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Set the FilePathRoot on moved run #6292

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Merged
labkey-jeckels merged 3 commits into from
Feb 18, 2025
Merged

Set the FilePathRoot on moved run #6292

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e4dfdd8
Fix ExpRuns's FilePathRoot.
vagisha Feb 4, 2025
d990456
Added getJobRootPath() to XarSource. Use this to set the FilePathRoot…
vagisha Feb 5, 2025
eca8bb2
CR changes
vagisha Feb 9, 2025
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2 changes: 2 additions & 0 deletions api/src/org/labkey/api/exp/XarSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@ public XarSource(PipelineJob job)

public abstract Path getRootPath();

public Path getJobRootPath() { return getRootPath(); }

/**
* Should be true if this was uploaded XML that was not part of a full XAR
*/
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2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/XarReader.java
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Expand Up @@ -1109,7 +1109,7 @@ private void loadExperimentRun(ExperimentRunType a, List<ExpMaterial> startingMa
vals.setProtocolLSID(protocol.getLSID());
vals.setComments(trimString(a.getComments()));

vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath())); // FileUtil.getAbsolutePath(runContext.getContainer(), _job.getPipeRoot().getRootNioPath()));
vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getJobRootPath()));
vals.setContainer(getContainer());
String workflowTaskLSID = a.getWorkflowTaskLSID();

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9 changes: 9 additions & 0 deletions experiment/src/org/labkey/experiment/pipeline/MoveRunsTask.java
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Expand Up @@ -220,6 +220,15 @@ public Path getRootPath()
return FileUtil.stringToPath(_sourceContainer, _root);
}

@Override
public Path getJobRootPath()
{
var pipelineJob = getXarContext().getJob();
return pipelineJob != null
? pipelineJob.getPipeRoot().getRootFileLike().toNioPathForRead()
: super.getJobRootPath();
}

@Override
public boolean shouldIgnoreDataFiles()
{
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