Item 7490: Migration from log4j1 to log4j2 - update java methods and package names (#41)

labkey-ankurj · web-flow · commit aed1f9957682 · 2020-08-05T13:29:37.000-07:00
diff --git a/LDK/api-src/org/labkey/api/ldk/notification/AbstractNotification.java b/LDK/api-src/org/labkey/api/ldk/notification/AbstractNotification.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.api.ldk.notification;
 
-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.SimpleFilter;
@@ -36,7 +37,7 @@ abstract public class AbstractNotification implements Notification
 {
     private Module _owner;
 
-    protected final static Logger log = Logger.getLogger(AbstractNotification.class);
+    protected final static Logger log = LogManager.getLogger(AbstractNotification.class);
     protected final static SimpleDateFormat _timeFormat = new SimpleDateFormat("kk:mm");
 
     public AbstractNotification(Module owner)
diff --git a/LDK/src/org/labkey/ldk/LDKController.java b/LDK/src/org/labkey/ldk/LDKController.java
@@ -17,7 +17,8 @@
 package org.labkey.ldk;
 
 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.JSONArray;
 import org.json.JSONObject;
@@ -103,7 +104,7 @@
 public class LDKController extends SpringActionController
 {
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(LDKController.class);
-    private static Logger _log = Logger.getLogger(LDKController.class);
+    private static Logger _log = LogManager.getLogger(LDKController.class);
 
     public LDKController()
     {
diff --git a/LDK/src/org/labkey/ldk/LDKServiceImpl.java b/LDK/src/org/labkey/ldk/LDKServiceImpl.java
@@ -3,8 +3,9 @@
 import org.apache.commons.collections4.MultiValuedMap;
 import org.apache.commons.io.FileUtils;
 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.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
@@ -55,7 +56,7 @@
  */
 public class LDKServiceImpl extends LDKService
 {
-    private static final Logger _log = Logger.getLogger(LDKServiceImpl.class);
+    private static final Logger _log = LogManager.getLogger(LDKServiceImpl.class);
     private Set<NotificationSection> _summaryNotificationSections = new HashSet<>();
     private List<List<String>> _containerScopedTables = new ArrayList<>();
     private Boolean _isNaturalizeInstalled = null;
diff --git a/LDK/src/org/labkey/ldk/notification/NotificationJob.java b/LDK/src/org/labkey/ldk/notification/NotificationJob.java
@@ -1,7 +1,8 @@
 package org.labkey.ldk.notification;
 
 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.ldk.notification.Notification;
 import org.labkey.api.ldk.notification.NotificationService;
@@ -36,7 +37,7 @@
  */
 public class NotificationJob implements Job
 {
-    private static final Logger _log = Logger.getLogger(NotificationJob.class);
+    private static final Logger _log = LogManager.getLogger(NotificationJob.class);
     private Notification _notification;
 
     @Override
diff --git a/LDK/src/org/labkey/ldk/notification/NotificationServiceImpl.java b/LDK/src/org/labkey/ldk/notification/NotificationServiceImpl.java
@@ -17,7 +17,8 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DurationFormatUtils;
-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.JSONObject;
@@ -77,7 +78,7 @@
  */
 public class NotificationServiceImpl extends NotificationService
 {
-    private final static Logger _log = Logger.getLogger(NotificationServiceImpl.class);
+    private final static Logger _log = LogManager.getLogger(NotificationServiceImpl.class);
 
     public final static String TIMESTAMP_PROPERTY_DOMAIN = "org.labkey.ldk.notifications.timestamp";
     public final static String STATUS_PROPERTY_DOMAIN = "org.labkey.ldk.notifications.status";
diff --git a/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java b/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java
@@ -19,7 +19,8 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.commons.lang3.time.DurationFormatUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.json.JSONArray;
 import org.json.JSONObject;
 import org.labkey.api.audit.AuditLogService;
@@ -78,7 +79,7 @@
  */
 public class SiteSummaryNotification implements Notification
 {
-    protected final static Logger log = Logger.getLogger(SiteSummaryNotification.class);
+    protected final static Logger log = LogManager.getLogger(SiteSummaryNotification.class);
     private static final String lastSave = "lastSave";
     private NumberFormat _pctFormat = null;
 
diff --git a/LDK/src/org/labkey/ldk/query/BuiltInColumnsCustomizer.java b/LDK/src/org/labkey/ldk/query/BuiltInColumnsCustomizer.java
@@ -1,6 +1,7 @@
 package org.labkey.ldk.query;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.BaseColumnInfo;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.TableCustomizer;
@@ -17,7 +18,7 @@
  */
 public class BuiltInColumnsCustomizer implements TableCustomizer
 {
-    private static final Logger _log = Logger.getLogger(TableCustomizer.class);
+    private static final Logger _log = LogManager.getLogger(TableCustomizer.class);
     private boolean _disableFacetingForNumericCols = true;
 
     public BuiltInColumnsCustomizer()
diff --git a/LDK/src/org/labkey/ldk/query/DefaultTableCustomizer.java b/LDK/src/org/labkey/ldk/query/DefaultTableCustomizer.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.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.assay.AssayResultTable;
@@ -67,7 +68,7 @@ public class DefaultTableCustomizer implements TableCustomizer
 {
     private static final String MORE_ACTIONS = "More Actions";
 
-    private static final Logger _log = Logger.getLogger(TableCustomizer.class);
+    private static final Logger _log = LogManager.getLogger(TableCustomizer.class);
     private Settings _settings;
 
     public DefaultTableCustomizer()
diff --git a/LDK/src/org/labkey/ldk/query/LookupValidationHelper.java b/LDK/src/org/labkey/ldk/query/LookupValidationHelper.java
@@ -1,7 +1,8 @@
 package org.labkey.ldk.query;
 
 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.CaseInsensitiveHashMap;
 import org.labkey.api.data.ColumnInfo;
@@ -39,7 +40,7 @@ public class LookupValidationHelper
     private Container _container;
     private User _user;
     private TableInfo _table;
-    private static final Logger _log = Logger.getLogger(LookupValidationHelper.class);
+    private static final Logger _log = LogManager.getLogger(LookupValidationHelper.class);
 
     private Map<String, UserSchema> _userSchemaMap = new HashMap<String, UserSchema>();
     private Map<String, Map<String, String>> _allowableValueMap = new HashMap<String, Map<String, String>>();
diff --git a/LDK/src/org/labkey/ldk/query/UniqueConstraintHelper.java b/LDK/src/org/labkey/ldk/query/UniqueConstraintHelper.java
@@ -1,6 +1,7 @@
 package org.labkey.ldk.query;
 
-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.Container;
 import org.labkey.api.data.ContainerManager;
@@ -32,7 +33,7 @@ public class UniqueConstraintHelper
 
     private List<Object> _encounteredKeys = new ArrayList<>();
 
-    private static final Logger _log = Logger.getLogger(UniqueConstraintHelper.class);
+    private static final Logger _log = LogManager.getLogger(UniqueConstraintHelper.class);
 
     private UniqueConstraintHelper(String containerId, int userId, String schemaName, String queryName, String targetColName)
     {
diff --git a/laboratory/api-src/org/labkey/api/laboratory/assay/AbstractAssayDataProvider.java b/laboratory/api-src/org/labkey/api/laboratory/assay/AbstractAssayDataProvider.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.api.laboratory.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.json.JSONObject;
 import org.labkey.api.data.ColumnInfo;
@@ -64,7 +65,7 @@
 abstract public class AbstractAssayDataProvider extends AbstractDataProvider implements AssayDataProvider
 {
     public static final String PROPERTY_CATEGORY = "laboratory.importMethodDefaults";
-    protected static final Logger _log = Logger.getLogger(AbstractDataProvider.class);
+    protected static final Logger _log = LogManager.getLogger(AbstractDataProvider.class);
 
     protected String _providerName = null;
     protected Collection<AssayImportMethod> _importMethods = new LinkedHashSet<>();
diff --git a/laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayParser.java b/laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayParser.java
@@ -19,8 +19,9 @@
 import au.com.bytecode.opencsv.CSVWriter;
 import org.apache.commons.beanutils.ConversionException;
 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.apache.poi.openxml4j.exceptions.InvalidFormatException;
 import org.json.JSONArray;
 import org.json.JSONObject;
@@ -88,7 +89,7 @@ public class DefaultAssayParser implements AssayParser
 
     protected String RESULT_FIELD = "result";
 
-    private static final Logger _log = Logger.getLogger(AssayParser.class);
+    private static final Logger _log = LogManager.getLogger(AssayParser.class);
 
     public DefaultAssayParser(AssayImportMethod method, Container c, User u, int assayId)
     {
diff --git a/laboratory/api-src/org/labkey/api/laboratory/assay/ImportContext.java b/laboratory/api-src/org/labkey/api/laboratory/assay/ImportContext.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.api.laboratory.assay;
 
-import org.apache.log4j.Level;
+import org.apache.logging.log4j.Level;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONArray;
 import org.json.JSONObject;
diff --git a/laboratory/api-src/org/labkey/api/laboratory/assay/ParserErrors.java b/laboratory/api-src/org/labkey/api/laboratory/assay/ParserErrors.java
@@ -15,7 +15,7 @@
  */
 package org.labkey.api.laboratory.assay;
 
-import org.apache.log4j.Level;
+import org.apache.logging.log4j.Level;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.query.BatchValidationException;
@@ -49,7 +49,7 @@ public void addError(String msg)
 
     public void addError(String msg, Level level)
     {
-        if (level.isGreaterOrEqual(_threshold))
+        if (level.intLevel() >= _threshold.intLevel())
             _errors.add(Pair.of(msg, level));
     }
 
diff --git a/laboratory/src/org/labkey/laboratory/AbstractDataSource.java b/laboratory/src/org/labkey/laboratory/AbstractDataSource.java
@@ -1,6 +1,7 @@
 package org.labkey.laboratory;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
 import org.labkey.api.data.Container;
@@ -33,7 +34,7 @@ abstract public class AbstractDataSource
     private String _queryName;
     private String _label;
     protected static final String DELIM = "<>";
-    protected static final Logger _log = Logger.getLogger(AbstractDataSource.class);
+    protected static final Logger _log = LogManager.getLogger(AbstractDataSource.class);
     private Map<String, TableInfo> _cachedTables = new HashMap<>();
     
     public AbstractDataSource(String label, @Nullable String containerId, String schemaName, String queryName)
diff --git a/laboratory/src/org/labkey/laboratory/AdditionalDataSource.java b/laboratory/src/org/labkey/laboratory/AdditionalDataSource.java
@@ -1,7 +1,8 @@
 package org.labkey.laboratory;
 
 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.json.JSONException;
 import org.json.JSONObject;
@@ -25,7 +26,7 @@ public class AdditionalDataSource extends AbstractDataSource
     private boolean _importIntoWorkbooks;
     private String _subjectFieldKey;
     private String _sampleDateFieldKey;
-    private static final Logger _log = Logger.getLogger(AdditionalDataSource.class);
+    private static final Logger _log = LogManager.getLogger(AdditionalDataSource.class);
 
     public AdditionalDataSource(LaboratoryService.NavItemCategory itemType, String label, @Nullable String containerId, String schemaName, String queryName, String reportCategory, boolean importIntoWorkbooks, String subjectFieldKey, String sampleDateFieldKey)
     {
diff --git a/laboratory/src/org/labkey/laboratory/DemographicsSource.java b/laboratory/src/org/labkey/laboratory/DemographicsSource.java
@@ -1,7 +1,8 @@
 package org.labkey.laboratory;
 
 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.json.JSONException;
 import org.json.JSONObject;
@@ -29,7 +30,7 @@
 public class DemographicsSource extends AbstractDataSource
 {
     private String _targetColumn;
-    private static final Logger _log = Logger.getLogger(DemographicsSource.class);
+    private static final Logger _log = LogManager.getLogger(DemographicsSource.class);
     
     public DemographicsSource(String label, String containerId, String schemaName, String queryName, String targetColumn)
     {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java b/laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java
@@ -1,6 +1,7 @@
 package org.labkey.laboratory;
 
-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.ContainerManager;
 import org.labkey.api.data.SQLFragment;
@@ -30,7 +31,7 @@
  */
 public class LaboratoryContainerListener extends SimpleModuleContainerListener
 {
-    Logger _log = Logger.getLogger(LaboratoryContainerListener.class);
+    Logger _log = LogManager.getLogger(LaboratoryContainerListener.class);
 
     public LaboratoryContainerListener(Module owner)
     {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryController.java b/laboratory/src/org/labkey/laboratory/LaboratoryController.java
@@ -18,7 +18,8 @@
 
 import org.apache.commons.lang3.ArrayUtils;
 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.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
@@ -106,7 +107,7 @@
 public class LaboratoryController extends SpringActionController
 {
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(LaboratoryController.class);
-    private static final Logger _log = Logger.getLogger(LaboratoryController.class);
+    private static final Logger _log = LogManager.getLogger(LaboratoryController.class);
 
     public LaboratoryController()
     {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryManager.java b/laboratory/src/org/labkey/laboratory/LaboratoryManager.java
@@ -16,7 +16,8 @@
 package org.labkey.laboratory;
 
 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.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
@@ -83,7 +84,7 @@ public class LaboratoryManager
 {
     private static final LaboratoryManager _instance = new LaboratoryManager();
     public static final String DEFAULT_WORKBOOK_FOLDERTYPE_PROPNAME = "DefaultWorkbookFolderType";
-    private static final Logger _log = Logger.getLogger(LaboratoryManager.class);
+    private static final Logger _log = LogManager.getLogger(LaboratoryManager.class);
 
     private LaboratoryManager()
     {
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java b/laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.laboratory;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.json.JSONObject;
 import org.labkey.api.assay.AssayFileWriter;
 import org.labkey.api.assay.AssayProvider;
@@ -73,7 +74,7 @@
 public class LaboratoryServiceImpl extends LaboratoryService
 {
     private static final LaboratoryServiceImpl _instance = new LaboratoryServiceImpl();
-    private static final Logger _log = Logger.getLogger(LaboratoryServiceImpl.class);
+    private static final Logger _log = LogManager.getLogger(LaboratoryServiceImpl.class);
 
     private Set<Module> _registeredModules = new HashSet<>();
     private Map<String, Map<String, List<ButtonConfigFactory>>> _assayButtons = new CaseInsensitiveHashMap<>();
diff --git a/laboratory/src/org/labkey/laboratory/LaboratoryUpgradeCode.java b/laboratory/src/org/labkey/laboratory/LaboratoryUpgradeCode.java
diff --git a/laboratory/src/org/labkey/laboratory/URLDataSource.java b/laboratory/src/org/labkey/laboratory/URLDataSource.java
diff --git a/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java b/laboratory/src/org/labkey/laboratory/assay/AssayHelper.java
diff --git a/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java b/laboratory/src/org/labkey/laboratory/assay/RunUploadContext.java
diff --git a/laboratory/src/org/labkey/laboratory/notification/LabSummaryNotification.java b/laboratory/src/org/labkey/laboratory/notification/LabSummaryNotification.java
diff --git a/laboratory/src/org/labkey/laboratory/query/DefaultAssayCustomizer.java b/laboratory/src/org/labkey/laboratory/query/DefaultAssayCustomizer.java
diff --git a/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java b/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
diff --git a/laboratory/src/org/labkey/laboratory/query/LaboratoryWorkbooksTable.java b/laboratory/src/org/labkey/laboratory/query/LaboratoryWorkbooksTable.java
