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Merged
labkey-ankurj merged 1 commit into from
Aug 5, 2020
Merged

Item 7490: upgrade log4j #46

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27 changes: 14 additions & 13 deletions OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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<Map<String, Object>> updateResult;
try
{
Expand All @@ -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"));
Expand All @@ -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);
Expand Down Expand Up @@ -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"));
}
}
}
Expand All @@ -283,15 +284,15 @@ 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);
}
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;
}

Expand All @@ -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
{
Expand All @@ -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"));
}
}
}
Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/GenotypingController.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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);

Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -78,7 +79,7 @@ public class GenotypingQuerySchema extends UserSchema
private static final Set<String> 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<Integer, Map<String, String>> _allHaplotypes;

Expand Down
3 changes: 2 additions & 1 deletion genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
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Expand Up @@ -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;
Expand Down
11 changes: 6 additions & 5 deletions genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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<File, File> files = new HashMap<>();
files.put(new File("a"), new File("b"));
files.put(new File("c"), new File("d"));
Expand All @@ -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<File, File> files = new HashMap<>();
files.put(new File("a"), new File("b"));
files.put(new File("c"), new File("b"));
Expand Down Expand Up @@ -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<Pair<Integer, Integer>, FileInfo> outputs = parser.parseFastqFiles(null);
Assert.assertEquals("Outputs from parseFastqFiles with old headers were not as expected.", expectedOutputs, outputs.keySet());

Expand All @@ -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());
}
Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/SampleManager.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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<String> POSSIBLE_SAMPLE_KEYS = new CaseInsensitiveHashSet(MID5_COLUMN_NAME, MID3_COLUMN_NAME, AMPLICON_COLUMN_NAME);

Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java
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Expand Up @@ -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;
Expand All @@ -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()
Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
}
}
Expand Down
5 changes: 3 additions & 2 deletions genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java
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Expand Up @@ -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;
Expand All @@ -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"));
Expand Down