Item 7490: upgrade log4j (#72)

Author: labkey-ankurj

src/org/labkey/trialshare/ITNSpecimenRequestCustomizer.java

@@ -1,6 +1,7 @@
 package org.labkey.trialshare;
 
-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.security.Group;
@@ -16,7 +17,7 @@
 
 public class ITNSpecimenRequestCustomizer implements SpecimenService.SpecimenRequestCustomizer
 {
-    private static final Logger LOG = Logger.getLogger(ITNSpecimenRequestCustomizer.class);
+    private static final Logger LOG = LogManager.getLogger(ITNSpecimenRequestCustomizer.class);
 
     @Override
     public boolean allowEmptyRequests()

src/org/labkey/trialshare/PublicationDocumentProvider.java

@@ -15,7 +15,8 @@
  */
 package org.labkey.trialshare;
 
-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.ContainerManager;
@@ -39,7 +40,7 @@
 
 public class PublicationDocumentProvider implements SearchService.DocumentProvider
 {
-    private static final Logger _logger = Logger.getLogger(PublicationDocumentProvider.class);
+    private static final Logger _logger = LogManager.getLogger(PublicationDocumentProvider.class);
 
     public static Container getDocumentContainer()
     {

src/org/labkey/trialshare/StudyDocumentProvider.java

@@ -15,7 +15,8 @@
  */
 package org.labkey.trialshare;
 
-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.query.QuerySchema;
@@ -36,7 +37,7 @@
 
 public class StudyDocumentProvider implements SearchService.DocumentProvider
 {
-    private static final Logger _logger = Logger.getLogger(StudyDocumentProvider.class);
+    private static final Logger _logger = LogManager.getLogger(StudyDocumentProvider.class);
     public static Container getDocumentContainer()
     {
         return TrialShareManager.get().getCubeContainer(null);

src/org/labkey/trialshare/TrialShareController.java

@@ -20,7 +20,7 @@
 import com.fasterxml.jackson.databind.ObjectReader;
 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.jetbrains.annotations.Nullable;
 import org.junit.Assert;
@@ -594,7 +594,7 @@ public ApiResponse execute(TrialShareExportForm form, BindException errors) thro
             // todo: super important boolean false in 17.2 replaced by PHI enum.  what is new correct setting? PHI.Limited
             FolderExportContext ctx = new FolderExportContext(getUser(), container, types.stream().map(FolderDataTypes::getDescription).collect(Collectors.toSet()),
                     "new", false, PHI.NotPHI, false,
-                    false, false, new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class)));
+                    false, false, new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class)));
 
             PipeRoot root = PipelineService.get().findPipelineRoot(container);
             if (root == null || !root.isValid())

src/org/labkey/trialshare/TrialShareManager.java

@@ -17,7 +17,8 @@
 package org.labkey.trialshare;
 
 import org.apache.commons.lang3.BooleanUtils;
-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;
@@ -58,7 +59,7 @@
 public class TrialShareManager
 {
 
-    private static final Logger _logger = Logger.getLogger(TrialShareManager.class);
+    private static final Logger _logger = LogManager.getLogger(TrialShareManager.class);
     private static final TrialShareManager _instance = new TrialShareManager();
 
     private TrialShareManager()

src/org/labkey/trialshare/data/FacetFilter.java

@@ -15,9 +15,6 @@
  */
 package org.labkey.trialshare.data;
 
-import org.labkey.api.action.Marshal;
-import org.labkey.api.action.Marshaller;
-
 /**
  * Created by susanh on 12/14/15.
  */

src/org/labkey/trialshare/data/StudyFacetMember.java

@@ -16,7 +16,6 @@
 package org.labkey.trialshare.data;
 
 import java.util.List;
-import java.util.Map;
 
 /**
  * Created by susanh on 12/8/15.

src/org/labkey/trialshare/query/ManageCubeObjectQueryView.java

@@ -18,7 +18,6 @@
 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.query.DetailsURL;
 import org.labkey.api.query.QueryAction;