From 7b1ce52f31fa09d019c01dd39bdb725f72085405 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Fri, 10 Jul 2020 16:59:36 -0700 Subject: [PATCH] Item 7490: upgrade log4j --- .../OConnorExperimentsController.java | 27 ++++++++++--------- .../genotyping/GenotypingController.java | 5 ++-- .../genotyping/GenotypingQuerySchema.java | 5 ++-- .../genotyping/HaplotypeDataHandler.java | 3 ++- .../genotyping/IlluminaFastqParser.java | 11 ++++---- .../org/labkey/genotyping/SampleManager.java | 5 ++-- .../genotyping/galaxy/GalaxyManager.java | 5 ++-- .../genotyping/galaxy/GalaxyServer.java | 5 ++-- .../galaxy/WorkflowCompletionMonitor.java | 5 ++-- 9 files changed, 40 insertions(+), 31 deletions(-) diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java index f4f4a03..48a4d61 100644 --- a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java +++ b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java @@ -17,7 +17,8 @@ package org.labkey.oconnorexperiments; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.FormHandlerAction; @@ -124,7 +125,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception { if (form.isFinalMigration()) { - Logger.getLogger(OConnorExperimentsController.class).info("Final migration to be performed - file move events will be performed (irreversible)."); + LogManager.getLogger(OConnorExperimentsController.class).info("Final migration to be performed - file move events will be performed (irreversible)."); } // global containers @@ -192,7 +193,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception User user = UserManager.getUserByDisplayName((String) databaseMap.get("initials")); if (user == null) { - Logger.getLogger(OConnorExperimentsController.class).warn("User '" + databaseMap.get("initials") + "' not found for experiment " + databaseMap.get("expnumber")); + LogManager.getLogger(OConnorExperimentsController.class).warn("User '" + databaseMap.get("initials") + "' not found for experiment " + databaseMap.get("expnumber")); effectiveUser = getUser(); } else @@ -202,7 +203,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception } databaseMap.put("EffectiveUser", effectiveUser); - Logger.getLogger(OConnorExperimentsController.class).info("Insert on experiment " + databaseMap.get("expnumber")); + LogManager.getLogger(OConnorExperimentsController.class).info("Insert on experiment " + databaseMap.get("expnumber")); List> updateResult; try { @@ -211,13 +212,13 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception catch (Exception e) { // log the error to the logfile and continue - Logger.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber + " with exception " + e.getMessage()); + LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber + " with exception " + e.getMessage()); continue; } if (batchErrors.hasErrors()) { // throw batchErrors.getLastRowError(); - Logger.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber); + LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber); } Container workbookContainer = ContainerManager.getForId((String)updateResult.get(0).get("EntityId")); @@ -232,7 +233,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception // Move files File sourceFile = new File(fileContentService.getFileRoot(sourceContainer).getPath() + File.separator + "@files", databaseMap.get("expnumber").toString()); File targetDir = new File(fileContentService.getFileRoot(targetContainer).getPath() + File.separator + databaseMap.get("expnumber").toString() + File.separator + "@files"); - Logger.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile.toString() + "' to directory '" + targetDir.toString() +"'" ); + LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile.toString() + "' to directory '" + targetDir.toString() +"'" ); if (sourceFile.exists()) { FileUtils.copyDirectory(sourceFile, targetDir); @@ -274,7 +275,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception } else { - Logger.getLogger(OConnorExperimentsController.class).warn("child container not found: " + parents[i] + " for experiment " + databaseMap.get("expnumber") + " with username " + databaseMap.get("initials")); + LogManager.getLogger(OConnorExperimentsController.class).warn("child container not found: " + parents[i] + " for experiment " + databaseMap.get("expnumber") + " with username " + databaseMap.get("initials")); } } } @@ -283,7 +284,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception map.put("ParentExperiments", parentsEntityId.toArray(new String[parentsEntityId.size()])); // workaround, pass user, container - databaseMap.get("Container"), singleton list - Logger.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber")); + LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber")); try { queryUpdateService.updateRows(getUser(), targetContainer, Collections.singletonList(map), null, null, null); @@ -291,7 +292,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception catch (Exception e) { // log the error to the logfile and continue - Logger.getLogger(OConnorExperimentsController.class).warn("Error updating parent experiments for experiment number " + expNumber + " with exception " + e.getMessage()); + LogManager.getLogger(OConnorExperimentsController.class).warn("Error updating parent experiments for experiment number " + expNumber + " with exception " + e.getMessage()); continue; } @@ -318,7 +319,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception Container workbookContainer = targetContainer.getChild(databaseMap.get("expnumber").toString()); if (workbookContainer == null) { - Logger.getLogger(OConnorExperimentsController.class).warn("Updating wiki, container not found: " + databaseMap.get("expnumber")); + LogManager.getLogger(OConnorExperimentsController.class).warn("Updating wiki, container not found: " + databaseMap.get("expnumber")); } else { @@ -334,14 +335,14 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception catch (Exception e) { // log the error to the logfile and continue - Logger.getLogger(OConnorExperimentsController.class).warn("Error wiki for experiment number " + expNumber + " with exception " + e.getMessage()); + LogManager.getLogger(OConnorExperimentsController.class).warn("Error wiki for experiment number " + expNumber + " with exception " + e.getMessage()); continue; } finally { in.closeInputStream(); } - Logger.getLogger(OConnorExperimentsController.class).info("Inserting wiki for experiment " + databaseMap.get("expnumber")); + LogManager.getLogger(OConnorExperimentsController.class).info("Inserting wiki for experiment " + databaseMap.get("expnumber")); } } } diff --git a/genotyping/src/org/labkey/genotyping/GenotypingController.java b/genotyping/src/org/labkey/genotyping/GenotypingController.java index 14a64c0..d297931 100644 --- a/genotyping/src/org/labkey/genotyping/GenotypingController.java +++ b/genotyping/src/org/labkey/genotyping/GenotypingController.java @@ -17,7 +17,8 @@ package org.labkey.genotyping; import org.apache.commons.io.IOUtils; -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.action.ExportAction; @@ -139,7 +140,7 @@ public class GenotypingController extends SpringActionController { - private static final Logger LOG = Logger.getLogger(GenotypingController.class); + private static final Logger LOG = LogManager.getLogger(GenotypingController.class); @SuppressWarnings({"unchecked"}) private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(GenotypingController.class); diff --git a/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java b/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java index cac99d6..8faa5c8 100644 --- a/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java +++ b/genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java @@ -15,7 +15,8 @@ */ package org.labkey.genotyping; -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.CaseInsensitiveHashSet; @@ -78,7 +79,7 @@ public class GenotypingQuerySchema extends UserSchema private static final Set TABLE_NAMES; /** When building up concatenated haplotypes, a placeholder for NULL values */ private static final String NULL_HAPLOTYPE_MARKER = "~"; - private static final Logger LOG = Logger.getLogger(GenotypingQuerySchema.class); + private static final Logger LOG = LogManager.getLogger(GenotypingQuerySchema.class); private SortedMap> _allHaplotypes; diff --git a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java index b999cb7..5b2e60f 100644 --- a/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java +++ b/genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java @@ -15,7 +15,8 @@ */ package org.labkey.genotyping; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.NotNull; import org.junit.Assert; import org.junit.Test; diff --git a/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java b/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java index fe977ec..7544f5b 100644 --- a/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java +++ b/genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java @@ -20,7 +20,8 @@ import org.apache.commons.collections4.ListValuedMap; import org.apache.commons.collections4.multimap.ArrayListValuedHashMap; import org.apache.commons.io.FileUtils; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.junit.Assert; import org.junit.Before; @@ -333,7 +334,7 @@ public static class DupeTestCase extends Assert @Test public void testNoDupes() throws PipelineJobException { - IlluminaFastqParser parser = new IlluminaFastqParser(null, Collections.emptyMap(), Collections.emptyMap(), Collections.emptyMap(), Logger.getLogger(DupeTestCase.class), Collections.emptyList()); + IlluminaFastqParser parser = new IlluminaFastqParser(null, Collections.emptyMap(), Collections.emptyMap(), Collections.emptyMap(), LogManager.getLogger(DupeTestCase.class), Collections.emptyList()); Map files = new HashMap<>(); files.put(new File("a"), new File("b")); files.put(new File("c"), new File("d")); @@ -343,7 +344,7 @@ public void testNoDupes() throws PipelineJobException @Test(expected = PipelineJobException.class) public void testDupeTargets() throws PipelineJobException { - IlluminaFastqParser parser = new IlluminaFastqParser(null, Collections.emptyMap(), Collections.emptyMap(), Collections.emptyMap(), Logger.getLogger(DupeTestCase.class), Collections.emptyList()); + IlluminaFastqParser parser = new IlluminaFastqParser(null, Collections.emptyMap(), Collections.emptyMap(), Collections.emptyMap(), LogManager.getLogger(DupeTestCase.class), Collections.emptyList()); Map files = new HashMap<>(); files.put(new File("a"), new File("b")); files.put(new File("c"), new File("b")); @@ -500,7 +501,7 @@ public void testHeaders() throws PipelineJobException, IOException i++; } - IlluminaFastqParser parser = new IlluminaFastqParser(null, sampleIndexToIdMap, sampleIdToIndexMap, Collections.emptyMap(), Logger.getLogger(HeaderTestCase.class), oldHeaderFiles); + IlluminaFastqParser parser = new IlluminaFastqParser(null, sampleIndexToIdMap, sampleIdToIndexMap, Collections.emptyMap(), LogManager.getLogger(HeaderTestCase.class), oldHeaderFiles); Map, FileInfo> outputs = parser.parseFastqFiles(null); Assert.assertEquals("Outputs from parseFastqFiles with old headers were not as expected.", expectedOutputs, outputs.keySet()); @@ -513,7 +514,7 @@ public void testHeaders() throws PipelineJobException, IOException newHeaderFiles.add(target); } - parser = new IlluminaFastqParser(null, sampleIndexToIdMap, sampleIdToIndexMap, Collections.emptyMap(), Logger.getLogger(HeaderTestCase.class), newHeaderFiles); + parser = new IlluminaFastqParser(null, sampleIndexToIdMap, sampleIdToIndexMap, Collections.emptyMap(), LogManager.getLogger(HeaderTestCase.class), newHeaderFiles); outputs = parser.parseFastqFiles(null); Assert.assertEquals("Outputs from parseFastqFiles with new headers were not as expected.", expectedOutputs, outputs.keySet()); } diff --git a/genotyping/src/org/labkey/genotyping/SampleManager.java b/genotyping/src/org/labkey/genotyping/SampleManager.java index a0bc91d..ab8e43e 100644 --- a/genotyping/src/org/labkey/genotyping/SampleManager.java +++ b/genotyping/src/org/labkey/genotyping/SampleManager.java @@ -16,7 +16,8 @@ package org.labkey.genotyping; 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.CaseInsensitiveHashSet; import org.labkey.api.data.ColumnInfo; @@ -52,7 +53,7 @@ public class SampleManager public static final String AMPLICON_COLUMN_NAME = "amplicon"; public static final String KEY_COLUMN_NAME = "key"; - private static final Logger LOG = Logger.getLogger(SampleManager.class); + private static final Logger LOG = LogManager.getLogger(SampleManager.class); static final Set POSSIBLE_SAMPLE_KEYS = new CaseInsensitiveHashSet(MID5_COLUMN_NAME, MID3_COLUMN_NAME, AMPLICON_COLUMN_NAME); diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java index 9877925..af8899c 100644 --- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java +++ b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java @@ -16,7 +16,8 @@ package org.labkey.genotyping.galaxy; -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.PropertyManager; import org.labkey.api.security.User; @@ -31,7 +32,7 @@ public class GalaxyManager { - private static final Logger LOG = Logger.getLogger(GalaxyManager.class); + private static final Logger LOG = LogManager.getLogger(GalaxyManager.class); private static final GalaxyManager _instance = new GalaxyManager(); private GalaxyManager() diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java index 16711f0..6fceaea 100644 --- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java +++ b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java @@ -24,7 +24,8 @@ import org.apache.http.client.methods.HttpRequestBase; import org.apache.http.entity.StringEntity; import org.apache.http.impl.client.DefaultHttpClient; -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.JSONArray; @@ -125,7 +126,7 @@ public boolean canConnect() } catch (IOException e) { - Logger.getLogger(GalaxyServer.class).info("Test connect to Galaxy server failed", e); + LogManager.getLogger(GalaxyServer.class).info("Test connect to Galaxy server failed", e); return false; } } diff --git a/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java b/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java index 8b58f58..be94951 100644 --- a/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java +++ b/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java @@ -15,7 +15,8 @@ */ package org.labkey.genotyping.galaxy; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.ContextListener; import org.labkey.api.util.ShutdownListener; import org.labkey.genotyping.GenotypingManager; @@ -41,7 +42,7 @@ */ public class WorkflowCompletionMonitor implements ShutdownListener { - private static final Logger LOG = Logger.getLogger(WorkflowCompletionMonitor.class); + private static final Logger LOG = LogManager.getLogger(WorkflowCompletionMonitor.class); private static final WorkflowCompletionMonitor INSTANCE = new WorkflowCompletionMonitor(); private final ScheduledExecutorService _executor = Executors.newSingleThreadScheduledExecutor(r -> new Thread(r, "Genotyping Workflow Completion Monitor"));