From 0deb6d4a3e233cc3a9a80453b290a438824a5f8a Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Fri, 10 Jul 2020 16:59:37 -0700 Subject: [PATCH 1/2] Item 7490: upgrade log4j --- .../src/org/labkey/GeneticsCore/GeneticsCoreController.java | 5 +++-- .../GeneticsCore/notification/GeneticsCoreNotification.java | 5 +++-- mergesync/src/org/labkey/mergesync/MergeSyncManager.java | 5 +++-- mergesync/src/org/labkey/mergesync/MergeSyncRunner.java | 5 +++-- mergesync/src/org/labkey/mergesync/RequestSyncHelper.java | 5 +++-- ogasync/src/org/labkey/ogasync/OGASyncManager.java | 5 +++-- ogasync/src/org/labkey/ogasync/OGASyncRunner.java | 5 +++-- .../org/labkey/onprc_billing/query/BillingTriggerHelper.java | 5 +++-- .../labkey/onprc_billing/table/ONPRC_BillingCustomizer.java | 5 +++-- .../org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java | 5 +++-- .../src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java | 5 +++-- sla/src/org/labkey/sla/etl/ETL.java | 5 +++-- sla/src/org/labkey/sla/etl/ETLRunnable.java | 5 +++-- 13 files changed, 39 insertions(+), 26 deletions(-) diff --git a/GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java b/GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java index 3756cd2fb..bd1e55248 100644 --- a/GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java +++ b/GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreController.java @@ -1,6 +1,7 @@ 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; /** @@ -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() { diff --git a/GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java b/GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java index 93663dff3..1b5f67d84 100644 --- a/GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java +++ b/GeneticsCore/src/org/labkey/GeneticsCore/notification/GeneticsCoreNotification.java @@ -1,6 +1,7 @@ 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; @@ -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(); diff --git a/mergesync/src/org/labkey/mergesync/MergeSyncManager.java b/mergesync/src/org/labkey/mergesync/MergeSyncManager.java index 25cc76445..bb5a0a96f 100644 --- a/mergesync/src/org/labkey/mergesync/MergeSyncManager.java +++ b/mergesync/src/org/labkey/mergesync/MergeSyncManager.java @@ -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; @@ -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"; diff --git a/mergesync/src/org/labkey/mergesync/MergeSyncRunner.java b/mergesync/src/org/labkey/mergesync/MergeSyncRunner.java index cfe7c367c..9fca6f8d9 100644 --- a/mergesync/src/org/labkey/mergesync/MergeSyncRunner.java +++ b/mergesync/src/org/labkey/mergesync/MergeSyncRunner.java @@ -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; @@ -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 EXCLUDED_RESULTS = PageFlowUtil.set("received", "recieved", ".", "SENT TO RHEIN CONSULTING LAB"); diff --git a/mergesync/src/org/labkey/mergesync/RequestSyncHelper.java b/mergesync/src/org/labkey/mergesync/RequestSyncHelper.java index 13b2c341c..0b1473110 100644 --- a/mergesync/src/org/labkey/mergesync/RequestSyncHelper.java +++ b/mergesync/src/org/labkey/mergesync/RequestSyncHelper.java @@ -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; @@ -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; diff --git a/ogasync/src/org/labkey/ogasync/OGASyncManager.java b/ogasync/src/org/labkey/ogasync/OGASyncManager.java index b54303ed9..4711f787f 100644 --- a/ogasync/src/org/labkey/ogasync/OGASyncManager.java +++ b/ogasync/src/org/labkey/ogasync/OGASyncManager.java @@ -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; @@ -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"; diff --git a/ogasync/src/org/labkey/ogasync/OGASyncRunner.java b/ogasync/src/org/labkey/ogasync/OGASyncRunner.java index c67ced4f4..97dc9402c 100644 --- a/ogasync/src/org/labkey/ogasync/OGASyncRunner.java +++ b/ogasync/src/org/labkey/ogasync/OGASyncRunner.java @@ -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; @@ -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"; diff --git a/onprc_billing/src/org/labkey/onprc_billing/query/BillingTriggerHelper.java b/onprc_billing/src/org/labkey/onprc_billing/query/BillingTriggerHelper.java index 9d0da4ff8..dc25bf273 100644 --- a/onprc_billing/src/org/labkey/onprc_billing/query/BillingTriggerHelper.java +++ b/onprc_billing/src/org/labkey/onprc_billing/query/BillingTriggerHelper.java @@ -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; @@ -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) { diff --git a/onprc_billing/src/org/labkey/onprc_billing/table/ONPRC_BillingCustomizer.java b/onprc_billing/src/org/labkey/onprc_billing/table/ONPRC_BillingCustomizer.java index 9709d2a39..3c678ea9d 100644 --- a/onprc_billing/src/org/labkey/onprc_billing/table/ONPRC_BillingCustomizer.java +++ b/onprc_billing/src/org/labkey/onprc_billing/table/ONPRC_BillingCustomizer.java @@ -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; @@ -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) diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java b/onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java index 3e17cead0..0bb5075c2 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/query/ONPRC_EHRTriggerHelper.java @@ -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; @@ -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 _cachedTables = new HashMap<>(); private List> _cachedCageSizeRecords = null; diff --git a/onprc_ehr/src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java b/onprc_ehr/src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java index 0ecc0d611..61da6b7e8 100644 --- a/onprc_ehr/src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java +++ b/onprc_ehr/src/org/labkey/onprc_ehr/table/ONPRC_EHRCustomizer.java @@ -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; @@ -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() { diff --git a/sla/src/org/labkey/sla/etl/ETL.java b/sla/src/org/labkey/sla/etl/ETL.java index 7b995b022..f79d0378f 100644 --- a/sla/src/org/labkey/sla/etl/ETL.java +++ b/sla/src/org/labkey/sla/etl/ETL.java @@ -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; @@ -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; diff --git a/sla/src/org/labkey/sla/etl/ETLRunnable.java b/sla/src/org/labkey/sla/etl/ETLRunnable.java index d41345e23..8a7995006 100644 --- a/sla/src/org/labkey/sla/etl/ETLRunnable.java +++ b/sla/src/org/labkey/sla/etl/ETLRunnable.java @@ -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; @@ -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; From 765158088b843550ff837ff4e9f3230d4fa731d4 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Wed, 29 Jul 2020 18:03:46 -0700 Subject: [PATCH 2/2] fix compilation error in ehr build --- .../src/org/labkey/hormoneassay/assay/PivotedImportMethod.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HormoneAssay/src/org/labkey/hormoneassay/assay/PivotedImportMethod.java b/HormoneAssay/src/org/labkey/hormoneassay/assay/PivotedImportMethod.java index 353435e86..38bf667fc 100644 --- a/HormoneAssay/src/org/labkey/hormoneassay/assay/PivotedImportMethod.java +++ b/HormoneAssay/src/org/labkey/hormoneassay/assay/PivotedImportMethod.java @@ -1,6 +1,6 @@ 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;