XNAT Rejects Sessions
bennett landman
The SOP Class is 1.2.840.10008.5.1.4.1.1.4.1, Enhanced MR Image Storage same as everything else.
Any thoughts?
-Bennett
Herrick, Rick
Where is this message occurring? I can’t find anywhere in our code or dcm4che that the word “non-secondary” appears, so I don’t think XNAT itself is generating that message.
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Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
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Brian Boyd
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Moore, Charlie
The location in the source code is here: https://bitbucket.org/xnatdev/xnat-web/src/b6611b9ebdcd2ca64c3d85112bc9430ba85155a4/src/main/java/org/nrg/xnat/archive/PrearcSessionArchiver.java?at=master#lines-672 . It doesn’t show up in a direct search since “secondary” is actually pulling from the resource name.
Thanks,
Charlie
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Herrick, Rick
Okay here’s the relevant bit of code:
final List<String> unreferenced = CatalogUtils.getUnreferencedFiles(f.getParentFile());
if (unreferenced.size() > 0) {
warn(20, String.format("Scan %1$s has %2$s non-%3$s (or non-parsable %3$s) files", scan.getId(), unreferenced.size(), resource.getLabel()));
}
This means that one of the files for scan 901 isn’t in the catalog. Why is it not in the catalog?
🤷🏽♂️
But you can at least find out what the particular file is that’s causing the problem. Go to the prearchive folder for your session, go to that scan, and then the DICOM folder for that scan. There should be X DICOM files in that folder and X – 1 <cat:entry> elements in the accompanying scan_901_catalog.xml. It’s just a matter of diff’ing those:
$ diff <(fgrep cat:entry scan_901_catalog.xml | sed 's/^.*URI="\(.*\.dcm\)".*$/\1/' | sort) <(ls *.dcm | sort)
I copied a file from one scan into another in one of my sessions and did this:
$ diff <(fgrep cat:entry scan_1_catalog.xml | sed 's/^.*URI="\(.*\.dcm\)".*$/\1/' | sort) <(ls *.dcm | sort)
9a10
> 1.2.840.113654.2.45.2.108105-2-1-1jadmt2.dcm
Give that a try and that will at least tell you which files are causing the problem.
I’ll create an issue for this in JIRA, but there are some things that I’m not sure XNAT can tell you at this point. Where it’s issuing this message it’s just checking to see whether files aren’t in the catalog XML. The problem is that the files not getting included has already happened and all it can see is the symptom. Maybe once you figure out which file is causing the problem we can look into why it’s not getting picked up during the session XML building process.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
To view this discussion on the web visit
https://groups.google.com/d/msgid/xnat_discussion/CAH2LwGty_ZwHXO09dGe6%3D-8THAdwg5yW_Qu9FPYyGBwSw6%2B4kA%40mail.gmail.com.