From ae6a35d4d6c80cbbcb3e43087bbb19411c42f4a4 Mon Sep 17 00:00:00 2001 From: labkey-ankurj Date: Fri, 10 Jul 2020 16:59:35 -0700 Subject: [PATCH] Item 7490: upgrade log4j --- lincs/src/org/labkey/lincs/CustomGctBuilder.java | 5 +++-- lincs/src/org/labkey/lincs/DocImportListenter.java | 5 +++-- lincs/src/org/labkey/lincs/LincsManager.java | 5 +++-- lincs/src/org/labkey/lincs/psp/LincsPspTask.java | 3 ++- lincs/src/org/labkey/lincs/psp/LincsPspUtil.java | 3 ++- .../org/labkey/panoramapublic/PanoramaPublicController.java | 5 +++-- .../panoramapublic/pipeline/CopyExperimentFinalTask.java | 3 ++- .../labkey/panoramapublic/pipeline/ExperimentExportTask.java | 5 +++-- .../proteomexchange/ExperimentModificationGetter.java | 5 +++-- .../org/labkey/panoramapublic/proteomexchange/NcbiUtils.java | 2 +- .../labkey/panoramapublic/proteomexchange/PxHtmlWriter.java | 5 +++-- .../proteomexchange/SubmissionDataValidator.java | 5 +++-- .../src/org/labkey/panoramapublic/query/JournalManager.java | 5 +++-- signup/src/org/labkey/signup/SignUpController.java | 5 +++-- signup/src/org/labkey/signup/SignUpListener.java | 5 +++-- .../src/org/labkey/testresults/SendTestResultsEmail.java | 5 +++-- .../src/org/labkey/testresults/TestResultsController.java | 5 +++-- 17 files changed, 46 insertions(+), 30 deletions(-) diff --git a/lincs/src/org/labkey/lincs/CustomGctBuilder.java b/lincs/src/org/labkey/lincs/CustomGctBuilder.java index 0e446e66..f6fa8f52 100644 --- a/lincs/src/org/labkey/lincs/CustomGctBuilder.java +++ b/lincs/src/org/labkey/lincs/CustomGctBuilder.java @@ -15,7 +15,8 @@ */ package org.labkey.lincs; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.util.FileUtil; import org.labkey.lincs.view.GctUtils; @@ -34,7 +35,7 @@ public class CustomGctBuilder { private final String[] multiValueProbeAnnotations = new String[] {"pr_probe_normalization_group", "pr_probe_suitability_manual", "pr_normalization_peptide_id"}; - private final static Logger _log = Logger.getLogger(CustomGctBuilder.class); + private final static Logger _log = LogManager.getLogger(CustomGctBuilder.class); public Gct build(List files, List selectedAnnotations, Set ignoredProbeAnnotations, Set ignoredReplicateAnnotations) throws Gct.GctFileException diff --git a/lincs/src/org/labkey/lincs/DocImportListenter.java b/lincs/src/org/labkey/lincs/DocImportListenter.java index 0408dd10..8655d502 100644 --- a/lincs/src/org/labkey/lincs/DocImportListenter.java +++ b/lincs/src/org/labkey/lincs/DocImportListenter.java @@ -1,6 +1,7 @@ package org.labkey.lincs; -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.exp.api.ExpProtocol; import org.labkey.api.exp.api.ExpRun; @@ -33,7 +34,7 @@ public class DocImportListenter implements ExperimentListener { - private static Logger _log = Logger.getLogger(DocImportListenter.class); + private static Logger _log = LogManager.getLogger(DocImportListenter.class); @Override public void beforeRunCreated(Container container, User user, ExpProtocol protocol, ExpRun run) diff --git a/lincs/src/org/labkey/lincs/LincsManager.java b/lincs/src/org/labkey/lincs/LincsManager.java index f76c94ba..b25c2717 100644 --- a/lincs/src/org/labkey/lincs/LincsManager.java +++ b/lincs/src/org/labkey/lincs/LincsManager.java @@ -16,7 +16,8 @@ package org.labkey.lincs; -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.DbSchema; import org.labkey.api.data.DbSchemaType; @@ -48,7 +49,7 @@ public class LincsManager { private static final LincsManager _instance = new LincsManager(); - private static Logger _log = Logger.getLogger(LincsManager.class); + private static Logger _log = LogManager.getLogger(LincsManager.class); private LincsManager() { diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspTask.java b/lincs/src/org/labkey/lincs/psp/LincsPspTask.java index 9b369a9d..40ae86ee 100644 --- a/lincs/src/org/labkey/lincs/psp/LincsPspTask.java +++ b/lincs/src/org/labkey/lincs/psp/LincsPspTask.java @@ -1,6 +1,7 @@ package org.labkey.lincs.psp; -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.Container; import org.labkey.api.module.ModuleLoader; diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java b/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java index 65d35faa..a81e6a3b 100644 --- a/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java +++ b/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java @@ -2,7 +2,8 @@ import org.apache.commons.io.IOUtils; 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.JSONObject; import org.json.simple.JSONArray; import org.json.simple.parser.JSONParser; diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java index 7845bf53..45827998 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java @@ -19,7 +19,8 @@ import org.apache.commons.lang3.StringUtils; import org.apache.commons.validator.routines.EmailValidator; import org.apache.commons.validator.routines.UrlValidator; -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.action.ApiResponse; @@ -171,7 +172,7 @@ public PanoramaPublicController() setActionResolver(_actionResolver); } - private static final Logger LOG = Logger.getLogger(PanoramaPublicController.class); + private static final Logger LOG = LogManager.getLogger(PanoramaPublicController.class); // ------------------------------------------------------------------------ // BEGIN Actions for journal groups. diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java index a4b4fa9f..a48be3a6 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java @@ -15,7 +15,8 @@ */ package org.labkey.panoramapublic.pipeline; -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.Container; import org.labkey.api.data.ContainerManager; diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java index b469da5b..474a4a56 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java +++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java @@ -15,7 +15,8 @@ */ package org.labkey.panoramapublic.pipeline; -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.admin.FolderExportContext; import org.labkey.api.admin.FolderWriterImpl; @@ -109,7 +110,7 @@ public void writeExperiment(CopyExperimentJobSupport support, ExperimentAnnotati FolderExportContext ctx = new FolderExportContext(user, source, PageFlowUtil.set(templateWriterTypes), null, includeSubfolders, PHI.NotPHI, false, - false, false, new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class))); + false, false, new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class))); File exportDir = support.getExportDir(); diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java index 7e25d86b..1a415f72 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java @@ -16,7 +16,8 @@ package org.labkey.panoramapublic.proteomexchange; 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.junit.Assert; import org.junit.Test; import org.labkey.api.data.Container; @@ -38,7 +39,7 @@ public class ExperimentModificationGetter { - private static final Logger LOG = Logger.getLogger(ExperimentModificationGetter.class); + private static final Logger LOG = LogManager.getLogger(ExperimentModificationGetter.class); public static List getModifications(ExperimentAnnotations expAnnot) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java index cc0a4c41..b1149a0f 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java @@ -48,7 +48,7 @@ public class NcbiUtils private static final String eutilsUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy"; private static final String autoCompUrl = "https://blast.ncbi.nlm.nih.gov/portal/utils/autocomp.fcgi?dict=taxids_sg&q="; - // private static final Logger LOG = Logger.getLogger(NcbiUtils.class); + // private static final Logger LOG = LogManager.getLogger(NcbiUtils.class); public static List getCompletions(String token) throws PxException { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java index 9e49de27..a1292a75 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java @@ -16,7 +16,8 @@ package org.labkey.panoramapublic.proteomexchange; 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.security.User; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.view.ShortURLRecord; @@ -33,7 +34,7 @@ public class PxHtmlWriter extends PxWriter private final StringBuilder _output; private boolean _usePxTestDb; - private static final Logger LOG = Logger.getLogger(PxHtmlWriter.class); + private static final Logger LOG = LogManager.getLogger(PxHtmlWriter.class); public PxHtmlWriter(StringBuilder out) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java index fb03235a..1e9a157c 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java +++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java @@ -17,7 +17,8 @@ import org.apache.commons.io.FilenameUtils; 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.junit.Assert; import org.junit.Test; import org.labkey.api.data.CompareType; @@ -50,7 +51,7 @@ public class SubmissionDataValidator public static final int MIN_ABSTRACT_LENGTH = 50; public static final int MIN_TITLE_LENGTH = 30; - private static final Logger LOG = Logger.getLogger(SubmissionDataValidator.class); + private static final Logger LOG = LogManager.getLogger(SubmissionDataValidator.class); public static boolean isValid(ExperimentAnnotations expAnnot, boolean skipMetaDataCheck, boolean skipRawDataCheck, boolean skipModificationCheck) { diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java index ebb34887..1472d14a 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java @@ -15,7 +15,8 @@ */ package org.labkey.panoramapublic.query; -import org.apache.log4j.Logger; +import org.apache.logging.log4j.Logger; +import org.apache.logging.log4j.LogManager; import org.labkey.api.admin.FolderExportPermission; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; @@ -70,7 +71,7 @@ */ public class JournalManager { - private static final Logger LOG = Logger.getLogger(JournalManager.class); + private static final Logger LOG = LogManager.getLogger(JournalManager.class); public static List getJournals() { diff --git a/signup/src/org/labkey/signup/SignUpController.java b/signup/src/org/labkey/signup/SignUpController.java index 75ff2d1d..a0844372 100644 --- a/signup/src/org/labkey/signup/SignUpController.java +++ b/signup/src/org/labkey/signup/SignUpController.java @@ -17,7 +17,8 @@ package org.labkey.signup; 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.action.ReadOnlyApiAction; import org.labkey.api.action.MutatingApiAction; import org.labkey.api.action.ApiResponse; @@ -66,7 +67,7 @@ public class SignUpController extends SpringActionController { - private static final Logger _log = Logger.getLogger(SignUpController.class); + private static final Logger _log = LogManager.getLogger(SignUpController.class); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(SignUpController.class); diff --git a/signup/src/org/labkey/signup/SignUpListener.java b/signup/src/org/labkey/signup/SignUpListener.java index 0a684c7a..7062879e 100644 --- a/signup/src/org/labkey/signup/SignUpListener.java +++ b/signup/src/org/labkey/signup/SignUpListener.java @@ -16,7 +16,8 @@ package org.labkey.signup; -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.Container; import org.labkey.api.data.ContainerManager.ContainerListener; @@ -30,7 +31,7 @@ public class SignUpListener implements ContainerListener, UserManager.UserListener { - private static final Logger _log = Logger.getLogger(SignUpListener.class); + private static final Logger _log = LogManager.getLogger(SignUpListener.class); @Override public void userDeletedFromSite(User user) diff --git a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java index 8f345e83..0314d56f 100644 --- a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java +++ b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java @@ -1,6 +1,7 @@ package org.labkey.testresults; -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; @@ -46,7 +47,7 @@ public interface DEFAULT_EMAIL { String ADMIN_EMAIL = "yuval@uw.edu"; } - private static final Logger LOG = Logger.getLogger(SendTestResultsEmail.class); + private static final Logger LOG = LogManager.getLogger(SendTestResultsEmail.class); public SendTestResultsEmail() { diff --git a/testresults/src/org/labkey/testresults/TestResultsController.java b/testresults/src/org/labkey/testresults/TestResultsController.java index 83ede95d..6a9de8e4 100644 --- a/testresults/src/org/labkey/testresults/TestResultsController.java +++ b/testresults/src/org/labkey/testresults/TestResultsController.java @@ -19,7 +19,8 @@ import org.apache.commons.lang3.ArrayUtils; import org.apache.commons.lang3.time.DateUtils; import org.apache.commons.validator.routines.EmailValidator; -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.action.ApiSimpleResponse; import org.labkey.api.action.MutatingApiAction; @@ -118,7 +119,7 @@ */ public class TestResultsController extends SpringActionController { - private static final Logger _log = Logger.getLogger(TestResultsController.class); + private static final Logger _log = LogManager.getLogger(TestResultsController.class); private static final SimpleDateFormat MDYFormat = new SimpleDateFormat("MM/dd/yyyy"); private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(TestResultsController.class);