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Fix MS2 filepath #934

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Merged
XingY merged 1 commit into from
Sep 29, 2025
Merged

Fix MS2 filepath #934

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9 changes: 8 additions & 1 deletion ms2/src/org/labkey/ms2/PepXmlImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -301,9 +301,16 @@ protected File getMzXMLFile(MS2Loader.PeptideFraction fraction)
{
return f;
}

if (NetworkDrive.exists(mzXMLFile) && mzXMLFile.isFile())
{
return mzXMLFile;
}

return f; // return file under root, even if it doesn't exist
}

return mzXmlFileName == null ? null : new File(mzXmlFileName);
return null;
}

public static boolean isFractionsFile(File pepXmlFile, String joinedBaseName)
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4 changes: 2 additions & 2 deletions ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java
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Expand Up @@ -63,11 +63,11 @@ public static void doSetup()
protected void configure()
{
_containerHelper.createProject(getProjectName(), "MS2");
setPipelineRoot(TestFileUtils.getSampleData("xarfiles/ms2pipe/iTRAQ/").getAbsolutePath());
setPipelineRoot(TestFileUtils.getSampleData("xarfiles/ms2pipe/").getAbsolutePath());
clickProject(getProjectName());

clickButton("Process and Import Data");
_fileBrowserHelper.importFile("xtandem/Libra/iTRAQ.search.xar.xml", "Import Experiment");
_fileBrowserHelper.importFile("/iTRAQ/xtandem/Libra/iTRAQ.search.xar.xml", "Import Experiment");
goToModule("Pipeline");
waitForPipelineJobsToComplete(1, "Experiment Import - iTRAQ.search.xar.xml", false);
}
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