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Merged
labkey-jeckels merged 6 commits into from
Dec 3, 2025
Merged

Continue adopting FileLike instead of File or Path #399

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0b3cdec
Continue adopting FileLike instead of File or Path
labkey-jeckels Nov 17, 2025
f8d587e
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Dec 1, 2025
4a30259
More cleanup
labkey-jeckels Dec 1, 2025
a632c45
Prep for merge
labkey-jeckels Dec 2, 2025
6632524
Handle nulls
labkey-jeckels Dec 3, 2025
6d0aab3
Handle nulls
labkey-jeckels Dec 3, 2025
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3 changes: 2 additions & 1 deletion SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractResumer.java
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Expand Up @@ -7,6 +7,7 @@
import org.labkey.api.pipeline.RecordedAction;
import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.util.Pair;
import org.labkey.vfs.FileSystemLike;

import java.io.BufferedInputStream;
import java.io.File;
Expand Down Expand Up @@ -240,7 +241,7 @@ public static <T extends AbstractResumer> T create(SequenceOutputHandler.JobCont
{
for (File orig : ret.getCopiedInputs().keySet())
{
ctx.getWorkDir().inputFile(orig, ret._copiedInputs.get(orig), false);
ctx.getWorkDir().inputFile(FileSystemLike.wrapFile(orig), FileSystemLike.wrapFile(ret._copiedInputs.get(orig)), false);
}
}
}
Expand Down
5 changes: 3 additions & 2 deletions SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java
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Expand Up @@ -5,6 +5,7 @@
import org.labkey.api.data.ConvertHelper;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.WorkDirectory;
import org.labkey.vfs.FileSystemLike;

import java.io.File;
import java.io.IOException;
Expand Down Expand Up @@ -89,7 +90,7 @@ private static boolean verifyOrCreateCachedIndex(PipelineContext ctx, @Nullable
if (doCopy)
{
ctx.getLogger().info("copying index files to work location");
File localSharedDir = new File(wd.getDir(), "Shared");
File localSharedDir = new File(wd.getDir().toNioPathForRead().toFile(), "Shared");
File destination = new File(localSharedDir, localName);
ctx.getLogger().debug(destination.getPath());
File[] files = webserverIndexDir.listFiles();
Expand All @@ -98,7 +99,7 @@ private static boolean verifyOrCreateCachedIndex(PipelineContext ctx, @Nullable
return false;
}

destination = wd.inputFile(webserverIndexDir, destination, true);
destination = wd.inputFile(FileSystemLike.wrapFile(webserverIndexDir), FileSystemLike.wrapFile(destination), true).toNioPathForRead().toFile();
if (output != null && !destination.equals(webserverIndexDir))
{
ctx.getLogger().debug("adding deferred delete file: " + destination.getPath());
Expand Down
4 changes: 2 additions & 2 deletions SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/HasJobParams.java
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@@ -1,8 +1,8 @@
package org.labkey.api.sequenceanalysis.pipeline;

import org.json.JSONObject;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.util.Map;

/**
Expand All @@ -14,5 +14,5 @@ public interface HasJobParams

JSONObject getParameterJson();

File getParametersFile();
FileLike getParametersFile();
}
19 changes: 10 additions & 9 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/OutputIntegrationTests.java
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Expand Up @@ -34,6 +34,7 @@
import org.labkey.api.view.ViewServlet;
import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler;
import org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerJob;
import org.labkey.vfs.FileLike;
import org.springframework.mock.web.MockHttpServletResponse;
import org.springframework.web.bind.annotation.RequestMethod;

Expand Down Expand Up @@ -110,15 +111,15 @@ public void testVariantProcessing() throws Exception
SequenceOutputHandlerJob job = (SequenceOutputHandlerJob)j;

Set<File> extraFiles = new HashSet<>();
extraFiles.add(new File(job.getAnalysisDirectory(), jobName + "." + outputFileId + ".log"));
extraFiles.add(new File(job.getAnalysisDirectory(), "sequenceOutput.json"));
extraFiles.add(new File(job.getAnalysisDirectory(), "sequenceSupport.json.gz"));
extraFiles.add(ProcessVariantsHandler.getPedigreeFile(job.getAnalysisDirectory(), "laboratory.subjects"));
extraFiles.add(new File(job.getAnalysisDirectory(), basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz"));
extraFiles.add(new File(job.getAnalysisDirectory(), basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz.tbi"));
extraFiles.add(new File(job.getAnalysisDirectory(), job.getBaseName() + ".pipe.xar.xml"));

verifyFileOutputs(job.getAnalysisDirectory(), extraFiles);
extraFiles.add(job.getAnalysisDirectory().resolveChild(jobName + "." + outputFileId + ".log").toNioPathForRead().toFile());
extraFiles.add(job.getAnalysisDirectory().resolveChild("sequenceOutput.json").toNioPathForRead().toFile());
extraFiles.add(job.getAnalysisDirectory().resolveChild("sequenceSupport.json.gz").toNioPathForRead().toFile());
extraFiles.add(ProcessVariantsHandler.getPedigreeFile(job.getAnalysisDirectory(), "laboratory.subjects").toNioPathForRead().toFile());
extraFiles.add(job.getAnalysisDirectory().resolveChild(basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz").toNioPathForRead().toFile());
extraFiles.add(job.getAnalysisDirectory().resolveChild(basename + ".gfiltered.selectVariants.annotated.filtered.vcf.gz.tbi").toNioPathForRead().toFile());
extraFiles.add(job.getAnalysisDirectory().resolveChild(job.getBaseName() + ".pipe.xar.xml").toNioPathForRead().toFile());

verifyFileOutputs(job.getAnalysisDirectory().toNioPathForRead().toFile(), extraFiles);

//verify outputfile created:
TableSelector ts = new TableSelector(ti, PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("runId/jobid/job"), job.getJobGUID()), null);
Expand Down
51 changes: 24 additions & 27 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java
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Expand Up @@ -1876,14 +1876,14 @@ public boolean isSubmitJobToReadsetContainer()
return getJobParameters() != null && getJobParameters().optBoolean("submitJobToReadsetContainer", false);
}

public List<File> getFiles(PipeRoot pr) throws PipelineValidationException
public List<FileLike> getFiles(PipeRoot pr) throws PipelineValidationException
{
if (getJobParameters() == null || getJobParameters().get("inputFiles") == null)
{
return null;
}

List<File> ret = new ArrayList<>();
List<FileLike> ret = new ArrayList<>();
JSONArray inputFiles = getJobParameters().getJSONArray("inputFiles");
String path = getJobParameters().optString("path");
for (JSONObject o : JsonUtil.toJSONObjectList(inputFiles))
Expand All @@ -1900,7 +1900,7 @@ else if (!d.getFile().exists())
throw new PipelineValidationException("Missing file for data: " + o.get("dataId"));
}

ret.add(d.getFile());
ret.add(d.getFileLike());
}
else if (o.has("relPath") || o.has("fileName"))
{
Expand All @@ -1927,7 +1927,7 @@ else if (o.has("relPath") || o.has("fileName"))
throw new PipelineValidationException("Unknown file: " + o.getString("relPath") + " / " + o.getString("fileName"));
}

ret.add(f.toNioPathForRead().toFile());
ret.add(f);
}
else if (o.opt("filePath") != null)
{
Expand Down Expand Up @@ -2145,27 +2145,24 @@ protected void setContentType(HttpServletResponse response)
}

@Override
protected File getTargetFile(String filename) throws IOException
protected FileLike getTargetFile(String filename) throws IOException
{
if (!PipelineService.get().hasValidPipelineRoot(getContainer()))
throw new UploadException("Pipeline root must be configured before uploading FASTA files", HttpServletResponse.SC_NOT_FOUND);

PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());

File targetDirectory = root.getRootPath();

return FileUtil.findUniqueFileName(filename, targetDirectory);
return FileUtil.findUniqueFileName(filename, root.getRootFileLike());
}

@Override
public String getResponse(ImportFastaSequencesForm form, Map<String, Pair<File, String>> files)
public String getResponse(ImportFastaSequencesForm form, Map<String, Pair<FileLike, String>> files)
{
JSONObject resp = new JSONObject();
try
{
for (Map.Entry<String, Pair<File, String>> entry : files.entrySet())
for (Map.Entry<String, Pair<FileLike, String>> entry : files.entrySet())
{
File file = entry.getValue().getKey();
File file = entry.getValue().getKey().toNioPathForRead().toFile();

Map<String, String> params = form.getNtParams();
Map<String, Object> libraryParams = form.getLibraryParams();
Expand Down Expand Up @@ -2444,15 +2441,15 @@ protected void setContentType(HttpServletResponse response)
}

@Override
protected File getTargetFile(String filename) throws IOException
protected FileLike getTargetFile(String filename) throws IOException
{
if (!PipelineService.get().hasValidPipelineRoot(getContainer()))
throw new UploadException("Pipeline root must be configured before uploading files", HttpServletResponse.SC_NOT_FOUND);

try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer(), "sequenceOutputs");
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory);
}
catch (ExperimentException e)
{
Expand All @@ -2461,14 +2458,14 @@ protected File getTargetFile(String filename) throws IOException
}

@Override
public String getResponse(ImportOutputFileForm form, Map<String, Pair<File, String>> files)
public String getResponse(ImportOutputFileForm form, Map<String, Pair<FileLike, String>> files)
{
JSONObject resp = new JSONObject();
try
{
for (Map.Entry<String, Pair<File, String>> entry : files.entrySet())
for (Map.Entry<String, Pair<FileLike, String>> entry : files.entrySet())
{
File file = entry.getValue().getKey();
FileLike file = entry.getValue().getKey();

Map<String, Object> params = new CaseInsensitiveHashMap<>();
params.put("name", form.getName());
Expand Down Expand Up @@ -2577,15 +2574,15 @@ protected void setContentType(HttpServletResponse response)
}

@Override
protected File getTargetFile(String filename) throws IOException
protected FileLike getTargetFile(String filename) throws IOException
{
if (!PipelineService.get().hasValidPipelineRoot(getContainer()))
throw new UploadException("Pipeline root must be configured before uploading files", HttpServletResponse.SC_NOT_FOUND);

try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory);
}
catch (ExperimentException e)
{
Expand All @@ -2610,7 +2607,7 @@ public void validateCommand(ImportTrackForm form, Errors errors)
}

@Override
public String getResponse(ImportTrackForm form, Map<String, Pair<File, String>> files) throws UploadException
public String getResponse(ImportTrackForm form, Map<String, Pair<FileLike, String>> files) throws UploadException
{
JSONObject resp = new JSONObject();
if (form.getTrackName() == null || form.getLibraryId() == null)
Expand All @@ -2620,9 +2617,9 @@ public String getResponse(ImportTrackForm form, Map<String, Pair<File, String>>

try
{
for (Map.Entry<String, Pair<File, String>> entry : files.entrySet())
for (Map.Entry<String, Pair<FileLike, String>> entry : files.entrySet())
{
File file = entry.getValue().getKey();
File file = entry.getValue().getKey().toNioPathForRead().toFile();

try
{
Expand Down Expand Up @@ -2742,15 +2739,15 @@ protected void setContentType(HttpServletResponse response)
}

@Override
protected File getTargetFile(String filename) throws IOException
protected FileLike getTargetFile(String filename) throws IOException
{
if (!PipelineService.get().hasValidPipelineRoot(getContainer()))
throw new UploadException("Pipeline root must be configured before uploading files", HttpServletResponse.SC_NOT_FOUND);

try
{
FileLike targetDirectory = AssayFileWriter.ensureUploadDirectory(getContainer());
return FileUtil.findUniqueFileName(filename, targetDirectory).toNioPathForWrite().toFile();
return FileUtil.findUniqueFileName(filename, targetDirectory);
}
catch (ExperimentException e)
{
Expand All @@ -2759,14 +2756,14 @@ protected File getTargetFile(String filename) throws IOException
}

@Override
public String getResponse(ImportChainFileForm form, Map<String, Pair<File, String>> files)
public String getResponse(ImportChainFileForm form, Map<String, Pair<FileLike, String>> files)
{
JSONObject resp = new JSONObject();
try
{
for (Map.Entry<String, Pair<File, String>> entry : files.entrySet())
for (Map.Entry<String, Pair<FileLike, String>> entry : files.entrySet())
{
File file = entry.getValue().getKey();
File file = entry.getValue().getKey().toNioPathForRead().toFile();

if (form.getGenomeId1() == null || form.getGenomeId2() == null)
{
Expand Down
16 changes: 8 additions & 8 deletions SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceIntegrationTests.java
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Expand Up @@ -1144,7 +1144,7 @@ public void barcodeTest() throws Exception

private File getBaseDir(PipelineJob job)
{
return ((SequenceJob)job).getAnalysisDirectory();
return ((SequenceJob)job).getAnalysisDirectory().toNioPathForRead().toFile();
}

/**
Expand Down Expand Up @@ -1489,7 +1489,7 @@ protected void validateAlignmentJob(Set<PipelineJob> jobs, Collection<String> ad
protected void validateAlignmentJob(Set<PipelineJob> jobs, Collection<String> additionalFiles, SequenceReadsetImpl rs, Integer aligned, Integer unaligned, boolean includeRefFiles) throws Exception
{
SequenceAlignmentJob job = getAlignmentJob(jobs, rs);
File basedir = job.getAnalysisDirectory();
File basedir = job.getAnalysisDirectory().toNioPathForRead().toFile();
String outDir = SequenceTaskHelper.getUnzippedBaseName(rs.getReadDataImpl().get(0).getFile1());

Set<File> expectedOutputs = new HashSet<>();
Expand Down Expand Up @@ -2982,7 +2982,7 @@ public void testBismarkWithSavedLibraryAndAdapters() throws Exception
//job1Files.add("paired1/Alignment/TestReadset1.insertsize.metrics");
//job1Files.add("paired1/Alignment/TestReadset1.insertsize.metrics.pdf");

File basedir1 = getAlignmentJob(jobs, _readsets.get(0)).getAnalysisDirectory();
File basedir1 = getAlignmentJob(jobs, _readsets.get(0)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job1Files, basedir1, "paired1/Alignment/CpG_OB_TestReadset1.txt.gz");
addOptionalFile(job1Files, basedir1, "paired1/Alignment/CpG_OT_TestReadset1.txt.gz");
addOptionalFile(job1Files, basedir1, "paired1/Alignment/Non_CpG_OB_TestReadset1.bam.txt.gz");
Expand All @@ -3008,7 +3008,7 @@ public void testBismarkWithSavedLibraryAndAdapters() throws Exception
//job2Files.add("paired3/Alignment/TestReadset2.summary.metrics");
//job2Files.add("paired3/Alignment/TestReadset2.insertsize.metrics");

File basedir2 = getAlignmentJob(jobs, _readsets.get(1)).getAnalysisDirectory();
File basedir2 = getAlignmentJob(jobs, _readsets.get(1)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job2Files, basedir2, "paired3/Alignment/CpG_OB_TestReadset2.txt.gz");
addOptionalFile(job2Files, basedir2, "paired3/Alignment/CpG_OT_TestReadset2.txt.gz");
addOptionalFile(job2Files, basedir2, "paired3/Alignment/Non_CpG_OB_TestReadset2.bam.txt.gz");
Expand All @@ -3032,7 +3032,7 @@ public void testBismarkWithSavedLibraryAndAdapters() throws Exception
//job3Files.add("paired4/Alignment/TestReadset3.summary.metrics");
//job3Files.add("paired4/Alignment/TestReadset3.insertsize.metrics");

File basedir3 = getAlignmentJob(jobs, _readsets.get(2)).getAnalysisDirectory();
File basedir3 = getAlignmentJob(jobs, _readsets.get(2)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job3Files, basedir3, "paired4/Alignment/CpG_OB_TestReadset3.txt.gz");
addOptionalFile(job3Files, basedir3, "paired4/Alignment/CpG_OT_TestReadset3.txt.gz");
addOptionalFile(job3Files, basedir3, "paired4/Alignment/Non_CpG_OB_TestReadset3.bam.txt.gz");
Expand Down Expand Up @@ -3109,7 +3109,7 @@ public void testBismarkWithSavedLibraryAdaptersAndDelete() throws Exception
job1Files.add("paired1/Alignment/TestReadset1.insertsize.metrics");
job1Files.add("paired1/Alignment/TestReadset1.insertsize.metrics.pdf");

File basedir1 = getAlignmentJob(jobs, _readsets.get(0)).getAnalysisDirectory();
File basedir1 = getAlignmentJob(jobs, _readsets.get(0)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job1Files, basedir1, "paired1/Alignment/CpG_OB_TestReadset1.txt.gz");
addOptionalFile(job1Files, basedir1, "paired1/Alignment/CpG_OT_TestReadset1.txt.gz");
addOptionalFile(job1Files, basedir1, "paired1/Alignment/Non_CpG_OB_TestReadset1.bam.txt.gz");
Expand All @@ -3132,7 +3132,7 @@ public void testBismarkWithSavedLibraryAdaptersAndDelete() throws Exception
job2Files.add("paired3/Alignment/TestReadset2.summary.metrics");
//job2Files.add("paired3/Alignment/TestReadset2.insertsize.metrics");

File basedir2 = getAlignmentJob(jobs, _readsets.get(1)).getAnalysisDirectory();
File basedir2 = getAlignmentJob(jobs, _readsets.get(1)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job2Files, basedir2, "paired3/Alignment/CpG_OB_TestReadset2.txt.gz");
addOptionalFile(job2Files, basedir2, "paired3/Alignment/CpG_OT_TestReadset2.txt.gz");
addOptionalFile(job2Files, basedir2, "paired3/Alignment/Non_CpG_OB_TestReadset2.bam.txt.gz");
Expand All @@ -3154,7 +3154,7 @@ public void testBismarkWithSavedLibraryAdaptersAndDelete() throws Exception
job3Files.add("paired4/Alignment/TestReadset3.summary.metrics");
//job3Files.add("paired4/Alignment/TestReadset3.insertsize.metrics");

File basedir3 = getAlignmentJob(jobs, _readsets.get(2)).getAnalysisDirectory();
File basedir3 = getAlignmentJob(jobs, _readsets.get(2)).getAnalysisDirectory().toNioPathForRead().toFile();
addOptionalFile(job3Files, basedir3, "paired4/Alignment/CpG_OB_TestReadset3.txt.gz");
addOptionalFile(job3Files, basedir3, "paired4/Alignment/CpG_OT_TestReadset3.txt.gz");
addOptionalFile(job3Files, basedir3, "paired4/Alignment/Non_CpG_OB_TestReadset3.bam.txt.gz");
Expand Down
2 changes: 1 addition & 1 deletion SequenceAnalysis/src/org/labkey/sequenceanalysis/SequencePipelineServiceImpl.java
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Expand Up @@ -514,7 +514,7 @@ public List<File> getSequenceJobInputFiles(PipelineJob job)
return null;
}

return ((SequenceJob) job).getInputFiles();
return ((SequenceJob) job).getInputFiles().stream().map(f -> f.toNioPathForRead().toFile()).toList();
}

@Override
Expand Down
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