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Merged
labkey-ankurj merged 1 commit into from
Aug 5, 2020
Merged

Item 7490: Upgrade log4j #41

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5 changes: 3 additions & 2 deletions LDK/api-src/org/labkey/api/ldk/notification/AbstractNotification.java
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Expand Up @@ -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;
Expand All @@ -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)
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/LDKController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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()
{
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7 changes: 4 additions & 3 deletions LDK/src/org/labkey/ldk/LDKServiceImpl.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/notification/NotificationJob.java
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@@ -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;
Expand Down Expand Up @@ -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
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/notification/NotificationServiceImpl.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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";
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;

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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/query/BuiltInColumnsCustomizer.java
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@@ -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;
Expand All @@ -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()
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/query/DefaultTableCustomizer.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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()
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/query/LookupValidationHelper.java
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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;
Expand Down Expand Up @@ -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>>();
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5 changes: 3 additions & 2 deletions LDK/src/org/labkey/ldk/query/UniqueConstraintHelper.java
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@@ -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;
Expand Down Expand Up @@ -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)
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/api-src/org/labkey/api/laboratory/assay/AbstractAssayDataProvider.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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<>();
Expand Down
7 changes: 4 additions & 3 deletions laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayParser.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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)
{
Expand Down
2 changes: 1 addition & 1 deletion laboratory/api-src/org/labkey/api/laboratory/assay/ImportContext.java
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Expand Up @@ -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;
Expand Down
4 changes: 2 additions & 2 deletions laboratory/api-src/org/labkey/api/laboratory/assay/ParserErrors.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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));
}

Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/AbstractDataSource.java
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@@ -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;
Expand Down Expand Up @@ -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)
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/AdditionalDataSource.java
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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;
Expand All @@ -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)
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/DemographicsSource.java
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@@ -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;
Expand Down Expand Up @@ -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)
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/LaboratoryContainerListener.java
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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;
Expand Down Expand Up @@ -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)
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/LaboratoryController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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()
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/LaboratoryManager.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -82,7 +83,7 @@ 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()
{
Expand Down
5 changes: 3 additions & 2 deletions laboratory/src/org/labkey/laboratory/LaboratoryServiceImpl.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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<>();
Expand Down
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