Commit 08d86c92 authored by Sébastien Tourbier's avatar Sébastien Tourbier
Browse files

feat(handlers.participants): call Datalad's create() and save() methods

parent fca0a5c4

datahipy/handlers/participants.py

+37 −3
Original line number Diff line number Diff line
@@ -9,6 +9,8 @@ import shutil 
from datetime import datetime

from sre_constants import SUCCESS



import datalad.api



# BIDS Manager Python package has to be accessible.

try:

    from bids_manager.ins_bids_class import (
@@ -66,6 +68,13 @@ class ParticipantHandler: 
        # Post-importation BIDS Manager output refinements

        # to make BIDS Validator happy

        post_import_bids_refinement(ds_obj.dirname)

        # Save dataset state with Datalad

        save_msg = f'Add files for subject(s): {input_data["subjects"]}'

        datalad.api.save(

            dataset=ds_obj.dirname,

            message=save_msg,

            recursive=True

        )

        print(SUCCESS)



    def sub_delete(self, input_data=None):
@@ -84,6 +93,14 @@ class ParticipantHandler: 
        ds_obj.remove(sub_dict, with_issues=True, in_deriv=None)

        # Refresh

        ds_obj.parse_bids()

        # Save dataset state with Datalad

        save_msg = f'Remove files for subject {input_data["subject"]}'

        datalad.api.save(

            dataset=ds_obj.dirname,

            message=save_msg,

            recursive=True

        )

        print(SUCCESS)



    def sub_delete_file(self, input_data=None):

        """Delete data files from /raw and /source."""
@@ -91,6 +108,7 @@ class ParticipantHandler: 
        input_data = self.load_input_data(input_data)

        # Load the targeted BIDS dataset in BIDS Manager

        ds_obj = BidsDataset(self.dataset_path)

        subjects = list()

        for file in input_data["files"]:

            sub_dict = self.find_subject_dict(

                ds_obj=ds_obj, subject=file["subject"]
@@ -102,6 +120,15 @@ class ParticipantHandler: 
                    # but not from derivatives

                    ds_obj.remove(file_dict, with_issues=True, in_deriv=None)

                    print("{} was deleted.".format(file["fullpath"]))

                    if file["subject"] not in subjects:

                        subjects.append(file["subject"])

        # Save dataset state with Datalad

        save_msg = f'Remove files for subjects {subjects}'

        datalad.api.save(

            dataset=ds_obj.dirname,

            message=save_msg,

            recursive=True

        )

        print(SUCCESS)



    def sub_get(self, input_data=None, output_file=None):
@@ -142,6 +169,13 @@ class ParticipantHandler: 
                input_data["subject"], sub_info

            )

            ds_obj["ParticipantsTSV"].write_file()

            # Save dataset state with Datalad

            save_msg = f'Update participants.tsv file for subject {input_data["subject"]}'

            datalad.api.save(

                dataset=ds_obj.dirname,

                message=save_msg,

                recursive=True

            )

        print(SUCCESS)



    @staticmethod