[Loris-dev] Scan upload data path

[Christine Rogers]

For the Loris-dev community:

Detailed information on the Imaging Insertion (pipeline) scripts and the
Imaging Uploader can be found in our main GitHub Wiki, within the Loris
Setup Guide - Imaging Database page:
https://github.com/aces/Loris/wiki/Imaging-Database
This documentation includes diagrams, setup instructions, and
troubleshooting notes - some links are enclosed in the text below.

Yes, there's no need to re-upload data in order to re-run and troubleshoot
<https://github.com/aces/Loris/wiki/Imaging-Database#troubleshooting-insertion-of-uploaded-datasets>
the imaging insertion scripts, for projects using the Imaging Uploader
module.  The GitHub Wiki contains details on how to execute, troubleshoot
<https://github.com/aces/Loris/wiki/Imaging-Database#3-executing-and-troubleshooting-the-imaging-insertion-scripts>
and re-run
<https://github.com/aces/Loris/wiki/Imaging-Database#re-running-the-imaging-pipeline>
individual scripts.
In Matthew's case, the last step which is run by the tarchiveLoader
<https://github.com/aces/Loris/wiki/Imaging-Database#3-executing-and-troubleshooting-the-imaging-insertion-scripts>
script may be all you need to re-run.

Log files <https://github.com/aces/Loris/wiki/Imaging-Database#log-files>
containing error and output messages from the imaging insertion scripts are
created under the /data/$PROJ/data/logs/ directory. To view messages from
the last script run, consult the most recent log file modified in this
directory. These log files reference an upload ID used to identify each
imaging dataset -- consult the mri_upload database table to look up which
upload ID has been assigned to your scans.

Loris 16.0 was recently released with improvements to message logging and
notifications (main <https://github.com/aces/Loris/releases> and Imaging
<https://github.com/aces/Loris-MRI/releases> repos).

Best,
Christine
-- 
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada


On Mon, Jul 4, 2016 at 4:46 PM, Matthew Lee <matthew at biospective.com> wrote:

> Hi,
>
> I am trying to upload some scan data, using a wrapper around dcm2mnc
> instead of calling it directly.  I am running into problems though, and the
> upload process is failing after the call to tarchiveLoader with the message
> "The insertion scripts have failed".  When I tweak something, and try to
> run imaging_upload_file.pl again, I can't unless I get a new UploadID.
>
> Is there a quick way to rerun this without having to start from the
> imaging uploader module or an equivalent script?
> Is there documentation anywhere about the program execution flow of the
> upload process?  A diagram would be ideal, but something showing the order
> scripts that get called, and what they each do/check would be really
> helpful.
> What are some places I should check first to debug this process?
>
> I am running a modified version of LORIS v15.10.2 and LORIS_MRI v15.10 on
> Ubuntu 14.04.
>
> Thanks,
>
> Matthew
>
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>
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