Rationale

When a Skyline document is moved to another folder, FilePathRoot on the moved ExpRun continues to point to the source container.

• FilePathRoot gets set incorrectly in XarReader:
  vals.setFilePathRoot(FileUtil.getAbsolutePath(_xarSource.getRootPath()))
• getRootPath() method in MoveRunsXarSource returns the root path in the source container.
• Incorrect FilePathRoot causes the PanoramaPublic data copy pipeline to fail in PanoramaPublicFileImporter.alignDataFileUrls()

Questions:

• Would it be better to fix this in XarReader instead of the targetedms? This draft PR has a potential fix: Set the FilePathRoot on moved run platform#6292
• Would it be better to fix the FilePathRoot in the panoramapublic module instead, so that it only impacts PanoramaWeb?

Related issues and tickets:

• Issue 33712: Moving an assay file does not update exp.ExperimentRun.filepathRoot
• Issue 47189: Error moving Skyline documents across folders
• Ticket 35288: Issue 33712 is not fixed - Move Run doesn't update exp.ExperimentRun.filePathRoot column

Related Pull Requests

• Test for copying a folder containing moved Skyline documents to Panorama Public MacCossLabModules#502
• Set the FilePathRoot on moved run platform#6292 (Draft PR if better to fix in XarReader instead)

Changes

• Update FilePathRoot in TargetedMSDataHandler