python/scripts/run_dicom_archive_loader.py testing (+ addition of other automated tests)

[cmadjar]

Manual checks

• run run_dicom_archive_loader.py -h on a session with fieldmaps + BOLD images (or fieldmaps + DWI images)
  => should print the help of the script. Make sure the help documentation is up to date.
• run run_dicom_archive_loader.py -p database_config.py -u <UPLOAD ID> on a valid Upload ID and ensure the following:
  • if there are fieldmap and resting state scans, ensure that the IntendedFor field of the fieldmap files has been updated to include the path to the BOLD images
  • once the script is done running, ensure that the temporary directory that was used to run the script has been cleared out
• BONUS POINTS: verify that automated checks listed below are still implemented

Bugs found

• [ ]

Automatic checks

List of automatic checks to implement:

• run script on an invalid Upload ID
• run script on an invalid Tarchive Path
• run script on a tarchive that will result in a successful run and:
  • check Inserting=0 in the mri_upload table
  • check InsertionComplete=1 in the mri_upload table
  • check that the SessionID field of the mri_upload and tarchive tables has been updated properly
  • check that if a series description of a NIfTI file matches one of the regex listed in the excluded_series_description config, the NIfTI file is skipped from insertion (therefore cannot be found in files nor any of the violation tables) [tarchive_series count = 2 and files count = 1]
  • if this is the first time run_dicom_archive_loader.py is run on the upload ID and the tarchive, check that the tarchive has been moved into a year subdirectory and the path has been updated in the tarchive table