[Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend

[Carolina Makowski]

Hi there,

I have two queries that are related to the imaging and behavioral domains
of the database - please let me know if you would prefer that I separate
the issues since they pertain to different aspects of the database, but for
now I will put both issues here:

*1) Failure uploading .tgz file through Image Uploader*
Before getting to this point, we had completed everything outlined in the
documentation online for the Imaging Database.
The tgz file I tried to upload was anonymized and the header/Patient Name
was parsed accordingly, and the file did upload, but its status is marked
as "Failure".
Next, we looked for the tgz file in the backend, and it does indeed appear
in /data/incoming. We also followed all documentation in the Imaging
Uploader documentation, changing the paths appropriately in the
configuration module and updating the apache configuration file.
After running the imaging_upload_file.pl script, we received the following
error:

lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_
file.pl -profile prod -verbose -upload_id 5 /data/incoming/
NDARINV1ET4JE3B_174450_baselineyear1arm1_T1.tgz

    ERROR: You don't have a
    configuration file named 'prod' in:
    /data/abcd/bin/mri/dicom-archive/.loris_mri/

The prod file does indeed exist in that directory, and we have tried
running this as root and lorisadmin, with appropriate permissions, and can
access prod independently of this script. Has this error come up before in
your experience?

*2) Registering an instrument that was created using the Instrument Builder
GUI.*
I am having a bit of trouble following the documentation online for this.
In particular, we are getting stuck in populating the test_subgroups table.
According to the documentation online, this statement should apply to us
(from section 3: populate test_names and test_subgroups tables): "For all
*.linst instruments created via the Instrument Builder, sourcing the *.sql file
takes care of this step". However, test_subgroups was not automatically
populated (test_names was populated properly). We started delving into the
"Instrument Coding Guide" documentation but I am under the impression that
creation of an instrument through the instrument builder and using a linst
file should bypass some of the steps that are required in this Instrument
Coding Guide. Perhaps some clarification on the steps after building a
linst file and after creating and adding the instrument table to the
database would be helpful here.

Thanks in advance! I know I've been bombarding you guys with a lot of
questions lately but I really appreciate the help :)

Have a nice weekend,
Carolina
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