Creation of a generic file insertion script

[cmadjar]

This is a first iteration of a generic file insertion script. The script will insert files that are not MINC files into the files and parameter_file tables. Will probably still be modifying it as I will implement the PET HRRT insertion script and EEG insertion script which is why I tagged it as "Needs Work Before Merging".

Refers to following Redmine ticket: https://redmine.cbrain.mcgill.ca/issues/10557

PR sent to the LORIS repo to add imaging non minc file insertion to the notification_types table: aces/Loris#4144

Notes:

• the following arguments are required to run the script:

   -profile        name of config file in ./dicom-archive/.loris_mri.

   -file_path      file to register into the database (full path from the root
                   directory is required)

   -upload_id      ID of the uploaded imaging archive containing the file
                   given as argument with -file_path option

   -output_type    file's output type (e.g. native, qc, processed...)

   -scan_type      file's scan type (from the mri_scan_type table)

   -date_acquired  acquisition date for the file (YYYY-MM-DD)

   -scanner_id     ID of the scanner stored in the mri_scanner table

   -coordin_space  Coordinate space of the file to register (e.g. native,
                   linear, nonlinear, nativeT1)

• the following arguments are optional

   -patient_name   patient name, if cannot be found in the file name (in the
                   form of PSCID_CandID_VisitLabel)

   -metadata_file  file that can be read to look for metadata information to
                   attach to the file to be inserted

   -reckless       upload data to database even if study protocol is not
                   defined or violated.

   -noreckless     opposite of -reckless [default]

   -verbose        Be verbose

   -noverbose      opposite of -verbose [default]

Notes for existing projects

In order to be able to use this new script, you need to install the CPAN JSON library:

sudo cpan install JSON

[cmadjar]

@nicolasbrossard Thank you for the great feedback! I integrated all your comments. Ready for another review

[cmadjar]

@PapillonMcGill Thank you for the comments. They should all be taken care of in the last commit.

[PapillonMcGill]

LGTM

[nicolasbrossard]

I know it is not directly related to your code but I think there is no point in having method registerScanIntoDB (the method that contains the code above) receive a reference to a MINC file. Since $minc_file is a File object, it already is a reference. I think every time you see a double dollar sign access (as in $${minc_file}), it is a sign that too many levels of indirection are used...Anyway, leave it like this for now and let's try to "keep it cheap" in future PRs and minimize the number of $ used when accessing variables.

[cmadjar]

totally agree!

[nicolasbrossard]

I think that for this PR to work, you need the new module JSON.pm from cpan. The steps to retrieve it should go into the install script and something should be written in the release notes regarding the use of a new Perl module.

[cmadjar]

@nicolasbrossard Thank you for the good catches!! Fixed now. Ready for another review.

[nicolasbrossard]

All the issues have been addressed. Tagging as PassedCodeReview. 👍