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Merged
labkey-ankurj merged 2 commits into from
Aug 5, 2020
Merged

Item 7490: Migration from log4j1 to log4j2 #57

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3a492ac
Item 7490: Migration from log4j1 to log4j2 - update java methods and …
labkey-ankurj Jul 7, 2020
80a470e
update package
labkey-ankurj Jul 29, 2020
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5 changes: 3 additions & 2 deletions EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/EHR_ComplianceDBController.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr_compliancedb;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.action.SpringActionController;

/**
Expand All @@ -26,7 +27,7 @@
public class EHR_ComplianceDBController extends SpringActionController
{
private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(EHR_ComplianceDBController.class);
private static final Logger _log = Logger.getLogger(EHR_ComplianceDBController.class);
private static final Logger _log = LogManager.getLogger(EHR_ComplianceDBController.class);

public EHR_ComplianceDBController()
{
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2 changes: 1 addition & 1 deletion Viral_Load_Assay/src/org/labkey/viral_load_assay/Viral_Load_Manager.java
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Expand Up @@ -29,7 +29,7 @@ public class Viral_Load_Manager

public static String VL_ASSAY_PROVIDER_NAME = "Viral Loads";

//private static final Logger _log = Logger.getLogger(Viral_Load_Manager.class);
//private static final Logger _log = LogManager.getLogger(Viral_Load_Manager.class);

private Viral_Load_Manager()
{
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2 changes: 1 addition & 1 deletion Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java
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Expand Up @@ -19,7 +19,7 @@
import org.apache.commons.beanutils.ConversionException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.math3.stat.descriptive.moment.StandardDeviation;
import org.apache.log4j.Level;
import org.apache.logging.log4j.Level;
import org.jetbrains.annotations.Nullable;
import org.json.JSONArray;
import org.json.JSONException;
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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java
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*/
package org.labkey.api.ehr.dataentry;

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.TableInfo;
Expand Down Expand Up @@ -68,7 +69,7 @@ abstract public class AbstractFormSection implements FormSection

private List<Supplier<ClientDependency>> _clientDependencies = new ArrayList<>();

protected static final Logger _log = Logger.getLogger(AbstractFormSection.class);
protected static final Logger _log = LogManager.getLogger(AbstractFormSection.class);

public AbstractFormSection(String name, String label, String xtype)
{
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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java
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*/
package org.labkey.api.ehr.dataentry;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.module.Module;

Expand All @@ -31,7 +32,7 @@
*/
public class DefaultDataEntryFormFactory implements DataEntryFormFactory
{
private Logger _log = Logger.getLogger(DefaultDataEntryFormFactory.class);
private Logger _log = LogManager.getLogger(DefaultDataEntryFormFactory.class);
Class<? extends DataEntryForm> _clazz;
Module _module;

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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/demographics/AbstractDemographicsProvider.java
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Expand Up @@ -16,7 +16,8 @@
package org.labkey.api.ehr.demographics;

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.labkey.api.data.ColumnInfo;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
Expand Down Expand Up @@ -56,7 +57,7 @@
*/
abstract public class AbstractDemographicsProvider extends EHROwnable implements DemographicsProvider
{
protected static final Logger _log = Logger.getLogger(AbstractDemographicsProvider.class);
protected static final Logger _log = LogManager.getLogger(AbstractDemographicsProvider.class);

private String _schemaName;
private String _queryName;
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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/history/AbstractDataSource.java
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Expand Up @@ -16,7 +16,8 @@
package org.labkey.api.ehr.history;

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.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.data.ColumnInfo;
Expand Down Expand Up @@ -64,7 +65,7 @@ abstract public class AbstractDataSource extends EHROwnable implements HistoryDa
private String _name;
private boolean _showTime = false;
protected String _subjectIdField = "Id";
protected static final Logger _log = Logger.getLogger(HistoryDataSource.class);
protected static final Logger _log = LogManager.getLogger(HistoryDataSource.class);

public AbstractDataSource(String schema, String query, Module module)
{
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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java
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package org.labkey.api.ehr.history;

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.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.collections.CaseInsensitiveHashMap;
Expand Down Expand Up @@ -74,7 +75,7 @@ public class DefaultLabworkType implements LabworkType
protected String _normalRangeField = null;
protected String _normalRangeStatusField = null;

private static final Logger _log = Logger.getLogger(DefaultLabworkType.class);
private static final Logger _log = LogManager.getLogger(DefaultLabworkType.class);
@NotNull
private final Module _declaringModule;

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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/history/HistoryRowImpl.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.api.ehr.history;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.json.JSONObject;

import java.text.SimpleDateFormat;
Expand Down Expand Up @@ -49,7 +50,7 @@ public class HistoryRowImpl implements HistoryRow
private String _objectId;
private String _html;

protected static final Logger _log = Logger.getLogger(HistoryRowImpl.class);
protected static final Logger _log = LogManager.getLogger(HistoryRowImpl.class);

protected final SimpleDateFormat _timeFormat = new SimpleDateFormat("kk:mm");

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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/table/AssignedAtTimeForeignKey.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.api.ehr.table;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.BaseColumnInfo;
import org.labkey.api.data.ColumnInfo;
Expand All @@ -31,7 +32,7 @@

public class AssignedAtTimeForeignKey extends LookupForeignKey
{
private static final Logger _log = Logger.getLogger(AssignedAtTimeForeignKey.class);
private static final Logger _log = LogManager.getLogger(AssignedAtTimeForeignKey.class);

private AbstractTableInfo _tableInfo;
private ColumnInfo _pkCol;
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5 changes: 3 additions & 2 deletions ehr/api-src/org/labkey/api/ehr/table/AssignmentAtTimeForeignKey.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.api.ehr.table;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.data.AbstractTableInfo;
import org.labkey.api.data.BaseColumnInfo;
import org.labkey.api.data.ColumnInfo;
Expand All @@ -31,7 +32,7 @@

public class AssignmentAtTimeForeignKey extends LookupForeignKey
{
private static final Logger _log = Logger.getLogger(AssignmentAtTimeForeignKey.class);
private static final Logger _log = LogManager.getLogger(AssignmentAtTimeForeignKey.class);

private AbstractTableInfo _tableInfo;
private ColumnInfo _pkCol;
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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/EHRManager.java
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Expand Up @@ -17,7 +17,8 @@

import com.google.common.collect.Sets;
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.apache.xmlbeans.XmlException;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
Expand Down Expand Up @@ -125,7 +126,7 @@ public class EHRManager
@Queryable
public static final String OBS_CATEGORY_OBSERVATIONS = "Observations";

private static final Logger _log = Logger.getLogger(EHRManager.class);
private static final Logger _log = LogManager.getLogger(EHRManager.class);

private EHRManager()
{
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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/EHRServiceImpl.java
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Expand Up @@ -17,7 +17,8 @@

import org.apache.commons.collections4.MultiValuedMap;
import org.apache.commons.collections4.multimap.ArrayListValuedHashMap;
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 @@ -105,7 +106,7 @@ public class EHRServiceImpl extends EHRService
private Set<Module> _modulesRequiringLegacyExt3UI = new HashSet<>();
private ProjectValidator _projectValidator = null;

private static final Logger _log = Logger.getLogger(EHRServiceImpl.class);
private static final Logger _log = LogManager.getLogger(EHRServiceImpl.class);

public EHRServiceImpl()
{
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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/dataentry/DataEntryManager.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.dataentry;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.cache.Cache;
import org.labkey.api.cache.CacheManager;
import org.labkey.api.data.ColumnInfo;
Expand Down Expand Up @@ -54,7 +55,7 @@
public class DataEntryManager
{
private static final DataEntryManager _instance = new DataEntryManager();
private static final Logger _log = Logger.getLogger(DataEntryManager.class);
private static final Logger _log = LogManager.getLogger(DataEntryManager.class);
private List<DataEntryFormFactory> _forms = new ArrayList<>();
private Map<String, List<FieldKey>> _defaultFieldKeys = new HashMap<>();
private List<SingleQueryFormProvider> _queryProviders = new ArrayList<>();
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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/dataentry/RecordDeleteRunner.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.dataentry;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
Expand Down Expand Up @@ -65,7 +66,7 @@ public class RecordDeleteRunner implements Job
{
public static final String PROPERTY_DOMAIN = "org.labkey.ehr.recorddeletion";
public static final String ENABLED_PROP = "isEnabled";
private static final Logger _log = Logger.getLogger(RecordDeleteRunner.class);
private static final Logger _log = LogManager.getLogger(RecordDeleteRunner.class);
private static final int _hour = 23;
private static final int _minute = 30;

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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/demographics/EHRDemographicsServiceImpl.java
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Expand Up @@ -18,7 +18,8 @@
import com.google.common.collect.MapDifference;
import com.google.common.collect.Maps;
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.NotNull;
import org.labkey.api.cache.Cache;
import org.labkey.api.cache.CacheManager;
Expand Down Expand Up @@ -78,7 +79,7 @@
*/
public class EHRDemographicsServiceImpl extends EHRDemographicsService
{
private static final Logger _log = Logger.getLogger(EHRDemographicsServiceImpl.class);
private static final Logger _log = LogManager.getLogger(EHRDemographicsServiceImpl.class);
private static JobDetail _job = null;

private Cache<String, AnimalRecordImpl> _cache;
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3 changes: 2 additions & 1 deletion ehr/src/org/labkey/ehr/demographics/EHRProjectValidator.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.demographics;

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.CompareType;
import org.labkey.api.data.Container;
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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/history/ClinicalHistoryManager.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.history;

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.ehr.history.HistoryDataSource;
import org.labkey.api.ehr.history.HistoryRow;
Expand All @@ -38,7 +39,7 @@
public class ClinicalHistoryManager
{
private static final ClinicalHistoryManager _instance = new ClinicalHistoryManager();
private static final Logger _log = Logger.getLogger(ClinicalHistoryManager.class);
private static final Logger _log = LogManager.getLogger(ClinicalHistoryManager.class);

private final List<HistoryDataSource> _dataSources = new ArrayList<>();

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5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsJob.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.pipeline;

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.PropertyManager;
Expand Down Expand Up @@ -48,7 +49,7 @@
public class GeneticCalculationsJob implements Job
{
public final static String GENETICCALCULATIONS_PROPERTY_DOMAIN = "org.labkey.ehr.geneticcalculations";
private static final Logger _log = Logger.getLogger(GeneticCalculationsJob.class);
private static final Logger _log = LogManager.getLogger(GeneticCalculationsJob.class);
private static TriggerKey _jobKey = null;

public GeneticCalculationsJob()
Expand Down
5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRunnable.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.pipeline;

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.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineJobException;
Expand Down Expand Up @@ -53,7 +54,7 @@
public class GeneticCalculationsRunnable
{
private final String KINSHIP_PIPELINE_NAME = "kinshipPipeline";
private final Logger _log = Logger.getLogger(GeneticCalculationsRunnable.class);
private final Logger _log = LogManager.getLogger(GeneticCalculationsRunnable.class);

public boolean run(Container c, boolean allowRunningDuringDay) throws PipelineJobException
{
Expand Down
5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/table/DefaultEHRCustomizer.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.ehr.table;

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 @@ -92,7 +93,7 @@ public class DefaultEHRCustomizer extends AbstractTableCustomizer
public static final String ID_COL = "Id";
public static final String PARTICIPANT_CONCEPT_URI = "http://cpas.labkey.com/Study#ParticipantId";

private static final Logger _log = Logger.getLogger(DefaultEHRCustomizer.class);
private static final Logger _log = LogManager.getLogger(DefaultEHRCustomizer.class);
private boolean _addLinkDisablers = true;
private static final String MORE_ACTIONS = "More Actions";

Expand Down
5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/table/SNOMEDCodesDisplayColumn.java
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Expand Up @@ -16,7 +16,8 @@
package org.labkey.ehr.table;

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.NotNull;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.DataColumn;
Expand All @@ -38,7 +39,7 @@
*/
public class SNOMEDCodesDisplayColumn extends DataColumn
{
private static final Logger _log = Logger.getLogger(SNOMEDCodesDisplayColumn.class);
private static final Logger _log = LogManager.getLogger(SNOMEDCodesDisplayColumn.class);

public SNOMEDCodesDisplayColumn(ColumnInfo col)
{
Expand Down
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