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Merged
labkey-susanh merged 4 commits into from
Jul 30, 2025
Merged

Relocate methods related to file name uniqueness to FileUtil #370

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6de6d5c
Move `findUniqueFileName` from `AssayFileWriter` to `FileUtil`
labkey-susanh Jul 10, 2025
786c0b5
Merge remote-tracking branch 'origin/develop' into fb_fileNameAudit
labkey-susanh Jul 14, 2025
3c0845f
Bump schema version
labkey-susanh Jul 22, 2025
8d4b596
Merge remote-tracking branch 'origin/develop' into fb_fileNameAudit
labkey-susanh Jul 24, 2025
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4 changes: 2 additions & 2 deletions QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsModule.java
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Expand Up @@ -40,7 +40,7 @@ public String getName()
@Override
public @Nullable Double getSchemaVersion()
{
return 23.000;
return 25.000;
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@labkey-adam labkey-adam Jul 31, 2025

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@labkey-susanh was this schema bump necessary for some reason?

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@labkey-susanh labkey-susanh Jul 31, 2025

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No. I had thought so initially, but it wasn't. Is it causing issues?

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@labkey-adam labkey-adam Jul 31, 2025

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No, just unusual for us to be bumping versions in modules we don't manage. If deployed without any other upgrading modules, it will cause a no-op "upgrade" (drop and recreate all views), but that's harmless.

}

@Override
Expand Down Expand Up @@ -81,4 +81,4 @@ public Set<String> getSchemaNames()
{
return Collections.singleton(QueryExtensionsSchema.NAME);
}
}
}
10 changes: 5 additions & 5 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java
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Expand Up @@ -2151,7 +2151,7 @@ protected File getTargetFile(String filename) throws IOException

File targetDirectory = root.getRootPath();

return AssayFileWriter.findUniqueFileName(filename, targetDirectory);
return FileUtil.findUniqueFileName(filename, targetDirectory);
}

@Override
Expand Down Expand Up @@ -2449,7 +2449,7 @@ protected File getTargetFile(String filename) throws IOException
try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
}
catch (ExperimentException e)
{
Expand Down Expand Up @@ -2582,7 +2582,7 @@ protected File getTargetFile(String filename) throws IOException
try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
}
catch (ExperimentException e)
{
Expand Down Expand Up @@ -2747,7 +2747,7 @@ protected File getTargetFile(String filename) throws IOException
try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
}
catch (ExperimentException e)
{
Expand Down Expand Up @@ -4089,7 +4089,7 @@ public ApiResponse execute(ImportOutputFilesForm form, BindException errors) thr

for (File file : toCreate.keySet())
{
FileLike target = AssayFileWriter.findUniqueFileName(file.getName(), targetDirectory);
FileLike target = FileUtil.findUniqueFileName(file.getName(), targetDirectory);
FileUtils.moveFile(file, target.toNioPathForWrite().toFile());

ExpData data = ExperimentService.get().createData(getContainer(), new DataType("Sequence Output"));
Expand Down
6 changes: 3 additions & 3 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisManager.java
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Expand Up @@ -24,7 +24,6 @@
import org.jetbrains.annotations.Nullable;
import org.junit.Assert;
import org.junit.Test;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
Expand Down Expand Up @@ -67,6 +66,7 @@
import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.Job;
import org.labkey.api.util.JobRunner;
import org.labkey.api.util.PageFlowUtil;
Expand Down Expand Up @@ -827,7 +827,7 @@ public void addChainFile(Container c, User u, File file, int genomeId1, int geno

//create file
String expectedName = "chain-" + genomeId1 + "to" + genomeId2 + ".chain";
File outputFile = AssayFileWriter.findUniqueFileName(expectedName, targetDir);
File outputFile = FileUtil.findUniqueFileName(expectedName, targetDir);

FileUtils.moveFile(file, outputFile);
ExpData chainFile = ExperimentService.get().createData(c, new DataType("Sequence Track"));
Expand Down Expand Up @@ -939,4 +939,4 @@ public void testJars()
assertTrue("fastqcDir dir does not exist: " + fastqcDir.getPath(), fastqcDir.exists());
}
}
}
}
2 changes: 1 addition & 1 deletion ...nceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportFastaSequencesPipelineJob.java
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Expand Up @@ -69,7 +69,7 @@ public static File createLocalDirectory(PipeRoot pipeRoot) throws IOException

AssayFileWriter writer = new AssayFileWriter();
String folderName = "SequenceImport_" + FileUtil.getTimestamp();
webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir);
webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir);
if (!webserverOutDir.exists())
{
webserverOutDir.mkdirs();
Expand Down
4 changes: 2 additions & 2 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java
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Expand Up @@ -33,7 +33,6 @@
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.SystemUtils;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
Expand Down Expand Up @@ -61,6 +60,7 @@
import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenomeManager;
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
import org.labkey.api.util.FileType;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.Job;
import org.labkey.api.util.JobRunner;
import org.labkey.api.util.PageFlowUtil;
Expand Down Expand Up @@ -354,7 +354,7 @@ private void sortGxf(File gxf) throws PipelineJobException
}
private File getOutputFile(File file, File tracksDir)
{
return AssayFileWriter.findUniqueFileName(file.getName().replaceAll(" ", "_"), tracksDir);
return FileUtil.findUniqueFileName(file.getName().replaceAll(" ", "_"), tracksDir);
}

private Map<String, Pair<String, Integer>> getNameTranslationMap(List<RefNtSequenceModel> refNtSequenceModels) throws PipelineJobException
Expand Down
7 changes: 3 additions & 4 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJob.java
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Expand Up @@ -10,7 +10,6 @@
import org.json.JSONObject;
import org.junit.Assert;
import org.junit.Test;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.exp.api.DataType;
Expand Down Expand Up @@ -164,7 +163,7 @@ protected void addCustomParams(JSONObject params)

private Path _getLogFile()
{
var file = AssayFileWriter.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());
var file = FileUtil.findUniqueFileName((FileUtil.makeLegalName(_jobName) + ".log"), getDataDirectoryFileObject());
return file.toNioPathForWrite();
}

Expand Down Expand Up @@ -228,7 +227,7 @@ protected FileLike createLocalDirectory(PipeRoot pipeRoot) throws IOException
}

String folderName = FileUtil.makeLegalName(StringUtils.capitalize(_folderPrefix) + "_" + FileUtil.getTimestamp());
webserverOutDir = AssayFileWriter.findUniqueFileName(folderName, webserverOutDir);
webserverOutDir = FileUtil.findUniqueFileName(folderName, webserverOutDir);
if (!webserverOutDir.exists())
{
webserverOutDir.mkdir();
Expand Down Expand Up @@ -681,4 +680,4 @@ public File getLocationForCachedInputs(WorkDirectory wd, boolean createIfDoesntE

return ret;
}
}
}
5 changes: 3 additions & 2 deletions blast/src/org/labkey/blast/BLASTController.java
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Expand Up @@ -50,6 +50,7 @@
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.util.ExceptionUtil;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.util.StringUtilsLabKey;
Expand Down Expand Up @@ -217,7 +218,7 @@ protected File getTargetFile(String filename) throws IOException
try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
return AssayFileWriter.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
}
catch (ExperimentException e)
{
Expand Down Expand Up @@ -265,7 +266,7 @@ public String getResponse(RunBlastForm form, Map<String, Pair<File, String>> fil
try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
FileLike input = AssayFileWriter.findUniqueFileName("blast", targetDirectory);
FileLike input = FileUtil.findUniqueFileName("blast", targetDirectory);
input.createFile();
try (PrintWriter fw = PrintWriters.getPrintWriter(input.openOutputStream()))
{
Expand Down
3 changes: 1 addition & 2 deletions jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseLucenePipelineJob.java
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Expand Up @@ -3,7 +3,6 @@
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.SystemUtils;
import org.apache.logging.log4j.Logger;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.data.Container;
import org.labkey.api.files.FileUrls;
import org.labkey.api.module.Module;
Expand Down Expand Up @@ -59,7 +58,7 @@ public JBrowseLucenePipelineJob(Container c, User user, PipeRoot pipeRoot, Strin
_infoFields = infoFields;
_allowLenientLuceneProcessing = allowLenientLuceneProcessing;

setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-lucene" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true)));
setLogFile(FileUtil.findUniqueFileName("jbrowse-lucene" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true)));
}

public static class JBrowseLucenePipelineProvider extends PipelineProvider
Expand Down
6 changes: 3 additions & 3 deletions jbrowse/src/org/labkey/jbrowse/pipeline/JBrowseSessionPipelineJob.java
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@@ -1,7 +1,6 @@
package org.labkey.jbrowse.pipeline;

import org.jetbrains.annotations.Nullable;
import org.labkey.api.assay.AssayFileWriter;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.SimpleFilter;
Expand All @@ -15,6 +14,7 @@
import org.labkey.api.query.DetailsURL;
import org.labkey.api.query.FieldKey;
import org.labkey.api.security.User;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.GUID;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
Expand Down Expand Up @@ -101,7 +101,7 @@ private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, Lis
_sourceContainerId = databaseGuid == null ? getContainerId() : getSourceContainerId(databaseGuid);
_mode = mode;

setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true)));
setLogFile(FileUtil.findUniqueFileName("jbrowse-" + new GUID() + ".log", JBrowseManager.get().getBaseDir(c, true)));
}

private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, String name, String description, Integer libraryId, List<Integer> trackIds, List<Integer> outputFileIds, @Nullable String existingDatabaseGuid, boolean isTemporarySession)
Expand All @@ -118,7 +118,7 @@ private JBrowseSessionPipelineJob(Container c, User user, PipeRoot pipeRoot, Str
_sourceContainerId = existingDatabaseGuid == null ? getContainerId() : getSourceContainerId(existingDatabaseGuid);
_isTemporarySession = isTemporarySession;

setLogFile(AssayFileWriter.findUniqueFileName("jbrowse-" + _databaseGuid + ".log", JBrowseManager.get().getBaseDir(c, true)));
setLogFile(FileUtil.findUniqueFileName("jbrowse-" + _databaseGuid + ".log", JBrowseManager.get().getBaseDir(c, true)));
}

private String getSourceContainerId(String databaseGuid)
Expand Down