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Fix NPE #375

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Merged
bbimber merged 10 commits into from
Feb 3, 2026
Merged

Fix NPE #375

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6a48a8f
Fix NPE
bbimber Feb 2, 2026
71ceb1b
Merge branch 'discvr-25.11' into 25.11_fb_jb
bbimber Feb 2, 2026
618dd60
Fix NPE
bbimber Feb 2, 2026
5a95c30
Bugfix to GTF/GFF and jbrowse
bbimber Feb 3, 2026
b08bce7
Bugfix to GTF/GFF and jbrowse
bbimber Feb 3, 2026
100b0eb
Bugfix to GTF/GFF and jbrowse
bbimber Feb 3, 2026
8b2c512
Bugfix to GTF/GFF and jbrowse
bbimber Feb 3, 2026
4a5aa5b
Reduce warnings
bbimber Feb 3, 2026
85179e0
Allow JBrowse to run when picard not present
bbimber Feb 3, 2026
87d5a2e
Merge branch 'discvr-25.11' into 25.11_fb_jb
bbimber Feb 3, 2026
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73 changes: 66 additions & 7 deletions jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@
import org.labkey.api.sequenceanalysis.SequenceOutputFile;
import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
import org.labkey.api.sequenceanalysis.run.PicardWrapper;
import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
import org.labkey.api.settings.AppProps;
import org.labkey.api.util.FileType;
Expand Down Expand Up @@ -587,8 +588,7 @@ public boolean matchesTrackSelector(List<String> toTest)

public String getJsonTrackId()
{
final File finalLocation = getLocationOfProcessedTrack(false);
return finalLocation == null ? null : finalLocation.getName();
return getSourceFileName();
}

private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGenome rg)
Expand Down Expand Up @@ -627,6 +627,11 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
{{
put("location", new JSONObject()
{{
if (!new File(targetFile.getFile() + ".bai").exists())
{
log.error("Track lacks an index: {}, expected: {}", getObjectId(), targetFile.getFile().getPath() + ".bai");
}

put("uri", url + ".bai");
}});
put("indexType", "BAI");
Expand All @@ -646,6 +651,11 @@ private JSONObject getBamOrCramTrack(Logger log, ExpData targetFile, ReferenceGe
}});
put("craiLocation", new JSONObject()
{{
if (!new File(targetFile.getFile() + ".bai").exists())
{
log.error("Track lacks an index: {}, expected: {}", getObjectId(), targetFile.getFile().getPath() + ".crai");
}

put("uri", url + ".crai");
}});
put("sequenceAdapter", JBrowseSession.getBgZippedIndexedFastaAdapter(rg));
Expand Down Expand Up @@ -771,6 +781,11 @@ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, Referen
return null;
}

if (!new File(gzipped.getPath() + ".tbi").exists())
{
log.error("Track lacks an index: {}, expected: {}", getObjectId(), gzipped.getPath() + ".tbi");
}

ret.put("adapter", new JSONObject(){{
put("type", adapterType);
put(prefix + "GzLocation", new JSONObject(){{
Expand All @@ -790,12 +805,12 @@ private JSONObject getTabixTrack(User u, Logger log, ExpData targetFile, Referen

public boolean needsProcessing()
{
return (needsGzip() && !isGzipped()) || doIndex() || shouldHaveFreeTextSearch();
return (needsGzip() && !isGzipped()) || shouldBeReSorted() || doIndex() || shouldHaveFreeTextSearch();
}

public boolean shouldBeCopiedToProcessDir()
{
return (needsGzip() && !isGzipped());
return (needsGzip() && !isGzipped()) || shouldBeReSorted();
}

public boolean isGzipped()
Expand Down Expand Up @@ -828,10 +843,16 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
throw new PipelineJobException("No ExpData for JsonFile: " + getObjectId());
}

final File processedTrackFile = getLocationOfProcessedTrack(true);
final File processedTrackDir = processedTrackFile.getParentFile();
File processedTrackFile = getLocationOfProcessedTrack(true);
final File processedTrackDir = processedTrackFile == null ? null : processedTrackFile.getParentFile();
if (processedTrackFile == null)
{
processedTrackFile = expData.getFile();
log.debug("Track does not require processing or indexing, using original location: " + processedTrackFile.getPath());
}

File targetFile = expData.getFile();
if (needsGzip() && !isGzipped())
if ((needsGzip() && !isGzipped()) || shouldBeReSorted())
{
//need to gzip and tabix index:
if (processedTrackFile.exists() && !SequencePipelineService.get().hasMinLineCount(processedTrackFile, 1))
Expand Down Expand Up @@ -896,8 +917,30 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
createIndex(targetFile, log, idx, throwIfNotPrepared);
}

if (TRACK_TYPES.bam.getFileType().isType(targetFile) || TRACK_TYPES.cram.getFileType().isType(targetFile))
{
File fileIdx = SequenceAnalysisService.get().getExpectedBamOrCramIndex(targetFile);
if (!fileIdx.exists())
{
if (throwIfNotPrepared)
{
throw new IllegalStateException("This track should have been previously indexed: " + targetFile.getName());
}

if (PicardWrapper.getPicardJar(false) != null)
{
SequenceAnalysisService.get().ensureBamOrCramIdx(targetFile, log, false);
}
}
}

if (doIndex())
{
if (processedTrackDir == null)
{
throw new PipelineJobException("processedTrackDir should not be null");
}

File trixDir = FileUtil.appendName(processedTrackDir, "trix");
if (forceReprocess && trixDir.exists())
{
Expand Down Expand Up @@ -1154,6 +1197,17 @@ else if (TRACK_TYPES.gff.getFileType().isType(finalLocation) || TRACK_TYPES.gtf.
}
}

private boolean shouldBeReSorted()
{
String sourceFilename = getSourceFileName();
if (sourceFilename == null)
{
return false;
}

return TRACK_TYPES.gff.getFileType().isType(sourceFilename) || TRACK_TYPES.gtf.getFileType().isType(sourceFilename) || TRACK_TYPES.bed.getFileType().isType(sourceFilename);
}

public File getLocationOfProcessedTrack(boolean createDir)
{
ExpData expData = getExpData();
Expand All @@ -1163,6 +1217,11 @@ public File getLocationOfProcessedTrack(boolean createDir)
}

File trackDir = getBaseDir();
if (trackDir == null)
{
return null;
}

if (createDir && !trackDir.exists())
{
trackDir.mkdirs();
Expand Down