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

Item 7490: upgrade log4j #21

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0deb6d4
Item 7490: upgrade log4j
labkey-ankurj Jul 10, 2020
7651580
fix compilation error in ehr build
labkey-ankurj Jul 30, 2020
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5 changes: 3 additions & 2 deletions GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java
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package org.labkey.GeneticsCore;

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 @@ -11,7 +12,7 @@
public class GeneticsCoreController extends SpringActionController
{
private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(GeneticsCoreController.class);
private static final Logger _log = Logger.getLogger(GeneticsCoreController.class);
private static final Logger _log = LogManager.getLogger(GeneticsCoreController.class);

public GeneticsCoreController()
{
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5 changes: 3 additions & 2 deletions GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java
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package org.labkey.GeneticsCore.notification;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.GeneticsCore.GeneticsCoreManager;
import org.labkey.GeneticsCore.GeneticsCoreModule;
import org.labkey.api.data.CompareType;
Expand Down Expand Up @@ -30,7 +31,7 @@
*/
public class GeneticsCoreNotification implements Notification
{
protected final static Logger _log = Logger.getLogger(GeneticsCoreNotification.class);
protected final static Logger _log = LogManager.getLogger(GeneticsCoreNotification.class);
protected final static SimpleDateFormat _dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd kk:mm");
protected final static SimpleDateFormat _dateFormat = new SimpleDateFormat("yyyy-MM-dd");
protected NotificationService _ns = NotificationService.get();
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2 changes: 1 addition & 1 deletion HormoneAssay/src/org/labkey/hormoneassay/assay/PivotedImportMethod.java
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package org.labkey.hormoneassay.assay;

import org.apache.log4j.Level;
import org.apache.logging.log4j.Level;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
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5 changes: 3 additions & 2 deletions mergesync/src/org/labkey/mergesync/MergeSyncManager.java
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Expand Up @@ -17,7 +17,8 @@
package org.labkey.mergesync;

import org.apache.commons.lang3.time.DateUtils;
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.DbSchema;
Expand Down Expand Up @@ -70,7 +71,7 @@ public static MergeSyncManager get()
return _instance;
}

private static final Logger _log = Logger.getLogger(MergeSyncManager.class);
private static final Logger _log = LogManager.getLogger(MergeSyncManager.class);
private Integer _syncInterval;

public static final String DATA_SOURCE_PROP_NAME = "dataSourceName";
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5 changes: 3 additions & 2 deletions mergesync/src/org/labkey/mergesync/MergeSyncRunner.java
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Expand Up @@ -2,7 +2,8 @@

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
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.cache.CacheManager;
import org.labkey.api.collections.CaseInsensitiveHashMap;
Expand Down Expand Up @@ -62,7 +63,7 @@
*/
public class MergeSyncRunner implements Job
{
private static final Logger _log = Logger.getLogger(MergeSyncRunner.class);
private static final Logger _log = LogManager.getLogger(MergeSyncRunner.class);
protected final static SimpleDateFormat _dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd kk:mm");
protected final static SimpleDateFormat _dateFormat = new SimpleDateFormat("yyyy-MM-dd");
private final Set<String> EXCLUDED_RESULTS = PageFlowUtil.set("received", "recieved", ".", "SENT TO RHEIN CONSULTING LAB");
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5 changes: 3 additions & 2 deletions mergesync/src/org/labkey/mergesync/RequestSyncHelper.java
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Expand Up @@ -2,7 +2,8 @@

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
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.ColumnInfo;
import org.labkey.api.data.CompareType;
Expand Down Expand Up @@ -51,7 +52,7 @@
*/
public class RequestSyncHelper
{
private static final Logger _log = Logger.getLogger(RequestSyncHelper.class);
private static final Logger _log = LogManager.getLogger(RequestSyncHelper.class);
protected final static SimpleDateFormat _dateFormat = new SimpleDateFormat("yyyy-MM-dd");

private Container _container = null;
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5 changes: 3 additions & 2 deletions ogasync/src/org/labkey/ogasync/OGASyncManager.java
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Expand Up @@ -16,7 +16,8 @@

package org.labkey.ogasync;

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.DbSchema;
Expand Down Expand Up @@ -58,7 +59,7 @@ public static OGASyncManager get()
return _instance;
}

private static final Logger _log = Logger.getLogger(OGASyncManager.class);
private static final Logger _log = LogManager.getLogger(OGASyncManager.class);
public static final String LABKEY_USER_PROP_NAME = "labkeyUser";
public static final String LABKEY_CONTAINER_PROP_NAME = "labkeyContainer";
public static final String ENABLED_PROP_NAME = "etlStatus";
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5 changes: 3 additions & 2 deletions ogasync/src/org/labkey/ogasync/OGASyncRunner.java
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@@ -1,6 +1,7 @@
package org.labkey.ogasync;

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.CompareType;
Expand Down Expand Up @@ -44,7 +45,7 @@
*/
public class OGASyncRunner implements Job
{
private static final Logger _log = Logger.getLogger(OGASyncRunner.class);
private static final Logger _log = LogManager.getLogger(OGASyncRunner.class);
private static final String INVESTIGATOR_EMPLOYYE_ID_NUMBER = "investigatorEmployeeNumber";
private static final String FISCAL_AUTHORITY_EMPLOYEE_ID_NUMBER = "fiscalAuthorityNumber";
private static final String ADFM_EMP_NUM = "ADFM_EMP_NUM";
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5 changes: 3 additions & 2 deletions onprc_billing/src/org/labkey/onprc_billing/query/BillingTriggerHelper.java
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@@ -1,7 +1,8 @@
package org.labkey.onprc_billing.query;

import org.apache.commons.lang3.time.DateUtils;
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.Aggregate;
import org.labkey.api.data.CompareType;
Expand Down Expand Up @@ -42,7 +43,7 @@ public class BillingTriggerHelper
{
private Container _container = null;
private User _user = null;
private static final Logger _log = Logger.getLogger(BillingTriggerHelper.class);
private static final Logger _log = LogManager.getLogger(BillingTriggerHelper.class);

public BillingTriggerHelper(int userId, String containerId)
{
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5 changes: 3 additions & 2 deletions onprc_billing/src/org/labkey/onprc_billing/table/ONPRC_BillingCustomizer.java
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@@ -1,6 +1,7 @@
package org.labkey.onprc_billing.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.ColumnInfo;
import org.labkey.api.data.Container;
Expand All @@ -27,7 +28,7 @@
*/
public class ONPRC_BillingCustomizer extends AbstractTableCustomizer
{
private static final Logger _log = Logger.getLogger(ONPRC_BillingCustomizer.class);
private static final Logger _log = LogManager.getLogger(ONPRC_BillingCustomizer.class);

// consider moving this helper to AbstractTableCustomizer
private QueryForeignKey.Builder qfk(AbstractTableInfo ti)
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5 changes: 3 additions & 2 deletions onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java
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Expand Up @@ -17,7 +17,8 @@

import org.apache.commons.beanutils.ConversionException;
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.collections.CaseInsensitiveHashMap;
import org.labkey.api.collections.CaseInsensitiveHashSet;
Expand Down Expand Up @@ -99,7 +100,7 @@ public class ONPRC_EHRTriggerHelper
{
private Container _container = null;
private User _user = null;
private static final Logger _log = Logger.getLogger(ONPRC_EHRTriggerHelper.class);
private static final Logger _log = LogManager.getLogger(ONPRC_EHRTriggerHelper.class);
private Map<String, TableInfo> _cachedTables = new HashMap<>();

private List<Map<String, Object>> _cachedCageSizeRecords = null;
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5 changes: 3 additions & 2 deletions onprc_ehr/src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java
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Expand Up @@ -16,7 +16,8 @@
package org.labkey.onprc_ehr.table;

import org.apache.commons.beanutils.ConversionException;
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 Down Expand Up @@ -76,7 +77,7 @@
*/
public class ONPRC_EHRCustomizer extends AbstractTableCustomizer
{
private static final Logger _log = Logger.getLogger(ONPRC_EHRCustomizer.class);
private static final Logger _log = LogManager.getLogger(ONPRC_EHRCustomizer.class);

public ONPRC_EHRCustomizer()
{
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5 changes: 3 additions & 2 deletions sla/src/org/labkey/sla/etl/ETL.java
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Expand Up @@ -15,7 +15,8 @@
*/
package org.labkey.sla.etl;

import org.apache.log4j.Logger;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.labkey.api.data.PropertyManager;

import java.io.IOException;
Expand All @@ -32,7 +33,7 @@
*/
public class ETL
{
private final static Logger log = Logger.getLogger(ETL.class);
private final static Logger log = LogManager.getLogger(ETL.class);
private static ScheduledExecutorService executor;
private static ETLRunnable runnable;
private static boolean isScheduled = false;
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5 changes: 3 additions & 2 deletions sla/src/org/labkey/sla/etl/ETLRunnable.java
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Expand Up @@ -18,7 +18,8 @@
import com.google.common.base.Charsets;
import com.google.common.io.Files;
import org.apache.commons.codec.binary.Base64;
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.ColumnInfo;
import org.labkey.api.data.CompareType;
Expand Down Expand Up @@ -91,7 +92,7 @@ public class ETLRunnable implements Runnable
public final static String CONFIG_PROPERTY_DOMAIN = "org.labkey.sla.etl.config";
public final static byte[] DEFAULT_VERSION = new byte[0];

private final static Logger log = Logger.getLogger(ETLRunnable.class);
private final static Logger log = LogManager.getLogger(ETLRunnable.class);
private static final int UPSERT_BATCH_SIZE = 500;
private boolean isRunning = false;
private boolean shutdown;
Expand Down