[GENFI] Enable use of tsv to extract more clinical data

[MatthieuJoulot]

In its current state, this converter extracts only the most essential data from the spreadsheets.
This PR proposes to use a tsv given by the user specifying the name of the fields he wants, regardless of which spreadsheet the data is in.
The data must be given in the with underscores instead of spaces, and no capital letters
The data will then be written in the right place (participants.tsv/sessions.tsv/scans.tsv) using a mapping of the data.

[pep8speaks]

Hello @MatthieuJoulot! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2023-10-25 12:12:06 UTC

[NicolasGensollen]

Thanks @MatthieuJoulot !
I made a first pass with some minor suggestions along the way.
Are you planning to add some clinical data to the CI dataset as well ?

[NicolasGensollen]

Thanks @MatthieuJoulot !

The PR LGTM. I have a few additional suggestions but should be good to go once implemented.

[NicolasGensollen]

I think we should use Path objects consistently across the code base rather than strings. Especially when it makes the code much easier to read. I would modify both path_to_mapping_tsv and path_to_ref_csv.

To be verified, but this would become:

from clinica.utils.filemanip import get_parent
genfi_data_folder = get_parent(__file__, 3) / "data"
path_to_ref_csv = genfi_data_folder / "genfi_ref.csv"
...
path_to_mapping_tsv = genfi_data_folder / "genfi_data_mapping.tsv"

[NicolasGensollen]

I can imagine users getting stuck here when providing only path_to_clinical_tsv but not path_to_clinical since these concepts are quite close for the distracted reader of the documentation.

I would be very explicit to ease debugging. Maybe something like:

raise ValueError(
    "The Genfi2BIDS converter is unable to convert the clinical data because "
    "the path to these data was not provided while a TSV file with additional "
    f"data was given ({path_to_clinical_tsv}). You can either use the appropriate "
    "option from the clinica command line interface to provide the missing path, "
    "or chose to not convert clinical data at all."
)

[MatthieuJoulot]

Sounds good

[NicolasGensollen]

Could you also add the = None to the path_to_clinical argument as well ?

Also, is gif optional ? If not, it should be before the optional arguments, if yes, it should be declared as optional with a default value.

[NicolasGensollen]

LGTM, thanks @MatthieuJoulot !