Item 7490: upgrade log4j

src/org/labkey/targetedms/SkylineAuditLogManager.java

@@ -15,7 +15,8 @@
  */
 package org.labkey.targetedms;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.AfterClass;
 import org.junit.Assert;
 import org.junit.BeforeClass;
@@ -80,7 +81,7 @@ private class AuditLogImportContext{
     }
 
     public SkylineAuditLogManager(@NotNull Container pContainer, @NotNull User pUser) throws AuditLogException{
-        _logger = Logger.getLogger(this.getClass());
+        _logger = LogManager.getLogger(this.getClass());
         _securityMgr = new SkylineAuditLogSecurityManager(pContainer, pUser);
     }
 
@@ -448,7 +449,7 @@ public static class TestCase extends Assert
         @BeforeClass
         public static void InitTest(){
 
-            _logger = Logger.getLogger(SkylineAuditLogManager.TestCase.class.getPackageName() + ".test");
+            _logger = LogManager.getLogger(SkylineAuditLogManager.TestCase.class.getPackageName() + ".test");
             UnitTestUtil.cleanupDatabase(_docGUID);
             _user = TestContext.get().getUser();
             _container = ContainerManager.ensureContainer(JunitUtil.getTestContainer(), FOLDER_NAME);

src/org/labkey/targetedms/SkylineBinaryDataHandler.java

@@ -15,7 +15,7 @@
  */
 package org.labkey.targetedms;
 
-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;

src/org/labkey/targetedms/SkylineDocImporter.java

@@ -19,7 +19,8 @@
 import com.fasterxml.jackson.annotation.JsonCreator;
 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.labkey.api.collections.CaseInsensitiveHashMap;
@@ -128,7 +129,7 @@ public class SkylineDocImporter
     private ProgressMonitor _progressMonitor;
 
     // Use system logger for bugs & system problems, and in cases where we don't have a pipeline logger
-    protected static final Logger _systemLog = Logger.getLogger(SkylineDocImporter.class);
+    protected static final Logger _systemLog = LogManager.getLogger(SkylineDocImporter.class);
     protected final XarContext _context;
     private int blankLabelIndex;
 

src/org/labkey/targetedms/SkylineFileUtils.java

@@ -15,18 +15,17 @@
  */
 package org.labkey.targetedms;
 
-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;
 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.util.FileUtil;
 
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.List;
 
 /**
  * User: vsharma
@@ -43,7 +42,7 @@ public class SkylineFileUtils
     public static final String EXT_BLIB = "blib";
     public static final String EXT_SKY_LOG = "skyl";
 
-    private static final Logger LOG = Logger.getLogger(SkylineFileUtils.class);
+    private static final Logger LOG = LogManager.getLogger(SkylineFileUtils.class);
 
     public static String getBaseName(String fileName)
     {

src/org/labkey/targetedms/SkylinePort/Irt/IrtRegressionCalculator.java

@@ -1,12 +1,11 @@
 package org.labkey.targetedms.SkylinePort.Irt;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.targetedms.IrtPeptide;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedHashMap;
-import java.util.List;
 
 /**
  * User: tgaluhn

src/org/labkey/targetedms/TargetedMSController.java

@@ -20,45 +20,55 @@
 import com.keypoint.PngEncoder;
 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.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartUtilities;
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.plot.PlotOrientation;
-import org.labkey.api.action.*;
-import org.labkey.api.analytics.AnalyticsService;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.PipelineValidationException;
-import org.labkey.api.query.QueryDefinition;
-import org.labkey.api.security.permissions.ApplicationAdminPermission;
-import org.labkey.api.settings.AppProps;
-import org.labkey.api.targetedms.TargetedMSService;
-import org.labkey.api.targetedms.TargetedMSUrls;
-import org.labkey.api.targetedms.model.SampleFileInfo;
-import org.labkey.api.util.Button;
-import org.labkey.api.util.DOM;
-import org.labkey.api.util.DateUtil;
-import org.labkey.api.util.StringUtilsLabKey;
-import org.labkey.api.util.UnexpectedException;
-import org.labkey.api.view.*;
-import org.labkey.api.view.PopupMenu;
-import org.labkey.api.view.template.ClientDependency;
-import org.labkey.targetedms.model.GuideSet;
-import org.labkey.targetedms.model.GuideSetKey;
-import org.labkey.targetedms.model.GuideSetStats;
-import org.labkey.targetedms.model.QCPlotFragment;
-import org.labkey.targetedms.model.RawMetricDataSet;
-import org.labkey.targetedms.outliers.OutlierGenerator;
 import org.jfree.chart.title.TextTitle;
 import org.jfree.data.category.DefaultCategoryDataset;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.junit.Assert;
 import org.junit.Test;
-import org.labkey.api.data.*;
+import org.labkey.api.action.ApiResponse;
+import org.labkey.api.action.ApiSimpleResponse;
+import org.labkey.api.action.ApiUsageException;
+import org.labkey.api.action.CustomApiForm;
+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.SimpleErrorView;
+import org.labkey.api.action.SimpleViewAction;
+import org.labkey.api.action.SpringActionController;
+import org.labkey.api.analytics.AnalyticsService;
+import org.labkey.api.data.ButtonBar;
+import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerFilter;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.DataRegion;
+import org.labkey.api.data.DbScope;
+import org.labkey.api.data.PropertyManager;
+import org.labkey.api.data.SQLFragment;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.Sort;
+import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.Table;
+import org.labkey.api.data.TableCustomizer;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
@@ -71,15 +81,18 @@
 import org.labkey.api.ms2.MS2Urls;
 import org.labkey.api.pipeline.LocalDirectory;
 import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.pipeline.PipelineUrls;
+import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.pipeline.browse.PipelinePathForm;
 import org.labkey.api.portal.ProjectUrls;
 import org.labkey.api.protein.ProteinService;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.FilteredTable;
+import org.labkey.api.query.QueryDefinition;
 import org.labkey.api.query.QueryParam;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QuerySettings;
@@ -96,15 +109,41 @@
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
 import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.security.permissions.ApplicationAdminPermission;
 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.settings.AppProps;
+import org.labkey.api.targetedms.TargetedMSService;
+import org.labkey.api.targetedms.TargetedMSUrls;
+import org.labkey.api.targetedms.model.SampleFileInfo;
+import org.labkey.api.util.Button;
 import org.labkey.api.util.ContainerContext;
+import org.labkey.api.util.DOM;
+import org.labkey.api.util.DateUtil;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.HelpTopic;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
+import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.util.UnexpectedException;
+import org.labkey.api.view.ActionURL;
+import org.labkey.api.view.DetailsView;
+import org.labkey.api.view.GridView;
+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.api.view.NotFoundException;
+import org.labkey.api.view.PopupMenu;
+import org.labkey.api.view.Portal;
+import org.labkey.api.view.RedirectException;
+import org.labkey.api.view.VBox;
+import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.api.view.ViewContext;
+import org.labkey.api.view.WebPartView;
+import org.labkey.api.view.template.ClientDependency;
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.targetedms.chart.ChromatogramChartMakerFactory;
 import org.labkey.targetedms.chart.ComparisonChartMaker;
@@ -115,7 +154,13 @@
 import org.labkey.targetedms.conflict.ConflictPrecursor;
 import org.labkey.targetedms.conflict.ConflictProtein;
 import org.labkey.targetedms.conflict.ConflictTransition;
+import org.labkey.targetedms.model.GuideSet;
+import org.labkey.targetedms.model.GuideSetKey;
+import org.labkey.targetedms.model.GuideSetStats;
 import org.labkey.targetedms.model.QCMetricConfiguration;
+import org.labkey.targetedms.model.QCPlotFragment;
+import org.labkey.targetedms.model.RawMetricDataSet;
+import org.labkey.targetedms.outliers.OutlierGenerator;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.GeneralMoleculeChromInfo;
 import org.labkey.targetedms.parser.Molecule;
@@ -136,9 +181,26 @@
 import org.labkey.targetedms.parser.TransitionChromInfo;
 import org.labkey.targetedms.parser.blib.BlibSpectrumReader;
 import org.labkey.targetedms.parser.list.ListDefinition;
-import org.labkey.targetedms.pipeline.ChromatogramCrawlerJob;
 import org.labkey.targetedms.parser.skyaudit.AuditLogEntry;
-import org.labkey.targetedms.query.*;
+import org.labkey.targetedms.pipeline.ChromatogramCrawlerJob;
+import org.labkey.targetedms.query.ChromatogramDisplayColumnFactory;
+import org.labkey.targetedms.query.ConflictResultsManager;
+import org.labkey.targetedms.query.IsotopeLabelManager;
+import org.labkey.targetedms.query.LibraryManager;
+import org.labkey.targetedms.query.ModificationManager;
+import org.labkey.targetedms.query.ModifiedSequenceDisplayColumn;
+import org.labkey.targetedms.query.MoleculeManager;
+import org.labkey.targetedms.query.MoleculePrecursorManager;
+import org.labkey.targetedms.query.PeptideChromatogramsTableInfo;
+import org.labkey.targetedms.query.PeptideGroupManager;
+import org.labkey.targetedms.query.PeptideManager;
+import org.labkey.targetedms.query.PrecursorChromatogramsTableInfo;
+import org.labkey.targetedms.query.PrecursorManager;
+import org.labkey.targetedms.query.ReplicateManager;
+import org.labkey.targetedms.query.SkylineListManager;
+import org.labkey.targetedms.query.SkylineListSchema;
+import org.labkey.targetedms.query.TargetedMSTable;
+import org.labkey.targetedms.query.TransitionManager;
 import org.labkey.targetedms.search.ModificationSearchWebPart;
 import org.labkey.targetedms.view.CalibrationCurveChart;
 import org.labkey.targetedms.view.CalibrationCurvesView;
@@ -163,7 +225,6 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-
 import javax.servlet.http.HttpServletResponse;
 import java.awt.*;
 import java.awt.image.BufferedImage;
@@ -194,10 +255,11 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
+import static org.labkey.api.targetedms.TargetedMSService.FolderType;
 import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
-import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_TAB;
 import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_DIR;
-import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
+import static org.labkey.api.targetedms.TargetedMSService.RAW_FILES_TAB;
 import static org.labkey.api.util.DOM.Attribute.method;
 import static org.labkey.api.util.DOM.Attribute.src;
 import static org.labkey.api.util.DOM.DIV;
@@ -207,14 +269,13 @@
 import static org.labkey.api.util.DOM.at;
 import static org.labkey.api.util.DOM.cl;
 import static org.labkey.targetedms.TargetedMSModule.EXPERIMENT_FOLDER_WEB_PARTS;
-import static org.labkey.api.targetedms.TargetedMSService.FolderType;
 import static org.labkey.targetedms.TargetedMSModule.LIBRARY_FOLDER_WEB_PARTS;
 import static org.labkey.targetedms.TargetedMSModule.PROTEIN_LIBRARY_FOLDER_WEB_PARTS;
 import static org.labkey.targetedms.TargetedMSModule.QC_FOLDER_WEB_PARTS;
 
 public class TargetedMSController extends SpringActionController
 {
-    private static final Logger LOG = Logger.getLogger(TargetedMSController.class);
+    private static final Logger LOG = LogManager.getLogger(TargetedMSController.class);
 
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(TargetedMSController.class);
     public static final String CONFIGURE_TARGETED_MS_FOLDER = "Configure Panorama Folder";

src/org/labkey/targetedms/TargetedMSDataHandler.java

@@ -17,7 +17,8 @@
 package org.labkey.targetedms;
 
 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.Container;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.exp.ExperimentException;
@@ -58,7 +59,7 @@
  */
 public class TargetedMSDataHandler extends AbstractExperimentDataHandler
 {
-    private static final Logger _log = Logger.getLogger(TargetedMSDataHandler.class);
+    private static final Logger _log = LogManager.getLogger(TargetedMSDataHandler.class);
 
     @Override
     public DataType getDataType()

src/org/labkey/targetedms/TargetedMSManager.java

@@ -19,7 +19,8 @@
 import com.google.common.base.Joiner;
 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.fhcrc.cpas.exp.xml.ExperimentArchiveDocument;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -123,7 +124,7 @@ public class TargetedMSManager
 {
     private static final TargetedMSManager _instance = new TargetedMSManager();
 
-    private static Logger _log = Logger.getLogger(TargetedMSManager.class);
+    private static Logger _log = LogManager.getLogger(TargetedMSManager.class);
 
     private TargetedMSManager()
     {

src/org/labkey/targetedms/TargetedMSServiceImpl.java

@@ -23,14 +23,14 @@
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.User;
+import org.labkey.api.targetedms.BlibSourceFiles;
 import org.labkey.api.targetedms.IModification;
 import org.labkey.api.targetedms.ITargetedMSRun;
-import org.labkey.api.targetedms.SkylineDocumentImportListener;
 import org.labkey.api.targetedms.SkylineAnnotation;
+import org.labkey.api.targetedms.SkylineDocumentImportListener;
 import org.labkey.api.targetedms.TargetedMSFolderTypeListener;
 import org.labkey.api.targetedms.TargetedMSService;
 import org.labkey.api.targetedms.model.SampleFileInfo;
-import org.labkey.api.targetedms.BlibSourceFiles;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.targetedms.parser.blib.BlibSpectrumReader;
 import org.labkey.targetedms.query.ModificationManager;