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

Item 7490: upgrade log4j #60

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ae6a35d
Item 7490: upgrade log4j
labkey-ankurj Jul 10, 2020
e3758d6
Merge branch 'develop' into fb_log4J_upgrade
labkey-ankurj Aug 5, 2020
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5 changes: 3 additions & 2 deletions lincs/src/org/labkey/lincs/CustomGctBuilder.java
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Expand Up @@ -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;

Expand All @@ -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<Path> files, List<LincsController.SelectedAnnotation> selectedAnnotations,
Set<String> ignoredProbeAnnotations, Set<String> ignoredReplicateAnnotations) throws Gct.GctFileException
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5 changes: 3 additions & 2 deletions lincs/src/org/labkey/lincs/DocImportListenter.java
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@@ -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;
Expand Down Expand Up @@ -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)
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5 changes: 3 additions & 2 deletions lincs/src/org/labkey/lincs/LincsManager.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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()
{
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3 changes: 2 additions & 1 deletion lincs/src/org/labkey/lincs/psp/LincsPspTask.java
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@@ -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;
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3 changes: 2 additions & 1 deletion lincs/src/org/labkey/lincs/psp/LincsPspUtil.java
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Expand Up @@ -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;
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5 changes: 3 additions & 2 deletions panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -185,7 +186,7 @@ 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.
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3 changes: 2 additions & 1 deletion panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
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Expand Up @@ -15,9 +15,10 @@
*/
package org.labkey.panoramapublic.pipeline;

import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
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5 changes: 3 additions & 2 deletions panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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();
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5 changes: 3 additions & 2 deletions ...amapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java
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Expand Up @@ -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;
Expand All @@ -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<PxModification> getModifications(ExperimentAnnotations expAnnot)
{
Expand Down
2 changes: 1 addition & 1 deletion panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
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Expand Up @@ -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<JSONObject> getCompletions(String token) throws PxException
{
Expand Down
5 changes: 3 additions & 2 deletions panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java
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Expand Up @@ -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;
Expand All @@ -33,7 +34,7 @@ public class PxHtmlWriter extends PxWriter
{
private final StringBuilder _output;

private static final Logger LOG = Logger.getLogger(PxHtmlWriter.class);
private static final Logger LOG = LogManager.getLogger(PxHtmlWriter.class);

public PxHtmlWriter(StringBuilder out)
{
Expand Down
5 changes: 3 additions & 2 deletions panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -52,7 +53,7 @@ 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)
{
Expand Down
5 changes: 3 additions & 2 deletions panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -69,7 +70,7 @@
*/
public class JournalManager
{
private static final Logger LOG = Logger.getLogger(JournalManager.class);
private static final Logger LOG = LogManager.getLogger(JournalManager.class);

public static List<Journal> getJournals()
{
Expand Down
5 changes: 3 additions & 2 deletions signup/src/org/labkey/signup/SignUpController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);

Expand Down
5 changes: 3 additions & 2 deletions signup/src/org/labkey/signup/SignUpListener.java
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Expand Up @@ -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;
Expand All @@ -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)
Expand Down
5 changes: 3 additions & 2 deletions testresults/src/org/labkey/testresults/SendTestResultsEmail.java
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@@ -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;
Expand Down Expand Up @@ -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()
{
Expand Down
5 changes: 3 additions & 2 deletions testresults/src/org/labkey/testresults/TestResultsController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);
Expand Down