Item 7490: Upgrade to Log4J 2 - Part 1

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();

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;

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<SendMessageAction.MessageForm>
 {
-    private static final Logger _log = Logger.getLogger(SendMessageAction.class);
+    private static final Logger _log = LogManager.getLogger(SendMessageAction.class);
     private Map<String, Set<String>> _recipientMap = new HashMap<>();
 
     enum Props

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" %>
 

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.

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
         {

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

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;
 
 /**

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

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

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

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;

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

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
 {

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;
 

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

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;

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

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

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;

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

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

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

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

api/schemas/datStatExport.xsd

@@ -1,6 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
-            xmlns:rc="http://labkey.org/study/xml/datStatExport"
             targetNamespace="http://labkey.org/study/xml/datStatExport"
             elementFormDefault="qualified" attributeFormDefault="unqualified">
 

api/schemas/domainTemplate.xsd

@@ -1,12 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <xs:schema
-    xmlns:xs="http://www.w3.org/2001/XMLSchema"
-    xmlns:dat="http://labkey.org/data/xml"
-    xmlns:t="http://labkey.org/data/xml/domainTemplate"
-    xmlns="http://labkey.org/data/xml/domainTemplate"
-    targetNamespace="http://labkey.org/data/xml/domainTemplate"
-    elementFormDefault="qualified"
-    attributeFormDefault="unqualified">
+        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">
 
     <xs:import namespace="http://labkey.org/data/xml" schemaLocation="tableInfo.xsd"/>
 

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">
   <xsd:import namespace="http://labkey.org/data/xml/webpart" schemaLocation="webpart.xsd"/>
   <xsd:element name="folderType" type="ft:folderType" />