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Merged
labkey-jeckels merged 1 commit into from
May 12, 2026
Merged

Auto-refactor lint cleanup #197

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37 changes: 18 additions & 19 deletions OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,6 @@
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
import org.labkey.api.view.NotFoundException;
Expand All @@ -85,6 +84,7 @@ public class OConnorExperimentsController extends SpringActionController
{
public static final String EXPERIMENTS = "Experiments";
private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(OConnorExperimentsController.class);
public static final org.apache.logging.log4j.Logger LOG = LogManager.getLogger(OConnorExperimentsController.class);

public OConnorExperimentsController()
{
Expand All @@ -110,7 +110,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
{
if (form.isFinalMigration())
{
LogManager.getLogger(OConnorExperimentsController.class).info("Final migration to be performed - file move events will be performed (irreversible).");
LOG.info("Final migration to be performed - file move events will be performed (irreversible).");
}

// global containers
Expand Down Expand Up @@ -160,7 +160,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
newType.put("Name", currentType);
newType.put("Enabled", true);
List<Map<String, Object>> newTypes = typeUpdateService.insertRows(getUser(), getContainer(), Collections.singletonList(newType), new BatchValidationException(), null, null);
targetType = (Integer) newTypes.get(0).get("RowId");
targetType = (Integer) newTypes.getFirst().get("RowId");
}
}

Expand All @@ -178,7 +178,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
User user = UserManager.getUserByDisplayName((String) databaseMap.get("initials"));
if (user == null)
{
LogManager.getLogger(OConnorExperimentsController.class).warn("User '" + databaseMap.get("initials") + "' not found for experiment " + databaseMap.get("expnumber"));
LOG.warn("User '{}' not found for experiment {}", databaseMap.get("initials"), databaseMap.get("expnumber"));
effectiveUser = getUser();
}
else
Expand All @@ -188,7 +188,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
}

databaseMap.put("EffectiveUser", effectiveUser);
LogManager.getLogger(OConnorExperimentsController.class).info("Insert on experiment " + databaseMap.get("expnumber"));
LOG.info("Insert on experiment {}", databaseMap.get("expnumber"));
List<Map<String, Object>> updateResult;
try
{
Expand All @@ -197,18 +197,18 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
catch (Exception e)
{
// log the error to the logfile and continue
LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber + " with exception " + e.getMessage());
LOG.warn("Error inserting expNumber {} with exception {}", expNumber, e.getMessage());
continue;
}
if (batchErrors.hasErrors())
{
// throw batchErrors.getLastRowError();
LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber);
LOG.warn("Error inserting expNumber {}", expNumber);
}

Container workbookContainer = ContainerManager.getForId((String)updateResult.get(0).get("EntityId"));
Container workbookContainer = ContainerManager.getForId((String)updateResult.getFirst().get("EntityId"));
databaseMap.put("ContainerObj", workbookContainer);
databaseMap.put("ContainerStr", updateResult.get(0).get("EntityId"));
databaseMap.put("ContainerStr", updateResult.getFirst().get("EntityId"));

// We don't want these fields to be spoofable through the QueryUpdateService (and hence the Client API),
// so preserve the value from the source data manually
Expand All @@ -218,7 +218,7 @@ 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");
LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile + "' to directory '" + targetDir +"'" );
LOG.info("Copy from file '{}' to directory '{}'", sourceFile, targetDir);
if (sourceFile.exists())
{
FileUtils.copyDirectory(sourceFile, targetDir);
Expand Down Expand Up @@ -260,7 +260,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
}
else
{
LogManager.getLogger(OConnorExperimentsController.class).warn("child container not found: " + parents[i] + " for experiment " + databaseMap.get("expnumber") + " with username " + databaseMap.get("initials"));
LOG.warn("child container not found: {} for experiment {} with username {}", parents[i], databaseMap.get("expnumber"), databaseMap.get("initials"));
}
}
}
Expand All @@ -269,16 +269,15 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
map.put("ParentExperiments", parentsEntityId.toArray(new String[0]));

// workaround, pass user, container - databaseMap.get("Container"), singleton list
LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber"));
LOG.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
LogManager.getLogger(OConnorExperimentsController.class).warn("Error updating parent experiments for experiment number " + expNumber + " with exception " + e.getMessage());
continue;
LOG.warn("Error updating parent experiments for experiment number {} with exception {}", expNumber, e.getMessage());
}

}
Expand All @@ -304,7 +303,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
Container workbookContainer = targetContainer.getChild(databaseMap.get("expnumber").toString());
if (workbookContainer == null)
{
LogManager.getLogger(OConnorExperimentsController.class).warn("Updating wiki, container not found: " + databaseMap.get("expnumber"));
LOG.warn("Updating wiki, container not found: {}", databaseMap.get("expnumber"));
}
else
{
Expand All @@ -320,14 +319,14 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
catch (Exception e)
{
// log the error to the logfile and continue
LogManager.getLogger(OConnorExperimentsController.class).warn("Error wiki for experiment number " + expNumber + " with exception " + e.getMessage());
LOG.warn("Error wiki for experiment number {} with exception {}", expNumber, e.getMessage());
continue;
}
finally
{
in.closeInputStream();
}
LogManager.getLogger(OConnorExperimentsController.class).info("Inserting wiki for experiment " + databaseMap.get("expnumber"));
LOG.info("Inserting wiki for experiment {}", databaseMap.get("expnumber"));
}
}
}
Expand Down Expand Up @@ -439,7 +438,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception

if (result != null && !result.isEmpty())
{
String entityId = (String)result.get(0).get("Container");
String entityId = (String)result.getFirst().get("Container");
newExperiment = ContainerManager.getForId(entityId);
return true;
}
Expand All @@ -464,7 +463,7 @@ public ApiResponse execute(Object o, BindException errors) throws Exception
ApiSimpleResponse resp = new ApiSimpleResponse();
if (result != null && !result.isEmpty())
{
Map<String, Object> exp = result.get(0);
Map<String, Object> exp = result.getFirst();

resp.put("success", true);
resp.put("experiment", exp);
Expand Down
3 changes: 2 additions & 1 deletion OConnorExperiments/src/org/labkey/oconnorexperiments/query/OConnorExperimentsUserSchema.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
package org.labkey.oconnorexperiments.query;

import org.jetbrains.annotations.Nullable;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.collections.Sets;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerFilter;
Expand Down Expand Up @@ -139,7 +140,7 @@ private TableInfo createParentExperimentsTable(String name, ContainerFilter cf)
}

@Override
public QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
public @NotNull QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
{
if (OConnorExperimentsController.EXPERIMENTS.equalsIgnoreCase(settings.getQueryName()))
{
Expand Down
12 changes: 3 additions & 9 deletions genotyping/src/org/labkey/genotyping/GenotypingController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,6 @@
import java.math.BigInteger;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.sql.ResultSet;
import java.sql.SQLException;
Expand Down Expand Up @@ -381,7 +380,7 @@ public boolean handlePost(ReturnUrlForm returnUrlForm, BindException errors)
{
long startTime = System.currentTimeMillis();
SequenceManager.get().loadSequences(getContainer(), getUser());
LOG.info(DateUtil.formatDuration(System.currentTimeMillis() - startTime) + " to load sequences");
LOG.info("{} to load sequences", DateUtil.formatDuration(System.currentTimeMillis() - startTime));

return true;
}
Expand Down Expand Up @@ -1299,7 +1298,7 @@ public void validateForm(ImportAnalysisForm form, Errors errors)
@Override
public Object execute(ImportAnalysisForm form, BindException errors) throws Exception
{
LOG.info("Galaxy signaled the completion of analysis " + form.getAnalysis());
LOG.info("Galaxy signaled the completion of analysis {}", form.getAnalysis());
String message;

// Send any exceptions back to the Galaxy task so it can log it as well.
Expand Down Expand Up @@ -1337,7 +1336,7 @@ public Object execute(ImportAnalysisForm form, BindException errors) throws Exce
message = FAILURE_PREFACE + "Analysis path doesn't match import path (see system log for more details)";

// But log more detail to the administrator so they're aware
LOG.error(FAILURE_PREFACE + fnf.getMessage());
LOG.error("{}{}", FAILURE_PREFACE, fnf.getMessage());
}
catch (Exception e)
{
Expand Down Expand Up @@ -1657,11 +1656,6 @@ public static class RunForm extends QueryExportForm
public enum Platforms{

LS454 {
@Override
public String getTableName()
{
return TableType.Reads.toString();
}
},
ILLUMINA {
@Override
Expand Down
4 changes: 2 additions & 2 deletions genotyping/src/org/labkey/genotyping/GenotypingQuerySchema.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@

import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.collections.CaseInsensitiveHashSet;
import org.labkey.api.collections.Sets;
import org.labkey.api.data.*;
Expand Down Expand Up @@ -952,7 +952,7 @@ public Set<String> getTableNames()
}

@Override
public QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
public @NotNull QueryView createView(ViewContext context, QuerySettings settings, BindException errors)
{
TableType type = findTableType(settings.getQueryName());
return type == null ? super.createView(context, settings, errors) : type.createQueryView(context, settings, errors, this);
Expand Down
1 change: 0 additions & 1 deletion genotyping/src/org/labkey/genotyping/HaplotypeAssayProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,6 @@
import org.labkey.api.view.NavTree;
import org.labkey.api.view.ViewContext;

import java.io.File;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedHashMap;
Expand Down
9 changes: 4 additions & 5 deletions genotyping/src/org/labkey/genotyping/HaplotypeDataHandler.java
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Expand Up @@ -49,7 +49,6 @@
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
Expand All @@ -75,7 +74,7 @@ public void importFile(@NotNull ExpData data, @NotNull FileLike dataFile, @NotNu
{
if (!dataFile.exists())
{
log.warn("Could not find file " + dataFile + " on disk for data with LSID " + data.getLSID());
log.warn("Could not find file {} on disk for data with LSID {}", dataFile, data.getLSID());
return;
}
ExpRun expRun = data.getRun();
Expand Down Expand Up @@ -226,7 +225,7 @@ private Map<String, Integer> ensureAnimalIds(Map<String, String> ids, Map<String
{
throw new ExperimentException("Unable to insert a row into the Animal table for " + animalKey);
}
row.put("rowid", insertedRow.get(0).get("RowId"));
row.put("rowid", insertedRow.getFirst().get("RowId"));
}
}

Expand Down Expand Up @@ -299,7 +298,7 @@ private Map<HaplotypeIdentifier, Integer> ensureHaplotypeNames(List<HaplotypeIde
{
throw new ExperimentException("Unable to insert a row into the Haplotype table for " + haplotypeName);
}
row.put("rowid", insertedRow.get(0).get("RowId"));
row.put("rowid", insertedRow.getFirst().get("RowId"));
}
}

Expand Down Expand Up @@ -462,7 +461,7 @@ private void throwFirstError(BatchValidationException errors) throws ExperimentE
{
if (errors.hasErrors())
{
throw new ExperimentException(errors.getRowErrors().get(0));
throw new ExperimentException(errors.getRowErrors().getFirst());
}
}

Expand Down
14 changes: 7 additions & 7 deletions genotyping/src/org/labkey/genotyping/IlluminaFastqParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
long length = f.length();
if (length == 0)
{
_logger.info("File " + f.getName() + " has no content to parse.");
_logger.info("File {} has no content to parse.", f.getName());
continue;
}

Expand All @@ -138,10 +138,10 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
// good way to check if a file is truly local
tempFile = FileUtil.createTempFile(FileUtil.getBaseName(f) + ".", "." + FileUtil.getExtension(f));
tempFile.deleteOnExit();
_logger.debug("Copying to temp file " + tempFile + ", size is " + f.length() + " bytes");
_logger.debug("Copying to temp file {}, size is {} bytes", tempFile, f.length());
FileUtil.copyFile(f, tempFile);

_logger.info("Beginning to parse file: " + f.getName());
_logger.info("Beginning to parse file: {}", f.getName());
try (FastqReader reader = new FastqReader(tempFile))
{
File targetDir = f.getParentFile();
Expand Down Expand Up @@ -197,7 +197,7 @@ public Map<Pair<Integer, Integer>, FileInfo> parseFastqFiles(PipelineJob job) th
}
else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains("null"))//empty file
{
_logger.warn("File " + fileName + " has no content to parse.");
_logger.warn("File {} has no content to parse.", fileName);
reader.close();
continue;
}
Expand All @@ -223,7 +223,7 @@ else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains
Pair<Integer, Integer> key = Pair.of(sampleId, pairNumber);
_fileInfo.put(key, new FileInfo(newFile, totalReads));

_logger.info("Finished parsing file: " + f.getName());
_logger.info("Finished parsing file: {}", f.getName());
}
}
}
Expand Down Expand Up @@ -252,7 +252,7 @@ else if (reader.getLineNumber() == 1 && totalReads == 0 && !f.getName().contains
File oldFile = entry.getKey();
File newFile = entry.getValue();
FileUtils.moveFile(oldFile, newFile);
_logger.info("Moved file " + oldFile.getName() + " to " + newFile.getName() );
_logger.info("Moved file {} to {}", oldFile.getName(), newFile.getName());
}
}
catch (IOException e)
Expand Down Expand Up @@ -317,7 +317,7 @@ private void checkForDuplicateTargets(Map<File, File> filesToMove) throws Pipeli
if (sourceFiles.size() > 1)
{
error = true;
_logger.error("Multiple input files map to the target file " + targetFile + " - they are: " + sourceFiles);
_logger.error("Multiple input files map to the target file {} - they are: {}", targetFile, sourceFiles);
}
}
if (error)
Expand Down
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