From a53b5a1026db230b552efa5b0ea858d24ad30d9a Mon Sep 17 00:00:00 2001 From: XingY Date: Sun, 28 Sep 2025 17:28:20 -0700 Subject: [PATCH] Fix MS2 filepath --- ms2/src/org/labkey/ms2/PepXmlImporter.java | 9 ++++++++- ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java | 4 ++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/ms2/src/org/labkey/ms2/PepXmlImporter.java b/ms2/src/org/labkey/ms2/PepXmlImporter.java index ae006700c..5490f3234 100644 --- a/ms2/src/org/labkey/ms2/PepXmlImporter.java +++ b/ms2/src/org/labkey/ms2/PepXmlImporter.java @@ -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) diff --git a/ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java b/ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java index a5d4e7755..1e2b6a32e 100644 --- a/ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java +++ b/ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java @@ -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); }