unable to archive imported DICOMs

[Alle Meije Wink]

Following the advice on
   https://wiki.xnat.org/display/XKB/Importing+data+directly+into+XNAT
I pushed a set of images, which were already on the host, to the prearchive using
   $ find . -name *.dcm -exec storescu -aec XNAT xnat.oh.my 8104 {} \;

Then I went to the web interface and
   1. all the scans were there (import_step1)
   2. I then assigned them to a project (import_step2)
   3. archived them in the project (import_step3)
   4. but then I got an error because "unable to create new session ID" (import_step4)

I'm not sure why this is - do the sessions need to be manually created before uploading local data?
Another possibility is that (because the data are from an imaging study) session info is missing?

If there is a way to archive data that was imported this way, eg by supplying information to the DICOM command, that would be a great help.

Thanks for your help!

[McKay, Mike]

Are you able to archive any of them if you do so one at a time? I could seeing there being issues trying to archive two sessions with identical project/subject/session.

-Mike

---

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of Alle Meije Wink <a.m....@gmail.com>
Sent: Tuesday, February 6, 2018 8:07:08 AM
To: xnat_discussion
Subject: [XNAT Discussion] unable to archive imported DICOMs

 

Following the advice on
   https://wiki.xnat.org/display/XKB/Importing+data+directly+into+XNAT

Importing data directly into XNAT - XNAT Knowledge Base ... wiki.xnat.org These procedures are useful when you have a large amount of data on the same machine or local network as your XNAT installation. These procedures presume that you can ...

I pushed a set of images, which were already on the host, to the prearchive using
   $ find . -name *.dcm -exec storescu -aec XNAT xnat.oh.my 8104 {} \;

Then I went to the web interface and
   1. all the scans were there (import_step1)
   2. I then assigned them to a project (import_step2)
   3. archived them in the project (import_step3)
   4. but then I got an error because "unable to create new session ID" (import_step4)

I'm not sure why this is - do the sessions need to be manually created before uploading local data?
Another possibility is that (because the data are from an imaging study) session info is missing?

If there is a way to archive data that was imported this way, eg by supplying information to the DICOM command, that would be a great help.

Thanks for your help!

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[Alle Meije Wink]

Thanks for the suggestion! When I only do the project assignment for one of them (on the 'details' page) I first have this warning on the top of the page

   "This session is in the Unassigned folder. Move the session to a project to enable archiving."

and then as soon as I assign the session to the test project, these warnings appear below the scan details:

   Current Warnings

   FAIL-9: unable to create new session ID

   FAIL-13: unable to create new session ID

So it goes wrong even before archiving (see the screenshot). The data have been anonymised before they enter the prearchive, so could it be that information to set the XNAT session ID is missing?

[Alle Meije Wink]

If after that I do 'review and archive' instead of 'archive', then the 'review' page show this warning

* This subject does not exist, and will be automatically created. To populate demographic details for this subject please use the 'Add New Subject' link.

It seems that the idea is that, even with the missing information, the subject ID etc will be automatically created, only that this idea cannot be executed?


bw
AM

[Herrick, Rick]

That’s correct, the subject should be automatically created on the archive process. But I think the issue is not related to the subject creation. Those messages indicate that the session ID generator is failing. This is pretty stable code, so if it’s failing that likely indicates something weird going with your system configuration. Check the back-end logs and see if there are any error messages there that correlate with the failed archive operations. It’s impossible to say what the failure is without that info.

 

-- 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

Phone: +1 (314) 273-1645

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[Alle Meije Wink]

Hi Rick, thanks for the suggestion!

What I don't understand is that I get the warnings 'unable to create Session ID' as soon as I assign the subjects to the project, that is before archiving.
The access log shows the http calls that request the database record creations -- but no errors?

They all look like this

2018-02-07 09:24:10,101 - admin 127.0.0.1 GET http://145.121.54.181/data/projects?accessible=true&XNAT_XHR=xez9l96c7-1517995456023&format=json
2018-02-07 09:24:10,101 - admin 127.0.0.1 GET http://145.121.54.181/data/projects?favorite=true&XNAT_XHR=xjuvo2yed-1517995456033&format=json
2018-02-07 09:24:10,102 - admin 127.0.0.1 GET http://145.121.54.181/data/projects?accessible=true&users=true&XNAT_XHR=xy22bx54y-1517995456028&format=json
2018-02-07 09:24:10,108 - admin 145.121.46.135 GET http://127.0.0.1:8080/xapi/spawner/namespaces
2018-02-07 09:24:10,344 - admin 127.0.0.1 GET http://145.121.54.181/data/search/saved?format=json
2018-02-07 09:24:10,558 - admin 145.121.46.135 GET http://127.0.0.1:8080/xapi/siteConfig/buildInfo
2018-02-07 09:24:10,813 - admin 127.0.0.1 GET http://145.121.54.181/REST/projects?XNAT_CSRF=9d6be542-8422-4fd8-a1e4-c594dc813236&format=json&timestamp=1517995456739&creatableTypes=true&data-type=xnat:mrSessionData&rnd=1517995456740
2018-02-07 09:24:11,039 - admin 127.0.0.1 GET http://145.121.54.181/data/services/scan-quality-labels/epad-test?XNAT_CSRF=9d6be542-8422-4fd8-a1e4-c594dc813236&format=json&rnd=1517995456890
2018-02-07 09:24:11,040 - admin 127.0.0.1 GET http://145.121.54.181/REST/projects/epad-test/subjects?XNAT_CSRF=9d6be542-8422-4fd8-a1e4-c594dc813236&format=json&timestamp=1517995456959&rnd=1517995456959
2018-02-07 09:24:11,044 - admin 127.0.0.1 GET http://145.121.54.181/REST/projects/epad-test/experiments?XNAT_CSRF=9d6be542-8422-4fd8-a1e4-c594dc813236&format=json&timestamp=1517995456959&rnd=1517995456959
2018-02-07 09:24:11,046 - admin 127.0.0.1 GET http://145.121.54.181/REST/prearchive/projects/epad-test/20180207_082936293/010-00000/resources?format=json&sortBy=category,cat_id,label&timestamp=1517995456978&rnd=1517995456978
2018-02-07 09:24:11,066 - admin 127.0.0.1 GET http://145.121.54.181/REST/prearchive/projects/epad-test/20180207_082936293/010-00000/logs?template=details&format=html&requested_screen=PrearchiveDetailsLogs.vm&popup=true&rnd=1517995456979
2018-02-07 09:24:11,077 - admin 145.121.46.135 SCREEN: PrearchiveDetailsLogs
2018-02-07 09:24:11,209 - admin 145.121.46.135 GET http://127.0.0.1:8080/xapi/siteConfig/buildInfo
2018-02-07 09:24:11,422 - admin 145.121.46.135 GET http://127.0.0.1:8080/xapi/xnatTask/checkNodeConfigurationStatus

And then The PreArchive logs show this

2018-02-06 09:25:00,567 [Thread-64] ERROR org.nrg.xnat.helpers.prearchive.PrearcTableBuilder -
org.nrg.xnat.helpers.prearchive.PrearcDatabase$SyncFailedException: Operation Failed: unable to create new session ID
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.wrapException(PrearcDatabase.java:1028)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:1021)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase.access$800(PrearcDatabase.java:65)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$11.run(PrearcDatabase.java:948)
Caused by: org.nrg.action.ServerException: unable to create new session ID
    at org.nrg.xnat.archive.PrearcSessionArchiver.call(PrearcSessionArchiver.java:490)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$12.extSync(PrearcDatabase.java:988)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$12.extSync(PrearcDatabase.java:985)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase$LockAndSync.run(PrearcDatabase.java:1640)
    at org.nrg.xnat.helpers.prearchive.PrearcDatabase._archive(PrearcDatabase.java:1011)
    ... 2 more
Caused by: java.lang.NumberFormatException: For input string: ""
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:592)
    at java.lang.Integer.valueOf(Integer.java:766)
    at org.nrg.xnat.turbine.utils.IDGenerator.generateIdentifier(IDGenerator.java:68)
    at org.nrg.xdat.om.base.BaseXnatExperimentdata.CreateNewID(BaseXnatExperimentdata.java:407)
    at org.nrg.xnat.archive.PrearcSessionArchiver.call(PrearcSessionArchiver.java:487)
    ... 6 more

That suggests that an empty string for <somewhere in session creation> causes the error?

Thanks for your insights!
Alle Meije

[Alle Meije Wink]

I also tried the same actions in a new project with a different name: same problem.

One of my ideas was to use the menu for manually creating a session and then 'modify and archive', so that I could populate (make up) the session data that may be required.
But even when I fill out all the details about this subject I cannot complete the form (the window stays on after 'submit') and it shows an error saying [For input string: ""] -- even though there are no empty strings left on the form? I have attached a screenshot of the form.

If anyone has a suggestion it would really be appreciated!

On Thursday, 8 February 2018 20:16:38 UTC+1, Rick Herrick wrote:

[Alle Meije Wink]

I think I have found what the problem was. Nothing in XNAT.

Every time I used sudo (e.g. for installing DAX software) I got the otherwise innocuous-looking message
  sudo: unable to resolve host the_hostname
After solving this, just out of curiosity I tried to archive one of the images and the warning 9 and 13 were gone -- it was added to the project!

Not sure on which level this host name resolution caused a problem, but this seems to have done it.