile; /** * Used when running a job through a remote execution engine. The cluster itself may handle giving the web diff --git a/pipeline/src/org/labkey/pipeline/importer/FolderImportJob.java b/pipeline/src/org/labkey/pipeline/importer/FolderImportJob.java index 521e4d6b793..e97a0e2c697 100644 --- a/pipeline/src/org/labkey/pipeline/importer/FolderImportJob.java +++ b/pipeline/src/org/labkey/pipeline/importer/FolderImportJob.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.admin.FolderImportContext; import org.labkey.api.admin.ImportOptions; import org.labkey.api.admin.PipelineJobLoggerGetter; @@ -44,7 +45,7 @@ */ public class FolderImportJob extends PipelineJob implements FolderJobSupport { - private static final Logger LOG = Logger.getLogger(FolderImportJob.class); + private static final Logger LOG = LogManager.getLogger(FolderImportJob.class); private final FolderImportContext _ctx; private final VirtualFile _root; diff --git a/pipeline/src/org/labkey/pipeline/importer/FolderImportProvider.java b/pipeline/src/org/labkey/pipeline/importer/FolderImportProvider.java index 2e0b57a6517..2dd29b70a05 100644 --- a/pipeline/src/org/labkey/pipeline/importer/FolderImportProvider.java +++ b/pipeline/src/org/labkey/pipeline/importer/FolderImportProvider.java @@ -15,13 +15,13 @@ */ package org.labkey.pipeline.importer; +import org.labkey.api.module.Module; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineDirectory; import org.labkey.api.pipeline.PipelineProvider; +import org.labkey.api.security.permissions.AdminPermission; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ViewContext; -import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.module.Module; import org.labkey.pipeline.PipelineController; import java.io.File; diff --git a/pipeline/src/org/labkey/pipeline/importer/FolderJobSupport.java b/pipeline/src/org/labkey/pipeline/importer/FolderJobSupport.java index b4f640d296d..c6ba66e59b9 100644 --- a/pipeline/src/org/labkey/pipeline/importer/FolderJobSupport.java +++ b/pipeline/src/org/labkey/pipeline/importer/FolderJobSupport.java @@ -18,8 +18,6 @@ import org.labkey.api.admin.FolderImportContext; import org.labkey.api.writer.VirtualFile; -import java.io.File; - /** * User: cnathe * Date: Jan 18, 2012 diff --git a/pipeline/src/org/labkey/pipeline/mule/EPipelineQueueImpl.java b/pipeline/src/org/labkey/pipeline/mule/EPipelineQueueImpl.java index d4d8b1326cc..b596a78a8c4 100644 --- a/pipeline/src/org/labkey/pipeline/mule/EPipelineQueueImpl.java +++ b/pipeline/src/org/labkey/pipeline/mule/EPipelineQueueImpl.java @@ -16,14 +16,14 @@ package org.labkey.pipeline.mule; import org.apache.activemq.ActiveMQConnectionFactory; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobData; -import org.labkey.api.pipeline.PipelineJobService; import org.labkey.api.pipeline.PipelineStatusFile; -import org.labkey.api.pipeline.TaskFactory; import org.labkey.api.pipeline.RemoteExecutionEngine; +import org.labkey.api.pipeline.TaskFactory; import org.labkey.api.security.User; import org.labkey.api.util.JobRunner; import org.labkey.pipeline.api.AbstractPipelineQueue; @@ -59,7 +59,7 @@ */ public class EPipelineQueueImpl extends AbstractPipelineQueue { - private static Logger _log = Logger.getLogger(EPipelineQueueImpl.class); + private static Logger _log = LogManager.getLogger(EPipelineQueueImpl.class); private static final String PIPELINE_QUEUE_NAME = "PipelineQueue"; private static ThreadLocal> _outboundJobs = new ThreadLocal<>(); diff --git a/pipeline/src/org/labkey/pipeline/mule/JMSStatusWriter.java b/pipeline/src/org/labkey/pipeline/mule/JMSStatusWriter.java index 76afb817458..d9c50476715 100644 --- a/pipeline/src/org/labkey/pipeline/mule/JMSStatusWriter.java +++ b/pipeline/src/org/labkey/pipeline/mule/JMSStatusWriter.java @@ -16,8 +16,8 @@ package org.labkey.pipeline.mule; import org.jetbrains.annotations.NotNull; -import org.labkey.api.pipeline.PipelineStatusFile; import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineStatusFile; import org.mule.extras.client.MuleClient; import org.mule.impl.RequestContext; import org.mule.umo.UMOEvent; diff --git a/pipeline/src/org/labkey/pipeline/mule/LoggerUtil.java b/pipeline/src/org/labkey/pipeline/mule/LoggerUtil.java index d69f1dae163..e5189bdd63e 100644 --- a/pipeline/src/org/labkey/pipeline/mule/LoggerUtil.java +++ b/pipeline/src/org/labkey/pipeline/mule/LoggerUtil.java @@ -15,16 +15,17 @@ */ package org.labkey.pipeline.mule; -import org.apache.log4j.Appender; -import org.apache.log4j.Logger; -import org.apache.log4j.PropertyConfigurator; -import org.apache.log4j.RollingFileAppender; -import org.apache.log4j.xml.DOMConfigurator; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.core.LoggerContext; +import org.apache.logging.log4j.core.config.ConfigurationSource; +import org.apache.logging.log4j.core.config.Configurator; +import org.apache.logging.log4j.core.config.properties.PropertiesConfiguration; +import org.apache.logging.log4j.core.config.properties.PropertiesConfigurationFactory; -import java.io.InputStream; +import java.io.FileInputStream; import java.io.IOException; -import java.util.Enumeration; -import java.util.Properties; +import java.io.InputStream; +import java.util.Objects; /** * User: jeckels @@ -32,21 +33,23 @@ */ public class LoggerUtil { - public static void initLogging(String classloaderResource) throws IOException + public static void initLogging(String name, String classloaderResource) throws IOException { InputStream in = null; try { if (classloaderResource.toLowerCase().endsWith(".properties")) { - in = LoggerUtil.class.getClassLoader().getResourceAsStream(classloaderResource); - Properties props = new Properties(); - props.load(in); - PropertyConfigurator.configure(props); + ConfigurationSource source = new ConfigurationSource(Objects.requireNonNull(LoggerUtil.class.getClassLoader().getResourceAsStream(classloaderResource))); + PropertiesConfigurationFactory factory = new PropertiesConfigurationFactory(); + LoggerContext context = (LoggerContext) LogManager.getContext(false); + PropertiesConfiguration propertiesConfiguration = factory.getConfiguration(context, source); + context.setConfiguration(propertiesConfiguration); + Configurator.initialize(null, propertiesConfiguration); } else { - DOMConfigurator.configure(LoggerUtil.class.getClassLoader().getResource(classloaderResource)); + Configurator.initialize(name, LoggerUtil.class.getClassLoader(), classloaderResource); } } finally @@ -55,28 +58,4 @@ public static void initLogging(String classloaderResource) throws IOException } } - /** We want to roll the file every time the server starts, which isn't directly supported by Log4J so we do it manually */ - public static void rollErrorLogFile(Logger logger) - { - while (logger != null && !logger.getAllAppenders().hasMoreElements()) - { - logger = (Logger)logger.getParent(); - } - - if (logger == null) - { - return; - } - - for (Enumeration e2 = logger.getAllAppenders(); e2.hasMoreElements();) - { - final Appender appender = (Appender)e2.nextElement(); - if (appender instanceof RollingFileAppender && "ERRORS".equals(appender.getName())) - { - RollingFileAppender rfa = (RollingFileAppender)appender; - rfa.rollOver(); - } - } - } - } \ No newline at end of file diff --git a/pipeline/src/org/labkey/pipeline/mule/MuleListenerHelper.java b/pipeline/src/org/labkey/pipeline/mule/MuleListenerHelper.java index ae1bca88b3a..63d5864b449 100644 --- a/pipeline/src/org/labkey/pipeline/mule/MuleListenerHelper.java +++ b/pipeline/src/org/labkey/pipeline/mule/MuleListenerHelper.java @@ -17,7 +17,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.module.SpringModule; import org.labkey.api.settings.AppProps; @@ -58,7 +59,7 @@ */ public class MuleListenerHelper implements ServletContext { - private static final Logger _log = Logger.getLogger(MuleListenerHelper.class); + private static final Logger _log = LogManager.getLogger(MuleListenerHelper.class); private final MuleXmlBuilderContextListener _muleContextListener; private final ServletContext _parentContext; diff --git a/pipeline/src/org/labkey/pipeline/mule/PipelineJobExceptionStrategy.java b/pipeline/src/org/labkey/pipeline/mule/PipelineJobExceptionStrategy.java index 2e524d32e8f..61ee4ce2227 100644 --- a/pipeline/src/org/labkey/pipeline/mule/PipelineJobExceptionStrategy.java +++ b/pipeline/src/org/labkey/pipeline/mule/PipelineJobExceptionStrategy.java @@ -15,14 +15,14 @@ */ package org.labkey.pipeline.mule; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.CancelledException; +import org.labkey.api.pipeline.PipelineJob; import org.mule.impl.DefaultComponentExceptionStrategy; import org.mule.impl.RequestContext; -import org.mule.umo.UMOEvent; import org.mule.umo.ComponentException; -import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobService; +import org.mule.umo.UMOEvent; /* * User: jeckels @@ -30,7 +30,7 @@ */ public class PipelineJobExceptionStrategy extends DefaultComponentExceptionStrategy { - private static final Logger LOGGER = Logger.getLogger(PipelineJobExceptionStrategy.class); + private static final Logger LOGGER = LogManager.getLogger(PipelineJobExceptionStrategy.class); @Override protected void defaultHandler(Throwable t) diff --git a/pipeline/src/org/labkey/pipeline/mule/PipelineJobRunnerRemoteExecution.java b/pipeline/src/org/labkey/pipeline/mule/PipelineJobRunnerRemoteExecution.java index 0332362271b..f9006dc4093 100644 --- a/pipeline/src/org/labkey/pipeline/mule/PipelineJobRunnerRemoteExecution.java +++ b/pipeline/src/org/labkey/pipeline/mule/PipelineJobRunnerRemoteExecution.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.mule; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.pipeline.PipelineJob; @@ -41,7 +42,7 @@ public class PipelineJobRunnerRemoteExecution implements Callable, ResumableDescriptor { - private static Logger _log = Logger.getLogger(PipelineJobRunnerRemoteExecution.class); + private static Logger _log = LogManager.getLogger(PipelineJobRunnerRemoteExecution.class); public PipelineJobRunnerRemoteExecution() { diff --git a/pipeline/src/org/labkey/pipeline/mule/RemoteServerStartup.java b/pipeline/src/org/labkey/pipeline/mule/RemoteServerStartup.java index 957ca2a8f96..b224e345c27 100644 --- a/pipeline/src/org/labkey/pipeline/mule/RemoteServerStartup.java +++ b/pipeline/src/org/labkey/pipeline/mule/RemoteServerStartup.java @@ -15,23 +15,32 @@ */ package org.labkey.pipeline.mule; -import org.mule.config.builders.MuleXmlConfigurationBuilder; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.pipeline.PipelineJobService; +import org.labkey.pipeline.AbstractPipelineStartup; +import org.labkey.pipeline.api.PipelineJobServiceImpl; +import org.labkey.pipeline.mule.filters.TaskJmsSelectorFilter; import org.mule.extras.client.MuleClient; import org.mule.impl.RequestContext; import org.springframework.beans.factory.BeanFactory; -import org.labkey.pipeline.api.PipelineJobServiceImpl; -import org.labkey.pipeline.AbstractPipelineStartup; -import org.labkey.pipeline.mule.filters.TaskJmsSelectorFilter; -import org.labkey.api.pipeline.PipelineJobService; -import org.labkey.api.pipeline.PipelineService; -import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.util.BreakpointThread; -import org.apache.log4j.Logger; -import javax.jms.*; -import java.io.*; -import java.lang.IllegalStateException; -import java.util.*; +import javax.jms.Connection; +import javax.jms.ConnectionFactory; +import javax.jms.JMSException; +import javax.jms.Message; +import javax.jms.QueueBrowser; +import javax.jms.Session; +import javax.jms.TextMessage; +import java.io.File; +import java.util.Collection; +import java.util.Collections; +import java.util.Enumeration; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; /* * User: jeckels @@ -39,7 +48,7 @@ */ public class RemoteServerStartup extends AbstractPipelineStartup { - private static Logger _log = Logger.getLogger(RemoteServerStartup.class); + private static Logger _log = LogManager.getLogger(RemoteServerStartup.class); private static final String JOB_QUEUE_ADDRESS = "job.queue"; /** @@ -47,8 +56,7 @@ public class RemoteServerStartup extends AbstractPipelineStartup */ public void run(List moduleFiles, List moduleConfigFiles, List customConfigFiles, File webappDir, String[] args) throws Exception { - Map factories = initContext("log4j.xml", moduleFiles, moduleConfigFiles, customConfigFiles, webappDir, PipelineJobService.LocationType.RemoteServer); - LoggerUtil.rollErrorLogFile(_log); + Map factories = initContext("RemoteServerStartup", "log4j2.xml", moduleFiles, moduleConfigFiles, customConfigFiles, webappDir, PipelineJobService.LocationType.RemoteServer); _log.info("Starting up LabKey Remote Server"); diff --git a/pipeline/src/org/labkey/pipeline/mule/RequeueLostJobsRequest.java b/pipeline/src/org/labkey/pipeline/mule/RequeueLostJobsRequest.java index 380c2e286d8..dd1c805c4d2 100644 --- a/pipeline/src/org/labkey/pipeline/mule/RequeueLostJobsRequest.java +++ b/pipeline/src/org/labkey/pipeline/mule/RequeueLostJobsRequest.java @@ -15,7 +15,8 @@ */ package org.labkey.pipeline.mule; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.pipeline.NoSuchJobException; import org.labkey.api.pipeline.PipelineJob; @@ -36,7 +37,7 @@ */ public class RequeueLostJobsRequest implements StatusRequest { - private static final Logger _log = Logger.getLogger(RequeueLostJobsRequest.class); + private static final Logger _log = LogManager.getLogger(RequeueLostJobsRequest.class); private Collection _locations; private Collection _jobIds; diff --git a/pipeline/src/org/labkey/pipeline/mule/StatusChangeRequest.java b/pipeline/src/org/labkey/pipeline/mule/StatusChangeRequest.java index 7e73dccb3ff..b67b959b5e3 100644 --- a/pipeline/src/org/labkey/pipeline/mule/StatusChangeRequest.java +++ b/pipeline/src/org/labkey/pipeline/mule/StatusChangeRequest.java @@ -21,7 +21,6 @@ import org.labkey.pipeline.api.PipelineStatusManager; import java.io.Serializable; -import java.sql.SQLException; /** * Transfer object for remote status changes. diff --git a/pipeline/src/org/labkey/pipeline/mule/StatusRequest.java b/pipeline/src/org/labkey/pipeline/mule/StatusRequest.java index 44dc4b2c96c..748238ffe6d 100644 --- a/pipeline/src/org/labkey/pipeline/mule/StatusRequest.java +++ b/pipeline/src/org/labkey/pipeline/mule/StatusRequest.java @@ -15,7 +15,6 @@ */ package org.labkey.pipeline.mule; -import java.sql.SQLException; import java.io.Serializable; /** diff --git a/pipeline/src/org/labkey/pipeline/mule/StatusRequestHandler.java b/pipeline/src/org/labkey/pipeline/mule/StatusRequestHandler.java index 8bdc75fdc4a..753df608b04 100644 --- a/pipeline/src/org/labkey/pipeline/mule/StatusRequestHandler.java +++ b/pipeline/src/org/labkey/pipeline/mule/StatusRequestHandler.java @@ -15,8 +15,6 @@ */ package org.labkey.pipeline.mule; -import java.sql.SQLException; - /** * StatusRequestHandler * diff --git a/pipeline/src/org/labkey/pipeline/mule/config/cluster.log4j.properties b/pipeline/src/org/labkey/pipeline/mule/config/cluster.log4j.properties index 24cc4113fd2..4e599865fea 100644 --- a/pipeline/src/org/labkey/pipeline/mule/config/cluster.log4j.properties +++ b/pipeline/src/org/labkey/pipeline/mule/config/cluster.log4j.properties @@ -1,26 +1,36 @@ -# Default log level -log4j.rootCategory=INFO, console +appender.console.type = Console +appender.console.name = STDOUT +appender.console.layout.type = PatternLayout +appender.console.layout.pattern = %-5p %d [%t] %c: %m%n -log4j.appender.console=org.apache.log4j.ConsoleAppender -log4j.appender.console.layout=org.apache.log4j.PatternLayout -log4j.appender.console.layout.ConversionPattern=%-5p %d [%t] %c: %m%n ################################################ # You can set custom log levels per-package here ################################################ # Apache Commons tend to make a lot of noise which can clutter the log. -log4j.logger.org.apache=WARN +logger.apache.name = org.apache +logger.apache.level = warn # Don't write job log output into the system logs -log4j.logger.org.labkey.api.pipeline.PipelineJob=FATAL +logger.PipelineJob.name = org.labkey.api.pipeline.PipelineJob +logger.PipelineJob.level = fatal # Mule classes -log4j.logger.org.mule=INFO +logger.mule.name = org.mule +logger.mule.level = info # Thread dump requests -log4j.logger.org.labkey.api.util.BreakpointThread=DEBUG +logger.BreakpointThread.name = org.labkey.api.util.BreakpointThread +logger.BreakpointThread.level = debug # Don't write Spring initialization info into every job's log file -log4j.logger.org.springframework.beans=WARN -log4j.logger.org.springframework.context.support=WARN \ No newline at end of file +logger.springframeworkBeans.name = org.springframework.beans +logger.springframeworkBeans.level = warn + +logger.springframeworkContext.name = org.springframework.context.support +logger.springframeworkContext.level = warn + +# Default log level +rootLogger.level = info +rootLogger.appenderRef.stdout.ref = STDOUT \ No newline at end of file diff --git a/pipeline/src/org/labkey/pipeline/mule/config/remote.log4j.properties b/pipeline/src/org/labkey/pipeline/mule/config/remote.log4j.properties index bad7fee58ae..65c7a8d05ae 100644 --- a/pipeline/src/org/labkey/pipeline/mule/config/remote.log4j.properties +++ b/pipeline/src/org/labkey/pipeline/mule/config/remote.log4j.properties @@ -1,23 +1,32 @@ # Default log level log4j.rootCategory=INFO, console -log4j.appender.console=org.apache.log4j.ConsoleAppender -log4j.appender.console.layout=org.apache.log4j.PatternLayout -log4j.appender.console.layout.ConversionPattern=%-5p %d [%t] %c: %m%n +appender.console.type = Console +appender.console.name = STDOUT +appender.console.layout.type = PatternLayout +appender.console.layout.pattern = %-5p %d [%t] %c: %m%n ################################################ # You can set custom log levels per-package here ################################################ # Apache Commons tend to make a lot of noise which can clutter the log. -log4j.logger.org.apache=WARN +logger.apache.name = org.apache +logger.apache.level = warn # Mule classes -log4j.logger.org.mule=INFO +logger.mule.name = org.mule +logger.mule.level = info # Thread dump requests -log4j.logger.org.labkey.api.util.BreakpointThread=DEBUG +logger.BreakpointThread.name = org.labkey.api.util.BreakpointThread +logger.BreakpointThread.level = debug # Don't write job log output into the system logs -log4j.logger.org.labkey.api.pipeline.PipelineJob=FATAL +logger.PipelineJob.name = org.labkey.api.pipeline.PipelineJob +logger.PipelineJob.level = fatal + +# Default log level +rootLogger.level = info +rootLogger.appenderRef.stdout.ref = STDOUT diff --git a/pipeline/src/org/labkey/pipeline/mule/filters/TaskJmsSelectorFilter.java b/pipeline/src/org/labkey/pipeline/mule/filters/TaskJmsSelectorFilter.java index 8e1b20d40a9..a2aae2d4e30 100644 --- a/pipeline/src/org/labkey/pipeline/mule/filters/TaskJmsSelectorFilter.java +++ b/pipeline/src/org/labkey/pipeline/mule/filters/TaskJmsSelectorFilter.java @@ -15,9 +15,9 @@ */ package org.labkey.pipeline.mule.filters; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; -import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.collections.CaseInsensitiveTreeSet; import org.labkey.api.pipeline.PipelineJob; import org.mule.providers.jms.filters.JmsSelectorFilter; @@ -35,7 +35,7 @@ public class TaskJmsSelectorFilter extends JmsSelectorFilter { private static Set ALL_LOCAL_LOCATIONS = new HashSet<>(); - private static Logger _log = Logger.getLogger(TaskJmsSelectorFilter.class); + private static Logger _log = LogManager.getLogger(TaskJmsSelectorFilter.class); private boolean _includeMonolithic; diff --git a/pipeline/src/org/labkey/pipeline/mule/test/DummyPipelineJob.java b/pipeline/src/org/labkey/pipeline/mule/test/DummyPipelineJob.java index 9fcc454a918..0bf435655e5 100644 --- a/pipeline/src/org/labkey/pipeline/mule/test/DummyPipelineJob.java +++ b/pipeline/src/org/labkey/pipeline/mule/test/DummyPipelineJob.java @@ -16,8 +16,7 @@ package org.labkey.pipeline.mule.test; import com.fasterxml.jackson.annotation.JsonCreator; -import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.pipeline.PipelineJob; @@ -29,7 +28,6 @@ import org.labkey.api.util.URLHelper; import org.labkey.api.util.UnexpectedException; import org.labkey.api.view.ViewBackgroundInfo; -import org.labkey.pipeline.api.TaskPipelineImpl; import java.io.File; import java.io.IOException; diff --git a/pipeline/src/org/labkey/pipeline/mule/test/DummyRemoteExecutionEngine.java b/pipeline/src/org/labkey/pipeline/mule/test/DummyRemoteExecutionEngine.java index 787710be4c9..917d3ec0f78 100644 --- a/pipeline/src/org/labkey/pipeline/mule/test/DummyRemoteExecutionEngine.java +++ b/pipeline/src/org/labkey/pipeline/mule/test/DummyRemoteExecutionEngine.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.pipeline.AbstractRemoteExecutionEngineConfig; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.pipeline.RemoteExecutionEngine; import org.labkey.pipeline.api.PipelineStatusFileImpl; diff --git a/pipeline/src/org/labkey/pipeline/mule/test/DummyTask.java b/pipeline/src/org/labkey/pipeline/mule/test/DummyTask.java index 032dc83a184..4baf1830660 100644 --- a/pipeline/src/org/labkey/pipeline/mule/test/DummyTask.java +++ b/pipeline/src/org/labkey/pipeline/mule/test/DummyTask.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.RecordedActionSet; /** diff --git a/pipeline/src/org/labkey/pipeline/mule/transformers/JMSMessageToPipelineJob.java b/pipeline/src/org/labkey/pipeline/mule/transformers/JMSMessageToPipelineJob.java index 66c0b289786..d5a5477711d 100644 --- a/pipeline/src/org/labkey/pipeline/mule/transformers/JMSMessageToPipelineJob.java +++ b/pipeline/src/org/labkey/pipeline/mule/transformers/JMSMessageToPipelineJob.java @@ -15,9 +15,9 @@ */ package org.labkey.pipeline.mule.transformers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.PipelineJob; -import org.labkey.api.pipeline.PipelineJobService; import org.mule.providers.jms.transformers.JMSMessageToObject; import org.mule.transformers.AbstractEventAwareTransformer; import org.mule.umo.UMOEventContext; @@ -31,7 +31,7 @@ */ public class JMSMessageToPipelineJob extends AbstractEventAwareTransformer { - private static final Logger LOG = Logger.getLogger(JMSMessageToPipelineJob.class); + private static final Logger LOG = LogManager.getLogger(JMSMessageToPipelineJob.class); private JMSMessageToObject _transformerFromJMS; diff --git a/pipeline/src/org/labkey/pipeline/mule/transformers/NoOpTransformer.java b/pipeline/src/org/labkey/pipeline/mule/transformers/NoOpTransformer.java index 073b365fc56..9fd268d8a49 100644 --- a/pipeline/src/org/labkey/pipeline/mule/transformers/NoOpTransformer.java +++ b/pipeline/src/org/labkey/pipeline/mule/transformers/NoOpTransformer.java @@ -16,7 +16,6 @@ package org.labkey.pipeline.mule.transformers; import org.mule.transformers.AbstractTransformer; -import org.mule.umo.transformer.TransformerException; /** * NoOpTransformer class diff --git a/pipeline/src/org/labkey/pipeline/mule/transformers/PipelineJobToJMSMessage.java b/pipeline/src/org/labkey/pipeline/mule/transformers/PipelineJobToJMSMessage.java index 97127e0fc92..8c43e22b35c 100644 --- a/pipeline/src/org/labkey/pipeline/mule/transformers/PipelineJobToJMSMessage.java +++ b/pipeline/src/org/labkey/pipeline/mule/transformers/PipelineJobToJMSMessage.java @@ -27,8 +27,6 @@ import javax.jms.JMSException; import javax.jms.Message; -import java.io.IOException; -import java.sql.SQLException; /** * PipelineJobToJMSMessage transforms a PipelineJob to a JMS Message diff --git a/pipeline/src/org/labkey/pipeline/startPipelineImport.jsp b/pipeline/src/org/labkey/pipeline/startPipelineImport.jsp index f1fd6b6fe34..b3cfe15be46 100644 --- a/pipeline/src/org/labkey/pipeline/startPipelineImport.jsp +++ b/pipeline/src/org/labkey/pipeline/startPipelineImport.jsp @@ -19,12 +19,12 @@ <%@ page import="org.labkey.api.security.permissions.AdminPermission" %> <%@ page import="org.labkey.api.study.Study" %> <%@ page import="org.labkey.api.study.StudyService" %> +<%@ page import="org.labkey.api.study.TimepointType" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.pipeline.PipelineController" %> <%@ page import="org.labkey.pipeline.PipelineController.StartFolderImportForm" %> -<%@ page import="org.labkey.api.study.TimepointType" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/pipeline/src/org/labkey/pipeline/status/ProviderButtonBar.java b/pipeline/src/org/labkey/pipeline/status/ProviderButtonBar.java new file mode 100644 index 00000000000..e69de29bb2d diff --git a/pipeline/src/org/labkey/pipeline/status/StatusController.java b/pipeline/src/org/labkey/pipeline/status/StatusController.java index 84aa73dc6e3..79dd04fa9a2 100644 --- a/pipeline/src/org/labkey/pipeline/status/StatusController.java +++ b/pipeline/src/org/labkey/pipeline/status/StatusController.java @@ -16,7 +16,9 @@ package org.labkey.pipeline.status; -import org.apache.log4j.Logger; +import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.FormHandlerAction; @@ -107,7 +109,7 @@ public class StatusController extends SpringActionController { - private static final Logger _log = Logger.getLogger(StatusController.class); + private static final Logger _log = LogManager.getLogger(StatusController.class); private static final DefaultActionResolver _resolver = new DefaultActionResolver(StatusController.class); protected static final String _newline = System.getProperty("line.separator"); diff --git a/query/build.gradle b/query/build.gradle index b1566477b3b..5138aa6fcbc 100644 --- a/query/build.gradle +++ b/query/build.gradle @@ -14,6 +14,8 @@ dependencies { // exclude these because they cause interference with the tomcat versions exclude group: "javax.servlet", module:"jsp-api" exclude group: "javax.servlet", module:"servlet-api" + // exclude this because it brings older version of log4j + exclude group: "log4j", module:"log4j" } external "org.olap4j:olap4j:${olap4jVersion}" diff --git a/query/src/org/labkey/query/AutoGeneratedCustomView.java b/query/src/org/labkey/query/AutoGeneratedCustomView.java index dacba30da2c..c84545288eb 100644 --- a/query/src/org/labkey/query/AutoGeneratedCustomView.java +++ b/query/src/org/labkey/query/AutoGeneratedCustomView.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; import org.labkey.api.query.CustomView; import org.labkey.api.query.FieldKey; @@ -31,7 +30,6 @@ import org.springframework.validation.Errors; import javax.servlet.http.HttpServletRequest; -import java.io.IOException; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; diff --git a/query/src/org/labkey/query/CustomQueryDefinitionImpl.java b/query/src/org/labkey/query/CustomQueryDefinitionImpl.java index 33039df441d..d52bce7f0fe 100644 --- a/query/src/org/labkey/query/CustomQueryDefinitionImpl.java +++ b/query/src/org/labkey/query/CustomQueryDefinitionImpl.java @@ -15,11 +15,11 @@ */ package org.labkey.query; +import org.labkey.api.data.Container; import org.labkey.api.query.SchemaKey; import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; import org.labkey.query.persist.QueryDef; -import org.labkey.api.data.Container; /** * User: jeckels diff --git a/query/src/org/labkey/query/CustomViewImpl.java b/query/src/org/labkey/query/CustomViewImpl.java index d831814137f..0dac6cf821e 100644 --- a/query/src/org/labkey/query/CustomViewImpl.java +++ b/query/src/org/labkey/query/CustomViewImpl.java @@ -17,7 +17,8 @@ package org.labkey.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.AnalyticsProviderItem; @@ -72,7 +73,7 @@ */ public class CustomViewImpl extends CustomViewInfoImpl implements CustomView, EditableCustomView { - private static final Logger _log = Logger.getLogger(CustomViewImpl.class); + private static final Logger _log = LogManager.getLogger(CustomViewImpl.class); private final QueryDefinition _queryDef; private boolean _dirty; diff --git a/query/src/org/labkey/query/CustomViewImporter.java b/query/src/org/labkey/query/CustomViewImporter.java index 190d50db5f6..81a897b6ae9 100644 --- a/query/src/org/labkey/query/CustomViewImporter.java +++ b/query/src/org/labkey/query/CustomViewImporter.java @@ -16,20 +16,17 @@ package org.labkey.query; import org.jetbrains.annotations.NotNull; -import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobWarning; import org.labkey.api.query.QueryService; -import org.labkey.api.util.XmlValidationException; import org.labkey.api.writer.VirtualFile; import java.io.IOException; -import java.sql.SQLException; import java.util.Collection; import java.util.Collections; diff --git a/query/src/org/labkey/query/CustomViewInfoImpl.java b/query/src/org/labkey/query/CustomViewInfoImpl.java index ef4e82bf0ec..d994f491109 100644 --- a/query/src/org/labkey/query/CustomViewInfoImpl.java +++ b/query/src/org/labkey/query/CustomViewInfoImpl.java @@ -32,7 +32,12 @@ import org.labkey.query.persist.QueryManager; import java.net.URISyntaxException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.Date; +import java.util.EnumMap; +import java.util.List; +import java.util.Map; /** * User: klum diff --git a/query/src/org/labkey/query/CustomViewQueryChangeListener.java b/query/src/org/labkey/query/CustomViewQueryChangeListener.java index 741e8c68b23..428fbeff482 100644 --- a/query/src/org/labkey/query/CustomViewQueryChangeListener.java +++ b/query/src/org/labkey/query/CustomViewQueryChangeListener.java @@ -15,7 +15,7 @@ */ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.AnalyticsProviderItem; import org.labkey.api.data.Container; @@ -119,7 +119,7 @@ public Collection queryDependents(User user, Container container, Contai } catch (URISyntaxException e) { - Logger.getLogger(CustomViewQueryChangeListener.class).error("An error occurred finding custom view dependents: ", e); + LogManager.getLogger(CustomViewQueryChangeListener.class).error("An error occurred finding custom view dependents: ", e); continue VIEW_LOOP; } @@ -262,7 +262,7 @@ private void _updateCustomViewQueryNameChange(User user, Container container, Sc } catch (Exception e) { - Logger.getLogger(CustomViewQueryChangeListener.class).error("An error occurred upgrading custom view properties: ", e); + LogManager.getLogger(CustomViewQueryChangeListener.class).error("An error occurred upgrading custom view properties: ", e); } } } diff --git a/query/src/org/labkey/query/CustomViewUtil.java b/query/src/org/labkey/query/CustomViewUtil.java index 5f5d82b8344..27a1b436dea 100644 --- a/query/src/org/labkey/query/CustomViewUtil.java +++ b/query/src/org/labkey/query/CustomViewUtil.java @@ -20,7 +20,6 @@ import org.jetbrains.annotations.NotNull; import org.json.JSONArray; import org.json.JSONObject; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.AnalyticsProviderItem; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DisplayColumn; @@ -39,12 +38,12 @@ import org.labkey.api.query.QueryView; import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewContext; -import javax.servlet.ServletException; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.Collections; diff --git a/query/src/org/labkey/query/CustomViewWriter.java b/query/src/org/labkey/query/CustomViewWriter.java index 5eeb4d66ec3..ca46cf22e95 100644 --- a/query/src/org/labkey/query/CustomViewWriter.java +++ b/query/src/org/labkey/query/CustomViewWriter.java @@ -16,12 +16,11 @@ package org.labkey.query; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderExportContext; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; -import org.labkey.api.admin.ImportException; import org.labkey.api.data.Container; import org.labkey.api.query.CustomView; import org.labkey.api.query.DefaultSchema; diff --git a/query/src/org/labkey/query/CustomViewXmlReader.java b/query/src/org/labkey/query/CustomViewXmlReader.java index afe7568c51e..5488dbb8078 100644 --- a/query/src/org/labkey/query/CustomViewXmlReader.java +++ b/query/src/org/labkey/query/CustomViewXmlReader.java @@ -17,7 +17,8 @@ package org.labkey.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.labkey.api.data.Aggregate; import org.labkey.api.data.AnalyticsProviderItem; @@ -92,7 +93,7 @@ public class CustomViewXmlReader private List _errors; - private static final Logger LOG = Logger.getLogger(CustomViewXmlReader.class); + private static final Logger LOG = LogManager.getLogger(CustomViewXmlReader.class); private CustomViewXmlReader() { diff --git a/query/src/org/labkey/query/ExternalSchema.java b/query/src/org/labkey/query/ExternalSchema.java index 2aa6a4cf7b2..f7bbe645a52 100644 --- a/query/src/org/labkey/query/ExternalSchema.java +++ b/query/src/org/labkey/query/ExternalSchema.java @@ -16,7 +16,7 @@ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.apache.xmlbeans.XmlException; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -28,8 +28,8 @@ import org.labkey.api.data.DbSchemaType; import org.labkey.api.data.DbScope; import org.labkey.api.data.ExternalSchemaCustomizer; -import org.labkey.api.data.UserSchemaCustomizer; import org.labkey.api.data.TableInfo; +import org.labkey.api.data.UserSchemaCustomizer; import org.labkey.api.query.DefaultSchema; import org.labkey.api.query.QuerySchema; import org.labkey.api.query.QueryService; @@ -181,7 +181,7 @@ protected static TablesType parseTablesType(AbstractExternalSchemaDef def, Templ String containerPath = def.getContainerPath(); if (containerPath != null && !"".equals(containerPath)) sb.append(" in container '").append(containerPath).append("'"); - Logger.getLogger(ExternalSchema.class).warn(sb, e); + LogManager.getLogger(ExternalSchema.class).warn(sb, e); return null; } } diff --git a/query/src/org/labkey/query/ExternalSchemaDefWriterFactory.java b/query/src/org/labkey/query/ExternalSchemaDefWriterFactory.java index f3793dcde30..ea5cccf7fc5 100644 --- a/query/src/org/labkey/query/ExternalSchemaDefWriterFactory.java +++ b/query/src/org/labkey/query/ExternalSchemaDefWriterFactory.java @@ -17,9 +17,9 @@ import org.apache.xmlbeans.XmlException; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.writer.VirtualFile; diff --git a/query/src/org/labkey/query/ExternalSchemaDocumentProvider.java b/query/src/org/labkey/query/ExternalSchemaDocumentProvider.java index 2585b372aeb..198ac4481a1 100644 --- a/query/src/org/labkey/query/ExternalSchemaDocumentProvider.java +++ b/query/src/org/labkey/query/ExternalSchemaDocumentProvider.java @@ -16,7 +16,8 @@ package org.labkey.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; @@ -33,7 +34,6 @@ import org.labkey.api.view.UnauthorizedException; import org.labkey.api.webdav.SimpleDocumentResource; -import java.sql.SQLException; import java.util.Date; import java.util.HashMap; import java.util.Map; @@ -46,7 +46,7 @@ */ public class ExternalSchemaDocumentProvider implements SearchService.DocumentProvider { - private static final Logger LOG = Logger.getLogger(ExternalSchemaDocumentProvider.class); + private static final Logger LOG = LogManager.getLogger(ExternalSchemaDocumentProvider.class); private static final SearchService.DocumentProvider _instance = new ExternalSchemaDocumentProvider(); public static final SearchService.SearchCategory externalTableCategory = new SearchService.SearchCategory("externalTable", "External Table"); diff --git a/query/src/org/labkey/query/LinkedSchema.java b/query/src/org/labkey/query/LinkedSchema.java index b66363449ff..8b753f76344 100644 --- a/query/src/org/labkey/query/LinkedSchema.java +++ b/query/src/org/labkey/query/LinkedSchema.java @@ -16,7 +16,7 @@ package org.labkey.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -101,7 +101,7 @@ public static LinkedSchema get(User user, Container container, LinkedSchemaDef d Container sourceContainer = def.lookupSourceContainer(); if (sourceContainer == null) { - Logger.getLogger(LinkedSchema.class).warn("Source container '" + def.getSourceContainerId() + "' not found for linked schema " + def.getUserSchemaName()); + LogManager.getLogger(LinkedSchema.class).warn("Source container '" + def.getSourceContainerId() + "' not found for linked schema " + def.getUserSchemaName()); return null; } @@ -112,7 +112,7 @@ public static LinkedSchema get(User user, Container container, LinkedSchemaDef d UserSchema sourceSchema = getSourceSchema(def, sourceSchemaName, sourceContainer, user); if (sourceSchema == null) { - Logger.getLogger(LinkedSchema.class).warn("Source schema '" + sourceSchemaName + "' not found in container '" + sourceContainer.getPath() + "' for linked schema " + def.getUserSchemaName()); + LogManager.getLogger(LinkedSchema.class).warn("Source schema '" + sourceSchemaName + "' not found in container '" + sourceContainer.getPath() + "' for linked schema " + def.getUserSchemaName()); return null; } @@ -163,7 +163,7 @@ private static UserSchema getSourceSchema(LinkedSchemaDef def, String sourceSche // Disallow recursive linked schema if (def.lookupContainer() == sourceContainer && def.getUserSchemaName().equals(sourceSchemaName)) { - Logger.getLogger(LinkedSchema.class).warn("Disallowed recursive linked schema definition '" + sourceSchemaName + "' in container '" + sourceContainer.getPath() + "'"); + LogManager.getLogger(LinkedSchema.class).warn("Disallowed recursive linked schema definition '" + sourceSchemaName + "' in container '" + sourceContainer.getPath() + "'"); return null; } diff --git a/query/src/org/labkey/query/ModuleQueryMetadataDef.java b/query/src/org/labkey/query/ModuleQueryMetadataDef.java index 6cc4006737e..ef8a35c931a 100644 --- a/query/src/org/labkey/query/ModuleQueryMetadataDef.java +++ b/query/src/org/labkey/query/ModuleQueryMetadataDef.java @@ -15,7 +15,8 @@ */ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.query.SchemaKey; import org.labkey.api.resource.Resource; @@ -40,7 +41,7 @@ */ public class ModuleQueryMetadataDef { - private static final Logger LOG = Logger.getLogger(ModuleQueryMetadataDef.class); + private static final Logger LOG = LogManager.getLogger(ModuleQueryMetadataDef.class); private String _name; private Path _path; diff --git a/query/src/org/labkey/query/QueryBrowserWebPartFactory.java b/query/src/org/labkey/query/QueryBrowserWebPartFactory.java index 1ebd4394f86..51ef12175cb 100644 --- a/query/src/org/labkey/query/QueryBrowserWebPartFactory.java +++ b/query/src/org/labkey/query/QueryBrowserWebPartFactory.java @@ -20,7 +20,6 @@ import org.labkey.api.view.JspView; import org.labkey.api.view.Portal; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.WebPartConfigurationException; import org.labkey.api.view.WebPartView; public class QueryBrowserWebPartFactory extends BaseWebPartFactory diff --git a/query/src/org/labkey/query/QueryDefinitionImpl.java b/query/src/org/labkey/query/QueryDefinitionImpl.java index c5d46993a44..0d8299497c0 100644 --- a/query/src/org/labkey/query/QueryDefinitionImpl.java +++ b/query/src/org/labkey/query/QueryDefinitionImpl.java @@ -18,7 +18,8 @@ import com.google.common.collect.ImmutableSet; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; @@ -61,7 +62,6 @@ import org.labkey.api.view.NotFoundException; import org.labkey.data.xml.TableType; import org.labkey.data.xml.TablesDocument; -import org.labkey.data.xml.TablesType; import org.labkey.data.xml.queryCustomView.NamedFiltersType; import org.labkey.query.persist.CstmView; import org.labkey.query.persist.QueryDef; @@ -86,7 +86,7 @@ public abstract class QueryDefinitionImpl implements QueryDefinition { private static final QueryManager mgr = QueryManager.get(); - private static final Logger log = Logger.getLogger(QueryDefinitionImpl.class); + private static final Logger log = LogManager.getLogger(QueryDefinitionImpl.class); protected final User _user; protected final Container _container; diff --git a/query/src/org/labkey/query/QueryModule.java b/query/src/org/labkey/query/QueryModule.java index 08f9c9ad6e7..d555c5bcfe4 100644 --- a/query/src/org/labkey/query/QueryModule.java +++ b/query/src/org/labkey/query/QueryModule.java @@ -129,7 +129,6 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; -import java.util.HashSet; import java.util.List; import java.util.Set; diff --git a/query/src/org/labkey/query/QueryServiceImpl.java b/query/src/org/labkey/query/QueryServiceImpl.java index bc7ac80bf38..cb2b30fb649 100644 --- a/query/src/org/labkey/query/QueryServiceImpl.java +++ b/query/src/org/labkey/query/QueryServiceImpl.java @@ -20,7 +20,8 @@ import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.collections4.SetValuedMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; import org.jetbrains.annotations.NotNull; @@ -29,10 +30,10 @@ import org.junit.Assert; import org.junit.Test; import org.labkey.api.assay.AssayService; +import org.labkey.api.audit.AuditHandler; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; import org.labkey.api.audit.DetailedAuditTypeEvent; -import org.labkey.api.audit.AuditHandler; import org.labkey.api.cache.Cache; import org.labkey.api.cache.CacheManager; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -147,7 +148,7 @@ public class QueryServiceImpl extends AuditHandler implements QueryService { - private static final Logger LOG = Logger.getLogger(QueryServiceImpl.class); + private static final Logger LOG = LogManager.getLogger(QueryServiceImpl.class); private static final ResourceRootProvider QUERY_AND_ASSAY_PROVIDER = new ResourceRootProvider() { private final ResourceRootProvider ASSAY_QUERY = ResourceRootProvider.chain(ResourceRootProvider.getAssayProviders(Path.rootPath), ResourceRootProvider.QUERY); @@ -1742,7 +1743,7 @@ public Map getExternalSchemas(User user, Container c) } catch (Exception e) { - Logger.getLogger(QueryServiceImpl.class).warn("Could not load schema " + def.getSourceSchemaName() + " from " + def.getDataSource(), e); + LogManager.getLogger(QueryServiceImpl.class).warn("Could not load schema " + def.getSourceSchemaName() + " from " + def.getDataSource(), e); } } @@ -1761,7 +1762,7 @@ public UserSchema getExternalSchema(User user, Container c, String name) } catch (Exception e) { - Logger.getLogger(QueryServiceImpl.class).warn("Could not load schema " + def.getSourceSchemaName() + " from " + def.getDataSource(), e); + LogManager.getLogger(QueryServiceImpl.class).warn("Could not load schema " + def.getSourceSchemaName() + " from " + def.getDataSource(), e); } } @@ -1783,7 +1784,7 @@ public Map getLinkedSchemas(User user, Container c) } catch (Exception e) { - Logger.getLogger(QueryServiceImpl.class).error("Error creating linked schema " + def.getUserSchemaName(), e); + LogManager.getLogger(QueryServiceImpl.class).error("Error creating linked schema " + def.getUserSchemaName(), e); } } @@ -1803,7 +1804,7 @@ public UserSchema getLinkedSchema(User user, Container c, String name) } catch (Exception e) { - Logger.getLogger(QueryServiceImpl.class).error("Error creating linked schema " + def.getUserSchemaName(), e); + LogManager.getLogger(QueryServiceImpl.class).error("Error creating linked schema " + def.getUserSchemaName(), e); } } @@ -1835,7 +1836,7 @@ public void deleteLinkedSchema(User user, Container c, String name) } catch (Exception e) { - Logger.getLogger(QueryServiceImpl.class).error("Error deleting linked schema " + name, e); + LogManager.getLogger(QueryServiceImpl.class).error("Error deleting linked schema " + name, e); } } diff --git a/query/src/org/labkey/query/QuerySnapshotDefImpl.java b/query/src/org/labkey/query/QuerySnapshotDefImpl.java index a68a8930033..21b2737a6d5 100644 --- a/query/src/org/labkey/query/QuerySnapshotDefImpl.java +++ b/query/src/org/labkey/query/QuerySnapshotDefImpl.java @@ -17,7 +17,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.query.FieldKey; @@ -45,7 +46,7 @@ public class QuerySnapshotDefImpl implements QuerySnapshotDefinition { - final static private Logger LOG = Logger.getLogger(QuerySnapshotDefImpl.class); + final static private Logger LOG = LogManager.getLogger(QuerySnapshotDefImpl.class); // data models private QueryDef _queryDef; diff --git a/query/src/org/labkey/query/QuerySnapshotQueryChangeListener.java b/query/src/org/labkey/query/QuerySnapshotQueryChangeListener.java index f0963738d00..74c0d829e86 100644 --- a/query/src/org/labkey/query/QuerySnapshotQueryChangeListener.java +++ b/query/src/org/labkey/query/QuerySnapshotQueryChangeListener.java @@ -15,7 +15,7 @@ */ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -96,7 +96,7 @@ private void _updateQuerySnapshotQueryNameChange(User user, Container container, } catch (Exception e) { - Logger.getLogger(QuerySnapshotQueryChangeListener.class).error("An error occurred upgrading query snapshot properties: ", e); + LogManager.getLogger(QuerySnapshotQueryChangeListener.class).error("An error occurred upgrading query snapshot properties: ", e); } } } diff --git a/query/src/org/labkey/query/QueryUpgradeCode.java b/query/src/org/labkey/query/QueryUpgradeCode.java index 6ff68367b48..0899c2e1dfa 100644 --- a/query/src/org/labkey/query/QueryUpgradeCode.java +++ b/query/src/org/labkey/query/QueryUpgradeCode.java @@ -15,7 +15,8 @@ */ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; import org.labkey.api.data.DbScope; @@ -34,7 +35,7 @@ public class QueryUpgradeCode implements UpgradeCode { - private static final Logger _log = Logger.getLogger(QueryUpgradeCode.class); + private static final Logger _log = LogManager.getLogger(QueryUpgradeCode.class); /** * Migrate the legacy chart views to the new json-based versions diff --git a/query/src/org/labkey/query/QueryWriter.java b/query/src/org/labkey/query/QueryWriter.java index 3e756e0a838..fec4dcd2371 100644 --- a/query/src/org/labkey/query/QueryWriter.java +++ b/query/src/org/labkey/query/QueryWriter.java @@ -16,7 +16,8 @@ package org.labkey.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.apache.xmlbeans.XmlOptions; import org.labkey.api.admin.BaseFolderWriter; @@ -45,7 +46,7 @@ */ public class QueryWriter extends BaseFolderWriter { - private static final Logger _log = Logger.getLogger(QueryWriter.class); + private static final Logger _log = LogManager.getLogger(QueryWriter.class); public static final String FILE_EXTENSION = ".sql"; public static final String META_FILE_EXTENSION = ".query.xml"; diff --git a/query/src/org/labkey/query/TableQueryDefinition.java b/query/src/org/labkey/query/TableQueryDefinition.java index fafc5d5fe23..a3b2c4336da 100644 --- a/query/src/org/labkey/query/TableQueryDefinition.java +++ b/query/src/org/labkey/query/TableQueryDefinition.java @@ -16,7 +16,8 @@ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.AbstractTableInfo; @@ -53,7 +54,7 @@ public class TableQueryDefinition extends QueryDefinitionImpl { private String _sql; private String _title; - private static final Logger log = Logger.getLogger(TableQueryDefinition.class); + private static final Logger log = LogManager.getLogger(TableQueryDefinition.class); public TableQueryDefinition(UserSchema schema, String tableName) { diff --git a/query/src/org/labkey/query/TableXML.java b/query/src/org/labkey/query/TableXML.java index 0a0e6497b06..c98d00b7fb9 100644 --- a/query/src/org/labkey/query/TableXML.java +++ b/query/src/org/labkey/query/TableXML.java @@ -16,14 +16,14 @@ package org.labkey.query; -import org.labkey.api.query.QueryParseException; -import org.labkey.data.xml.TableType; -import org.labkey.data.xml.ColumnType; -import org.labkey.api.data.TableInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ForeignKey; -import org.labkey.api.query.RowIdForeignKey; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryParseException; +import org.labkey.api.query.RowIdForeignKey; +import org.labkey.data.xml.ColumnType; +import org.labkey.data.xml.TableType; import java.util.Collection; import java.util.Collections; diff --git a/query/src/org/labkey/query/ValidateQueriesVisitor.java b/query/src/org/labkey/query/ValidateQueriesVisitor.java index e2d2893f599..fd283347530 100644 --- a/query/src/org/labkey/query/ValidateQueriesVisitor.java +++ b/query/src/org/labkey/query/ValidateQueriesVisitor.java @@ -15,7 +15,7 @@ */ package org.labkey.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.TableInfo; import org.labkey.api.query.QueryParseException; import org.labkey.api.query.SchemaTreeWalker; diff --git a/query/src/org/labkey/query/analytics/AggregatesCountNonBlankAnalyticsProvider.java b/query/src/org/labkey/query/analytics/AggregatesCountNonBlankAnalyticsProvider.java index 4e2a7e59f82..fea0dca23fa 100644 --- a/query/src/org/labkey/query/analytics/AggregatesCountNonBlankAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/AggregatesCountNonBlankAnalyticsProvider.java @@ -16,9 +16,9 @@ package org.labkey.query.analytics; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.Aggregate; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; public class AggregatesCountNonBlankAnalyticsProvider extends BaseAggregatesAnalyticsProvider { diff --git a/query/src/org/labkey/query/analytics/AggregatesMaxAnalyticsProvider.java b/query/src/org/labkey/query/analytics/AggregatesMaxAnalyticsProvider.java index 514726a2019..bb7b7be3b85 100644 --- a/query/src/org/labkey/query/analytics/AggregatesMaxAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/AggregatesMaxAnalyticsProvider.java @@ -16,9 +16,9 @@ package org.labkey.query.analytics; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.Aggregate; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; public class AggregatesMaxAnalyticsProvider extends BaseAggregatesAnalyticsProvider { diff --git a/query/src/org/labkey/query/analytics/AggregatesMeanAnalyticsProvider.java b/query/src/org/labkey/query/analytics/AggregatesMeanAnalyticsProvider.java index d601a8ec52d..16114fb4a28 100644 --- a/query/src/org/labkey/query/analytics/AggregatesMeanAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/AggregatesMeanAnalyticsProvider.java @@ -16,9 +16,9 @@ package org.labkey.query.analytics; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.Aggregate; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; public class AggregatesMeanAnalyticsProvider extends BaseAggregatesAnalyticsProvider { diff --git a/query/src/org/labkey/query/analytics/AggregatesMinAnalyticsProvider.java b/query/src/org/labkey/query/analytics/AggregatesMinAnalyticsProvider.java index 9bf0d471eab..fb0672c73b5 100644 --- a/query/src/org/labkey/query/analytics/AggregatesMinAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/AggregatesMinAnalyticsProvider.java @@ -16,9 +16,9 @@ package org.labkey.query.analytics; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.Aggregate; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; public class AggregatesMinAnalyticsProvider extends BaseAggregatesAnalyticsProvider { diff --git a/query/src/org/labkey/query/analytics/AggregatesSumAnalyticsProvider.java b/query/src/org/labkey/query/analytics/AggregatesSumAnalyticsProvider.java index 8e6409a02bc..767d71fec02 100644 --- a/query/src/org/labkey/query/analytics/AggregatesSumAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/AggregatesSumAnalyticsProvider.java @@ -16,9 +16,9 @@ package org.labkey.query.analytics; import org.jetbrains.annotations.NotNull; -import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; import org.labkey.api.data.Aggregate; import org.labkey.api.data.ColumnInfo; +import org.labkey.api.stats.BaseAggregatesAnalyticsProvider; public class AggregatesSumAnalyticsProvider extends BaseAggregatesAnalyticsProvider { diff --git a/query/src/org/labkey/query/analytics/RemoveColumnAnalyticsProvider.java b/query/src/org/labkey/query/analytics/RemoveColumnAnalyticsProvider.java index ed0eda28663..53e959cf6b8 100644 --- a/query/src/org/labkey/query/analytics/RemoveColumnAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/RemoveColumnAnalyticsProvider.java @@ -17,10 +17,10 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.RenderContext; import org.labkey.api.query.QuerySettings; +import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.template.ClientDependency; diff --git a/query/src/org/labkey/query/analytics/SummaryStatisticsAnalyticsProvider.java b/query/src/org/labkey/query/analytics/SummaryStatisticsAnalyticsProvider.java index 67ce2e52018..99e2a1145ec 100644 --- a/query/src/org/labkey/query/analytics/SummaryStatisticsAnalyticsProvider.java +++ b/query/src/org/labkey/query/analytics/SummaryStatisticsAnalyticsProvider.java @@ -17,10 +17,10 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; -import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.RenderContext; import org.labkey.api.query.QuerySettings; +import org.labkey.api.stats.ColumnAnalyticsProvider; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.template.ClientDependency; diff --git a/query/src/org/labkey/query/audit/QueryUpdateAuditProvider.java b/query/src/org/labkey/query/audit/QueryUpdateAuditProvider.java index c64986d9410..cfcb62c8ac9 100644 --- a/query/src/org/labkey/query/audit/QueryUpdateAuditProvider.java +++ b/query/src/org/labkey/query/audit/QueryUpdateAuditProvider.java @@ -22,7 +22,6 @@ import org.labkey.api.audit.DetailedAuditTypeEvent; import org.labkey.api.audit.query.AbstractAuditDomainKind; import org.labkey.api.audit.query.DefaultAuditTypeTable; -import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.SimpleFilter; diff --git a/query/src/org/labkey/query/controllers/GetQueryDetailsAction.java b/query/src/org/labkey/query/controllers/GetQueryDetailsAction.java index 1ef4bb1fb60..e7a0e7cc295 100644 --- a/query/src/org/labkey/query/controllers/GetQueryDetailsAction.java +++ b/query/src/org/labkey/query/controllers/GetQueryDetailsAction.java @@ -16,7 +16,8 @@ package org.labkey.query.controllers; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.json.JSONArray; import org.json.JSONObject; import org.labkey.api.action.Action; @@ -81,7 +82,7 @@ @Action(ActionType.SelectMetaData.class) public class GetQueryDetailsAction extends ReadOnlyApiAction { - private static final Logger LOG = Logger.getLogger(GetQueryDetailsAction.class); + private static final Logger LOG = LogManager.getLogger(GetQueryDetailsAction.class); @Override protected long getLastModified(Form form) diff --git a/query/src/org/labkey/query/controllers/NewQueryForm.java b/query/src/org/labkey/query/controllers/NewQueryForm.java index 3ec273b5cf3..750695c7388 100644 --- a/query/src/org/labkey/query/controllers/NewQueryForm.java +++ b/query/src/org/labkey/query/controllers/NewQueryForm.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - + package org.labkey.query.controllers; -import org.labkey.api.query.QueryForm; import org.labkey.api.query.QueryAction; +import org.labkey.api.query.QueryForm; public class NewQueryForm extends QueryForm { diff --git a/query/src/org/labkey/query/controllers/OlapController.java b/query/src/org/labkey/query/controllers/OlapController.java index d50e2d13cd7..4fbec3a5f5b 100644 --- a/query/src/org/labkey/query/controllers/OlapController.java +++ b/query/src/org/labkey/query/controllers/OlapController.java @@ -21,7 +21,8 @@ import mondrian.olap.MondrianServer; import mondrian.xmla.impl.MondrianXmlaServlet; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -146,7 +147,7 @@ */ public class OlapController extends SpringActionController { - private static final Logger _log = Logger.getLogger(OlapController.class); + private static final Logger _log = LogManager.getLogger(OlapController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(OlapController.class); @@ -637,7 +638,7 @@ public ApiResponse execute(ExecuteMdxForm form, BindException errors) throws Exc } catch (RuntimeException x) { - Logger.getLogger(OlapController.class).error("mondrian error", x); + LogManager.getLogger(OlapController.class).error("mondrian error", x); Throwable t = x; while (null != t.getCause() && t != t.getCause()) t = t.getCause(); diff --git a/query/src/org/labkey/query/controllers/QueryController.java b/query/src/org/labkey/query/controllers/QueryController.java index 96c008042fb..8612cc54914 100644 --- a/query/src/org/labkey/query/controllers/QueryController.java +++ b/query/src/org/labkey/query/controllers/QueryController.java @@ -25,7 +25,8 @@ import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; import org.apache.xmlbeans.XmlValidationError; @@ -200,7 +201,7 @@ public class QueryController extends SpringActionController { - private static final Logger LOG = Logger.getLogger(QueryController.class); + private static final Logger LOG = LogManager.getLogger(QueryController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(QueryController.class, ValidateQueryAction.class, @@ -957,7 +958,7 @@ public ModelAndView getView(SourceForm form, BindException errors) // } errors.reject("ERROR_MSG", e.toString()); - Logger.getLogger(QueryController.class).error("Error", e); + LogManager.getLogger(QueryController.class).error("Error", e); } Renderable moduleWarning = null; @@ -5271,7 +5272,7 @@ public boolean handlePost(InternalNewViewForm form, BindException errors) } catch (Exception e) { - Logger.getLogger(QueryController.class).error("Error", e); + LogManager.getLogger(QueryController.class).error("Error", e); errors.reject(ERROR_MSG, "An exception occurred: " + e); return false; } @@ -6045,7 +6046,7 @@ public ModelAndView getView(Object o, BindException errors) if (null != x.getCause() && x != x.getCause()) x = x.getCause(); html.add("
" + PageFlowUtil.filter(x.toString())); - Logger.getLogger(QueryController.class).debug(expr,x); + LogManager.getLogger(QueryController.class).debug(expr,x); } if (null != e) { diff --git a/query/src/org/labkey/query/controllers/TableInfoForm.java b/query/src/org/labkey/query/controllers/TableInfoForm.java index 63bf5dd44e9..94fc017f245 100644 --- a/query/src/org/labkey/query/controllers/TableInfoForm.java +++ b/query/src/org/labkey/query/controllers/TableInfoForm.java @@ -17,17 +17,20 @@ package org.labkey.query.controllers; import org.jetbrains.annotations.NotNull; -import org.labkey.api.query.QueryForm; -import org.labkey.api.query.FieldKey; -import org.labkey.api.data.TableInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ForeignKey; -import org.labkey.query.sql.Query; +import org.labkey.api.data.TableInfo; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryForm; import org.labkey.query.QueryDefinitionImpl; -import org.springframework.validation.BindException; +import org.labkey.query.sql.Query; import org.springframework.beans.PropertyValues; +import org.springframework.validation.BindException; -import java.util.*; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; public class TableInfoForm extends QueryForm { diff --git a/query/src/org/labkey/query/data/ExternalSchemaTable.java b/query/src/org/labkey/query/data/ExternalSchemaTable.java index 2d19ddda9c0..01116612f4b 100644 --- a/query/src/org/labkey/query/data/ExternalSchemaTable.java +++ b/query/src/org/labkey/query/data/ExternalSchemaTable.java @@ -16,9 +16,15 @@ package org.labkey.query.data; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DatabaseTableType; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.UpdateableTableInfo; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryException; import org.labkey.api.query.QueryUpdateService; @@ -39,7 +45,7 @@ public class ExternalSchemaTable extends SimpleUserSchema.SimpleTable implements UpdateableTableInfo { - private static final Logger _logger = Logger.getLogger(ExternalSchemaTable.class); + private static final Logger _logger = LogManager.getLogger(ExternalSchemaTable.class); private Container _container; protected TableType _metadata; diff --git a/query/src/org/labkey/query/jdbc/QueryConnection.java b/query/src/org/labkey/query/jdbc/QueryConnection.java index e3148dba98d..6948ca4f2d8 100644 --- a/query/src/org/labkey/query/jdbc/QueryConnection.java +++ b/query/src/org/labkey/query/jdbc/QueryConnection.java @@ -21,7 +21,6 @@ import org.labkey.api.query.QuerySchema; import org.labkey.api.security.PrincipalType; import org.labkey.api.security.User; -import org.labkey.api.security.UserManager; import java.sql.Array; import java.sql.Blob; @@ -31,8 +30,6 @@ import java.sql.DatabaseMetaData; import java.sql.NClob; import java.sql.PreparedStatement; -import java.sql.SQLClientInfoException; -import java.sql.SQLException; import java.sql.SQLWarning; import java.sql.SQLXML; import java.sql.Savepoint; diff --git a/query/src/org/labkey/query/jdbc/QueryDatabaseMetaData.java b/query/src/org/labkey/query/jdbc/QueryDatabaseMetaData.java index 43ad4e6a06a..63a0ab143c0 100644 --- a/query/src/org/labkey/query/jdbc/QueryDatabaseMetaData.java +++ b/query/src/org/labkey/query/jdbc/QueryDatabaseMetaData.java @@ -19,7 +19,6 @@ import java.sql.DatabaseMetaData; import java.sql.ResultSet; import java.sql.RowIdLifetime; -import java.sql.SQLException; /** * User: matthewb diff --git a/query/src/org/labkey/query/jdbc/QueryDriver.java b/query/src/org/labkey/query/jdbc/QueryDriver.java index 9c2a7e14a83..35d526e5790 100644 --- a/query/src/org/labkey/query/jdbc/QueryDriver.java +++ b/query/src/org/labkey/query/jdbc/QueryDriver.java @@ -15,7 +15,6 @@ */ package org.labkey.query.jdbc; -import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; diff --git a/query/src/org/labkey/query/jdbc/QueryStatement.java b/query/src/org/labkey/query/jdbc/QueryStatement.java index 6823605a5b3..abb6f62a0ba 100644 --- a/query/src/org/labkey/query/jdbc/QueryStatement.java +++ b/query/src/org/labkey/query/jdbc/QueryStatement.java @@ -15,7 +15,8 @@ */ package org.labkey.query.jdbc; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.CachedResultSet; import org.labkey.api.query.QuerySchema; import org.labkey.api.query.QueryService; @@ -37,7 +38,7 @@ public class QueryStatement implements Statement final QueryConnection _conn; boolean _closed = false; ResultSet _rs = null; - static Logger _log = Logger.getLogger(QueryStatement.class); + static Logger _log = LogManager.getLogger(QueryStatement.class); QueryStatement(QueryConnection conn) { diff --git a/query/src/org/labkey/query/olap/BitSetQueryImpl.java b/query/src/org/labkey/query/olap/BitSetQueryImpl.java index 62fc6da8fdb..30a49c39090 100644 --- a/query/src/org/labkey/query/olap/BitSetQueryImpl.java +++ b/query/src/org/labkey/query/olap/BitSetQueryImpl.java @@ -16,7 +16,8 @@ package org.labkey.query.olap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.Cache; @@ -82,7 +83,7 @@ public class BitSetQueryImpl { private final boolean mondrianCompatibleNullHandling = false; - private static Logger _log = Logger.getLogger(BitSetQueryImpl.class); + private static Logger _log = LogManager.getLogger(BitSetQueryImpl.class); private final static User olapServiceUser = new LimitedUser(User.guest, new int[0], Collections.singleton(RoleManager.getRole(ReaderRole.class)), false); static { diff --git a/query/src/org/labkey/query/olap/CustomOlapSchemaDescriptor.java b/query/src/org/labkey/query/olap/CustomOlapSchemaDescriptor.java index 5011d4bf751..2e435202046 100644 --- a/query/src/org/labkey/query/olap/CustomOlapSchemaDescriptor.java +++ b/query/src/org/labkey/query/olap/CustomOlapSchemaDescriptor.java @@ -18,11 +18,9 @@ import org.apache.commons.io.IOUtils; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; -import org.labkey.api.module.Module; import org.labkey.api.view.ActionURL; import org.labkey.query.controllers.OlapController; -import java.io.IOException; import java.io.InputStream; /** diff --git a/query/src/org/labkey/query/olap/OlapTestCase.jsp b/query/src/org/labkey/query/olap/OlapTestCase.jsp index 72f5d9f37d2..09a9b4f1b02 100644 --- a/query/src/org/labkey/query/olap/OlapTestCase.jsp +++ b/query/src/org/labkey/query/olap/OlapTestCase.jsp @@ -1,12 +1,14 @@ <%@ page import="org.json.JSONObject" %> -<%@ page import="org.labkey.api.view.ActionURL" %> -<%@ page import="org.labkey.api.security.User" %> -<%@ page import="java.util.Map" %> -<%@ page import="org.labkey.api.view.ViewServlet" %> <%@ page import="org.junit.Test" %> -<%@ page import="static org.junit.Assert.*" %> -<%@ page import="org.labkey.api.util.TestContext" %> +<%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.util.JunitUtil" %> +<%@ page import="org.labkey.api.util.TestContext" %> +<%@ page import="org.labkey.api.view.ActionURL" %> +<%@ page import="static org.junit.Assert.*" %> +<%@ page import="org.labkey.api.view.ViewServlet" %> +<%@ page import="java.util.Map" %> +<%@ page import="org.apache.logging.log4j.LogManager" %> +<%@ page import="org.labkey.query.controllers.OlapController" %> <%@ page extends="org.labkey.api.jsp.JspTest.DRT" %> <%! @@ -28,7 +30,6 @@ boolean canExecuteMdx(String configId) throws Exception config.put("query", "SELECT [Measures].[RowCount] ON COLUMNS, [Fact.ptid].[ptid].Members ON ROWS FROM [Facts]"); config.put("configId", configId); config.put("schemaName", "OlapTest"); - JSONObject result = executeJsonApi(new ActionURL("olap","executeMdx", JunitUtil.getTestContainer()), TestContext.get().getUser(), config.toString()); if (null != result.get("success") && Boolean.FALSE == result.getBoolean("success")) return false; diff --git a/query/src/org/labkey/query/olap/Qube.java b/query/src/org/labkey/query/olap/Qube.java index f1107439829..81b3fefb155 100644 --- a/query/src/org/labkey/query/olap/Qube.java +++ b/query/src/org/labkey/query/olap/Qube.java @@ -17,22 +17,10 @@ import org.json.JSONObject; -import org.olap4j.Axis; import org.olap4j.CellSet; -import org.olap4j.CellSetAxis; -import org.olap4j.CellSetAxisMetaData; import org.olap4j.OlapConnection; -import org.olap4j.OlapException; -import org.olap4j.Position; import org.olap4j.metadata.Cube; -import org.olap4j.metadata.Hierarchy; import org.olap4j.metadata.Level; -import org.olap4j.metadata.Member; - -import java.util.ArrayList; -import java.util.Collections; -import java.util.List; -import java.util.ListIterator; /** diff --git a/query/src/org/labkey/query/olap/ServerManager.java b/query/src/org/labkey/query/olap/ServerManager.java index 9717e2e3686..6b8c6d5295e 100644 --- a/query/src/org/labkey/query/olap/ServerManager.java +++ b/query/src/org/labkey/query/olap/ServerManager.java @@ -25,7 +25,8 @@ import mondrian.spi.CatalogLocator; import mondrian.spi.DataSourceChangeListener; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -112,7 +113,7 @@ public class ServerManager { - private static final Logger LOG = Logger.getLogger(ServerManager.class); + private static final Logger LOG = LogManager.getLogger(ServerManager.class); private static final Map SERVERS = new HashMap<>(); private static final Object SERVERS_LOCK = new Object(); diff --git a/query/src/org/labkey/query/olap/SqlQueryImpl.java b/query/src/org/labkey/query/olap/SqlQueryImpl.java index 905ead4ce58..e3c38a10c97 100644 --- a/query/src/org/labkey/query/olap/SqlQueryImpl.java +++ b/query/src/org/labkey/query/olap/SqlQueryImpl.java @@ -15,21 +15,8 @@ */ package org.labkey.query.olap; -import org.labkey.api.action.SpringActionController; -import org.olap4j.metadata.Level; -import org.olap4j.metadata.Member; -import org.olap4j.metadata.MetadataElement; import org.springframework.validation.BindException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; - -import static org.labkey.query.olap.QubeQuery.QubeExpr; -import static org.labkey.query.olap.QubeQuery.QubeMembersExpr; - /** * Created by matthew on 3/13/14. */ diff --git a/query/src/org/labkey/query/olap/metadata/CachedCube.java b/query/src/org/labkey/query/olap/metadata/CachedCube.java index c3b839f38f7..0a76213b614 100644 --- a/query/src/org/labkey/query/olap/metadata/CachedCube.java +++ b/query/src/org/labkey/query/olap/metadata/CachedCube.java @@ -38,7 +38,6 @@ import org.olap4j.metadata.Property; import org.olap4j.metadata.Schema; -import java.sql.SQLException; import java.util.AbstractMap; import java.util.ArrayList; import java.util.Collection; diff --git a/query/src/org/labkey/query/olap/metadata/MetadataElementBase.java b/query/src/org/labkey/query/olap/metadata/MetadataElementBase.java index 6fd8cfe9ebf..cda5356face 100644 --- a/query/src/org/labkey/query/olap/metadata/MetadataElementBase.java +++ b/query/src/org/labkey/query/olap/metadata/MetadataElementBase.java @@ -15,9 +15,9 @@ */ package org.labkey.query.olap.metadata; -import org.junit.Assert; import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.Nullable; +import org.junit.Assert; import org.junit.Test; import org.labkey.api.query.FieldKey; import org.olap4j.impl.Named; diff --git a/query/src/org/labkey/query/olap/metadata/Olap4JCachedCubeFactory.java b/query/src/org/labkey/query/olap/metadata/Olap4JCachedCubeFactory.java index 5f7112011ee..7e5e69136a8 100644 --- a/query/src/org/labkey/query/olap/metadata/Olap4JCachedCubeFactory.java +++ b/query/src/org/labkey/query/olap/metadata/Olap4JCachedCubeFactory.java @@ -39,12 +39,12 @@ import java.util.TreeMap; import static org.labkey.query.olap.metadata.CachedCube._Dimension; +import static org.labkey.query.olap.metadata.CachedCube._EmptyNamedList; import static org.labkey.query.olap.metadata.CachedCube._Hierarchy; import static org.labkey.query.olap.metadata.CachedCube._Level; -import static org.labkey.query.olap.metadata.CachedCube._Member; import static org.labkey.query.olap.metadata.CachedCube._Measure; +import static org.labkey.query.olap.metadata.CachedCube._Member; import static org.labkey.query.olap.metadata.CachedCube._NamedList; -import static org.labkey.query.olap.metadata.CachedCube._EmptyNamedList; /** * Created by matthew on 4/25/14. diff --git a/query/src/org/labkey/query/olap/rolap/RolapCubeDef.java b/query/src/org/labkey/query/olap/rolap/RolapCubeDef.java index 44b0f4a7553..59e9182013a 100644 --- a/query/src/org/labkey/query/olap/rolap/RolapCubeDef.java +++ b/query/src/org/labkey/query/olap/rolap/RolapCubeDef.java @@ -16,9 +16,7 @@ package org.labkey.query.olap.rolap; import org.apache.commons.lang3.StringUtils; -import static org.apache.commons.lang3.StringUtils.*; - -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -44,7 +42,6 @@ import java.util.Collection; import java.util.Collections; import java.util.Date; -import java.util.HashMap; import java.util.LinkedHashSet; import java.util.LinkedList; import java.util.List; @@ -52,6 +49,8 @@ import java.util.Set; import java.util.TreeMap; +import static org.apache.commons.lang3.StringUtils.defaultString; + /** * Created by matthew on 8/16/14. * @@ -901,7 +900,7 @@ public JdbcType computeKeyType(ResultSet rs) throws SQLException JdbcType j = JdbcType.valueOf(columnType); if (j.isText() != jdbcType.isText() || j.isDateOrTime() != jdbcType.isDateOrTime()) { - Logger.getLogger(RolapCubeDef.class).info("jdbc types do not match, expected: " + jdbcType + " found: " + j + ". Alias: \"" + keyAlias + "\""); + LogManager.getLogger(RolapCubeDef.class).info("jdbc types do not match, expected: " + jdbcType + " found: " + j + ". Alias: \"" + keyAlias + "\""); } return jdbcType; } diff --git a/query/src/org/labkey/query/olap/rolap/RolapReader.java b/query/src/org/labkey/query/olap/rolap/RolapReader.java index 904c28ed4ae..320e6dd2031 100644 --- a/query/src/org/labkey/query/olap/rolap/RolapReader.java +++ b/query/src/org/labkey/query/olap/rolap/RolapReader.java @@ -57,7 +57,7 @@ public class RolapReader { -// static Logger _log = Logger.getLogger(RolapReader.class); +// static Logger _log = LogManager.getLogger(RolapReader.class); private Document _document; private String schemaName; diff --git a/query/src/org/labkey/query/persist/QueryManager.java b/query/src/org/labkey/query/persist/QueryManager.java index d93fd3a196d..e6fdb89a7ce 100644 --- a/query/src/org/labkey/query/persist/QueryManager.java +++ b/query/src/org/labkey/query/persist/QueryManager.java @@ -19,7 +19,8 @@ import org.apache.commons.collections4.Bag; import org.apache.commons.collections4.bag.HashBag; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -78,7 +79,7 @@ public class QueryManager { - private static final Logger _log = Logger.getLogger(QueryManager.class); + private static final Logger _log = LogManager.getLogger(QueryManager.class); private static final QueryManager instance = new QueryManager(); private static final String SCHEMA_NAME = "query"; private static final List QUERY_LISTENERS = new CopyOnWriteArrayList<>(); diff --git a/query/src/org/labkey/query/reports/AttachmentReport.java b/query/src/org/labkey/query/reports/AttachmentReport.java index f84a115ed93..6d4dcd80312 100644 --- a/query/src/org/labkey/query/reports/AttachmentReport.java +++ b/query/src/org/labkey/query/reports/AttachmentReport.java @@ -18,7 +18,7 @@ import org.apache.batik.transcoder.TranscoderException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; @@ -280,7 +280,7 @@ Thumbnail getDynamicThumbnail(AttachmentReport report) throws IOException } catch (TranscoderException e) { - Logger.getLogger(AttachmentReport.class).error("Couldn't generate thumbnail", e); + LogManager.getLogger(AttachmentReport.class).error("Couldn't generate thumbnail", e); } } diff --git a/query/src/org/labkey/query/reports/LinkReport.java b/query/src/org/labkey/query/reports/LinkReport.java index 38cf863887a..f49b90c6846 100644 --- a/query/src/org/labkey/query/reports/LinkReport.java +++ b/query/src/org/labkey/query/reports/LinkReport.java @@ -15,7 +15,7 @@ */ package org.labkey.query.reports; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.reports.ReportService; import org.labkey.api.thumbnail.Thumbnail; @@ -64,7 +64,7 @@ public Thumbnail generateThumbnail(@Nullable ViewContext context) } catch (UnknownHostException uhe) { - Logger.getLogger(LinkReport.class).warn("Error rendering link report thumbnail: " + uhe.getMessage()); + LogManager.getLogger(LinkReport.class).warn("Error rendering link report thumbnail: " + uhe.getMessage()); } catch (Exception e) { diff --git a/query/src/org/labkey/query/reports/ModuleReportCache.java b/query/src/org/labkey/query/reports/ModuleReportCache.java index 486137e10e9..57251e75438 100644 --- a/query/src/org/labkey/query/reports/ModuleReportCache.java +++ b/query/src/org/labkey/query/reports/ModuleReportCache.java @@ -17,7 +17,8 @@ import org.apache.commons.collections4.ListValuedMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -56,7 +57,7 @@ */ public class ModuleReportCache { - private static final Logger LOG = Logger.getLogger(ModuleResourceCache.class); + private static final Logger LOG = LogManager.getLogger(ModuleResourceCache.class); private static final String REPORT_PATH_STRING = "reports/schemas"; private static final Path REPORT_PATH = Path.parse(REPORT_PATH_STRING); private static final ReportCollections EMPTY_REPORT_COLLECTIONS = new ReportCollections(Collections.emptyMap()); diff --git a/query/src/org/labkey/query/reports/ReportImporter.java b/query/src/org/labkey/query/reports/ReportImporter.java index 09c28b1944a..95f3c900220 100644 --- a/query/src/org/labkey/query/reports/ReportImporter.java +++ b/query/src/org/labkey/query/reports/ReportImporter.java @@ -17,8 +17,8 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.admin.InvalidFileException; diff --git a/query/src/org/labkey/query/reports/ReportQueryChangeListener.java b/query/src/org/labkey/query/reports/ReportQueryChangeListener.java index fb333653e91..dd67d38e176 100644 --- a/query/src/org/labkey/query/reports/ReportQueryChangeListener.java +++ b/query/src/org/labkey/query/reports/ReportQueryChangeListener.java @@ -16,7 +16,8 @@ package org.labkey.query.reports; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -61,7 +62,7 @@ protected void _uncacheDependent(CustomView view) } catch (Exception e) { - Logger.getLogger(ReportQueryChangeListener.class).error("An error occurred uncaching dependent reports", e); + LogManager.getLogger(ReportQueryChangeListener.class).error("An error occurred uncaching dependent reports", e); } } @@ -118,7 +119,7 @@ public Collection viewDependents(CustomView view) private void _updateReportQueryNameChange(User user, Container container, SchemaKey schemaKey, Collection changes) { - Logger logger = Logger.getLogger(ReportQueryChangeListener.class); + Logger logger = LogManager.getLogger(ReportQueryChangeListener.class); // most property updates only care about the query name old value string and new value string Map queryNameChangeMap = new HashMap<>(); diff --git a/query/src/org/labkey/query/reports/ReportServiceImpl.java b/query/src/org/labkey/query/reports/ReportServiceImpl.java index 2cf5185e3f6..be8ebcecba7 100644 --- a/query/src/org/labkey/query/reports/ReportServiceImpl.java +++ b/query/src/org/labkey/query/reports/ReportServiceImpl.java @@ -21,7 +21,8 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; @@ -115,7 +116,7 @@ */ public class ReportServiceImpl extends AbstractContainerListener implements ReportService { - private static final Logger _log = Logger.getLogger(ReportService.class); + private static final Logger _log = LogManager.getLogger(ReportService.class); private static final List _uiProviders = new CopyOnWriteArrayList<>(); private static final Map _typeToProviderMap = new ConcurrentHashMap<>(); private static final List _globalItemFilterTypes = new CopyOnWriteArrayList<>(); diff --git a/query/src/org/labkey/query/reports/ReportWriter.java b/query/src/org/labkey/query/reports/ReportWriter.java index 340838e5dbe..a1b0164cbbc 100644 --- a/query/src/org/labkey/query/reports/ReportWriter.java +++ b/query/src/org/labkey/query/reports/ReportWriter.java @@ -16,10 +16,10 @@ package org.labkey.query.reports; import org.labkey.api.admin.BaseFolderWriter; +import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.FolderExportContext; import org.labkey.api.admin.FolderWriter; import org.labkey.api.admin.FolderWriterFactory; -import org.labkey.api.admin.FolderArchiveDataTypes; import org.labkey.api.admin.ImportContext; import org.labkey.api.data.Container; import org.labkey.api.reports.Report; diff --git a/query/src/org/labkey/query/reports/ReportsController.java b/query/src/org/labkey/query/reports/ReportsController.java index 7658ef47336..6dca529d2c7 100644 --- a/query/src/org/labkey/query/reports/ReportsController.java +++ b/query/src/org/labkey/query/reports/ReportsController.java @@ -19,7 +19,8 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; import org.json.JSONException; @@ -60,8 +61,6 @@ import org.labkey.api.exceptions.OptimisticConflictException; import org.labkey.api.message.digest.DailyMessageDigest; import org.labkey.api.message.digest.ReportAndDatasetChangeDigestProvider; -import org.labkey.api.module.Module; -import org.labkey.api.moduleeditor.api.ModuleEditorService; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineService; @@ -86,7 +85,6 @@ import org.labkey.api.reports.report.AbstractReport; import org.labkey.api.reports.report.AbstractReportIdentifier; import org.labkey.api.reports.report.ChartReport; -import org.labkey.api.reports.report.ModuleReportDescriptor; import org.labkey.api.reports.report.QueryReport; import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.RReportJob; @@ -188,8 +186,8 @@ import java.util.TreeSet; import static org.apache.commons.lang3.StringUtils.isBlank; -import static org.labkey.api.util.DOM.*; -import static org.labkey.api.util.HtmlString.NBSP; +import static org.labkey.api.util.DOM.SPAN; +import static org.labkey.api.util.DOM.cl; /** * User: Karl Lum @@ -197,7 +195,7 @@ */ public class ReportsController extends SpringActionController { - private static final Logger _log = Logger.getLogger(ReportsController.class); + private static final Logger _log = LogManager.getLogger(ReportsController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(ReportsController.class); private static final MimeMap _mimeMap = new MimeMap(); diff --git a/query/src/org/labkey/query/reports/ReportsPipelineProvider.java b/query/src/org/labkey/query/reports/ReportsPipelineProvider.java index 80634206b22..46d325b7f16 100644 --- a/query/src/org/labkey/query/reports/ReportsPipelineProvider.java +++ b/query/src/org/labkey/query/reports/ReportsPipelineProvider.java @@ -16,11 +16,11 @@ package org.labkey.query.reports; +import org.labkey.api.module.Module; +import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineDirectory; import org.labkey.api.pipeline.PipelineProvider; import org.labkey.api.pipeline.PipelineStatusFile; -import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.module.Module; import org.labkey.api.security.User; import org.labkey.api.view.ViewContext; diff --git a/query/src/org/labkey/query/reports/getdata/JSONReportDataRenderer.java b/query/src/org/labkey/query/reports/getdata/JSONReportDataRenderer.java index 16f66f34d4f..343318005df 100644 --- a/query/src/org/labkey/query/reports/getdata/JSONReportDataRenderer.java +++ b/query/src/org/labkey/query/reports/getdata/JSONReportDataRenderer.java @@ -18,17 +18,7 @@ import com.fasterxml.jackson.annotation.JsonTypeName; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ReportingApiQueryResponse; -import org.labkey.api.data.ShowRows; -import org.labkey.api.data.Sort; -import org.labkey.api.query.QueryDefinition; -import org.labkey.api.query.QueryService; -import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; -import org.labkey.api.view.ViewContext; -import org.labkey.query.controllers.QueryController; -import org.springframework.validation.Errors; - -import java.util.List; /** * Writes a JSON response containing the column metadata and actual data rows back to the client diff --git a/query/src/org/labkey/query/reports/getdata/SchemaQueryReportDataSource.java b/query/src/org/labkey/query/reports/getdata/SchemaQueryReportDataSource.java index 28e0e854435..abd7ec0ce1b 100644 --- a/query/src/org/labkey/query/reports/getdata/SchemaQueryReportDataSource.java +++ b/query/src/org/labkey/query/reports/getdata/SchemaQueryReportDataSource.java @@ -22,7 +22,6 @@ import org.labkey.api.data.TableInfo; import org.labkey.api.query.QueryDefinition; import org.labkey.api.query.QueryException; -import org.labkey.api.query.QueryService; import org.labkey.api.query.SchemaKey; import org.labkey.api.security.User; import org.labkey.api.view.NotFoundException; diff --git a/query/src/org/labkey/query/reports/view/ReportAndDatasetChangeDigestEmailTemplate.java b/query/src/org/labkey/query/reports/view/ReportAndDatasetChangeDigestEmailTemplate.java index 6bc1caac2e8..ae62d21a10c 100644 --- a/query/src/org/labkey/query/reports/view/ReportAndDatasetChangeDigestEmailTemplate.java +++ b/query/src/org/labkey/query/reports/view/ReportAndDatasetChangeDigestEmailTemplate.java @@ -15,7 +15,6 @@ */ package org.labkey.query.reports.view; -import org.apache.commons.io.IOUtils; import org.labkey.api.data.Container; import org.labkey.api.portal.ProjectUrls; import org.labkey.api.reports.model.NotificationInfo; diff --git a/query/src/org/labkey/query/reports/view/ReportsWebPart.java b/query/src/org/labkey/query/reports/view/ReportsWebPart.java index 348d0f1df13..ed34d3bcc54 100644 --- a/query/src/org/labkey/query/reports/view/ReportsWebPart.java +++ b/query/src/org/labkey/query/reports/view/ReportsWebPart.java @@ -21,13 +21,16 @@ import org.labkey.api.premium.PremiumService; import org.labkey.api.query.QueryParam; import org.labkey.api.reports.Report; -import org.labkey.api.reports.ReportService; import org.labkey.api.reports.report.RReport; import org.labkey.api.reports.report.ReportDescriptor; import org.labkey.api.reports.report.ScriptReportDescriptor; import org.labkey.api.reports.report.view.RenderBackgroundRReportView; import org.labkey.api.reports.report.view.ReportUtil; -import org.labkey.api.view.*; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.Portal; +import org.labkey.api.view.ViewContext; +import org.labkey.api.view.WebPartView; import java.io.PrintWriter; import java.util.Map; diff --git a/query/src/org/labkey/query/reports/view/ReportsWebPartConfig.java b/query/src/org/labkey/query/reports/view/ReportsWebPartConfig.java index eba8bbd479e..07d15046e9b 100644 --- a/query/src/org/labkey/query/reports/view/ReportsWebPartConfig.java +++ b/query/src/org/labkey/query/reports/view/ReportsWebPartConfig.java @@ -17,8 +17,8 @@ package org.labkey.query.reports.view; import org.labkey.api.view.HttpView; -import org.labkey.api.view.Portal; import org.labkey.api.view.JspView; +import org.labkey.api.view.Portal; import java.io.PrintWriter; diff --git a/query/src/org/labkey/query/reports/view/createQueryReport.jsp b/query/src/org/labkey/query/reports/view/createQueryReport.jsp index dc786c2b9b8..5979b1c2f8a 100644 --- a/query/src/org/labkey/query/reports/view/createQueryReport.jsp +++ b/query/src/org/labkey/query/reports/view/createQueryReport.jsp @@ -17,10 +17,9 @@ %> <%@ page import="org.labkey.api.view.HttpView"%> <%@ page import="org.labkey.api.view.JspView"%> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.query.reports.ReportsController" %> <%@ page import="org.springframework.validation.ObjectError" %> -<%@ page import="java.util.List" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/query/src/org/labkey/query/reports/view/linkReport.jsp b/query/src/org/labkey/query/reports/view/linkReport.jsp index 06cf0249a58..59176a7209b 100644 --- a/query/src/org/labkey/query/reports/view/linkReport.jsp +++ b/query/src/org/labkey/query/reports/view/linkReport.jsp @@ -21,7 +21,6 @@ <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.query.reports.ReportsController.LinkReportForm" %> -<%@ page import="org.labkey.api.util.HtmlString" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/query/src/org/labkey/query/reports/view/reportDetails.jsp b/query/src/org/labkey/query/reports/view/reportDetails.jsp index d60ac4dea41..9409bcbc0ba 100644 --- a/query/src/org/labkey/query/reports/view/reportDetails.jsp +++ b/query/src/org/labkey/query/reports/view/reportDetails.jsp @@ -29,8 +29,6 @@ <%@ page import="org.labkey.api.view.JspView" %> <%@ page import="org.labkey.api.view.ViewContext" %> <%@ page import="java.util.Date" %> -<%@ page import="java.util.Map" %> -<%@ page import="java.util.Collections" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% JspView me = (JspView) HttpView.currentView(); diff --git a/query/src/org/labkey/query/sql/Builder.java b/query/src/org/labkey/query/sql/Builder.java index 9b1f1c9cbb7..a48b8cf5b9e 100644 --- a/query/src/org/labkey/query/sql/Builder.java +++ b/query/src/org/labkey/query/sql/Builder.java @@ -19,8 +19,8 @@ import org.apache.commons.lang3.StringUtils; import org.labkey.api.data.SQLFragment; -import java.util.List; import java.util.ArrayList; +import java.util.List; public class Builder extends SQLFragment { diff --git a/query/src/org/labkey/query/sql/Operator.java b/query/src/org/labkey/query/sql/Operator.java index 296819787f5..12c9a33c4c3 100644 --- a/query/src/org/labkey/query/sql/Operator.java +++ b/query/src/org/labkey/query/sql/Operator.java @@ -21,7 +21,10 @@ import org.labkey.api.data.SQLFragment; import org.labkey.api.data.dialect.SqlDialect; -import java.util.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; import static org.labkey.query.sql.antlr.SqlBaseParser.*; diff --git a/query/src/org/labkey/query/sql/QJoinOrTable.java b/query/src/org/labkey/query/sql/QJoinOrTable.java index 00901fd8b07..04d889b078a 100644 --- a/query/src/org/labkey/query/sql/QJoinOrTable.java +++ b/query/src/org/labkey/query/sql/QJoinOrTable.java @@ -16,8 +16,6 @@ package org.labkey.query.sql; -import org.labkey.api.query.FieldKey; - /** * User: matthewb * Date: Dec 1, 2010 diff --git a/query/src/org/labkey/query/sql/QMethodCall.java b/query/src/org/labkey/query/sql/QMethodCall.java index 2fcce04759a..e615f13f122 100644 --- a/query/src/org/labkey/query/sql/QMethodCall.java +++ b/query/src/org/labkey/query/sql/QMethodCall.java @@ -17,13 +17,17 @@ package org.labkey.query.sql; import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.MethodInfo; +import org.labkey.api.data.SQLFragment; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.query.QueryException; import org.labkey.api.query.QueryParseException; -import org.labkey.api.data.*; -import java.util.List; import java.util.ArrayList; +import java.util.List; import java.util.ListIterator; diff --git a/query/src/org/labkey/query/sql/QOrder.java b/query/src/org/labkey/query/sql/QOrder.java index 44188d4fd18..826f54bc40a 100644 --- a/query/src/org/labkey/query/sql/QOrder.java +++ b/query/src/org/labkey/query/sql/QOrder.java @@ -20,10 +20,10 @@ import org.labkey.api.util.Pair; import org.labkey.query.sql.antlr.SqlBaseParser; -import java.util.Map; -import java.util.List; import java.util.ArrayList; import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; public class QOrder extends QNode { diff --git a/query/src/org/labkey/query/sql/QTimestamp.java b/query/src/org/labkey/query/sql/QTimestamp.java index 4ea4a11e060..eb3159043ad 100644 --- a/query/src/org/labkey/query/sql/QTimestamp.java +++ b/query/src/org/labkey/query/sql/QTimestamp.java @@ -19,6 +19,7 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.data.JdbcType; import org.labkey.api.util.DateUtil; + import java.sql.Timestamp; /** diff --git a/query/src/org/labkey/query/sql/QUnion.java b/query/src/org/labkey/query/sql/QUnion.java index 341acc5af4e..fd584fad71d 100644 --- a/query/src/org/labkey/query/sql/QUnion.java +++ b/query/src/org/labkey/query/sql/QUnion.java @@ -17,7 +17,6 @@ package org.labkey.query.sql; import org.antlr.runtime.tree.CommonTree; -import org.labkey.query.sql.antlr.SqlBaseParser; public class QUnion extends QExpr diff --git a/query/src/org/labkey/query/sql/Query.java b/query/src/org/labkey/query/sql/Query.java index 94815368d10..ed96284a862 100644 --- a/query/src/org/labkey/query/sql/Query.java +++ b/query/src/org/labkey/query/sql/Query.java @@ -19,7 +19,7 @@ import org.apache.commons.collections4.multimap.HashSetValuedHashMap; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; @@ -248,7 +248,7 @@ public void parseQuerySource(boolean skipSuggestedColumns) if (null == _querySource) throw new IllegalStateException("SQL has not been specified"); - Logger.getLogger(Query.class).debug("Query.parse()\n" + _querySource); + LogManager.getLogger(Query.class).debug("Query.parse()\n" + _querySource); _parse(_querySource, skipSuggestedColumns); for (QueryException e : _parseErrors) @@ -644,7 +644,7 @@ public TableInfo getTableInfo() } catch (RuntimeException x) { - Logger.getLogger(Query.class).error("error", x); + LogManager.getLogger(Query.class).error("error", x); throw Query.wrapRuntimeException(x, _querySource); } } diff --git a/query/src/org/labkey/query/sql/QueryLookupWrapper.java b/query/src/org/labkey/query/sql/QueryLookupWrapper.java index ca6479e415a..6122fbc06e0 100644 --- a/query/src/org/labkey/query/sql/QueryLookupWrapper.java +++ b/query/src/org/labkey/query/sql/QueryLookupWrapper.java @@ -15,18 +15,31 @@ */ package org.labkey.query.sql; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; -import org.labkey.api.data.*; +import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ForeignKey; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasManager; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryParseException; import org.labkey.data.xml.ColumnType; import org.labkey.data.xml.TableType; -import java.util.*; +import java.util.Collection; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.Set; /** * User: matthewb @@ -44,7 +57,7 @@ */ public class QueryLookupWrapper extends QueryRelation { - private static final Logger _log = Logger.getLogger(QueryLookupWrapper.class); + private static final Logger _log = LogManager.getLogger(QueryLookupWrapper.class); final AliasManager _aliasManager; final QueryRelation _source; diff --git a/query/src/org/labkey/query/sql/QueryPivot.java b/query/src/org/labkey/query/sql/QueryPivot.java index 6b27360c61a..ba1b11a19d3 100644 --- a/query/src/org/labkey/query/sql/QueryPivot.java +++ b/query/src/org/labkey/query/sql/QueryPivot.java @@ -20,27 +20,7 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveMapWrapper; import org.labkey.api.collections.NamedObjectList; -import org.labkey.api.data.AbstractTableInfo; -import org.labkey.api.data.AggregateColumnInfo; -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.CrosstabDimension; -import org.labkey.api.data.CrosstabMeasure; -import org.labkey.api.data.CrosstabMember; -import org.labkey.api.data.CrosstabSettings; -import org.labkey.api.data.CrosstabTableInfo; -import org.labkey.api.data.Filter; -import org.labkey.api.data.ForeignKey; -import org.labkey.api.data.JdbcType; -import org.labkey.api.data.NullColumnInfo; -import org.labkey.api.data.RenderContext; -import org.labkey.api.data.RuntimeSQLException; -import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.Sort; -import org.labkey.api.data.SqlSelector; -import org.labkey.api.data.TableInfo; +import org.labkey.api.data.*; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.queryprofiler.QueryProfiler; import org.labkey.api.query.AliasManager; diff --git a/query/src/org/labkey/query/sql/QueryRelation.java b/query/src/org/labkey/query/sql/QueryRelation.java index 2c3813cf449..a1641d72bc1 100644 --- a/query/src/org/labkey/query/sql/QueryRelation.java +++ b/query/src/org/labkey/query/sql/QueryRelation.java @@ -15,7 +15,8 @@ */ package org.labkey.query.sql; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.BaseColumnInfo; @@ -51,7 +52,7 @@ */ public abstract class QueryRelation { - private static final Logger _log = Logger.getLogger(QuerySelect.class); + private static final Logger _log = LogManager.getLogger(QuerySelect.class); protected String _savedName = null; protected Query _query; diff --git a/query/src/org/labkey/query/sql/QuerySelect.java b/query/src/org/labkey/query/sql/QuerySelect.java index f1d2313ab0f..2f5e663a910 100644 --- a/query/src/org/labkey/query/sql/QuerySelect.java +++ b/query/src/org/labkey/query/sql/QuerySelect.java @@ -16,7 +16,8 @@ package org.labkey.query.sql; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; @@ -63,7 +64,7 @@ public class QuerySelect extends QueryRelation implements Cloneable { - private static final Logger _log = Logger.getLogger(QuerySelect.class); + private static final Logger _log = LogManager.getLogger(QuerySelect.class); String _queryText; private Map _columns; diff --git a/query/src/org/labkey/query/sql/QueryTable.java b/query/src/org/labkey/query/sql/QueryTable.java index b1a25f7faf9..5549b3b62c3 100644 --- a/query/src/org/labkey/query/sql/QueryTable.java +++ b/query/src/org/labkey/query/sql/QueryTable.java @@ -16,7 +16,8 @@ package org.labkey.query.sql; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.AbstractTableInfo; @@ -60,7 +61,7 @@ public class QueryTable extends QueryRelation { - private static final Logger _log = Logger.getLogger(QueryTable.class); + private static final Logger _log = LogManager.getLogger(QueryTable.class); private final String _originalAlias; // as passed in from QuerySelect for error messages private final int _uniqueAliasCounter; diff --git a/query/src/org/labkey/query/sql/QueryTableInfo.java b/query/src/org/labkey/query/sql/QueryTableInfo.java index c8391b9dd08..007cdec9592 100644 --- a/query/src/org/labkey/query/sql/QueryTableInfo.java +++ b/query/src/org/labkey/query/sql/QueryTableInfo.java @@ -16,14 +16,13 @@ package org.labkey.query.sql; -import org.apache.commons.lang3.StringUtils; import org.jetbrains.annotations.NotNull; import org.labkey.api.data.AbstractTableInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerFilterable; -import org.labkey.api.data.SQLFragment; import org.labkey.api.data.HasResolvedTables; +import org.labkey.api.data.SQLFragment; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryService; import org.labkey.api.query.SchemaKey; diff --git a/query/src/org/labkey/query/sql/ReferenceCount.java b/query/src/org/labkey/query/sql/ReferenceCount.java index fd0aafebbec..a4035188f90 100644 --- a/query/src/org/labkey/query/sql/ReferenceCount.java +++ b/query/src/org/labkey/query/sql/ReferenceCount.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; -import java.util.HashSet; import java.util.IdentityHashMap; import java.util.Set; diff --git a/query/src/org/labkey/query/sql/SQLTableInfo.java b/query/src/org/labkey/query/sql/SQLTableInfo.java index afcb69beaef..31ca5a61404 100644 --- a/query/src/org/labkey/query/sql/SQLTableInfo.java +++ b/query/src/org/labkey/query/sql/SQLTableInfo.java @@ -16,8 +16,12 @@ package org.labkey.query.sql; -import org.labkey.api.data.*; import org.jetbrains.annotations.NotNull; +import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.ContainerFilterable; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.SQLFragment; import org.labkey.api.query.UserSchema; diff --git a/query/src/org/labkey/query/sql/SqlBase.g b/query/src/org/labkey/query/sql/SqlBase.g index c0b761c96a1..ec4084c7b4a 100644 --- a/query/src/org/labkey/query/sql/SqlBase.g +++ b/query/src/org/labkey/query/sql/SqlBase.g @@ -56,8 +56,8 @@ tokens { package org.labkey.query.sql.antlr; - import org.apache.log4j.Category; - import org.labkey.query.sql.SqlParser; + import org.apache.logging.log4j.Logger; + import org.apache.logging.log4j.LogManager; } @@ -108,7 +108,7 @@ tokens @lexer::members { - Category _log = Category.getInstance(SqlParser.class); + Logger _log = LogManager.getLogger(org.labkey.query.sql.SqlParser.class); protected void setPossibleID(boolean possibleID) { diff --git a/query/src/org/labkey/query/sql/SqlBuilder.java b/query/src/org/labkey/query/sql/SqlBuilder.java index 54b795cf2cd..df411d17e38 100644 --- a/query/src/org/labkey/query/sql/SqlBuilder.java +++ b/query/src/org/labkey/query/sql/SqlBuilder.java @@ -16,10 +16,11 @@ package org.labkey.query.sql; -import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.data.DbSchema; +import org.labkey.api.data.dialect.SqlDialect; -import java.util.*; +import java.util.Arrays; +import java.util.Collection; public class SqlBuilder extends Builder { diff --git a/query/src/org/labkey/query/sql/SqlParser.java b/query/src/org/labkey/query/sql/SqlParser.java index e8844e1ac2e..3a081323dae 100644 --- a/query/src/org/labkey/query/sql/SqlParser.java +++ b/query/src/org/labkey/query/sql/SqlParser.java @@ -28,7 +28,8 @@ import org.antlr.runtime.tree.Tree; import org.apache.commons.beanutils.ConversionException; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -90,7 +91,7 @@ @SuppressWarnings({"ThrowableResultOfMethodCallIgnored","ThrowableInstanceNeverThrown"}) public class SqlParser { - private static final Logger _log = Logger.getLogger(SqlParser.class); + private static final Logger _log = LogManager.getLogger(SqlParser.class); ArrayList _parseErrors; List _parseWarnings; diff --git a/query/src/org/labkey/query/view/AbstractQueryDataViewProvider.java b/query/src/org/labkey/query/view/AbstractQueryDataViewProvider.java index 1188e3fd288..ac6f97e2463 100644 --- a/query/src/org/labkey/query/view/AbstractQueryDataViewProvider.java +++ b/query/src/org/labkey/query/view/AbstractQueryDataViewProvider.java @@ -31,7 +31,6 @@ import org.labkey.api.reports.report.view.ReportUtil; import org.labkey.api.security.User; import org.labkey.api.settings.ResourceURL; -import org.labkey.api.study.StudyService; import org.labkey.api.view.ActionURL; import org.labkey.api.view.ViewContext; import org.labkey.api.writer.ContainerUser; diff --git a/query/src/org/labkey/query/view/InheritedQueryDataViewProvider.java b/query/src/org/labkey/query/view/InheritedQueryDataViewProvider.java index 8abfbd3faac..b27c6f3cbcb 100644 --- a/query/src/org/labkey/query/view/InheritedQueryDataViewProvider.java +++ b/query/src/org/labkey/query/view/InheritedQueryDataViewProvider.java @@ -18,7 +18,6 @@ import org.labkey.api.data.views.DataViewProvider; import org.labkey.api.data.views.ProviderType; import org.labkey.api.query.CustomView; -import org.labkey.api.query.CustomViewInfo; import org.labkey.api.reports.report.view.ReportUtil; import org.labkey.api.view.ViewContext; diff --git a/query/src/org/labkey/query/view/QueryDataViewProvider.java b/query/src/org/labkey/query/view/QueryDataViewProvider.java index 964dafffbbc..3fc6c23055e 100644 --- a/query/src/org/labkey/query/view/QueryDataViewProvider.java +++ b/query/src/org/labkey/query/view/QueryDataViewProvider.java @@ -27,7 +27,6 @@ import org.labkey.query.persist.CstmView; import org.labkey.query.persist.QueryManager; -import java.sql.SQLException; import java.util.Map; /** diff --git a/query/src/org/labkey/query/view/browse.jsp b/query/src/org/labkey/query/view/browse.jsp index 7f6b343c07e..3ee9e8339d9 100644 --- a/query/src/org/labkey/query/view/browse.jsp +++ b/query/src/org/labkey/query/view/browse.jsp @@ -15,10 +15,10 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.query.QueryService" %> <%@ page import="org.labkey.api.util.UniqueID" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> -<%@ page import="org.labkey.api.query.QueryService" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/query/src/org/labkey/query/view/confirmDeleteConnection.jsp b/query/src/org/labkey/query/view/confirmDeleteConnection.jsp index cefc26d1a4a..d111e156971 100644 --- a/query/src/org/labkey/query/view/confirmDeleteConnection.jsp +++ b/query/src/org/labkey/query/view/confirmDeleteConnection.jsp @@ -17,10 +17,10 @@ %> <%@ page extends="org.labkey.api.jsp.FormPage" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> -<%@ page import="org.labkey.query.controllers.QueryController" %> -<%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.data.Container" %> +<%@ page import="org.labkey.api.view.HttpView" %> +<%@ page import="org.labkey.api.view.JspView" %> +<%@ page import="org.labkey.query.controllers.QueryController" %> <%@ page import="org.labkey.remoteapi.RemoteConnections" %> <% Container c = getContainer(); diff --git a/query/src/org/labkey/query/view/deleteQuery.jsp b/query/src/org/labkey/query/view/deleteQuery.jsp index 15f1b48fa31..a3010103f94 100644 --- a/query/src/org/labkey/query/view/deleteQuery.jsp +++ b/query/src/org/labkey/query/view/deleteQuery.jsp @@ -16,10 +16,10 @@ */ --%> <%@ page extends="org.labkey.query.controllers.Page" %> -<%@ page import="org.labkey.api.view.HttpView"%> -<%@ page import="org.labkey.api.query.QueryDefinition" %> -<%@ page import="java.util.Collection" %> +<%@ page import="org.labkey.api.query.QueryDefinition"%> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.query.controllers.QueryController" %> +<%@ page import="java.util.Collection" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% QueryController.DeleteQueryAction action = (QueryController.DeleteQueryAction) HttpView.currentModel(); diff --git a/query/src/org/labkey/query/view/exportTables.jsp b/query/src/org/labkey/query/view/exportTables.jsp index 88369939846..f25cd823463 100644 --- a/query/src/org/labkey/query/view/exportTables.jsp +++ b/query/src/org/labkey/query/view/exportTables.jsp @@ -17,10 +17,10 @@ %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.query.controllers.QueryController" %> <%@ page import="org.springframework.validation.Errors" %> <%@ page import="org.springframework.validation.ObjectError" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! @Override diff --git a/query/src/org/labkey/query/view/generateSchema.jsp b/query/src/org/labkey/query/view/generateSchema.jsp index 89c5beef6e2..aa45a128194 100644 --- a/query/src/org/labkey/query/view/generateSchema.jsp +++ b/query/src/org/labkey/query/view/generateSchema.jsp @@ -17,8 +17,8 @@ %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.query.controllers.QueryController" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> +<%@ page import="org.labkey.query.controllers.QueryController" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%! diff --git a/query/src/org/labkey/query/view/internalDeleteView.jsp b/query/src/org/labkey/query/view/internalDeleteView.jsp index dad0816331e..90bab721e7b 100644 --- a/query/src/org/labkey/query/view/internalDeleteView.jsp +++ b/query/src/org/labkey/query/view/internalDeleteView.jsp @@ -15,9 +15,9 @@ * limitations under the License. */ %> +<%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.query.controllers.InternalViewForm" %> <%@ page import="org.labkey.query.persist.CstmView" %> -<%@ page import="org.labkey.api.view.HttpView" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% InternalViewForm form = (InternalViewForm)HttpView.currentModel(); diff --git a/query/src/org/labkey/query/view/mdx.jsp b/query/src/org/labkey/query/view/mdx.jsp index 81a13b8de5a..c05d184226a 100644 --- a/query/src/org/labkey/query/view/mdx.jsp +++ b/query/src/org/labkey/query/view/mdx.jsp @@ -15,10 +15,10 @@ * limitations under the License. */ %> +<%@ page import="org.apache.commons.lang3.StringUtils" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.query.controllers.OlapController" %> -<%@ page import="org.apache.commons.lang3.StringUtils" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <%! diff --git a/search/src/org/labkey/search/SearchModule.java b/search/src/org/labkey/search/SearchModule.java index d7b13ae62a9..7f81ae7caf2 100644 --- a/search/src/org/labkey/search/SearchModule.java +++ b/search/src/org/labkey/search/SearchModule.java @@ -16,7 +16,8 @@ package org.labkey.search; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.attachments.DocumentConversionService; import org.labkey.api.audit.AuditLogService; @@ -54,7 +55,7 @@ public class SearchModule extends DefaultModule { // package logger for use with logger-manage.view - static final Logger _logPackage = Logger.getLogger(SearchModule.class.getPackage().getName()); + static final Logger _logPackage = LogManager.getLogger(SearchModule.class.getPackage().getName()); @Override public String getName() @@ -136,7 +137,7 @@ public void doStartup(ModuleContext moduleContext) AdminConsole.addLink(AdminConsole.SettingsLinkType.Management, "full-text search", new ActionURL(SearchController.AdminAction.class, null)); CacheManager.addListener(() -> { - Logger.getLogger(SearchService.class).info("Purging SearchService queues"); + LogManager.getLogger(SearchService.class).info("Purging SearchService queues"); ss.purgeQueues(); }); } diff --git a/search/src/org/labkey/search/model/AbstractSearchService.java b/search/src/org/labkey/search/model/AbstractSearchService.java index 235297c801b..a65a291d4ef 100644 --- a/search/src/org/labkey/search/model/AbstractSearchService.java +++ b/search/src/org/labkey/search/model/AbstractSearchService.java @@ -19,7 +19,8 @@ import com.google.common.collect.Multiset.Entry; import org.apache.commons.collections4.MultiValuedMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; @@ -76,7 +77,7 @@ */ public abstract class AbstractSearchService implements SearchService, ShutdownListener { - private static final Logger _log = Logger.getLogger(AbstractSearchService.class); + private static final Logger _log = LogManager.getLogger(AbstractSearchService.class); // Runnables go here, and get pulled off in a single threaded manner (assumption is that Runnables can create work very quickly) final PriorityBlockingQueue _runQueue = new PriorityBlockingQueue<>(1000, itemCompare); diff --git a/search/src/org/labkey/search/model/DavCrawler.java b/search/src/org/labkey/search/model/DavCrawler.java index 0c340dff65d..4b155374279 100644 --- a/search/src/org/labkey/search/model/DavCrawler.java +++ b/search/src/org/labkey/search/model/DavCrawler.java @@ -15,7 +15,8 @@ */ package org.labkey.search.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.cache.Cache; @@ -142,7 +143,7 @@ public interface SavePaths } - final static Logger _log = Logger.getLogger(DavCrawler.class); + final static Logger _log = LogManager.getLogger(DavCrawler.class); DavCrawler() diff --git a/search/src/org/labkey/search/model/IndexInspector.java b/search/src/org/labkey/search/model/IndexInspector.java index d4014fcc0b5..0ca1bb99699 100644 --- a/search/src/org/labkey/search/model/IndexInspector.java +++ b/search/src/org/labkey/search/model/IndexInspector.java @@ -29,8 +29,6 @@ import org.labkey.api.data.ContainerManager; import org.labkey.api.data.ExcelWriter; import org.labkey.api.data.TSVWriter; -import org.labkey.api.data.TextWriter; -import org.labkey.api.util.PageFlowUtil; import javax.servlet.http.HttpServletResponse; import java.io.IOException; diff --git a/search/src/org/labkey/search/model/LuceneAnalyzer.java b/search/src/org/labkey/search/model/LuceneAnalyzer.java index 5696d2954ec..c8d24b06349 100644 --- a/search/src/org/labkey/search/model/LuceneAnalyzer.java +++ b/search/src/org/labkey/search/model/LuceneAnalyzer.java @@ -20,7 +20,6 @@ import org.apache.lucene.analysis.core.KeywordAnalyzer; import org.apache.lucene.analysis.core.LowerCaseFilterFactory; import org.apache.lucene.analysis.core.SimpleAnalyzer; -import org.apache.lucene.analysis.core.StopFilterFactory; import org.apache.lucene.analysis.core.WhitespaceTokenizerFactory; import org.apache.lucene.analysis.custom.CustomAnalyzer; import org.apache.lucene.analysis.en.EnglishAnalyzer; diff --git a/search/src/org/labkey/search/model/LuceneSearchServiceImpl.java b/search/src/org/labkey/search/model/LuceneSearchServiceImpl.java index 147ddd52892..a1e019f81b8 100644 --- a/search/src/org/labkey/search/model/LuceneSearchServiceImpl.java +++ b/search/src/org/labkey/search/model/LuceneSearchServiceImpl.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.iterators.ArrayIterator; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.lucene.analysis.Analyzer; import org.apache.lucene.analysis.TokenStream; import org.apache.lucene.analysis.tokenattributes.CharTermAttribute; @@ -141,7 +142,7 @@ */ public class LuceneSearchServiceImpl extends AbstractSearchService { - private static final Logger _log = Logger.getLogger(LuceneSearchServiceImpl.class); + private static final Logger _log = LogManager.getLogger(LuceneSearchServiceImpl.class); // Changes to _index are rare (only when admin changes the index path), but we want any changes to be visible to // other threads immediately. Initialize to Noop class to prevent rare NPE (e.g., system maintenance runs before index diff --git a/search/src/org/labkey/search/model/NoopWritableIndex.java b/search/src/org/labkey/search/model/NoopWritableIndex.java index 09729114572..97d09361938 100644 --- a/search/src/org/labkey/search/model/NoopWritableIndex.java +++ b/search/src/org/labkey/search/model/NoopWritableIndex.java @@ -16,7 +16,7 @@ package org.labkey.search.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.apache.lucene.document.Document; import org.apache.lucene.search.IndexSearcher; import org.apache.lucene.search.Query; diff --git a/search/src/org/labkey/search/model/ProblemHandler.java b/search/src/org/labkey/search/model/ProblemHandler.java index c42c35e0dc2..22ad9e19c26 100644 --- a/search/src/org/labkey/search/model/ProblemHandler.java +++ b/search/src/org/labkey/search/model/ProblemHandler.java @@ -15,12 +15,13 @@ */ package org.labkey.search.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.tika.config.InitializableProblemHandler; public class ProblemHandler implements InitializableProblemHandler { - private final Logger LOG = Logger.getLogger(LuceneSearchServiceImpl.class); + private final Logger LOG = LogManager.getLogger(LuceneSearchServiceImpl.class); @Override public void handleInitializableProblem(String className, String message) diff --git a/search/src/org/labkey/search/model/WritableIndexManagerImpl.java b/search/src/org/labkey/search/model/WritableIndexManagerImpl.java index 0bc4f353ad2..78a8d53d04a 100644 --- a/search/src/org/labkey/search/model/WritableIndexManagerImpl.java +++ b/search/src/org/labkey/search/model/WritableIndexManagerImpl.java @@ -17,7 +17,8 @@ import com.google.common.collect.ImmutableMap; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.lucene.analysis.Analyzer; import org.apache.lucene.document.Document; import org.apache.lucene.index.IndexReader; @@ -65,7 +66,7 @@ // Adds synchronization for writing, in addition to searching synchronization provided by IndexManager class WritableIndexManagerImpl extends IndexManager implements WritableIndexManager { - private static final Logger _log = Logger.getLogger(WritableIndexManagerImpl.class); + private static final Logger _log = LogManager.getLogger(WritableIndexManagerImpl.class); private static final AtomicInteger _maybeRefreshRequests = new AtomicInteger(); private final Object _writerLock = new Object(); diff --git a/search/src/org/labkey/search/umls/ConceptName.java b/search/src/org/labkey/search/umls/ConceptName.java index 0cc7085afdf..3cf49a7d7b7 100644 --- a/search/src/org/labkey/search/umls/ConceptName.java +++ b/search/src/org/labkey/search/umls/ConceptName.java @@ -20,7 +20,6 @@ import org.labkey.api.data.ResultSetSelector; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/search/src/org/labkey/search/umls/Definition.java b/search/src/org/labkey/search/umls/Definition.java index 6fff54731a1..c4619d18cd6 100644 --- a/search/src/org/labkey/search/umls/Definition.java +++ b/search/src/org/labkey/search/umls/Definition.java @@ -20,7 +20,6 @@ import org.labkey.api.data.ResultSetSelector; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/search/src/org/labkey/search/umls/RRF_Loader.java b/search/src/org/labkey/search/umls/RRF_Loader.java index b1600c3e9ee..3e60fab41c1 100644 --- a/search/src/org/labkey/search/umls/RRF_Loader.java +++ b/search/src/org/labkey/search/umls/RRF_Loader.java @@ -16,7 +16,6 @@ package org.labkey.search.umls; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.ColumnInfo; diff --git a/search/src/org/labkey/search/umls/Related.java b/search/src/org/labkey/search/umls/Related.java index 7ca5c7f845c..9a3ecf5b422 100644 --- a/search/src/org/labkey/search/umls/Related.java +++ b/search/src/org/labkey/search/umls/Related.java @@ -20,7 +20,6 @@ import org.labkey.api.data.ResultSetSelector; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/search/src/org/labkey/search/umls/SemanticType.java b/search/src/org/labkey/search/umls/SemanticType.java index 8b2d1ab1d08..a7d3e964d73 100644 --- a/search/src/org/labkey/search/umls/SemanticType.java +++ b/search/src/org/labkey/search/umls/SemanticType.java @@ -20,7 +20,6 @@ import org.labkey.api.data.ResultSetSelector; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/search/src/org/labkey/search/view/exportContents.jsp b/search/src/org/labkey/search/view/exportContents.jsp index 4053f724b71..584ccb5a81c 100644 --- a/search/src/org/labkey/search/view/exportContents.jsp +++ b/search/src/org/labkey/search/view/exportContents.jsp @@ -16,8 +16,8 @@ */ %> <%@ page import="org.labkey.api.data.ContainerManager" %> -<%@ page import="org.labkey.search.SearchController" %> <%@ page import="org.labkey.api.view.ActionURL" %> +<%@ page import="org.labkey.search.SearchController" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/study/src/org/labkey/study/DefragmentParticipantVisitIndexesTask.java b/study/src/org/labkey/study/DefragmentParticipantVisitIndexesTask.java index 04d66cfc0a1..0c71a93a9d4 100644 --- a/study/src/org/labkey/study/DefragmentParticipantVisitIndexesTask.java +++ b/study/src/org/labkey/study/DefragmentParticipantVisitIndexesTask.java @@ -15,7 +15,7 @@ */ package org.labkey.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.DbSchema; import org.labkey.api.data.TableInfo; import org.labkey.api.data.dialect.SqlDialect; diff --git a/study/src/org/labkey/study/MasterPatientIndexMaintenanceTask.java b/study/src/org/labkey/study/MasterPatientIndexMaintenanceTask.java index e476f39ad50..c10e7b260bb 100644 --- a/study/src/org/labkey/study/MasterPatientIndexMaintenanceTask.java +++ b/study/src/org/labkey/study/MasterPatientIndexMaintenanceTask.java @@ -15,7 +15,7 @@ */ package org.labkey.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.PropertyManager; diff --git a/study/src/org/labkey/study/PurgeParticipantsMaintenanceTask.java b/study/src/org/labkey/study/PurgeParticipantsMaintenanceTask.java index 74bbc62197d..75455fde2e8 100644 --- a/study/src/org/labkey/study/PurgeParticipantsMaintenanceTask.java +++ b/study/src/org/labkey/study/PurgeParticipantsMaintenanceTask.java @@ -15,7 +15,7 @@ */ package org.labkey.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.util.SystemMaintenance.MaintenanceTask; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; diff --git a/study/src/org/labkey/study/SpecimenManager.java b/study/src/org/labkey/study/SpecimenManager.java index 857a2612a63..d8665b5c817 100644 --- a/study/src/org/labkey/study/SpecimenManager.java +++ b/study/src/org/labkey/study/SpecimenManager.java @@ -19,7 +19,7 @@ import org.apache.commons.beanutils.PropertyUtils; import org.apache.commons.collections4.comparators.ComparableComparator; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.SpringActionController; @@ -2727,7 +2727,7 @@ public RequestSummaryByVisitType[] getRequestSummaryBySite(Container container, } catch (IllegalAccessException | InvocationTargetException | NoSuchMethodException e) { - Logger.getLogger(SpecimenManager.class).error(e); + LogManager.getLogger(SpecimenManager.class).error(e); } } ret.add(summary); diff --git a/study/src/org/labkey/study/SpecimenRefreshMaintainanceTask.java b/study/src/org/labkey/study/SpecimenRefreshMaintainanceTask.java index c062935ed4b..d5591e54bd1 100644 --- a/study/src/org/labkey/study/SpecimenRefreshMaintainanceTask.java +++ b/study/src/org/labkey/study/SpecimenRefreshMaintainanceTask.java @@ -15,7 +15,7 @@ */ package org.labkey.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; diff --git a/study/src/org/labkey/study/SpecimenServiceImpl.java b/study/src/org/labkey/study/SpecimenServiceImpl.java index 9cfd20910e6..988e21eff5a 100644 --- a/study/src/org/labkey/study/SpecimenServiceImpl.java +++ b/study/src/org/labkey/study/SpecimenServiceImpl.java @@ -17,7 +17,7 @@ package org.labkey.study; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; diff --git a/study/src/org/labkey/study/StudyModule.java b/study/src/org/labkey/study/StudyModule.java index 53d73c8343d..93a93fb32ed 100644 --- a/study/src/org/labkey/study/StudyModule.java +++ b/study/src/org/labkey/study/StudyModule.java @@ -18,7 +18,8 @@ import org.apache.commons.collections4.bag.HashBag; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.json.JSONObject; import org.junit.Assert; @@ -188,7 +189,7 @@ public class StudyModule extends SpringModule implements SearchService.DocumentProvider { - private static final Logger LOG = Logger.getLogger(StudyModule.class); + private static final Logger LOG = LogManager.getLogger(StudyModule.class); public static final String MODULE_NAME = "Study"; diff --git a/study/src/org/labkey/study/StudyServiceImpl.java b/study/src/org/labkey/study/StudyServiceImpl.java index e374a0a5562..d07c3f8d4d4 100644 --- a/study/src/org/labkey/study/StudyServiceImpl.java +++ b/study/src/org/labkey/study/StudyServiceImpl.java @@ -21,6 +21,9 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportOptions; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayTableMetadata; import org.labkey.api.audit.AuditLogService; import org.labkey.api.audit.AuditTypeEvent; import org.labkey.api.collections.CaseInsensitiveHashSet; @@ -71,9 +74,6 @@ import org.labkey.api.study.StudyService; import org.labkey.api.study.TimepointType; import org.labkey.api.study.UnionTable; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayTableMetadata; import org.labkey.api.util.GUID; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; diff --git a/study/src/org/labkey/study/StudyUnionTableInfo.java b/study/src/org/labkey/study/StudyUnionTableInfo.java index 641f281be09..803fe25dc44 100644 --- a/study/src/org/labkey/study/StudyUnionTableInfo.java +++ b/study/src/org/labkey/study/StudyUnionTableInfo.java @@ -15,7 +15,7 @@ */ package org.labkey.study; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.BaseColumnInfo; @@ -103,7 +103,7 @@ public void init(Collection defs) String visitPropertyName = def.getVisitDateColumnName(); ColumnInfo visitColumn = null == visitPropertyName ? null : ti.getColumn(visitPropertyName); if (null != visitPropertyName && (null == visitColumn || visitColumn.getJdbcType() != JdbcType.TIMESTAMP)) - Logger.getLogger(StudySchema.class).info("Could not find visit column of correct type '" + visitPropertyName + "' in dataset '" + def.getName() + "'"); + LogManager.getLogger(StudySchema.class).info("Could not find visit column of correct type '" + visitPropertyName + "' in dataset '" + def.getName() + "'"); if (null != visitColumn && visitColumn.getJdbcType() == JdbcType.TIMESTAMP) sqlf.append(", ").append(visitColumn.getValueSql("D")).append(" AS _visitdate"); else diff --git a/study/src/org/labkey/study/assay/AssayPublishManager.java b/study/src/org/labkey/study/assay/AssayPublishManager.java index b99468572b1..6f69d0751e3 100644 --- a/study/src/org/labkey/study/assay/AssayPublishManager.java +++ b/study/src/org/labkey/study/assay/AssayPublishManager.java @@ -19,7 +19,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.assay.AbstractAssayProvider; @@ -125,7 +126,7 @@ public class AssayPublishManager implements AssayPublishService { private static final int MIN_ASSAY_ID = 5000; - private static final Logger LOG = Logger.getLogger(AssayPublishManager.class); + private static final Logger LOG = LogManager.getLogger(AssayPublishManager.class); public synchronized static AssayPublishManager getInstance() { diff --git a/study/src/org/labkey/study/assay/PublishConfirmAction.java b/study/src/org/labkey/study/assay/PublishConfirmAction.java index 7e1ccc7fe83..ceeebc9ede4 100644 --- a/study/src/org/labkey/study/assay/PublishConfirmAction.java +++ b/study/src/org/labkey/study/assay/PublishConfirmAction.java @@ -25,6 +25,11 @@ import org.labkey.api.action.FormViewAction; import org.labkey.api.action.HasBindParameters; import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.ActionButton; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -37,13 +42,8 @@ import org.labkey.api.study.StudyService; import org.labkey.api.study.StudyUrls; import org.labkey.api.study.TimepointType; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; import org.labkey.api.study.assay.AssayPublishKey; import org.labkey.api.study.assay.AssayPublishService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.study.query.PublishResultsQueryView; import org.labkey.api.util.HelpTopic; import org.labkey.api.util.PageFlowUtil; diff --git a/study/src/org/labkey/study/assay/PublishStartAction.java b/study/src/org/labkey/study/assay/PublishStartAction.java index 75d5ff78e1e..fcea6a35135 100644 --- a/study/src/org/labkey/study/assay/PublishStartAction.java +++ b/study/src/org/labkey/study/assay/PublishStartAction.java @@ -16,7 +16,13 @@ package org.labkey.study.assay; +import org.labkey.api.assay.AssayProtocolSchema; +import org.labkey.api.assay.AssayProvider; import org.labkey.api.assay.AssayQCService; +import org.labkey.api.assay.AssayTableMetadata; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -36,12 +42,6 @@ import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.study.StudyUrls; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.api.assay.AssayProtocolSchema; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayTableMetadata; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.HelpTopic; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; diff --git a/study/src/org/labkey/study/assay/view/publishHeader.jsp b/study/src/org/labkey/study/assay/view/publishHeader.jsp index ab0bf22ba93..7e55495ced3 100644 --- a/study/src/org/labkey/study/assay/view/publishHeader.jsp +++ b/study/src/org/labkey/study/assay/view/publishHeader.jsp @@ -15,10 +15,10 @@ * limitations under the License. */ %> -<%@ page import="org.labkey.study.assay.PublishConfirmAction"%> +<%@ page import="org.labkey.api.study.TimepointType"%> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> -<%@ page import="org.labkey.api.study.TimepointType" %> +<%@ page import="org.labkey.study.assay.PublishConfirmAction" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/study/src/org/labkey/study/controllers/CreateChildStudyAction.java b/study/src/org/labkey/study/controllers/CreateChildStudyAction.java index 04bc8226c5a..914262a8297 100644 --- a/study/src/org/labkey/study/controllers/CreateChildStudyAction.java +++ b/study/src/org/labkey/study/controllers/CreateChildStudyAction.java @@ -15,7 +15,8 @@ */ package org.labkey.study.controllers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.MutatingApiAction; @@ -65,7 +66,7 @@ @RequiresPermission(AdminPermission.class) public class CreateChildStudyAction extends MutatingApiAction { - private static final Logger LOG = Logger.getLogger(CreateChildStudyAction.class); + private static final Logger LOG = LogManager.getLogger(CreateChildStudyAction.class); public static final String CREATE_SPECIMEN_STUDY = "CreateSpecimenStudy"; private Container _dstContainer; diff --git a/study/src/org/labkey/study/controllers/PublishController.java b/study/src/org/labkey/study/controllers/PublishController.java index 159b553fd47..290aca6baa2 100644 --- a/study/src/org/labkey/study/controllers/PublishController.java +++ b/study/src/org/labkey/study/controllers/PublishController.java @@ -4,6 +4,13 @@ import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; +import org.labkey.api.assay.actions.AssayHeaderView; +import org.labkey.api.assay.actions.AssayRunsAction; +import org.labkey.api.assay.actions.BaseAssayAction; +import org.labkey.api.assay.actions.ProtocolIdForm; import org.labkey.api.audit.AuditLogService; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; @@ -24,16 +31,7 @@ import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.security.permissions.ReadPermission; import org.labkey.api.study.Study; -import org.labkey.api.assay.actions.AssayHeaderView; -import org.labkey.api.assay.actions.AssayRunsAction; -import org.labkey.api.assay.actions.BaseAssayAction; -import org.labkey.api.assay.actions.ProtocolIdForm; -import org.labkey.study.assay.PublishConfirmAction; -import org.labkey.study.assay.PublishStartAction; -import org.labkey.api.assay.AssayProvider; import org.labkey.api.study.assay.AssayPublishService; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.ConfigurationException; import org.labkey.api.util.FileUtil; import org.labkey.api.util.HelpTopic; @@ -44,6 +42,8 @@ import org.labkey.api.view.VBox; import org.labkey.api.view.ViewBackgroundInfo; import org.labkey.study.assay.AssayPublishManager; +import org.labkey.study.assay.PublishConfirmAction; +import org.labkey.study.assay.PublishStartAction; import org.labkey.study.assay.query.AssayAuditProvider; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/study/src/org/labkey/study/controllers/SharedStudyController.java b/study/src/org/labkey/study/controllers/SharedStudyController.java index 9ae1306b5d0..7c40745b43e 100644 --- a/study/src/org/labkey/study/controllers/SharedStudyController.java +++ b/study/src/org/labkey/study/controllers/SharedStudyController.java @@ -15,7 +15,8 @@ */ package org.labkey.study.controllers; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.action.Marshal; import org.labkey.api.action.Marshaller; @@ -58,7 +59,7 @@ */ public class SharedStudyController extends BaseStudyController { - private static final Logger _log = Logger.getLogger(SharedStudyController.class); + private static final Logger _log = LogManager.getLogger(SharedStudyController.class); private static final ActionResolver ACTION_RESOLVER = new DefaultActionResolver(SharedStudyController.class); diff --git a/study/src/org/labkey/study/controllers/StudyController.java b/study/src/org/labkey/study/controllers/StudyController.java index f35232b2a24..8b97f6c04e3 100644 --- a/study/src/org/labkey/study/controllers/StudyController.java +++ b/study/src/org/labkey/study/controllers/StudyController.java @@ -24,7 +24,8 @@ import org.apache.commons.lang3.BooleanUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONArray; @@ -250,7 +251,7 @@ */ public class StudyController extends BaseStudyController { - private static final Logger _log = Logger.getLogger(StudyController.class); + private static final Logger _log = LogManager.getLogger(StudyController.class); private static final String PARTICIPANT_CACHE_PREFIX = "Study_participants/participantCache"; private static final String EXPAND_CONTAINERS_KEY = StudyController.class.getName() + "/expandedContainers"; diff --git a/study/src/org/labkey/study/controllers/StudyDesignController.java b/study/src/org/labkey/study/controllers/StudyDesignController.java index 476a19ca1ce..71c55a64a1c 100644 --- a/study/src/org/labkey/study/controllers/StudyDesignController.java +++ b/study/src/org/labkey/study/controllers/StudyDesignController.java @@ -44,15 +44,15 @@ import org.labkey.study.StudySchema; import org.labkey.study.model.AssaySpecimenConfigImpl; import org.labkey.study.model.AssaySpecimenVisitImpl; -import org.labkey.study.model.CohortManager; -import org.labkey.study.model.StudyAssaySchedule; -import org.labkey.study.model.StudyTreatmentSchedule; import org.labkey.study.model.CohortImpl; +import org.labkey.study.model.CohortManager; import org.labkey.study.model.DoseAndRoute; import org.labkey.study.model.ProductAntigenImpl; import org.labkey.study.model.ProductImpl; +import org.labkey.study.model.StudyAssaySchedule; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; +import org.labkey.study.model.StudyTreatmentSchedule; import org.labkey.study.model.TreatmentImpl; import org.labkey.study.model.TreatmentManager; import org.labkey.study.model.TreatmentProductImpl; diff --git a/study/src/org/labkey/study/controllers/specimen/ParticipantCommentAction.java b/study/src/org/labkey/study/controllers/specimen/ParticipantCommentAction.java index a393e842b53..896abded095 100644 --- a/study/src/org/labkey/study/controllers/specimen/ParticipantCommentAction.java +++ b/study/src/org/labkey/study/controllers/specimen/ParticipantCommentAction.java @@ -17,23 +17,23 @@ package org.labkey.study.controllers.specimen; import org.apache.commons.lang3.StringUtils; +import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.query.QueryUpdateForm; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.User; import org.labkey.api.security.permissions.InsertPermission; import org.labkey.api.security.permissions.ReadPermission; +import org.labkey.api.study.StudyService; import org.labkey.api.view.DataView; import org.labkey.api.view.InsertView; import org.labkey.api.view.NavTree; import org.labkey.api.view.UpdateView; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.study.StudyService; +import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.InsertUpdateAction; +import org.labkey.study.model.SpecimenComment; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.Vial; -import org.labkey.study.model.SpecimenComment; -import org.labkey.study.SpecimenManager; import org.springframework.validation.BindException; import org.springframework.web.servlet.ModelAndView; diff --git a/study/src/org/labkey/study/controllers/specimen/ShowGroupMembersAction.java b/study/src/org/labkey/study/controllers/specimen/ShowGroupMembersAction.java index 43173306d97..bfcb7324d77 100644 --- a/study/src/org/labkey/study/controllers/specimen/ShowGroupMembersAction.java +++ b/study/src/org/labkey/study/controllers/specimen/ShowGroupMembersAction.java @@ -33,8 +33,8 @@ import org.labkey.api.view.NotFoundException; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.BaseStudyController; -import org.labkey.study.model.SpecimenRequestActor; import org.labkey.study.model.LocationImpl; +import org.labkey.study.model.SpecimenRequestActor; import org.labkey.study.model.StudyManager; import org.labkey.study.security.permissions.ManageSpecimenActorsPermission; import org.springframework.validation.BindException; diff --git a/study/src/org/labkey/study/controllers/specimen/ShowUploadSpecimensAction.java b/study/src/org/labkey/study/controllers/specimen/ShowUploadSpecimensAction.java index 90938b9b372..c9e963fa9e6 100644 --- a/study/src/org/labkey/study/controllers/specimen/ShowUploadSpecimensAction.java +++ b/study/src/org/labkey/study/controllers/specimen/ShowUploadSpecimensAction.java @@ -24,18 +24,22 @@ import org.labkey.api.data.Container; import org.labkey.api.data.RuntimeSQLException; import org.labkey.api.pipeline.PipelineUrls; +import org.labkey.api.portal.ProjectUrls; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.TabLoader; import org.labkey.api.security.RequiresPermission; import org.labkey.api.security.User; import org.labkey.api.security.permissions.AdminPermission; import org.labkey.api.study.Study; -import org.labkey.api.study.TimepointType; import org.labkey.api.study.StudyService; +import org.labkey.api.study.TimepointType; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; -import org.labkey.api.view.*; -import org.labkey.api.portal.ProjectUrls; +import org.labkey.api.view.ActionURL; +import org.labkey.api.view.HtmlView; +import org.labkey.api.view.HttpView; +import org.labkey.api.view.JspView; +import org.labkey.api.view.NavTree; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.StudyController; import org.labkey.study.importer.SimpleSpecimenImporter; @@ -47,7 +51,11 @@ import java.io.IOException; import java.sql.BatchUpdateException; -import java.util.*; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; @RequiresPermission(AdminPermission.class) public class ShowUploadSpecimensAction extends FormViewAction diff --git a/study/src/org/labkey/study/controllers/specimen/SpecimenApiController.java b/study/src/org/labkey/study/controllers/specimen/SpecimenApiController.java index 09fe14b0d56..6d13c9ce200 100644 --- a/study/src/org/labkey/study/controllers/specimen/SpecimenApiController.java +++ b/study/src/org/labkey/study/controllers/specimen/SpecimenApiController.java @@ -17,23 +17,46 @@ import org.apache.commons.lang3.StringUtils; import org.json.JSONObject; -import org.labkey.api.security.*; +import org.labkey.api.action.ApiResponse; +import org.labkey.api.action.ApiSimpleResponse; +import org.labkey.api.action.ApiVersion; +import org.labkey.api.action.HasViewContext; +import org.labkey.api.action.MutatingApiAction; +import org.labkey.api.action.ReadOnlyApiAction; +import org.labkey.api.data.Container; +import org.labkey.api.security.RequiresPermission; +import org.labkey.api.security.User; +import org.labkey.api.security.UserManager; import org.labkey.api.security.permissions.ReadPermission; -import org.labkey.api.action.*; +import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.NotFoundException; import org.labkey.api.view.ViewContext; -import org.labkey.api.data.Container; -import org.labkey.api.util.PageFlowUtil; import org.labkey.study.SpecimenManager; +import org.labkey.study.controllers.BaseStudyController; import org.labkey.study.importer.RequestabilityManager; -import org.labkey.study.specimen.settings.RepositorySettings; -import org.labkey.study.security.permissions.RequestSpecimensPermission; +import org.labkey.study.model.AdditiveType; +import org.labkey.study.model.DerivativeType; +import org.labkey.study.model.LocationImpl; +import org.labkey.study.model.PrimaryType; +import org.labkey.study.model.SpecimenRequest; +import org.labkey.study.model.SpecimenRequestStatus; +import org.labkey.study.model.SpecimenTypeSummary; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.Vial; import org.labkey.study.security.permissions.ManageRequestsPermission; -import org.labkey.study.controllers.BaseStudyController; -import org.labkey.study.model.*; +import org.labkey.study.security.permissions.RequestSpecimensPermission; +import org.labkey.study.specimen.settings.RepositorySettings; import org.springframework.validation.BindException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; /* * User: brittp diff --git a/study/src/org/labkey/study/controllers/specimen/SpecimenController.java b/study/src/org/labkey/study/controllers/specimen/SpecimenController.java index 7f97c010689..8a8a8776541 100644 --- a/study/src/org/labkey/study/controllers/specimen/SpecimenController.java +++ b/study/src/org/labkey/study/controllers/specimen/SpecimenController.java @@ -18,7 +18,8 @@ import org.apache.commons.io.Charsets; import org.apache.commons.lang3.time.DateUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.json.JSONObject; @@ -205,7 +206,7 @@ @SuppressWarnings("UnusedDeclaration") public class SpecimenController extends BaseStudyController { - private static final Logger _log = Logger.getLogger(SpecimenController.class); + private static final Logger _log = LogManager.getLogger(SpecimenController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver( SpecimenController.class, diff --git a/study/src/org/labkey/study/controllers/specimen/SpecimenUtils.java b/study/src/org/labkey/study/controllers/specimen/SpecimenUtils.java index dff4f5b052d..d742b45780b 100644 --- a/study/src/org/labkey/study/controllers/specimen/SpecimenUtils.java +++ b/study/src/org/labkey/study/controllers/specimen/SpecimenUtils.java @@ -21,7 +21,25 @@ import org.labkey.api.action.SpringActionController; import org.labkey.api.attachments.Attachment; import org.labkey.api.attachments.AttachmentService; -import org.labkey.api.data.*; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBarLineBreak; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.CompareType; +import org.labkey.api.data.Container; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DataRegionSelection; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.ExcelWriter; +import org.labkey.api.data.MenuButton; +import org.labkey.api.data.ObjectFactory; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.Results; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.TSVGridWriter; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.CustomView; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryDefinition; diff --git a/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java b/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java index 6f5dc2b1902..7017d9a4dcf 100644 --- a/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java +++ b/study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java @@ -16,10 +16,12 @@ package org.labkey.study.dataset; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.NullSafeBindException; import org.labkey.api.action.SpringActionController; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.audit.AuditLogService; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.ColumnHeaderType; @@ -56,7 +58,6 @@ import org.labkey.api.study.Dataset; import org.labkey.api.study.Study; import org.labkey.api.study.StudyService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.ContextListener; import org.labkey.api.util.ExceptionUtil; import org.labkey.api.util.PageFlowUtil; @@ -107,7 +108,7 @@ public class DatasetSnapshotProvider extends AbstractSnapshotProvider implements QuerySnapshotService.AutoUpdateable, DatasetManager.DatasetListener, ParticipantCategoryListener { private static final DatasetSnapshotProvider INSTANCE = new DatasetSnapshotProvider(); - private static final Logger LOG = Logger.getLogger(DatasetSnapshotProvider.class); + private static final Logger LOG = LogManager.getLogger(DatasetSnapshotProvider.class); private static final BlockingQueue QUEUE = new LinkedBlockingQueue<>(1000); private static final QuerySnapshotDependencyThread DEPENDENCY_THREAD = new QuerySnapshotDependencyThread(); diff --git a/study/src/org/labkey/study/dataset/SnapshotDependency.java b/study/src/org/labkey/study/dataset/SnapshotDependency.java index 7299202cfb5..6dd7cd8e129 100644 --- a/study/src/org/labkey/study/dataset/SnapshotDependency.java +++ b/study/src/org/labkey/study/dataset/SnapshotDependency.java @@ -16,7 +16,8 @@ package org.labkey.study.dataset; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.action.NullSafeBindException; @@ -25,8 +26,8 @@ import org.labkey.api.data.ContainerManager; import org.labkey.api.data.ConvertHelper; import org.labkey.api.data.DisplayColumn; -import org.labkey.api.data.TableInfo; import org.labkey.api.data.HasResolvedTables; +import org.labkey.api.data.TableInfo; import org.labkey.api.data.UnionTableInfo; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; @@ -56,7 +57,7 @@ */ public abstract class SnapshotDependency { - private static final Logger _log = Logger.getLogger(SnapshotDependency.class); + private static final Logger _log = LogManager.getLogger(SnapshotDependency.class); protected boolean isContainerValid(Container c) { diff --git a/study/src/org/labkey/study/designer/JSONSerializer.java b/study/src/org/labkey/study/designer/JSONSerializer.java index 3868a435385..ed384006c34 100644 --- a/study/src/org/labkey/study/designer/JSONSerializer.java +++ b/study/src/org/labkey/study/designer/JSONSerializer.java @@ -15,24 +15,44 @@ */ package org.labkey.study.designer; -import org.apache.log4j.Logger; +import gwt.client.org.labkey.study.designer.client.model.GWTAdjuvant; +import gwt.client.org.labkey.study.designer.client.model.GWTAntigen; +import gwt.client.org.labkey.study.designer.client.model.GWTAssayDefinition; +import gwt.client.org.labkey.study.designer.client.model.GWTAssayNote; +import gwt.client.org.labkey.study.designer.client.model.GWTAssaySchedule; +import gwt.client.org.labkey.study.designer.client.model.GWTCohort; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunization; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunizationSchedule; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunogen; +import gwt.client.org.labkey.study.designer.client.model.GWTSampleMeasure; +import gwt.client.org.labkey.study.designer.client.model.GWTStudyDefinition; +import gwt.client.org.labkey.study.designer.client.model.GWTTimepoint; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; -import org.apache.xmlbeans.XmlError; -import gwt.client.org.labkey.study.designer.client.model.*; -import org.labkey.study.xml.*; import org.json.JSONObject; - +import org.labkey.study.xml.Adjuvant; +import org.labkey.study.xml.AdjuvantRef; +import org.labkey.study.xml.Antigen; +import org.labkey.study.xml.AssayEvent; +import org.labkey.study.xml.AssaySchedule; +import org.labkey.study.xml.Cohort; +import org.labkey.study.xml.ImmunizationEvent; +import org.labkey.study.xml.Immunogen; +import org.labkey.study.xml.ImmunogenRef; +import org.labkey.study.xml.SampleMeasure; +import org.labkey.study.xml.StudyDesign; +import org.labkey.study.xml.StudyDesignDocument; +import org.labkey.study.xml.Timepoint; + +import java.util.ArrayList; import java.util.List; -import java.util.ArrayList;/* - * User: marki - * Date: Jun 15, 2009 - * Time: 2:55:48 PM - */ public class JSONSerializer { - private static Logger _log = Logger.getLogger(XMLSerializer.class); + private static Logger _log = LogManager.getLogger(XMLSerializer.class); public static JSONObject toJSON(String xml) { diff --git a/study/src/org/labkey/study/designer/StudyDefinitionServiceImpl.java b/study/src/org/labkey/study/designer/StudyDefinitionServiceImpl.java index 67e797bb317..d0e4e590fa9 100644 --- a/study/src/org/labkey/study/designer/StudyDefinitionServiceImpl.java +++ b/study/src/org/labkey/study/designer/StudyDefinitionServiceImpl.java @@ -16,9 +16,14 @@ package org.labkey.study.designer; +import gwt.client.org.labkey.study.designer.client.StudyDefinitionService; +import gwt.client.org.labkey.study.designer.client.model.GWTAssayDefinition; import gwt.client.org.labkey.study.designer.client.model.GWTCohort; +import gwt.client.org.labkey.study.designer.client.model.GWTStudyDefinition; +import gwt.client.org.labkey.study.designer.client.model.GWTStudyDesignVersion; import gwt.client.org.labkey.study.designer.client.model.GWTTimepoint; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.gwt.server.BaseRemoteService; import org.labkey.api.query.ValidationException; @@ -36,10 +41,6 @@ import org.labkey.api.view.ViewContext; import org.labkey.study.assay.AssayPublishManager; import org.labkey.study.controllers.designer.DesignerController; -import gwt.client.org.labkey.study.designer.client.StudyDefinitionService; -import gwt.client.org.labkey.study.designer.client.model.GWTAssayDefinition; -import gwt.client.org.labkey.study.designer.client.model.GWTStudyDefinition; -import gwt.client.org.labkey.study.designer.client.model.GWTStudyDesignVersion; import org.labkey.study.model.CohortImpl; import org.labkey.study.model.CohortManager; import org.labkey.study.model.DatasetDefinition; @@ -58,7 +59,7 @@ */ public class StudyDefinitionServiceImpl extends BaseRemoteService implements StudyDefinitionService { - private static Logger _log = Logger.getLogger(StudyDefinitionServiceImpl.class); + private static Logger _log = LogManager.getLogger(StudyDefinitionServiceImpl.class); public StudyDefinitionServiceImpl(ViewContext context) { diff --git a/study/src/org/labkey/study/designer/StudyDesignVersion.java b/study/src/org/labkey/study/designer/StudyDesignVersion.java index 8e0802aba18..00a5a68fac6 100644 --- a/study/src/org/labkey/study/designer/StudyDesignVersion.java +++ b/study/src/org/labkey/study/designer/StudyDesignVersion.java @@ -16,11 +16,11 @@ package org.labkey.study.designer; +import gwt.client.org.labkey.study.designer.client.model.GWTStudyDesignVersion; import org.labkey.api.data.Container; -import org.labkey.api.security.UserManager; import org.labkey.api.security.User; +import org.labkey.api.security.UserManager; import org.labkey.api.view.ViewContext; -import gwt.client.org.labkey.study.designer.client.model.GWTStudyDesignVersion; import java.util.Date; diff --git a/study/src/org/labkey/study/designer/XMLSerializer.java b/study/src/org/labkey/study/designer/XMLSerializer.java index adf62358da1..3e6e74882cb 100644 --- a/study/src/org/labkey/study/designer/XMLSerializer.java +++ b/study/src/org/labkey/study/designer/XMLSerializer.java @@ -16,17 +16,44 @@ package org.labkey.study.designer; -import org.apache.log4j.Logger; +import gwt.client.org.labkey.study.designer.client.model.GWTAdjuvant; +import gwt.client.org.labkey.study.designer.client.model.GWTAntigen; +import gwt.client.org.labkey.study.designer.client.model.GWTAssayDefinition; +import gwt.client.org.labkey.study.designer.client.model.GWTAssayNote; +import gwt.client.org.labkey.study.designer.client.model.GWTAssaySchedule; +import gwt.client.org.labkey.study.designer.client.model.GWTCohort; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunization; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunizationSchedule; +import gwt.client.org.labkey.study.designer.client.model.GWTImmunogen; +import gwt.client.org.labkey.study.designer.client.model.GWTSampleMeasure; +import gwt.client.org.labkey.study.designer.client.model.GWTStudyDefinition; +import gwt.client.org.labkey.study.designer.client.model.GWTTimepoint; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.apache.xmlbeans.XmlError; import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlOptions; -import gwt.client.org.labkey.study.designer.client.model.*; import org.labkey.api.data.Container; import org.labkey.api.security.User; import org.labkey.study.StudySchema; import org.labkey.study.model.CohortImpl; import org.labkey.study.model.StudyManager; -import org.labkey.study.xml.*; +import org.labkey.study.xml.Adjuvant; +import org.labkey.study.xml.AdjuvantRef; +import org.labkey.study.xml.Antigen; +import org.labkey.study.xml.AssayEvent; +import org.labkey.study.xml.AssayRef; +import org.labkey.study.xml.AssaySchedule; +import org.labkey.study.xml.Cohort; +import org.labkey.study.xml.Immunization; +import org.labkey.study.xml.ImmunizationEvent; +import org.labkey.study.xml.ImmunizationSchedule; +import org.labkey.study.xml.Immunogen; +import org.labkey.study.xml.ImmunogenRef; +import org.labkey.study.xml.SampleMeasure; +import org.labkey.study.xml.StudyDesign; +import org.labkey.study.xml.StudyDesignDocument; +import org.labkey.study.xml.Timepoint; import java.util.ArrayList; import java.util.List; @@ -38,7 +65,7 @@ */ public class XMLSerializer { - private static Logger _log = Logger.getLogger(XMLSerializer.class); + private static Logger _log = LogManager.getLogger(XMLSerializer.class); public static GWTStudyDefinition fromXML(String xml, User user, Container c) { diff --git a/study/src/org/labkey/study/designer/view/CreateRepositoryWizard.jsp b/study/src/org/labkey/study/designer/view/CreateRepositoryWizard.jsp index 45059ef17a3..cb65033d950 100644 --- a/study/src/org/labkey/study/designer/view/CreateRepositoryWizard.jsp +++ b/study/src/org/labkey/study/designer/view/CreateRepositoryWizard.jsp @@ -20,6 +20,7 @@ <%@ page import="org.labkey.api.data.ContainerManager" %> <%@ page import="org.labkey.api.security.User" %> <%@ page import="org.labkey.api.security.permissions.AdminPermission" %> +<%@ page import="org.labkey.api.util.DateUtil" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.study.controllers.designer.DesignerController" %> @@ -28,7 +29,6 @@ <%@ page import="java.util.Set" %> <%@ page import="java.util.SortedSet" %> <%@ page import="java.util.TreeSet" %> -<%@ page import="org.labkey.api.util.DateUtil" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% diff --git a/study/src/org/labkey/study/designer/view/StudyDesignsWebPart.java b/study/src/org/labkey/study/designer/view/StudyDesignsWebPart.java index e4579a4ef25..4461cd7ec9e 100644 --- a/study/src/org/labkey/study/designer/view/StudyDesignsWebPart.java +++ b/study/src/org/labkey/study/designer/view/StudyDesignsWebPart.java @@ -16,7 +16,16 @@ package org.labkey.study.designer.view; -import org.labkey.api.data.*; +import org.labkey.api.data.ActionButton; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DataRegionSelection; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.TableInfo; import org.labkey.api.portal.ProjectUrls; import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; @@ -36,8 +45,6 @@ import java.io.IOException; import java.io.Writer; -import java.util.HashMap; -import java.util.Map; /** * User: Mark Igra diff --git a/study/src/org/labkey/study/importer/CohortImporter.java b/study/src/org/labkey/study/importer/CohortImporter.java index c3a7baa2a17..cdac92ffdb4 100644 --- a/study/src/org/labkey/study/importer/CohortImporter.java +++ b/study/src/org/labkey/study/importer/CohortImporter.java @@ -35,9 +35,7 @@ import org.labkey.study.xml.StudyDocument; import org.springframework.validation.BindException; -import javax.servlet.ServletException; import java.io.IOException; -import java.sql.SQLException; import java.util.HashMap; import java.util.Map; diff --git a/study/src/org/labkey/study/importer/DatasetImportUtils.java b/study/src/org/labkey/study/importer/DatasetImportUtils.java index 85e8131e960..728b6608a69 100644 --- a/study/src/org/labkey/study/importer/DatasetImportUtils.java +++ b/study/src/org/labkey/study/importer/DatasetImportUtils.java @@ -31,7 +31,6 @@ import javax.servlet.ServletException; import java.io.File; import java.io.IOException; -import java.sql.SQLException; /* * User: adam diff --git a/study/src/org/labkey/study/importer/EditableSpecimenImporter.java b/study/src/org/labkey/study/importer/EditableSpecimenImporter.java index 6213ac34a56..d120ecbe308 100644 --- a/study/src/org/labkey/study/importer/EditableSpecimenImporter.java +++ b/study/src/org/labkey/study/importer/EditableSpecimenImporter.java @@ -15,7 +15,8 @@ */ package org.labkey.study.importer; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; @@ -30,7 +31,6 @@ import org.labkey.study.StudySchema; import java.io.IOException; -import java.sql.SQLException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; @@ -63,7 +63,7 @@ public void process(List> rows, boolean merge) throws IOExce public void process(List> rows, boolean merge, Logger logger) throws IOException, ValidationException { if (null == logger) - logger = Logger.getLogger(getClass()); + logger = LogManager.getLogger(getClass()); _process(rows, merge, logger); } diff --git a/study/src/org/labkey/study/importer/IteratorSpecimenImportFile.java b/study/src/org/labkey/study/importer/IteratorSpecimenImportFile.java index 22a1632e1d8..2a6dd2563dc 100644 --- a/study/src/org/labkey/study/importer/IteratorSpecimenImportFile.java +++ b/study/src/org/labkey/study/importer/IteratorSpecimenImportFile.java @@ -19,9 +19,8 @@ import org.labkey.api.reader.DataLoader; import org.labkey.api.reader.MapLoader; import org.labkey.api.study.SpecimenImportStrategy; -import org.labkey.study.importer.SpecimenImporter.*; +import org.labkey.study.importer.SpecimenImporter.SpecimenTableType; -import java.io.IOException; import java.util.List; import java.util.Map; diff --git a/study/src/org/labkey/study/importer/LDMSRecord.java b/study/src/org/labkey/study/importer/LDMSRecord.java index 39ddb3baebd..9ce211b5cf7 100644 --- a/study/src/org/labkey/study/importer/LDMSRecord.java +++ b/study/src/org/labkey/study/importer/LDMSRecord.java @@ -13,14 +13,14 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - + package org.labkey.study.importer; import org.labkey.api.exp.api.ExpMaterial; -import java.util.Map; -import java.util.Date; import java.util.Calendar; +import java.util.Date; +import java.util.Map; /** * User: brittp diff --git a/study/src/org/labkey/study/importer/MissingValueImporterFactory.java b/study/src/org/labkey/study/importer/MissingValueImporterFactory.java index 3c06984f75a..20b6f91b4af 100644 --- a/study/src/org/labkey/study/importer/MissingValueImporterFactory.java +++ b/study/src/org/labkey/study/importer/MissingValueImporterFactory.java @@ -19,8 +19,8 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.AbstractFolderImportFactory; -import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.FolderArchiveDataTypes; +import org.labkey.api.admin.FolderImporter; import org.labkey.api.admin.ImportContext; import org.labkey.api.admin.ImportException; import org.labkey.api.data.MvUtil; diff --git a/study/src/org/labkey/study/importer/ParticipantGroupImporter.java b/study/src/org/labkey/study/importer/ParticipantGroupImporter.java index f29070df00e..d9b356c329b 100644 --- a/study/src/org/labkey/study/importer/ParticipantGroupImporter.java +++ b/study/src/org/labkey/study/importer/ParticipantGroupImporter.java @@ -17,7 +17,6 @@ import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlObject; -import org.labkey.api.admin.ImportException; import org.labkey.api.admin.InvalidFileException; import org.labkey.api.data.DbScope; import org.labkey.api.util.XmlBeansUtil; diff --git a/study/src/org/labkey/study/importer/RequestabilityManager.java b/study/src/org/labkey/study/importer/RequestabilityManager.java index ca779f81359..4e6c6d55c82 100644 --- a/study/src/org/labkey/study/importer/RequestabilityManager.java +++ b/study/src/org/labkey/study/importer/RequestabilityManager.java @@ -15,18 +15,38 @@ */ package org.labkey.study.importer; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; -import org.labkey.api.data.*; -import org.labkey.api.query.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.CompareType; +import org.labkey.api.data.Container; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.SqlExecutor; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; +import org.labkey.api.query.CustomView; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryAction; +import org.labkey.api.query.QueryParam; +import org.labkey.api.query.QueryService; +import org.labkey.api.query.QueryView; +import org.labkey.api.query.UserSchema; import org.labkey.api.security.User; import org.labkey.api.view.ActionURL; import org.labkey.study.StudySchema; import org.labkey.study.controllers.specimen.SpecimenController; import org.labkey.study.model.Vial; -import java.sql.SQLException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Set; /** * User: brittp diff --git a/study/src/org/labkey/study/importer/SchemaReader.java b/study/src/org/labkey/study/importer/SchemaReader.java index 7e0e9af2b16..ea18c340b3d 100644 --- a/study/src/org/labkey/study/importer/SchemaReader.java +++ b/study/src/org/labkey/study/importer/SchemaReader.java @@ -25,7 +25,6 @@ import java.util.Collection; import java.util.HashSet; -import java.util.List; import java.util.Map; import java.util.Set; diff --git a/study/src/org/labkey/study/importer/SchemaXmlReader.java b/study/src/org/labkey/study/importer/SchemaXmlReader.java index bf1f1689efe..8dfd2326b71 100644 --- a/study/src/org/labkey/study/importer/SchemaXmlReader.java +++ b/study/src/org/labkey/study/importer/SchemaXmlReader.java @@ -15,7 +15,6 @@ */ package org.labkey.study.importer; -import org.apache.xmlbeans.XmlException; import org.apache.xmlbeans.XmlObject; import org.jetbrains.annotations.NotNull; import org.labkey.api.admin.ImportException; diff --git a/study/src/org/labkey/study/importer/SimpleSpecimenImporter.java b/study/src/org/labkey/study/importer/SimpleSpecimenImporter.java index c27a387e6a1..0868f09d363 100644 --- a/study/src/org/labkey/study/importer/SimpleSpecimenImporter.java +++ b/study/src/org/labkey/study/importer/SimpleSpecimenImporter.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConversionException; import org.apache.commons.beanutils.ConvertUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; import org.labkey.api.data.Filter; @@ -208,7 +209,7 @@ public ColumnDescriptor[] getSimpleSpecimenColumns() public void process(List> rows, boolean merge) throws IOException, ValidationException { - _process(rows, merge, Logger.getLogger(getClass())); + _process(rows, merge, LogManager.getLogger(getClass())); } // Avoid conflict with SpecimenImporter.process() (has similar signature) diff --git a/study/src/org/labkey/study/importer/SpecimenImporter.java b/study/src/org/labkey/study/importer/SpecimenImporter.java index 0d2440d9e87..4498623c1c4 100644 --- a/study/src/org/labkey/study/importer/SpecimenImporter.java +++ b/study/src/org/labkey/study/importer/SpecimenImporter.java @@ -18,7 +18,7 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.After; diff --git a/study/src/org/labkey/study/importer/StandardSpecimenImportStrategy.java b/study/src/org/labkey/study/importer/StandardSpecimenImportStrategy.java index e473efd8138..eeded276fdd 100644 --- a/study/src/org/labkey/study/importer/StandardSpecimenImportStrategy.java +++ b/study/src/org/labkey/study/importer/StandardSpecimenImportStrategy.java @@ -19,7 +19,6 @@ import org.labkey.api.data.Filter; import org.labkey.api.study.SpecimenImportStrategy; -import java.io.IOException; import java.util.Map; /** diff --git a/study/src/org/labkey/study/importer/StudyImportJob.java b/study/src/org/labkey/study/importer/StudyImportJob.java index 2c9b4773445..ad5276596ea 100644 --- a/study/src/org/labkey/study/importer/StudyImportJob.java +++ b/study/src/org/labkey/study/importer/StudyImportJob.java @@ -17,7 +17,8 @@ import com.fasterxml.jackson.annotation.JsonCreator; import com.fasterxml.jackson.annotation.JsonProperty; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.NullSafeBindException; import org.labkey.api.admin.ImportException; import org.labkey.api.admin.ImportOptions; @@ -48,7 +49,7 @@ */ public class StudyImportJob extends PipelineJob implements StudyJobSupport, StudyImporter { - private static final transient Logger LOG = Logger.getLogger(StudyImportJob.class); + private static final transient Logger LOG = LogManager.getLogger(StudyImportJob.class); private final StudyImportContext _ctx; private final VirtualFile _root; diff --git a/study/src/org/labkey/study/importer/StudyImportProvider.java b/study/src/org/labkey/study/importer/StudyImportProvider.java index 62b99d865a6..8b451c85c28 100644 --- a/study/src/org/labkey/study/importer/StudyImportProvider.java +++ b/study/src/org/labkey/study/importer/StudyImportProvider.java @@ -16,12 +16,12 @@ package org.labkey.study.importer; +import org.labkey.api.module.Module; import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineDirectory; import org.labkey.api.pipeline.PipelineProvider; -import org.labkey.api.view.ViewContext; import org.labkey.api.security.permissions.AdminPermission; -import org.labkey.api.module.Module; +import org.labkey.api.view.ViewContext; import org.labkey.study.controllers.StudyController; import org.labkey.study.model.StudyManager; diff --git a/study/src/org/labkey/study/importer/StudyPropertiesImporter.java b/study/src/org/labkey/study/importer/StudyPropertiesImporter.java index 5d4edbf6aa2..025af7b8f28 100644 --- a/study/src/org/labkey/study/importer/StudyPropertiesImporter.java +++ b/study/src/org/labkey/study/importer/StudyPropertiesImporter.java @@ -20,7 +20,6 @@ import org.labkey.api.admin.ImportException; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.collections.CaseInsensitiveHashSet; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.DbScope; import org.labkey.api.data.TableInfo; import org.labkey.api.security.User; diff --git a/study/src/org/labkey/study/importer/StudyReload.java b/study/src/org/labkey/study/importer/StudyReload.java index 6d73ab2f051..552004e887b 100644 --- a/study/src/org/labkey/study/importer/StudyReload.java +++ b/study/src/org/labkey/study/importer/StudyReload.java @@ -16,7 +16,8 @@ package org.labkey.study.importer; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.action.NullSafeBindException; import org.labkey.api.admin.FolderImportContext; @@ -28,11 +29,8 @@ import org.labkey.api.pipeline.PipeRoot; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.security.User; -import org.labkey.api.security.UserManager; import org.labkey.api.study.Study; -import org.labkey.api.util.ContextListener; import org.labkey.api.util.ExceptionUtil; -import org.labkey.api.util.ShutdownListener; import org.labkey.api.view.ActionURL; import org.labkey.api.view.NotFoundException; import org.labkey.folder.xml.FolderDocument; @@ -45,8 +43,6 @@ import java.io.File; import java.util.Date; -import java.util.concurrent.ArrayBlockingQueue; -import java.util.concurrent.BlockingQueue; /* * User: adam @@ -55,7 +51,7 @@ */ public class StudyReload { - private static final Logger LOG = Logger.getLogger(StudyReload.class); + private static final Logger LOG = LogManager.getLogger(StudyReload.class); private static String getDescription(Study study) { diff --git a/study/src/org/labkey/study/importer/TreatmentDataImporter.java b/study/src/org/labkey/study/importer/TreatmentDataImporter.java index f1f7092abaf..492b25a605a 100644 --- a/study/src/org/labkey/study/importer/TreatmentDataImporter.java +++ b/study/src/org/labkey/study/importer/TreatmentDataImporter.java @@ -18,7 +18,6 @@ import org.labkey.api.admin.ImportException; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.DbScope; import org.labkey.api.writer.VirtualFile; import org.labkey.study.StudySchema; diff --git a/study/src/org/labkey/study/importer/VisitMapImporter.java b/study/src/org/labkey/study/importer/VisitMapImporter.java index a4efef957b9..8c85900395c 100644 --- a/study/src/org/labkey/study/importer/VisitMapImporter.java +++ b/study/src/org/labkey/study/importer/VisitMapImporter.java @@ -17,7 +17,7 @@ package org.labkey.study.importer; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.Container; import org.labkey.api.data.DbScope; import org.labkey.api.query.ValidationException; diff --git a/study/src/org/labkey/study/importer/VisitMapReader.java b/study/src/org/labkey/study/importer/VisitMapReader.java index 21e2ac6d0d3..f5627db53bf 100644 --- a/study/src/org/labkey/study/importer/VisitMapReader.java +++ b/study/src/org/labkey/study/importer/VisitMapReader.java @@ -17,11 +17,9 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.study.TimepointType; -import org.labkey.study.model.StudyManager; import org.labkey.study.model.StudyManager.VisitAlias; import org.labkey.study.model.VisitTag; -import java.io.IOException; import java.util.List; /** diff --git a/study/src/org/labkey/study/model/AbstractSpecimenDomainKind.java b/study/src/org/labkey/study/model/AbstractSpecimenDomainKind.java index 906db0e2235..c5bb5ddce22 100644 --- a/study/src/org/labkey/study/model/AbstractSpecimenDomainKind.java +++ b/study/src/org/labkey/study/model/AbstractSpecimenDomainKind.java @@ -16,7 +16,6 @@ package org.labkey.study.model; import org.jetbrains.annotations.Nullable; -import org.json.JSONObject; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchema; diff --git a/study/src/org/labkey/study/model/AdditiveType.java b/study/src/org/labkey/study/model/AdditiveType.java index 41b05270027..296794b37d2 100644 --- a/study/src/org/labkey/study/model/AdditiveType.java +++ b/study/src/org/labkey/study/model/AdditiveType.java @@ -15,11 +15,7 @@ */ package org.labkey.study.model; -import org.labkey.api.data.Container;/* - * User: brittp - * Date: Dec 18, 2008 - * Time: 12:48:03 PM - */ +import org.labkey.api.data.Container; import java.util.Map; diff --git a/study/src/org/labkey/study/model/BaseStudyDomainKind.java b/study/src/org/labkey/study/model/BaseStudyDomainKind.java index 6c7f1a8760d..0ade2586e8f 100644 --- a/study/src/org/labkey/study/model/BaseStudyDomainKind.java +++ b/study/src/org/labkey/study/model/BaseStudyDomainKind.java @@ -15,7 +15,6 @@ */ package org.labkey.study.model; -import org.json.JSONObject; import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.TableInfo; diff --git a/study/src/org/labkey/study/model/ChildStudyDefinition.java b/study/src/org/labkey/study/model/ChildStudyDefinition.java index 2d65f6ef90d..c63b644e180 100644 --- a/study/src/org/labkey/study/model/ChildStudyDefinition.java +++ b/study/src/org/labkey/study/model/ChildStudyDefinition.java @@ -15,7 +15,7 @@ */ package org.labkey.study.model; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.data.PHI; import org.labkey.api.study.StudySnapshotType; diff --git a/study/src/org/labkey/study/model/CohortImpl.java b/study/src/org/labkey/study/model/CohortImpl.java index 9ea0dfd9dfc..04cfdbe545c 100644 --- a/study/src/org/labkey/study/model/CohortImpl.java +++ b/study/src/org/labkey/study/model/CohortImpl.java @@ -18,8 +18,8 @@ import org.jetbrains.annotations.NotNull; import org.json.JSONArray; import org.json.JSONObject; -import org.labkey.api.study.Cohort; import org.labkey.api.exp.Lsid; +import org.labkey.api.study.Cohort; import java.util.ArrayList; import java.util.HashSet; diff --git a/study/src/org/labkey/study/model/DatasetDataIteratorBuilder.java b/study/src/org/labkey/study/model/DatasetDataIteratorBuilder.java index ad2b339dbb2..9804ab0fe78 100644 --- a/study/src/org/labkey/study/model/DatasetDataIteratorBuilder.java +++ b/study/src/org/labkey/study/model/DatasetDataIteratorBuilder.java @@ -17,11 +17,10 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.beanutils.Converter; -import org.apache.log4j.Logger; -import org.labkey.api.data.BaseColumnInfo; -import org.labkey.api.dataiterator.ScrollableDataIterator; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.collections.CaseInsensitiveHashSet; +import org.labkey.api.data.BaseColumnInfo; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; @@ -33,6 +32,7 @@ import org.labkey.api.dataiterator.DataIteratorUtil; import org.labkey.api.dataiterator.ErrorIterator; import org.labkey.api.dataiterator.LoggingDataIterator; +import org.labkey.api.dataiterator.ScrollableDataIterator; import org.labkey.api.dataiterator.SimpleTranslator; import org.labkey.api.qc.QCState; import org.labkey.api.qc.QCStateManager; diff --git a/study/src/org/labkey/study/model/DatasetDefinition.java b/study/src/org/labkey/study/model/DatasetDefinition.java index 545f99ee769..c451d7a1752 100644 --- a/study/src/org/labkey/study/model/DatasetDefinition.java +++ b/study/src/org/labkey/study/model/DatasetDefinition.java @@ -18,7 +18,8 @@ import org.apache.commons.beanutils.ConvertUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -125,9 +126,6 @@ import java.util.Set; import java.util.TreeSet; import java.util.concurrent.locks.ReentrantLock; -import java.util.stream.Collectors; - -import static java.util.stream.Collectors.toSet; /** @@ -140,7 +138,7 @@ public class DatasetDefinition extends AbstractStudyEntity im // standard string to use in URLs etc. public static final String DATASETKEY = "datasetId"; // static final Object MANAGED_KEY_LOCK = new Object(); - private static Logger _log = Logger.getLogger(DatasetDefinition.class); + private static Logger _log = LogManager.getLogger(DatasetDefinition.class); private final ReentrantLock _lock = new ReentrantLock(); diff --git a/study/src/org/labkey/study/model/DatasetReorderer.java b/study/src/org/labkey/study/model/DatasetReorderer.java index eece149bd22..0880ef04d32 100644 --- a/study/src/org/labkey/study/model/DatasetReorderer.java +++ b/study/src/org/labkey/study/model/DatasetReorderer.java @@ -18,7 +18,6 @@ import org.labkey.api.security.User; import org.labkey.api.study.Study; -import java.sql.SQLException; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; diff --git a/study/src/org/labkey/study/model/ExtensibleStudyEntity.java b/study/src/org/labkey/study/model/ExtensibleStudyEntity.java index 788c6bddbd6..67948c52e64 100644 --- a/study/src/org/labkey/study/model/ExtensibleStudyEntity.java +++ b/study/src/org/labkey/study/model/ExtensibleStudyEntity.java @@ -17,7 +17,10 @@ import org.labkey.api.data.Container; import org.labkey.api.data.ImportAliasable; -import org.labkey.api.exp.*; +import org.labkey.api.exp.Lsid; +import org.labkey.api.exp.ObjectProperty; +import org.labkey.api.exp.OntologyManager; +import org.labkey.api.exp.PropertyType; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.exp.property.PropertyService; @@ -26,7 +29,6 @@ import java.util.ArrayList; import java.util.List; import java.util.Map; -import java.sql.SQLException; /** * Indicates that an object has virtual columns in Ontology Manager diff --git a/study/src/org/labkey/study/model/ParticipantGroup.java b/study/src/org/labkey/study/model/ParticipantGroup.java index 51929bd7a8c..74340f8ee34 100644 --- a/study/src/org/labkey/study/model/ParticipantGroup.java +++ b/study/src/org/labkey/study/model/ParticipantGroup.java @@ -18,9 +18,9 @@ import org.apache.commons.lang3.StringUtils; import org.json.JSONException; import org.json.JSONObject; +import org.labkey.api.data.AbstractParticipantGroup; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; -import org.labkey.api.data.AbstractParticipantGroup; import org.labkey.api.query.FieldKey; import org.labkey.api.study.StudyService; import org.labkey.api.util.Pair; diff --git a/study/src/org/labkey/study/model/PrimaryType.java b/study/src/org/labkey/study/model/PrimaryType.java index b9e61ee84e0..a8bd3bc60b0 100644 --- a/study/src/org/labkey/study/model/PrimaryType.java +++ b/study/src/org/labkey/study/model/PrimaryType.java @@ -15,11 +15,7 @@ */ package org.labkey.study.model; -import org.labkey.api.data.Container;/* - * User: brittp - * Date: Dec 18, 2008 - * Time: 12:48:03 PM - */ +import org.labkey.api.data.Container; import java.util.Map; diff --git a/study/src/org/labkey/study/model/SpecimenRequestActor.java b/study/src/org/labkey/study/model/SpecimenRequestActor.java index ae3a7c59fc9..b111324ffc4 100644 --- a/study/src/org/labkey/study/model/SpecimenRequestActor.java +++ b/study/src/org/labkey/study/model/SpecimenRequestActor.java @@ -20,8 +20,8 @@ import org.labkey.api.data.TableInfo; import org.labkey.api.study.StudyCachable; import org.labkey.api.util.MemTracker; -import org.labkey.study.requirements.DefaultActor; import org.labkey.study.StudySchema; +import org.labkey.study.requirements.DefaultActor; /** * User: brittp diff --git a/study/src/org/labkey/study/model/SpecimenTypeSummary.java b/study/src/org/labkey/study/model/SpecimenTypeSummary.java index 789f1b88ae8..c26b1eb08ad 100644 --- a/study/src/org/labkey/study/model/SpecimenTypeSummary.java +++ b/study/src/org/labkey/study/model/SpecimenTypeSummary.java @@ -20,7 +20,11 @@ import org.labkey.api.view.ActionURL; import org.labkey.study.controllers.specimen.SpecimenController; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; /** * User: brittp diff --git a/study/src/org/labkey/study/model/StudyImpl.java b/study/src/org/labkey/study/model/StudyImpl.java index 7c5ebc4b513..e317e2a4944 100644 --- a/study/src/org/labkey/study/model/StudyImpl.java +++ b/study/src/org/labkey/study/model/StudyImpl.java @@ -18,7 +18,8 @@ import gwt.client.org.labkey.study.designer.client.model.GWTStudyDefinition; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; @@ -97,7 +98,7 @@ */ public class StudyImpl extends ExtensibleStudyEntity implements Study { - private static final Logger LOG = Logger.getLogger(StudyImpl.class); + private static final Logger LOG = LogManager.getLogger(StudyImpl.class); private static final String DOMAIN_URI_PREFIX = "Study"; public static final DomainInfo DOMAIN_INFO = new StudyDomainInfo(DOMAIN_URI_PREFIX, true); diff --git a/study/src/org/labkey/study/model/StudyManager.java b/study/src/org/labkey/study/model/StudyManager.java index f9cce772ccd..12ca319ed8f 100644 --- a/study/src/org/labkey/study/model/StudyManager.java +++ b/study/src/org/labkey/study/model/StudyManager.java @@ -19,12 +19,14 @@ import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.mutable.MutableInt; -import org.apache.log4j.Level; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Level; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Test; +import org.labkey.api.assay.AssayService; import org.labkey.api.attachments.Attachment; import org.labkey.api.attachments.AttachmentParent; import org.labkey.api.attachments.AttachmentService; @@ -119,7 +121,6 @@ import org.labkey.api.study.StudyService; import org.labkey.api.study.TimepointType; import org.labkey.api.study.Visit; -import org.labkey.api.assay.AssayService; import org.labkey.api.test.TestWhen; import org.labkey.api.util.DateUtil; import org.labkey.api.util.GUID; @@ -188,7 +189,7 @@ public class StudyManager public static final SearchService.SearchCategory datasetCategory = new SearchService.SearchCategory("dataset", "Study Dataset"); public static final SearchService.SearchCategory subjectCategory = new SearchService.SearchCategory("subject", "Study Subject"); - private static final Logger _log = Logger.getLogger(StudyManager.class); + private static final Logger _log = LogManager.getLogger(StudyManager.class); private static final StudyManager _instance = new StudyManager(); private static final StudySchema SCHEMA = StudySchema.getInstance(); @@ -4869,7 +4870,7 @@ public Study getStudyForVisitTag(@NotNull Study study) // To see detailed logging from StatementDataIterator, configure org.labkey.study.model.StudyManager$DatasetImportTestCase to level TRACE - private static final Logger TEST_LOGGER = Logger.getLogger(DatasetImportTestCase.class); + private static final Logger TEST_LOGGER = LogManager.getLogger(DatasetImportTestCase.class); @TestWhen(TestWhen.When.BVT) public static class DatasetImportTestCase extends Assert diff --git a/study/src/org/labkey/study/model/TreatmentManager.java b/study/src/org/labkey/study/model/TreatmentManager.java index 142a075544a..5c0ca238d12 100644 --- a/study/src/org/labkey/study/model/TreatmentManager.java +++ b/study/src/org/labkey/study/model/TreatmentManager.java @@ -48,7 +48,6 @@ import org.labkey.study.query.StudyQuerySchema; import java.math.BigDecimal; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; diff --git a/study/src/org/labkey/study/model/TreatmentProductImpl.java b/study/src/org/labkey/study/model/TreatmentProductImpl.java index 476b2355fd4..a8c5ddfc280 100644 --- a/study/src/org/labkey/study/model/TreatmentProductImpl.java +++ b/study/src/org/labkey/study/model/TreatmentProductImpl.java @@ -18,14 +18,9 @@ import org.jetbrains.annotations.NotNull; import org.json.JSONObject; import org.labkey.api.data.Container; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.data.TableSelector; -import org.labkey.api.query.FieldKey; import org.labkey.api.study.TreatmentProduct; import org.labkey.api.util.Pair; -import org.labkey.study.StudySchema; -import java.util.Collection; import java.util.HashMap; import java.util.Map; diff --git a/study/src/org/labkey/study/model/VisitTag.java b/study/src/org/labkey/study/model/VisitTag.java index e20e1043922..4025e85407e 100644 --- a/study/src/org/labkey/study/model/VisitTag.java +++ b/study/src/org/labkey/study/model/VisitTag.java @@ -18,7 +18,6 @@ import org.labkey.api.data.ObjectFactory; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/study/src/org/labkey/study/model/VisitTagMapEntry.java b/study/src/org/labkey/study/model/VisitTagMapEntry.java index 471a36e6d40..52ce5098309 100644 --- a/study/src/org/labkey/study/model/VisitTagMapEntry.java +++ b/study/src/org/labkey/study/model/VisitTagMapEntry.java @@ -19,7 +19,6 @@ import org.labkey.api.data.ObjectFactory; import java.sql.ResultSet; -import java.sql.SQLException; import java.util.ArrayList; import java.util.Map; diff --git a/study/src/org/labkey/study/pipeline/AbstractDatasetImportTaskFactory.java b/study/src/org/labkey/study/pipeline/AbstractDatasetImportTaskFactory.java index 44113755b3b..9e3a3ef401d 100644 --- a/study/src/org/labkey/study/pipeline/AbstractDatasetImportTaskFactory.java +++ b/study/src/org/labkey/study/pipeline/AbstractDatasetImportTaskFactory.java @@ -16,13 +16,13 @@ package org.labkey.study.pipeline; -import org.labkey.api.pipeline.AbstractTaskFactorySettings; import org.labkey.api.pipeline.AbstractTaskFactory; +import org.labkey.api.pipeline.AbstractTaskFactorySettings; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.util.FileType; -import java.util.List; import java.util.Collections; +import java.util.List; public abstract class AbstractDatasetImportTaskFactory> extends AbstractTaskFactory { diff --git a/study/src/org/labkey/study/pipeline/AbstractSpecimenTask.java b/study/src/org/labkey/study/pipeline/AbstractSpecimenTask.java index 5ca96307292..ce29ba0a17e 100644 --- a/study/src/org/labkey/study/pipeline/AbstractSpecimenTask.java +++ b/study/src/org/labkey/study/pipeline/AbstractSpecimenTask.java @@ -16,7 +16,7 @@ package org.labkey.study.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.admin.ImportException; diff --git a/study/src/org/labkey/study/pipeline/AbstractSpecimenTaskFactory.java b/study/src/org/labkey/study/pipeline/AbstractSpecimenTaskFactory.java index fb8fbd2346e..9ea6e648061 100644 --- a/study/src/org/labkey/study/pipeline/AbstractSpecimenTaskFactory.java +++ b/study/src/org/labkey/study/pipeline/AbstractSpecimenTaskFactory.java @@ -16,13 +16,13 @@ package org.labkey.study.pipeline; -import org.labkey.api.pipeline.AbstractTaskFactorySettings; import org.labkey.api.pipeline.AbstractTaskFactory; +import org.labkey.api.pipeline.AbstractTaskFactorySettings; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.util.FileType; -import java.util.List; import java.util.Collections; +import java.util.List; public abstract class AbstractSpecimenTaskFactory> extends AbstractTaskFactory { diff --git a/study/src/org/labkey/study/pipeline/DatasetBatch.java b/study/src/org/labkey/study/pipeline/DatasetBatch.java index 5ec201cceba..5776087a731 100644 --- a/study/src/org/labkey/study/pipeline/DatasetBatch.java +++ b/study/src/org/labkey/study/pipeline/DatasetBatch.java @@ -27,7 +27,6 @@ import java.io.File; import java.io.Serializable; -import java.sql.SQLException; /** * User: Matthew diff --git a/study/src/org/labkey/study/pipeline/DatasetFileReader.java b/study/src/org/labkey/study/pipeline/DatasetFileReader.java index 569550d170d..3210c30d222 100644 --- a/study/src/org/labkey/study/pipeline/DatasetFileReader.java +++ b/study/src/org/labkey/study/pipeline/DatasetFileReader.java @@ -30,7 +30,6 @@ import org.labkey.study.pipeline.AbstractDatasetImportTask.Action; import java.io.IOException; -import java.io.InputStream; import java.text.ParseException; import java.util.AbstractMap; import java.util.ArrayList; @@ -40,7 +39,6 @@ import java.util.IdentityHashMap; import java.util.List; import java.util.Map; -import java.util.Properties; import java.util.Set; import java.util.regex.Matcher; import java.util.regex.Pattern; diff --git a/study/src/org/labkey/study/pipeline/DatasetImportRunnable.java b/study/src/org/labkey/study/pipeline/DatasetImportRunnable.java index d9adaadc5c8..ad60b884739 100644 --- a/study/src/org/labkey/study/pipeline/DatasetImportRunnable.java +++ b/study/src/org/labkey/study/pipeline/DatasetImportRunnable.java @@ -17,13 +17,14 @@ package org.labkey.study.pipeline; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.DbSchema; import org.labkey.api.data.DbScope; import org.labkey.api.data.TableInfo; import org.labkey.api.pipeline.PipelineJob; +import org.labkey.api.qc.QCState; import org.labkey.api.qc.QCStateManager; import org.labkey.api.reader.ColumnDescriptor; import org.labkey.api.reader.DataLoader; @@ -37,7 +38,6 @@ import org.labkey.study.StudySchema; import org.labkey.study.importer.StudyImportContext; import org.labkey.study.model.DatasetDefinition; -import org.labkey.api.qc.QCState; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; diff --git a/study/src/org/labkey/study/pipeline/DatasetJobSupport.java b/study/src/org/labkey/study/pipeline/DatasetJobSupport.java index 51496d0d99c..ae228f4e1ee 100644 --- a/study/src/org/labkey/study/pipeline/DatasetJobSupport.java +++ b/study/src/org/labkey/study/pipeline/DatasetJobSupport.java @@ -18,8 +18,6 @@ import org.labkey.api.writer.VirtualFile; -import java.io.File; - /* * User: adam * Date: Sep 2, 2009 diff --git a/study/src/org/labkey/study/pipeline/ParticipantImportRunnable.java b/study/src/org/labkey/study/pipeline/ParticipantImportRunnable.java index afa782f6021..c5993e3a08a 100644 --- a/study/src/org/labkey/study/pipeline/ParticipantImportRunnable.java +++ b/study/src/org/labkey/study/pipeline/ParticipantImportRunnable.java @@ -16,7 +16,7 @@ package org.labkey.study.pipeline; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; diff --git a/study/src/org/labkey/study/pipeline/SpecimenArchive.java b/study/src/org/labkey/study/pipeline/SpecimenArchive.java index 3191185e24c..f585c8df285 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenArchive.java +++ b/study/src/org/labkey/study/pipeline/SpecimenArchive.java @@ -20,14 +20,14 @@ import org.labkey.api.study.SpecimenService; import org.labkey.api.study.SpecimenTransform; -import java.util.Date; -import java.util.List; +import java.io.File; +import java.io.IOException; import java.util.ArrayList; +import java.util.Date; import java.util.Enumeration; -import java.util.zip.ZipFile; +import java.util.List; import java.util.zip.ZipEntry; -import java.io.IOException; -import java.io.File; +import java.util.zip.ZipFile; /* * User: adam diff --git a/study/src/org/labkey/study/pipeline/SpecimenBatch.java b/study/src/org/labkey/study/pipeline/SpecimenBatch.java index a1a83fd4533..a1f5f8a44b4 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenBatch.java +++ b/study/src/org/labkey/study/pipeline/SpecimenBatch.java @@ -35,7 +35,6 @@ import java.io.File; import java.io.Serializable; -import java.sql.SQLException; /** * User: brittp diff --git a/study/src/org/labkey/study/pipeline/SpecimenJobSupport.java b/study/src/org/labkey/study/pipeline/SpecimenJobSupport.java index 15e6b63d030..abf5185eda8 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenJobSupport.java +++ b/study/src/org/labkey/study/pipeline/SpecimenJobSupport.java @@ -19,7 +19,6 @@ import org.labkey.api.admin.ImportException; import java.io.File; -import java.sql.SQLException; /* * User: adam diff --git a/study/src/org/labkey/study/pipeline/SpecimenReloadJob.java b/study/src/org/labkey/study/pipeline/SpecimenReloadJob.java index 6f1db5877b8..f064d516080 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenReloadJob.java +++ b/study/src/org/labkey/study/pipeline/SpecimenReloadJob.java @@ -20,14 +20,11 @@ import org.labkey.api.pipeline.TaskId; import org.labkey.api.pipeline.TaskPipeline; import org.labkey.api.study.SpecimenTransform; -import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.view.ViewBackgroundInfo; import java.io.File; -import java.io.IOException; import java.io.Serializable; -import java.sql.SQLException; /** * Created by klum on 5/24/2014. diff --git a/study/src/org/labkey/study/pipeline/SpecimenReloadJobSupport.java b/study/src/org/labkey/study/pipeline/SpecimenReloadJobSupport.java index 44a4ed9be30..595f9c08638 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenReloadJobSupport.java +++ b/study/src/org/labkey/study/pipeline/SpecimenReloadJobSupport.java @@ -1,22 +1,21 @@ -/* - * Copyright (c) 2014 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ +/* + * Copyright (c) 2014 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ package org.labkey.study.pipeline; import org.labkey.api.study.SpecimenTransform; -import org.labkey.api.util.FileType; import java.io.File; diff --git a/study/src/org/labkey/study/pipeline/SpecimenReloadTask.java b/study/src/org/labkey/study/pipeline/SpecimenReloadTask.java index 805afb3c931..b3f58597fa0 100644 --- a/study/src/org/labkey/study/pipeline/SpecimenReloadTask.java +++ b/study/src/org/labkey/study/pipeline/SpecimenReloadTask.java @@ -27,8 +27,6 @@ import org.labkey.api.study.SpecimenTransform; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; -import org.labkey.study.importer.StudyImportContext; -import org.labkey.study.importer.StudyJobSupport; import java.io.File; import java.util.Collections; diff --git a/study/src/org/labkey/study/pipeline/StandaloneDatasetTask.java b/study/src/org/labkey/study/pipeline/StandaloneDatasetTask.java index 110c6754ee6..af9a772bd5f 100644 --- a/study/src/org/labkey/study/pipeline/StandaloneDatasetTask.java +++ b/study/src/org/labkey/study/pipeline/StandaloneDatasetTask.java @@ -16,7 +16,6 @@ package org.labkey.study.pipeline; -import org.labkey.api.admin.ImportException; import org.labkey.api.admin.PipelineJobLoggerGetter; import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.writer.VirtualFile; diff --git a/study/src/org/labkey/study/query/BaseSpecimenPivotTable.java b/study/src/org/labkey/study/query/BaseSpecimenPivotTable.java index 9271eaf74fc..d7b322ba720 100644 --- a/study/src/org/labkey/study/query/BaseSpecimenPivotTable.java +++ b/study/src/org/labkey/study/query/BaseSpecimenPivotTable.java @@ -15,19 +15,17 @@ */ package org.labkey.study.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.SpringActionController; import org.labkey.api.collections.CaseInsensitiveHashSet; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.MutableColumnInfo; import org.labkey.api.data.PropertyManager; import org.labkey.api.data.PropertyManager.PropertyMap; -import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasedColumn; -import org.labkey.api.query.FieldKey; import org.labkey.api.query.FilteredTable; import org.labkey.api.study.StudyService; import org.labkey.study.SpecimenManager; @@ -175,7 +173,7 @@ public BaseSpecimenPivotTable(final TableInfo tinfo, final StudyQuerySchema sche { super(tinfo, schema); - Logger.getLogger(BaseSpecimenPivotTable.class).debug("creating specimen pivot\n" + + LogManager.getLogger(BaseSpecimenPivotTable.class).debug("creating specimen pivot\n" + "SCHEMA=" + schema.getName() + " " + schema.getClass().getSimpleName()+"@"+System.identityHashCode(schema) + "\n" + "TABLE=" + tinfo.getName() + " " + this.getClass().getSimpleName() + "@" + System.identityHashCode(this), new Throwable("stack trace") diff --git a/study/src/org/labkey/study/query/CohortQueryView.java b/study/src/org/labkey/study/query/CohortQueryView.java index cdd3f681834..78e9652f664 100644 --- a/study/src/org/labkey/study/query/CohortQueryView.java +++ b/study/src/org/labkey/study/query/CohortQueryView.java @@ -26,7 +26,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.permissions.AdminPermission; import org.labkey.api.util.Link.LinkBuilder; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; import org.labkey.api.view.ViewContext; diff --git a/study/src/org/labkey/study/query/CohortUpdateService.java b/study/src/org/labkey/study/query/CohortUpdateService.java index 531efe97854..1bb4ac92ba5 100644 --- a/study/src/org/labkey/study/query/CohortUpdateService.java +++ b/study/src/org/labkey/study/query/CohortUpdateService.java @@ -23,9 +23,7 @@ import org.labkey.api.data.TableSelector; import org.labkey.api.gwt.client.util.PropertyUtil; import org.labkey.api.query.AbstractQueryUpdateService; -import org.labkey.api.query.DuplicateKeyException; import org.labkey.api.query.InvalidKeyException; -import org.labkey.api.query.QueryUpdateServiceException; import org.labkey.api.query.ValidationException; import org.labkey.api.security.User; import org.labkey.api.study.Study; @@ -35,7 +33,6 @@ import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; -import java.sql.SQLException; import java.util.HashMap; import java.util.Map; diff --git a/study/src/org/labkey/study/query/DatasetQuerySettings.java b/study/src/org/labkey/study/query/DatasetQuerySettings.java index 303f304dd3d..32e588ccd38 100644 --- a/study/src/org/labkey/study/query/DatasetQuerySettings.java +++ b/study/src/org/labkey/study/query/DatasetQuerySettings.java @@ -17,7 +17,6 @@ import org.apache.commons.beanutils.PropertyUtils; import org.labkey.api.query.QuerySettings; -import org.labkey.study.model.QCStateSet; import org.springframework.beans.PropertyValues; /** diff --git a/study/src/org/labkey/study/query/DatasetQueryView.java b/study/src/org/labkey/study/query/DatasetQueryView.java index 6b9fd869e8e..511058baa21 100644 --- a/study/src/org/labkey/study/query/DatasetQueryView.java +++ b/study/src/org/labkey/study/query/DatasetQueryView.java @@ -17,12 +17,16 @@ package org.labkey.study.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.junit.Assert; import org.junit.Test; import org.labkey.api.action.BaseViewAction; import org.labkey.api.action.QueryViewAction; +import org.labkey.api.assay.AssayProvider; +import org.labkey.api.assay.AssayService; +import org.labkey.api.assay.AssayUrls; import org.labkey.api.data.ActionButton; import org.labkey.api.data.ButtonBar; import org.labkey.api.data.ColumnInfo; @@ -61,9 +65,6 @@ import org.labkey.api.security.permissions.UpdatePermission; import org.labkey.api.study.DataspaceContainerFilter; import org.labkey.api.study.TimepointType; -import org.labkey.api.assay.AssayProvider; -import org.labkey.api.assay.AssayService; -import org.labkey.api.assay.AssayUrls; import org.labkey.api.util.GUID; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; @@ -116,7 +117,7 @@ public class DatasetQueryView extends StudyQueryView private QCStateSet _qcStateSet; private ExpProtocol _protocol; private AssayProvider _provider; - protected static Logger _systemLog = Logger.getLogger(DatasetQueryView.class); + protected static Logger _systemLog = LogManager.getLogger(DatasetQueryView.class); public DatasetQueryView(UserSchema schema, DatasetQuerySettings settings, BindException errors) { diff --git a/study/src/org/labkey/study/query/DatasetTableImpl.java b/study/src/org/labkey/study/query/DatasetTableImpl.java index ae30eff5a10..319256d051c 100644 --- a/study/src/org/labkey/study/query/DatasetTableImpl.java +++ b/study/src/org/labkey/study/query/DatasetTableImpl.java @@ -17,7 +17,8 @@ package org.labkey.study.query; import org.apache.commons.lang3.StringUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.labkey.api.assay.AbstractAssayProvider; import org.labkey.api.assay.AssayProtocolSchema; @@ -108,7 +109,7 @@ public class DatasetTableImpl extends BaseStudyTable implements DatasetTable */ public static final String ASSAY_RESULT_LSID = "AssayResultLsid"; - private static final Logger LOG = Logger.getLogger(DatasetTableImpl.class); + private static final Logger LOG = LogManager.getLogger(DatasetTableImpl.class); private final @NotNull DatasetDefinition _dsd; diff --git a/study/src/org/labkey/study/query/DatasetUpdateService.java b/study/src/org/labkey/study/query/DatasetUpdateService.java index 890cde3aff1..7834ed0ddb3 100644 --- a/study/src/org/labkey/study/query/DatasetUpdateService.java +++ b/study/src/org/labkey/study/query/DatasetUpdateService.java @@ -25,6 +25,7 @@ import org.labkey.api.dataiterator.DataIteratorBuilder; import org.labkey.api.dataiterator.DataIteratorContext; import org.labkey.api.exp.property.Domain; +import org.labkey.api.qc.QCState; import org.labkey.api.query.AbstractQueryUpdateService; import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.InvalidKeyException; @@ -35,7 +36,6 @@ import org.labkey.api.study.Dataset; import org.labkey.study.StudyServiceImpl; import org.labkey.study.model.DatasetDefinition; -import org.labkey.api.qc.QCState; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; import org.labkey.study.visitmanager.PurgeParticipantsTask; diff --git a/study/src/org/labkey/study/query/ExtensibleObjectQueryView.java b/study/src/org/labkey/study/query/ExtensibleObjectQueryView.java index 5ab700d772b..7694a40fb71 100644 --- a/study/src/org/labkey/study/query/ExtensibleObjectQueryView.java +++ b/study/src/org/labkey/study/query/ExtensibleObjectQueryView.java @@ -16,7 +16,6 @@ package org.labkey.study.query; import org.labkey.api.data.ButtonBar; -import org.labkey.api.data.PanelButton; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; import org.labkey.api.security.User; diff --git a/study/src/org/labkey/study/query/SimpleSpecimenTable.java b/study/src/org/labkey/study/query/SimpleSpecimenTable.java index 9d0b09ddcee..c41e94ec779 100644 --- a/study/src/org/labkey/study/query/SimpleSpecimenTable.java +++ b/study/src/org/labkey/study/query/SimpleSpecimenTable.java @@ -16,9 +16,9 @@ package org.labkey.study.query; import org.labkey.api.data.ContainerFilter; +import org.labkey.api.study.StudyService; import org.labkey.api.study.TimepointType; import org.labkey.study.StudySchema; -import org.labkey.api.study.StudyService; public class SimpleSpecimenTable extends AbstractSpecimenTable { diff --git a/study/src/org/labkey/study/query/SpecimenCommentTable.java b/study/src/org/labkey/study/query/SpecimenCommentTable.java index 88dc5f7ddfc..9f43d23fc65 100644 --- a/study/src/org/labkey/study/query/SpecimenCommentTable.java +++ b/study/src/org/labkey/study/query/SpecimenCommentTable.java @@ -15,13 +15,13 @@ */ package org.labkey.study.query; +import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerForeignKey; -import org.labkey.api.query.FilteredTable; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasedColumn; +import org.labkey.api.query.FilteredTable; import org.labkey.api.query.LookupForeignKey; -import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.TableInfo; import org.labkey.study.StudySchema; /** diff --git a/study/src/org/labkey/study/query/SpecimenDetailTable.java b/study/src/org/labkey/study/query/SpecimenDetailTable.java index bd9c5605618..db126a9b1e7 100644 --- a/study/src/org/labkey/study/query/SpecimenDetailTable.java +++ b/study/src/org/labkey/study/query/SpecimenDetailTable.java @@ -17,12 +17,30 @@ package org.labkey.study.query; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.*; +import org.labkey.api.data.BaseColumnInfo; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.JdbcType; +import org.labkey.api.data.NullColumnInfo; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.TableInfo; import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.exp.property.Domain; import org.labkey.api.exp.property.DomainProperty; -import org.labkey.api.query.*; +import org.labkey.api.query.AliasedColumn; +import org.labkey.api.query.ExprColumn; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.LookupForeignKey; +import org.labkey.api.query.QueryService; +import org.labkey.api.query.QueryUpdateService; import org.labkey.api.security.UserPrincipal; +import org.labkey.api.security.permissions.EditSpecimenDataPermission; import org.labkey.api.security.permissions.Permission; import org.labkey.api.study.StudyService; import org.labkey.study.CohortForeignKey; @@ -30,11 +48,15 @@ import org.labkey.study.StudySchema; import org.labkey.study.importer.SpecimenImporter; import org.labkey.study.model.StudyManager; -import org.labkey.api.security.permissions.EditSpecimenDataPermission; import java.io.IOException; import java.io.Writer; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; public class SpecimenDetailTable extends AbstractSpecimenTable { diff --git a/study/src/org/labkey/study/query/SpecimenEventQueryView.java b/study/src/org/labkey/study/query/SpecimenEventQueryView.java index db7040b9e5f..f47436f27a6 100644 --- a/study/src/org/labkey/study/query/SpecimenEventQueryView.java +++ b/study/src/org/labkey/study/query/SpecimenEventQueryView.java @@ -22,9 +22,9 @@ import org.labkey.api.query.QuerySettings; import org.labkey.api.query.UserSchema; import org.labkey.api.view.ViewContext; -import org.labkey.study.model.Vial; import org.labkey.study.model.StudyImpl; import org.labkey.study.model.StudyManager; +import org.labkey.study.model.Vial; /** * User: brittp diff --git a/study/src/org/labkey/study/query/SpecimenPivotByDerivativeType.java b/study/src/org/labkey/study/query/SpecimenPivotByDerivativeType.java index 195a6028cab..9122bda3e45 100644 --- a/study/src/org/labkey/study/query/SpecimenPivotByDerivativeType.java +++ b/study/src/org/labkey/study/query/SpecimenPivotByDerivativeType.java @@ -20,6 +20,7 @@ import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; import org.labkey.api.study.StudyService; + import java.util.Map; /** diff --git a/study/src/org/labkey/study/query/SpecimenQueryView.java b/study/src/org/labkey/study/query/SpecimenQueryView.java index 7ae7c033d30..08aaaba2233 100644 --- a/study/src/org/labkey/study/query/SpecimenQueryView.java +++ b/study/src/org/labkey/study/query/SpecimenQueryView.java @@ -18,7 +18,25 @@ import org.apache.commons.lang3.StringUtils; import org.labkey.api.collections.ResultSetRowMapFactory; -import org.labkey.api.data.*; +import org.labkey.api.data.AbstractTableInfo; +import org.labkey.api.data.Aggregate; +import org.labkey.api.data.ColumnHeaderType; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.Container; +import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DataRegion; +import org.labkey.api.data.DetailsColumn; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.MenuButton; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.Results; +import org.labkey.api.data.RuntimeSQLException; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SimpleDisplayColumn; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.Table; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.DetailsURL; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryParam; @@ -27,32 +45,39 @@ import org.labkey.api.query.UserSchema; import org.labkey.api.reports.report.ReportUrls; import org.labkey.api.security.User; +import org.labkey.api.security.permissions.EditSpecimenDataPermission; import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; import org.labkey.api.view.DataView; import org.labkey.api.view.ViewContext; -import org.labkey.api.security.permissions.EditSpecimenDataPermission; -import org.labkey.api.study.StudyService; -import org.labkey.study.SpecimenManager; import org.labkey.study.CohortFilter; +import org.labkey.study.SpecimenManager; import org.labkey.study.StudySchema; +import org.labkey.study.controllers.specimen.SpecimenController; +import org.labkey.study.controllers.specimen.SpecimenUtils; +import org.labkey.study.model.ParticipantDataset; +import org.labkey.study.model.StudyImpl; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.Vial; import org.labkey.study.reports.StudyCrosstabReport; import org.labkey.study.security.permissions.RequestSpecimensPermission; import org.labkey.study.specimen.settings.DisplaySettings; import org.labkey.study.specimen.settings.RepositorySettings; -import org.labkey.study.controllers.specimen.SpecimenUtils; -import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.study.model.ParticipantDataset; -import org.labkey.study.model.Vial; -import org.labkey.study.model.StudyManager; -import org.labkey.study.model.StudyImpl; import java.io.IOException; import java.io.Writer; import java.sql.ResultSet; import java.sql.SQLException; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; import static java.util.Objects.requireNonNull; diff --git a/study/src/org/labkey/study/query/SpecimenReportQuery.java b/study/src/org/labkey/study/query/SpecimenReportQuery.java index 711cf87a0f7..e5beeb22607 100644 --- a/study/src/org/labkey/study/query/SpecimenReportQuery.java +++ b/study/src/org/labkey/study/query/SpecimenReportQuery.java @@ -21,10 +21,8 @@ import org.labkey.api.query.QueryDefinition; import org.labkey.api.query.QueryException; import org.labkey.api.query.QueryService; -import org.labkey.api.security.User; import org.labkey.api.study.Study; import org.labkey.api.study.StudyService; -import org.labkey.study.StudySchema; import java.util.ArrayList; import java.util.List; diff --git a/study/src/org/labkey/study/query/SpecimenRequestDisplayColumn.java b/study/src/org/labkey/study/query/SpecimenRequestDisplayColumn.java index 1105bc06228..ad80670ea46 100644 --- a/study/src/org/labkey/study/query/SpecimenRequestDisplayColumn.java +++ b/study/src/org/labkey/study/query/SpecimenRequestDisplayColumn.java @@ -15,20 +15,16 @@ */ package org.labkey.study.query; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.RenderContext; import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.data.TableInfo; -import org.labkey.api.data.RenderContext; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.util.PageFlowUtil; import org.labkey.study.controllers.specimen.SpecimenUtils; -import java.io.Writer; import java.io.IOException; -import java.util.Set;/* - * User: brittp - * Date: Dec 18, 2008 - * Time: 11:22:25 AM - */ +import java.io.Writer; +import java.util.Set; public class SpecimenRequestDisplayColumn extends SimpleDisplayColumn { diff --git a/study/src/org/labkey/study/query/SpecimenUpdateService.java b/study/src/org/labkey/study/query/SpecimenUpdateService.java index 8c00e056e0f..13d744eb494 100644 --- a/study/src/org/labkey/study/query/SpecimenUpdateService.java +++ b/study/src/org/labkey/study/query/SpecimenUpdateService.java @@ -16,7 +16,7 @@ package org.labkey.study.query; import org.apache.commons.beanutils.converters.LongConverter; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ColumnInfo; @@ -43,9 +43,9 @@ import org.labkey.study.SpecimenManager; import org.labkey.study.StudySchema; import org.labkey.study.importer.EditableSpecimenImporter; -import org.labkey.study.model.Vial; import org.labkey.study.model.SpecimenEvent; import org.labkey.study.model.StudyManager; +import org.labkey.study.model.Vial; import java.io.IOException; import java.sql.SQLException; @@ -78,7 +78,7 @@ public int importRows(User user, Container container, DataIteratorBuilder rows, if (null != configParameters) { Object o = configParameters.get(ConfigParameters.Logger); - if (o instanceof org.apache.log4j.Logger) + if (o instanceof Logger) _logger = (Logger)o; } DataIteratorContext context = getDataIteratorContext(errors, InsertOption.IMPORT, configParameters); diff --git a/study/src/org/labkey/study/query/SpecimenWrapTable.java b/study/src/org/labkey/study/query/SpecimenWrapTable.java index 8325e393e45..b212172faef 100644 --- a/study/src/org/labkey/study/query/SpecimenWrapTable.java +++ b/study/src/org/labkey/study/query/SpecimenWrapTable.java @@ -17,7 +17,9 @@ package org.labkey.study.query; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.*; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.SQLFragment; import org.labkey.api.exp.property.DomainProperty; import org.labkey.api.util.Path; import org.labkey.study.StudySchema; diff --git a/study/src/org/labkey/study/query/StudyDataTable.java b/study/src/org/labkey/study/query/StudyDataTable.java index 5e4de97458b..e014395bffa 100644 --- a/study/src/org/labkey/study/query/StudyDataTable.java +++ b/study/src/org/labkey/study/query/StudyDataTable.java @@ -16,11 +16,14 @@ package org.labkey.study.query; -import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; import org.labkey.api.exp.PropertyDescriptor; -import org.labkey.api.query.*; +import org.labkey.api.query.AliasedColumn; +import org.labkey.api.query.DetailsURL; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.LookupForeignKey; +import org.labkey.api.query.QueryForeignKey; import org.labkey.api.study.StudyService; import org.labkey.api.view.ActionURL; import org.labkey.study.StudySchema; diff --git a/study/src/org/labkey/study/query/StudyPropertiesQueryView.java b/study/src/org/labkey/study/query/StudyPropertiesQueryView.java index 1c14da3c238..b000a693b11 100644 --- a/study/src/org/labkey/study/query/StudyPropertiesQueryView.java +++ b/study/src/org/labkey/study/query/StudyPropertiesQueryView.java @@ -15,7 +15,10 @@ */ package org.labkey.study.query; -import org.labkey.api.data.*; +import org.labkey.api.data.ButtonBar; +import org.labkey.api.data.Container; +import org.labkey.api.data.RenderContext; +import org.labkey.api.data.SimpleDisplayColumn; import org.labkey.api.security.User; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ActionURL; diff --git a/study/src/org/labkey/study/query/StudyQuerySchema.java b/study/src/org/labkey/study/query/StudyQuerySchema.java index 5d9d81b9a3c..e87e94d849d 100644 --- a/study/src/org/labkey/study/query/StudyQuerySchema.java +++ b/study/src/org/labkey/study/query/StudyQuerySchema.java @@ -32,7 +32,6 @@ import org.labkey.api.module.ModuleLoader; import org.labkey.api.query.FilteredTable; import org.labkey.api.query.QueryDefinition; -import org.labkey.api.query.QueryException; import org.labkey.api.query.QuerySchema; import org.labkey.api.query.QuerySettings; import org.labkey.api.query.QueryView; @@ -46,7 +45,6 @@ import org.labkey.api.study.Study; import org.labkey.api.study.StudyService; import org.labkey.api.study.TimepointType; -import org.labkey.api.util.Pair; import org.labkey.api.view.ActionURL; import org.labkey.api.view.HttpView; import org.labkey.api.view.NavTree; @@ -88,7 +86,6 @@ import org.springframework.validation.BindException; import java.util.Arrays; -import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; diff --git a/study/src/org/labkey/study/query/VialRequestTable.java b/study/src/org/labkey/study/query/VialRequestTable.java index f1124609c15..75fdff72a6b 100644 --- a/study/src/org/labkey/study/query/VialRequestTable.java +++ b/study/src/org/labkey/study/query/VialRequestTable.java @@ -15,10 +15,15 @@ */ package org.labkey.study.query; -import org.labkey.api.query.FilteredTable; +import org.labkey.api.data.ColumnInfo; +import org.labkey.api.data.ContainerFilter; +import org.labkey.api.data.DataColumn; +import org.labkey.api.data.DisplayColumn; +import org.labkey.api.data.DisplayColumnFactory; +import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasedColumn; +import org.labkey.api.query.FilteredTable; import org.labkey.api.query.LookupForeignKey; -import org.labkey.api.data.*; import org.labkey.study.StudySchema; /** diff --git a/study/src/org/labkey/study/query/VisitMapTable.java b/study/src/org/labkey/study/query/VisitMapTable.java index 3e34ff78fc1..1c5372ad8a6 100644 --- a/study/src/org/labkey/study/query/VisitMapTable.java +++ b/study/src/org/labkey/study/query/VisitMapTable.java @@ -1,7 +1,6 @@ package org.labkey.study.query; import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.JdbcType; import org.labkey.api.data.TableInfo; import org.labkey.api.query.AliasedColumn; import org.labkey.api.query.FieldKey; diff --git a/study/src/org/labkey/study/query/VisitTagTable.java b/study/src/org/labkey/study/query/VisitTagTable.java index 2772b3ee529..ae20edd4333 100644 --- a/study/src/org/labkey/study/query/VisitTagTable.java +++ b/study/src/org/labkey/study/query/VisitTagTable.java @@ -15,9 +15,8 @@ */ package org.labkey.study.query; -import org.jetbrains.annotations.Nullable; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.ColumnInfo; +import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.ContainerForeignKey; import org.labkey.api.data.SQLFragment; diff --git a/study/src/org/labkey/study/query/VisualizationVisitTagTable.java b/study/src/org/labkey/study/query/VisualizationVisitTagTable.java index 35539103cb2..0852402ebe2 100644 --- a/study/src/org/labkey/study/query/VisualizationVisitTagTable.java +++ b/study/src/org/labkey/study/query/VisualizationVisitTagTable.java @@ -23,7 +23,6 @@ import org.labkey.api.query.ExprColumn; import org.labkey.api.security.User; import org.labkey.api.study.StudyService; -import org.labkey.study.StudySchema; import org.labkey.study.model.StudyImpl; public class VisualizationVisitTagTable extends VirtualTable diff --git a/study/src/org/labkey/study/query/studydesign/AbstractStudyDesignDomainKind.java b/study/src/org/labkey/study/query/studydesign/AbstractStudyDesignDomainKind.java index 3e6d080aa4a..fc66d9a6fba 100644 --- a/study/src/org/labkey/study/query/studydesign/AbstractStudyDesignDomainKind.java +++ b/study/src/org/labkey/study/query/studydesign/AbstractStudyDesignDomainKind.java @@ -15,8 +15,6 @@ */ package org.labkey.study.query.studydesign; -import org.json.JSONObject; -import org.labkey.api.action.SpringActionController; import org.labkey.api.data.Container; import org.labkey.api.data.DbSchemaType; import org.labkey.api.data.DbScope; diff --git a/study/src/org/labkey/study/reports/BaseStudyView.java b/study/src/org/labkey/study/reports/BaseStudyView.java index 05156e5c6f4..ab62821579b 100644 --- a/study/src/org/labkey/study/reports/BaseStudyView.java +++ b/study/src/org/labkey/study/reports/BaseStudyView.java @@ -16,16 +16,13 @@ package org.labkey.study.reports; -import org.labkey.study.model.StudyManager; -import org.labkey.study.StudySchema; -import org.labkey.study.model.DatasetDefinition; -import org.labkey.study.model.VisitImpl; -import org.labkey.api.data.DbSchema; -import org.labkey.api.data.TableInfo; -import org.labkey.api.view.HttpView; -import org.labkey.api.study.Study; import org.labkey.api.study.Dataset; +import org.labkey.api.study.Study; import org.labkey.api.study.Visit; +import org.labkey.api.view.HttpView; +import org.labkey.study.model.DatasetDefinition; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.VisitImpl; import java.util.HashMap; import java.util.List; diff --git a/study/src/org/labkey/study/reports/ReportManager.java b/study/src/org/labkey/study/reports/ReportManager.java index d4b9fe0f74f..051f8858220 100644 --- a/study/src/org/labkey/study/reports/ReportManager.java +++ b/study/src/org/labkey/study/reports/ReportManager.java @@ -15,7 +15,8 @@ */ package org.labkey.study.reports; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.BaseColumnInfo; @@ -72,7 +73,7 @@ public class ReportManager implements DatasetManager.DatasetListener public static final String ALL_DATASETS_KEY = StudySchema.getInstance().getSchemaName() + "/*"; private static final ReportManager instance = new ReportManager(); - private static final Logger _log = Logger.getLogger(ReportManager.class); + private static final Logger _log = LogManager.getLogger(ReportManager.class); public static ReportManager get() { diff --git a/study/src/org/labkey/study/reports/StudyRReport.java b/study/src/org/labkey/study/reports/StudyRReport.java index 52e14cd109b..ee79110ff08 100644 --- a/study/src/org/labkey/study/reports/StudyRReport.java +++ b/study/src/org/labkey/study/reports/StudyRReport.java @@ -22,12 +22,12 @@ import org.labkey.api.reports.report.ReportUrls; import org.labkey.api.reports.report.view.ReportQueryView; import org.labkey.api.study.Study; +import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; import org.labkey.api.view.HttpView; +import org.labkey.api.view.TabStripView; import org.labkey.api.view.VBox; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.ActionURL; -import org.labkey.api.view.TabStripView; -import org.labkey.api.util.PageFlowUtil; import org.labkey.study.controllers.BaseStudyController; import org.labkey.study.controllers.StudyController; import org.labkey.study.controllers.reports.ReportsController; diff --git a/study/src/org/labkey/study/requirements/DefaultRequirementProvider.java b/study/src/org/labkey/study/requirements/DefaultRequirementProvider.java index 81cd0c90e4d..27aa4d2340b 100644 --- a/study/src/org/labkey/study/requirements/DefaultRequirementProvider.java +++ b/study/src/org/labkey/study/requirements/DefaultRequirementProvider.java @@ -16,15 +16,27 @@ package org.labkey.study.requirements; -import org.labkey.api.data.*; +import org.labkey.api.data.Container; +import org.labkey.api.data.DbScope; +import org.labkey.api.data.PropertyManager; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.data.Sort; +import org.labkey.api.data.TableInfo; +import org.labkey.api.data.TableSelector; import org.labkey.api.query.FieldKey; -import org.labkey.api.security.*; +import org.labkey.api.security.User; import org.labkey.api.util.GUID; import org.labkey.study.StudySchema; -import java.util.*; import java.lang.reflect.Array; -import java.sql.SQLException; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; /** * User: brittp diff --git a/study/src/org/labkey/study/requirements/RequirementOwner.java b/study/src/org/labkey/study/requirements/RequirementOwner.java index 8a9f13f4e57..35b358c4a15 100644 --- a/study/src/org/labkey/study/requirements/RequirementOwner.java +++ b/study/src/org/labkey/study/requirements/RequirementOwner.java @@ -13,11 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ - + package org.labkey.study.requirements; import org.labkey.api.data.Container; -import org.labkey.api.security.User; /** * User: brittp diff --git a/study/src/org/labkey/study/requirements/RequirementProvider.java b/study/src/org/labkey/study/requirements/RequirementProvider.java index d0fb1564b71..e7267210bb3 100644 --- a/study/src/org/labkey/study/requirements/RequirementProvider.java +++ b/study/src/org/labkey/study/requirements/RequirementProvider.java @@ -16,8 +16,8 @@ package org.labkey.study.requirements; -import org.labkey.api.security.User; import org.labkey.api.data.Container; +import org.labkey.api.security.User; import java.util.Collection; import java.util.List; diff --git a/study/src/org/labkey/study/requirements/SpecimenRequestRequirementProvider.java b/study/src/org/labkey/study/requirements/SpecimenRequestRequirementProvider.java index 90d4f9d5b9d..6225c98ffe0 100644 --- a/study/src/org/labkey/study/requirements/SpecimenRequestRequirementProvider.java +++ b/study/src/org/labkey/study/requirements/SpecimenRequestRequirementProvider.java @@ -18,7 +18,9 @@ import org.labkey.api.data.TableInfo; import org.labkey.study.StudySchema; -import org.labkey.study.model.*; +import org.labkey.study.model.SpecimenRequest; +import org.labkey.study.model.SpecimenRequestActor; +import org.labkey.study.model.SpecimenRequestRequirement; import java.util.List; diff --git a/study/src/org/labkey/study/security/roles/SpecimenCoordinatorRole.java b/study/src/org/labkey/study/security/roles/SpecimenCoordinatorRole.java index 39d9d5d420f..394f743b199 100644 --- a/study/src/org/labkey/study/security/roles/SpecimenCoordinatorRole.java +++ b/study/src/org/labkey/study/security/roles/SpecimenCoordinatorRole.java @@ -19,7 +19,18 @@ import org.labkey.api.security.SecurityManager; import org.labkey.api.security.permissions.EditSharedViewPermission; import org.labkey.api.security.permissions.EditSpecimenDataPermission; -import org.labkey.study.security.permissions.*; +import org.labkey.study.security.permissions.LockSpecimensPermission; +import org.labkey.study.security.permissions.ManageDisplaySettingsPermission; +import org.labkey.study.security.permissions.ManageNewRequestFormPermission; +import org.labkey.study.security.permissions.ManageNotificationsPermission; +import org.labkey.study.security.permissions.ManageRequestRequirementsPermission; +import org.labkey.study.security.permissions.ManageRequestSettingsPermission; +import org.labkey.study.security.permissions.ManageRequestStatusesPermission; +import org.labkey.study.security.permissions.ManageRequestsPermission; +import org.labkey.study.security.permissions.ManageSpecimenActorsPermission; +import org.labkey.study.security.permissions.ManageStudyPermission; +import org.labkey.study.security.permissions.RequestSpecimensPermission; +import org.labkey.study.security.permissions.SetSpecimenCommentsPermission; /* * User: Dave diff --git a/study/src/org/labkey/study/specimen/notifications/ActorNotificationRecipientSet.java b/study/src/org/labkey/study/specimen/notifications/ActorNotificationRecipientSet.java index 4fcd4d853a3..af2bf2baecd 100644 --- a/study/src/org/labkey/study/specimen/notifications/ActorNotificationRecipientSet.java +++ b/study/src/org/labkey/study/specimen/notifications/ActorNotificationRecipientSet.java @@ -24,8 +24,8 @@ import org.labkey.api.view.HttpView; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.specimen.ShowGroupMembersAction; -import org.labkey.study.model.SpecimenRequestActor; import org.labkey.study.model.LocationImpl; +import org.labkey.study.model.SpecimenRequestActor; import org.labkey.study.model.StudyManager; /** diff --git a/study/src/org/labkey/study/specimen/notifications/NotificationRecipientSet.java b/study/src/org/labkey/study/specimen/notifications/NotificationRecipientSet.java index cbcc5a7628e..e232e6a2f19 100644 --- a/study/src/org/labkey/study/specimen/notifications/NotificationRecipientSet.java +++ b/study/src/org/labkey/study/specimen/notifications/NotificationRecipientSet.java @@ -16,8 +16,6 @@ package org.labkey.study.specimen.notifications; -import org.labkey.api.security.ValidEmail; - import javax.mail.Address; /** diff --git a/study/src/org/labkey/study/specimen/report/SpecimenReportExcelWriter.java b/study/src/org/labkey/study/specimen/report/SpecimenReportExcelWriter.java index ab8d3cf8ccb..8c376f6555a 100644 --- a/study/src/org/labkey/study/specimen/report/SpecimenReportExcelWriter.java +++ b/study/src/org/labkey/study/specimen/report/SpecimenReportExcelWriter.java @@ -17,16 +17,20 @@ import jxl.Workbook; import jxl.WorkbookSettings; +import jxl.write.Label; +import jxl.write.Number; +import jxl.write.WritableCell; +import jxl.write.WritableCellFormat; +import jxl.write.WritableFont; +import jxl.write.WritableSheet; +import jxl.write.WritableWorkbook; +import jxl.write.WriteException; import org.labkey.api.data.ExcelWriter; import org.labkey.api.util.ExceptionUtil; import org.labkey.study.model.VisitImpl; -import javax.servlet.http.HttpServletResponse; import javax.servlet.ServletOutputStream; - -import jxl.write.*; -import jxl.write.Number; - +import javax.servlet.http.HttpServletResponse; import java.io.IOException; import java.util.Collection; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/SpecimenTypeVisitReport.java b/study/src/org/labkey/study/specimen/report/SpecimenTypeVisitReport.java index d81f4f19463..594b3feafb8 100644 --- a/study/src/org/labkey/study/specimen/report/SpecimenTypeVisitReport.java +++ b/study/src/org/labkey/study/specimen/report/SpecimenTypeVisitReport.java @@ -26,7 +26,6 @@ import org.labkey.study.controllers.specimen.SpecimenController; import org.labkey.study.model.VisitImpl; -import java.text.DecimalFormat; import java.util.Collection; import java.util.Iterator; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/SpecimenVisitReport.java b/study/src/org/labkey/study/specimen/report/SpecimenVisitReport.java index 2483e5cd6cd..f2af7782962 100644 --- a/study/src/org/labkey/study/specimen/report/SpecimenVisitReport.java +++ b/study/src/org/labkey/study/specimen/report/SpecimenVisitReport.java @@ -15,25 +15,32 @@ */ package org.labkey.study.specimen.report; +import org.labkey.api.data.Container; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.query.CustomView; +import org.labkey.api.query.FieldKey; +import org.labkey.api.query.QueryDefinition; +import org.labkey.api.query.QueryService; +import org.labkey.api.security.User; import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; import org.labkey.api.util.PageFlowUtil; +import org.labkey.api.view.ActionURL; import org.labkey.api.view.NotFoundException; +import org.labkey.study.CohortFilter; +import org.labkey.study.SpecimenManager; import org.labkey.study.model.ParticipantGroup; import org.labkey.study.model.ParticipantGroupManager; -import org.labkey.study.model.VisitImpl; import org.labkey.study.model.StudyManager; -import org.labkey.study.SpecimenManager; -import org.labkey.study.CohortFilter; -import org.labkey.study.query.StudyQuerySchema; +import org.labkey.study.model.VisitImpl; import org.labkey.study.query.SpecimenQueryView; -import org.labkey.api.view.ActionURL; -import org.labkey.api.data.Container; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.query.*; -import org.labkey.api.security.User; -import org.labkey.api.study.StudyService; +import org.labkey.study.query.StudyQuerySchema; -import java.util.*; +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReport.java b/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReport.java index 7e6219e38bf..7965fc1e63f 100644 --- a/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReport.java +++ b/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReport.java @@ -15,9 +15,9 @@ */ package org.labkey.study.specimen.report.participant; +import org.labkey.api.data.SimpleFilter; import org.labkey.study.model.VisitImpl; import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.api.data.SimpleFilter; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReportFactory.java b/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReportFactory.java index 8b869311cb3..0ccd042b402 100644 --- a/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/participant/ParticipantSiteReportFactory.java @@ -15,7 +15,6 @@ */ package org.labkey.study.specimen.report.participant; -import org.labkey.api.data.Container; import org.labkey.api.data.SimpleFilter; import org.labkey.api.query.FieldKey; import org.labkey.api.study.StudyService; diff --git a/study/src/org/labkey/study/specimen/report/participant/ParticipantSummaryReportFactory.java b/study/src/org/labkey/study/specimen/report/participant/ParticipantSummaryReportFactory.java index 5a7cdc04a08..1d615f90a34 100644 --- a/study/src/org/labkey/study/specimen/report/participant/ParticipantSummaryReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/participant/ParticipantSummaryReportFactory.java @@ -15,16 +15,16 @@ */ package org.labkey.study.specimen.report.participant; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.study.model.VisitImpl; -import org.labkey.study.SpecimenManager; import org.labkey.api.data.SimpleFilter; import org.labkey.api.study.StudyService; +import org.labkey.study.SpecimenManager; +import org.labkey.study.controllers.specimen.SpecimenController; +import org.labkey.study.model.VisitImpl; +import org.labkey.study.specimen.report.SpecimenVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import java.util.List; import java.util.Collections; +import java.util.List; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/participant/ParticipantTypeReportFactory.java b/study/src/org/labkey/study/specimen/report/participant/ParticipantTypeReportFactory.java index 8180e9783b4..36e7a9e7081 100644 --- a/study/src/org/labkey/study/specimen/report/participant/ParticipantTypeReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/participant/ParticipantTypeReportFactory.java @@ -16,23 +16,22 @@ package org.labkey.study.specimen.report.participant; import org.labkey.api.data.CompareType; -import org.labkey.api.data.Container; +import org.labkey.api.data.SimpleFilter; import org.labkey.api.study.StudyService; import org.labkey.api.util.HtmlString; +import org.labkey.api.util.Pair; import org.labkey.api.util.element.Option; import org.labkey.api.util.element.Select; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.study.model.SpecimenTypeSummary; -import org.labkey.study.model.VisitImpl; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.util.Pair; +import org.labkey.study.model.SpecimenTypeSummary; +import org.labkey.study.model.VisitImpl; +import org.labkey.study.specimen.report.SpecimenVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import java.util.List; import java.util.ArrayList; import java.util.Collections; +import java.util.List; import static org.labkey.api.util.HtmlString.unsafe; diff --git a/study/src/org/labkey/study/specimen/report/participant/ParticipantVisitReport.java b/study/src/org/labkey/study/specimen/report/participant/ParticipantVisitReport.java index 8a696e3dc5c..0357887d837 100644 --- a/study/src/org/labkey/study/specimen/report/participant/ParticipantVisitReport.java +++ b/study/src/org/labkey/study/specimen/report/participant/ParticipantVisitReport.java @@ -15,22 +15,24 @@ */ package org.labkey.study.specimen.report.participant; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.study.StudyService; import org.labkey.api.util.DemoMode; -import org.labkey.study.SpecimenManager.SummaryByVisitParticipant; -import org.labkey.study.model.VisitImpl; -import org.labkey.study.model.StudyManager; -import org.labkey.study.SpecimenManager; +import org.labkey.api.view.ActionURL; import org.labkey.study.CohortFilter; +import org.labkey.study.SpecimenManager; +import org.labkey.study.SpecimenManager.SummaryByVisitParticipant; import org.labkey.study.controllers.specimen.SpecimenController; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.VisitImpl; import org.labkey.study.specimen.report.SpecimenReportTitle; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.view.ActionURL; -import org.labkey.api.study.StudyService; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import java.util.*; -import java.sql.SQLException; +import java.util.Collection; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/request/BaseRequestReportFactory.java b/study/src/org/labkey/study/specimen/report/request/BaseRequestReportFactory.java index 17541e15676..fdfc57437cb 100644 --- a/study/src/org/labkey/study/specimen/report/request/BaseRequestReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/request/BaseRequestReportFactory.java @@ -15,12 +15,11 @@ */ package org.labkey.study.specimen.report.request; -import org.apache.xpath.operations.Bool; import org.labkey.api.util.HtmlString; +import org.labkey.api.util.Pair; import org.labkey.api.util.element.Option; import org.labkey.api.util.element.Select; import org.labkey.study.specimen.report.specimentype.TypeReportFactory; -import org.labkey.api.util.Pair; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentLocationReport.java b/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentLocationReport.java index 63554c734ed..cac5044a8c7 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentLocationReport.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentLocationReport.java @@ -16,11 +16,11 @@ package org.labkey.study.specimen.report.request; import org.labkey.api.data.SimpleFilter; +import org.labkey.study.SpecimenManager; import org.labkey.study.model.VisitImpl; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.study.specimen.report.SpecimenTypeVisitReport; import org.labkey.study.query.SpecimenQueryView; -import org.labkey.study.SpecimenManager; +import org.labkey.study.specimen.report.SpecimenTypeVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentSiteReportFactory.java b/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentSiteReportFactory.java index 5adaa1edfb1..daae3f0695f 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentSiteReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestEnrollmentSiteReportFactory.java @@ -15,7 +15,6 @@ */ package org.labkey.study.specimen.report.request; -import org.labkey.api.data.Container; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SimpleFilter; import org.labkey.api.query.FieldKey; diff --git a/study/src/org/labkey/study/specimen/report/request/RequestLocationReport.java b/study/src/org/labkey/study/specimen/report/request/RequestLocationReport.java index 0e2025fa4c4..28557470b65 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestLocationReport.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestLocationReport.java @@ -16,11 +16,11 @@ package org.labkey.study.specimen.report.request; import org.labkey.api.data.SimpleFilter; +import org.labkey.study.SpecimenManager; import org.labkey.study.model.VisitImpl; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.study.specimen.report.SpecimenTypeVisitReport; import org.labkey.study.query.SpecimenQueryView; -import org.labkey.study.SpecimenManager; +import org.labkey.study.specimen.report.SpecimenTypeVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/request/RequestLocationReportFactory.java b/study/src/org/labkey/study/specimen/report/request/RequestLocationReportFactory.java index a0e9cb1e397..1518c739496 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestLocationReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestLocationReportFactory.java @@ -15,11 +15,9 @@ */ package org.labkey.study.specimen.report.request; -import org.labkey.api.data.Container; import org.labkey.api.data.SimpleFilter; import org.labkey.api.study.Location; import org.labkey.api.util.HtmlString; -import org.labkey.api.util.PageFlowUtil; import org.labkey.api.util.Pair; import org.labkey.api.util.element.Option; import org.labkey.api.util.element.Select; diff --git a/study/src/org/labkey/study/specimen/report/request/RequestParticipantReport.java b/study/src/org/labkey/study/specimen/report/request/RequestParticipantReport.java index 2cbd57cb2b8..cf42dafbd53 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestParticipantReport.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestParticipantReport.java @@ -15,20 +15,19 @@ */ package org.labkey.study.specimen.report.request; +import org.labkey.api.data.SimpleFilter; +import org.labkey.api.view.ActionURL; import org.labkey.study.SpecimenManager; import org.labkey.study.SpecimenManager.RequestSummaryByVisitType; import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.study.query.SpecimenQueryView; import org.labkey.study.model.VisitImpl; +import org.labkey.study.query.SpecimenQueryView; import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.view.ActionURL; import java.util.Collection; import java.util.List; import java.util.Map; import java.util.TreeMap; -import java.sql.SQLException; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/request/RequestParticipantReportFactory.java b/study/src/org/labkey/study/specimen/report/request/RequestParticipantReportFactory.java index 6b89bc5b9c9..701048c9c24 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestParticipantReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestParticipantReportFactory.java @@ -15,24 +15,27 @@ */ package org.labkey.study.specimen.report.request; -import org.labkey.api.data.Container; +import org.labkey.api.data.SimpleFilter; import org.labkey.api.query.FieldKey; +import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; +import org.labkey.api.study.Visit; import org.labkey.api.util.DemoMode; import org.labkey.api.util.HtmlString; -import org.labkey.study.model.Participant; -import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.study.controllers.specimen.SpecimenController; +import org.labkey.api.util.Pair; import org.labkey.study.SpecimenManager; -import org.labkey.study.model.StudyManager; +import org.labkey.study.controllers.specimen.SpecimenController; import org.labkey.study.model.CohortImpl; +import org.labkey.study.model.Participant; +import org.labkey.study.model.StudyManager; import org.labkey.study.model.VisitImpl; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.study.Study; -import org.labkey.api.study.Visit; -import org.labkey.api.study.StudyService; -import org.labkey.api.util.Pair; +import org.labkey.study.specimen.report.SpecimenVisitReport; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/request/RequestReport.java b/study/src/org/labkey/study/specimen/report/request/RequestReport.java index 4e115b30215..a6becd935b1 100644 --- a/study/src/org/labkey/study/specimen/report/request/RequestReport.java +++ b/study/src/org/labkey/study/specimen/report/request/RequestReport.java @@ -16,11 +16,11 @@ package org.labkey.study.specimen.report.request; import org.labkey.api.data.SimpleFilter; +import org.labkey.study.SpecimenManager; import org.labkey.study.model.VisitImpl; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import org.labkey.study.specimen.report.SpecimenTypeVisitReport; import org.labkey.study.query.SpecimenQueryView; -import org.labkey.study.SpecimenManager; +import org.labkey.study.specimen.report.SpecimenTypeVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; import java.util.List; diff --git a/study/src/org/labkey/study/specimen/report/specimentype/TypeParticipantReportFactory.java b/study/src/org/labkey/study/specimen/report/specimentype/TypeParticipantReportFactory.java index 6a15f7f36ae..4ddd8b57dfa 100644 --- a/study/src/org/labkey/study/specimen/report/specimentype/TypeParticipantReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/specimentype/TypeParticipantReportFactory.java @@ -15,22 +15,28 @@ */ package org.labkey.study.specimen.report.specimentype; -import org.labkey.api.data.Container; +import org.labkey.api.data.SimpleFilter; import org.labkey.api.query.FieldKey; +import org.labkey.api.study.Study; +import org.labkey.api.study.StudyService; +import org.labkey.api.study.Visit; import org.labkey.api.util.DemoMode; import org.labkey.api.util.HtmlString; -import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.study.specimen.report.SpecimenTypeVisitReport; -import org.labkey.study.model.*; +import org.labkey.api.util.Pair; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.api.data.SimpleFilter; -import org.labkey.api.study.Study; -import org.labkey.api.study.Visit; -import org.labkey.api.study.StudyService; -import org.labkey.api.util.Pair; +import org.labkey.study.model.CohortImpl; +import org.labkey.study.model.Participant; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.VisitImpl; +import org.labkey.study.specimen.report.SpecimenTypeVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReport; -import java.util.*; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/report/specimentype/TypeReportFactory.java b/study/src/org/labkey/study/specimen/report/specimentype/TypeReportFactory.java index 70f42001516..9a826b8e029 100644 --- a/study/src/org/labkey/study/specimen/report/specimentype/TypeReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/specimentype/TypeReportFactory.java @@ -17,14 +17,14 @@ import org.labkey.api.study.SpecimenService; import org.labkey.api.util.HtmlString; +import org.labkey.api.util.Pair; import org.labkey.api.util.element.Option; import org.labkey.api.util.element.Select; -import org.labkey.study.specimen.report.SpecimenVisitReportParameters; import org.labkey.study.SpecimenManager; -import org.labkey.api.util.Pair; +import org.labkey.study.specimen.report.SpecimenVisitReportParameters; -import java.util.List; import java.util.ArrayList; +import java.util.List; import static org.labkey.api.util.HtmlString.unsafe; diff --git a/study/src/org/labkey/study/specimen/report/specimentype/TypeSummaryReportFactory.java b/study/src/org/labkey/study/specimen/report/specimentype/TypeSummaryReportFactory.java index 7174b14d671..8fa72b66aa0 100644 --- a/study/src/org/labkey/study/specimen/report/specimentype/TypeSummaryReportFactory.java +++ b/study/src/org/labkey/study/specimen/report/specimentype/TypeSummaryReportFactory.java @@ -15,15 +15,15 @@ */ package org.labkey.study.specimen.report.specimentype; -import org.labkey.study.specimen.report.SpecimenVisitReport; -import org.labkey.study.specimen.report.SpecimenTypeVisitReport; -import org.labkey.study.model.VisitImpl; +import org.labkey.api.data.SimpleFilter; import org.labkey.study.SpecimenManager; import org.labkey.study.controllers.specimen.SpecimenController; -import org.labkey.api.data.SimpleFilter; +import org.labkey.study.model.VisitImpl; +import org.labkey.study.specimen.report.SpecimenTypeVisitReport; +import org.labkey.study.specimen.report.SpecimenVisitReport; -import java.util.List; import java.util.Collections; +import java.util.List; /** * User: brittp diff --git a/study/src/org/labkey/study/specimen/settings/RepositorySettings.java b/study/src/org/labkey/study/specimen/settings/RepositorySettings.java index 5862cbfbb06..cac62991eb5 100644 --- a/study/src/org/labkey/study/specimen/settings/RepositorySettings.java +++ b/study/src/org/labkey/study/specimen/settings/RepositorySettings.java @@ -15,10 +15,10 @@ */ package org.labkey.study.specimen.settings; +import org.labkey.api.data.Container; import org.labkey.api.study.Study; import org.labkey.api.study.StudyService; import org.labkey.study.model.StudyManager; -import org.labkey.api.data.Container; import java.util.ArrayList; import java.util.HashMap; diff --git a/study/src/org/labkey/study/view/BaseStudyPage.java b/study/src/org/labkey/study/view/BaseStudyPage.java index 55d2934ec0f..4a20403c6ae 100644 --- a/study/src/org/labkey/study/view/BaseStudyPage.java +++ b/study/src/org/labkey/study/view/BaseStudyPage.java @@ -16,12 +16,20 @@ package org.labkey.study.view; -import org.labkey.api.wiki.WikiRendererType; -import org.labkey.study.model.*; -import org.labkey.api.jsp.JspBase; import org.labkey.api.data.Container; +import org.labkey.api.jsp.JspBase; import org.labkey.api.security.User; -import org.labkey.api.study.*; +import org.labkey.api.study.Visit; +import org.labkey.api.wiki.WikiRendererType; +import org.labkey.study.model.AssaySpecimenConfigImpl; +import org.labkey.study.model.CohortImpl; +import org.labkey.study.model.DatasetDefinition; +import org.labkey.study.model.LocationImpl; +import org.labkey.study.model.ProductImpl; +import org.labkey.study.model.StudyImpl; +import org.labkey.study.model.StudyManager; +import org.labkey.study.model.TreatmentImpl; +import org.labkey.study.model.VisitImpl; import java.util.List; diff --git a/study/src/org/labkey/study/view/DatasetsWebPartView.java b/study/src/org/labkey/study/view/DatasetsWebPartView.java index 787654a3d24..3fc4c17cdb0 100644 --- a/study/src/org/labkey/study/view/DatasetsWebPartView.java +++ b/study/src/org/labkey/study/view/DatasetsWebPartView.java @@ -18,8 +18,6 @@ import org.labkey.api.view.JspView; -import javax.servlet.ServletException; - /** * User: Mark Igra * Date: Aug 8, 2006 diff --git a/study/src/org/labkey/study/view/StudyListWebPartFactory.java b/study/src/org/labkey/study/view/StudyListWebPartFactory.java index 587372c7dcc..52c49fcb762 100644 --- a/study/src/org/labkey/study/view/StudyListWebPartFactory.java +++ b/study/src/org/labkey/study/view/StudyListWebPartFactory.java @@ -16,14 +16,11 @@ package org.labkey.study.view; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.Container; import org.labkey.api.view.AlwaysAvailableWebPartFactory; -import org.labkey.api.view.BaseWebPartFactory; import org.labkey.api.view.HttpView; import org.labkey.api.view.JspView; import org.labkey.api.view.Portal; import org.labkey.api.view.ViewContext; -import org.labkey.api.view.WebPartFactory; import org.labkey.api.view.WebPartView; /** diff --git a/study/src/org/labkey/study/view/VaccineStudyWebPart.java b/study/src/org/labkey/study/view/VaccineStudyWebPart.java index cebff9044dd..38a2ac99e68 100644 --- a/study/src/org/labkey/study/view/VaccineStudyWebPart.java +++ b/study/src/org/labkey/study/view/VaccineStudyWebPart.java @@ -15,16 +15,7 @@ */ package org.labkey.study.view; -import org.labkey.api.data.RuntimeSQLException; -import org.labkey.api.study.Study; -import org.labkey.api.view.HttpView; import org.labkey.api.view.JspView; -import org.labkey.study.designer.StudyDesignInfo; -import org.labkey.study.designer.StudyDesignManager; -import org.labkey.study.model.StudyManager; - -import java.awt.*; -import java.sql.SQLException; /** * User: markigra diff --git a/study/src/org/labkey/study/view/bulkImportDataTypes.jsp b/study/src/org/labkey/study/view/bulkImportDataTypes.jsp index 34d2f33bc97..ddedcd2c934 100644 --- a/study/src/org/labkey/study/view/bulkImportDataTypes.jsp +++ b/study/src/org/labkey/study/view/bulkImportDataTypes.jsp @@ -17,8 +17,8 @@ %> <%@ page import="org.labkey.api.view.HttpView"%> <%@ page import="org.labkey.study.controllers.BaseStudyController.StudyJspView"%> -<%@ page import="org.labkey.study.controllers.StudyController.BulkImportTypesForm"%> -<%@ page import="org.labkey.study.controllers.StudyController" %> +<%@ page import="org.labkey.study.controllers.StudyController"%> +<%@ page import="org.labkey.study.controllers.StudyController.BulkImportTypesForm" %> <%@ page extends="org.labkey.study.view.BaseStudyPage" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <% diff --git a/study/src/org/labkey/study/view/bulkVisitDelete.jsp b/study/src/org/labkey/study/view/bulkVisitDelete.jsp index 1ac81a5e107..f180181a3bd 100644 --- a/study/src/org/labkey/study/view/bulkVisitDelete.jsp +++ b/study/src/org/labkey/study/view/bulkVisitDelete.jsp @@ -17,24 +17,24 @@ %> <%@ page import="org.labkey.api.study.TimepointType"%> +<%@ page import="org.labkey.api.study.Visit" %> +<%@ page import="org.labkey.api.util.Formats" %> <%@ page import="org.labkey.api.view.ActionURL" %> <%@ page import="org.labkey.api.view.HttpView" %> <%@ page import="org.labkey.api.view.JspView" %> +<%@ page import="org.labkey.api.view.template.ClientDependencies" %> +<%@ page import="org.labkey.study.SpecimenManager" %> <%@ page import="org.labkey.study.controllers.StudyController" %> <%@ page import="org.labkey.study.controllers.StudyController.DeleteVisitsForm" %> <%@ page import="org.labkey.study.model.StudyImpl" %> <%@ page import="org.labkey.study.model.StudyManager" %> -<%@ page import="org.labkey.api.view.template.ClientDependencies" %> <%@ page import="org.labkey.study.model.VisitImpl" %> -<%@ page import="org.labkey.api.study.Visit" %> -<%@ page import="java.util.List" %> -<%@ page import="org.labkey.study.SpecimenManager" %> -<%@ page import="org.labkey.study.visitmanager.VisitManager" %> <%@ page import="org.labkey.study.model.VisitMapKey" %> +<%@ page import="org.labkey.study.visitmanager.VisitManager" %> <%@ page import="java.util.Collections" %> -<%@ page import="java.util.Map" %> <%@ page import="java.util.HashMap" %> -<%@ page import="org.labkey.api.util.Formats" %> +<%@ page import="java.util.List" %> +<%@ page import="java.util.Map" %> <%@ page extends="org.labkey.study.view.BaseStudyPage" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%! diff --git a/study/src/org/labkey/study/view/confirmDeleteStudy.jsp b/study/src/org/labkey/study/view/confirmDeleteStudy.jsp index 17f1ac5da12..ffc0993ce3a 100644 --- a/study/src/org/labkey/study/view/confirmDeleteStudy.jsp +++ b/study/src/org/labkey/study/view/confirmDeleteStudy.jsp @@ -16,8 +16,8 @@ */ %> <%@ page import="org.labkey.api.module.ModuleLoader" %> -<%@ page import="java.util.Collection" %> <%@ page import="org.labkey.study.controllers.StudyController" %> +<%@ page import="java.util.Collection" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.study.view.BaseStudyPage" %>