diff --git a/src/org/labkey/cds/CDSController.java b/src/org/labkey/cds/CDSController.java
index eff7cd7aa..e8a74c5f7 100644
--- a/src/org/labkey/cds/CDSController.java
+++ b/src/org/labkey/cds/CDSController.java
@@ -20,7 +20,8 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 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.json.JSONObject;
 import org.labkey.api.action.Action;
@@ -145,7 +146,7 @@ public class CDSController extends SpringActionController
         }
     }
 
-    private static final Logger LOG = Logger.getLogger(CDSController.class);
+    private static final Logger LOG = LogManager.getLogger(CDSController.class);
 
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(CDSController.class);
 
diff --git a/src/org/labkey/cds/CDSModule.java b/src/org/labkey/cds/CDSModule.java
index 5a5cf7fa1..e0be1184b 100644
--- a/src/org/labkey/cds/CDSModule.java
+++ b/src/org/labkey/cds/CDSModule.java
@@ -17,7 +17,7 @@
 package org.labkey.cds;
 
 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.data.Container;
@@ -258,7 +258,7 @@ private String ensureShortcut(ModuleProperty prop, String prevTarget, String sou
             }
             catch (IllegalArgumentException x)
             {
-                Logger.getLogger(CDSModule.class).warn("Could not create shortcut from '" + source + "' to '" + target + "'.");
+                LogManager.getLogger(CDSModule.class).warn("Could not create shortcut from '" + source + "' to '" + target + "'.");
             }
         }
         return target;
diff --git a/src/org/labkey/cds/data/CDSImportCopyConfig.java b/src/org/labkey/cds/data/CDSImportCopyConfig.java
index 5b812f761..63b52cf4d 100644
--- a/src/org/labkey/cds/data/CDSImportCopyConfig.java
+++ b/src/org/labkey/cds/data/CDSImportCopyConfig.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data;
 
-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.DbSchema;
diff --git a/src/org/labkey/cds/data/TSVCopyConfig.java b/src/org/labkey/cds/data/TSVCopyConfig.java
index 75f944805..eb1de6207 100644
--- a/src/org/labkey/cds/data/TSVCopyConfig.java
+++ b/src/org/labkey/cds/data/TSVCopyConfig.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data;
 
-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.dataiterator.DataIteratorBuilder;
diff --git a/src/org/labkey/cds/data/steps/AbstractPopulateTask.java b/src/org/labkey/cds/data/steps/AbstractPopulateTask.java
index e0d50e967..2a2ab4486 100644
--- a/src/org/labkey/cds/data/steps/AbstractPopulateTask.java
+++ b/src/org/labkey/cds/data/steps/AbstractPopulateTask.java
@@ -16,7 +16,7 @@
 package org.labkey.cds.data.steps;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.FolderTypeManager;
diff --git a/src/org/labkey/cds/data/steps/CDSImportTask.java b/src/org/labkey/cds/data/steps/CDSImportTask.java
index 1b688e9a8..facf25b92 100644
--- a/src/org/labkey/cds/data/steps/CDSImportTask.java
+++ b/src/org/labkey/cds/data/steps/CDSImportTask.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-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/src/org/labkey/cds/data/steps/CDSValidateTask.java b/src/org/labkey/cds/data/steps/CDSValidateTask.java
index 92546d894..5f68910ac 100644
--- a/src/org/labkey/cds/data/steps/CDSValidateTask.java
+++ b/src/org/labkey/cds/data/steps/CDSValidateTask.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/ClearAndWarmCube.java b/src/org/labkey/cds/data/steps/ClearAndWarmCube.java
index 5977d9578..15bdf6de0 100644
--- a/src/org/labkey/cds/data/steps/ClearAndWarmCube.java
+++ b/src/org/labkey/cds/data/steps/ClearAndWarmCube.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.QueryService;
diff --git a/src/org/labkey/cds/data/steps/ClearMappingTask.java b/src/org/labkey/cds/data/steps/ClearMappingTask.java
index 0b6c9085c..944ee88be 100644
--- a/src/org/labkey/cds/data/steps/ClearMappingTask.java
+++ b/src/org/labkey/cds/data/steps/ClearMappingTask.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/ContainerSensitivePopulateTask.java b/src/org/labkey/cds/data/steps/ContainerSensitivePopulateTask.java
index d56d85e05..d1ef81f24 100644
--- a/src/org/labkey/cds/data/steps/ContainerSensitivePopulateTask.java
+++ b/src/org/labkey/cds/data/steps/ContainerSensitivePopulateTask.java
@@ -15,10 +15,9 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateAssayTask.java b/src/org/labkey/cds/data/steps/PopulateAssayTask.java
index f653eca78..b9c85f79c 100644
--- a/src/org/labkey/cds/data/steps/PopulateAssayTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateAssayTask.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateDatasetTask.java b/src/org/labkey/cds/data/steps/PopulateDatasetTask.java
index 299eecc0d..634cba4b9 100644
--- a/src/org/labkey/cds/data/steps/PopulateDatasetTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateDatasetTask.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
@@ -27,7 +27,6 @@
 import org.labkey.api.query.QuerySchema;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.ValidationException;
-import org.labkey.api.security.User;
 import org.labkey.api.util.DateUtil;
 
 import java.util.Arrays;
diff --git a/src/org/labkey/cds/data/steps/PopulateFactsTask.java b/src/org/labkey/cds/data/steps/PopulateFactsTask.java
index ca12173ea..fb161a409 100644
--- a/src/org/labkey/cds/data/steps/PopulateFactsTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateFactsTask.java
@@ -15,10 +15,9 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateGridBaseTask.java b/src/org/labkey/cds/data/steps/PopulateGridBaseTask.java
index dced4bd16..676d8e928 100644
--- a/src/org/labkey/cds/data/steps/PopulateGridBaseTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateGridBaseTask.java
@@ -15,10 +15,9 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateRelationshipTask.java b/src/org/labkey/cds/data/steps/PopulateRelationshipTask.java
index 9c98bbd94..7278d7d05 100644
--- a/src/org/labkey/cds/data/steps/PopulateRelationshipTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateRelationshipTask.java
@@ -15,10 +15,9 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateStudiesTask.java b/src/org/labkey/cds/data/steps/PopulateStudiesTask.java
index 37bf1fdfc..cce0aa57f 100644
--- a/src/org/labkey/cds/data/steps/PopulateStudiesTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateStudiesTask.java
@@ -15,10 +15,9 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 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.NormalContainerType;
 import org.labkey.api.data.SQLFragment;
diff --git a/src/org/labkey/cds/data/steps/PopulateStudyVisitTask.java b/src/org/labkey/cds/data/steps/PopulateStudyVisitTask.java
index 85756a3ed..0f3c41cf9 100644
--- a/src/org/labkey/cds/data/steps/PopulateStudyVisitTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateStudyVisitTask.java
@@ -15,10 +15,8 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.Container;
-import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/data/steps/PopulateTreatmentArmTask.java b/src/org/labkey/cds/data/steps/PopulateTreatmentArmTask.java
index 9c5010db2..1b66fd465 100644
--- a/src/org/labkey/cds/data/steps/PopulateTreatmentArmTask.java
+++ b/src/org/labkey/cds/data/steps/PopulateTreatmentArmTask.java
@@ -15,11 +15,10 @@
  */
 package org.labkey.cds.data.steps;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerFilterable;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
 import org.labkey.api.data.TableInfo;
diff --git a/src/org/labkey/cds/query/MabGroupTable.java b/src/org/labkey/cds/query/MabGroupTable.java
index dcbc52593..33d8702fb 100644
--- a/src/org/labkey/cds/query/MabGroupTable.java
+++ b/src/org/labkey/cds/query/MabGroupTable.java
@@ -16,7 +16,6 @@
 package org.labkey.cds.query;
 
 import org.jetbrains.annotations.NotNull;
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
diff --git a/src/org/labkey/cds/view/cms.jsp b/src/org/labkey/cds/view/cms.jsp
index 0fd1e96f4..82bd8abd5 100644
--- a/src/org/labkey/cds/view/cms.jsp
+++ b/src/org/labkey/cds/view/cms.jsp
@@ -15,8 +15,8 @@
  * limitations under the License.
  */
 %>
-<%@ page import="org.labkey.cds.CDSController" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
+<%@ page import="org.labkey.cds.CDSController" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%