python/run_dicom_archive_loader.py

[cmadjar]

• [x] run run_dicom_archive_loader.py -h => should print the help of the script. Make sure the help documentation is up to date.
• [x] run run_dicom_archive_loader.py -p database_config.py -u <UPLOAD ID> on an invalid Upload ID => should return [ERROR ] Did not find an entry in mri_upload associated with 'UploadID' 150
• [x] run run_dicom_archive_loader.py -p database_config.py -t <TARCHIVE PATH> on an invalid Tarchive Path => should return [ERROR ] bla does not exist. Please provide a valid path for --tarchive_path
• [x] run run_dicom_archive_loader.py -p database_config.py -u <UPLOAD ID> on a valid Upload ID and ensure the following:
  • [x] check that the correct number of files are registered in the mri_upload table
  • [x] check that Inserting=0 and InsertionComplete=1 in the mri_upload table
  • [x] check that the SessionID field of the mri_upload and tarchive tables has been updated properly
  • [x] ensure 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)
  • [x] if this is the first time run_dicom_archive_loader.py is run on the upload ID and the tarchive, ensure that the tarchive has been moved into a year subdirectory and the path has been updated in the tarchive table
  • [x] 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
  • [x] once the script is done running, ensure that the temporary directory that was used to run the script has been cleared out