Use environment variable instead of CLI argument for the Python configuration file

[maximemulder]

Currently, there is the directory of the Python configuration file in the $LORIS_CONFIG variable (set in the environment file), and then each Python (and Perl) script takes the name of the configuration file as a CLI argument. The full path of the configuration file is obviously the environment variable joined with the CLI argument.

What is we instead put the full path to the configuration file in the environment variable such as $LORIS_CONFIG_PYTHON (example name) ? This would allow to not specify the configuration file each time and makes the scripts easier to use for new users.

For instance, on the new import_dicom_study.py script (#1117), we go from:

import_dicom_study.py --insert --source=/path/to/dicom/study

to:

import_dicom_study.py --profile database_config.py --insert --source=/path/to/dicom/study

(in comparison, the current command to get the same result is this one 👀)

dicomTar.pl -profile prod -database -source=/path/to/dicom/study -target=/path/to/tarchive/dir

[cmadjar]

You can have multiple configuration files. Hardcoding it in $LORIS_CONFIG_PYTHON makes switching between configuration files more complex for little benefits IMO. I constantly switch the configuration file when testing on different LORIS versions.

[maximemulder]

Discussion at the LORIS-MRI meeting: This might be nice to have, but is not a priority. One option would be to have a default configuration file that can be overridden with --profile.