Commit 4d6a1265 authored by Sebastien Tourbier's avatar Sebastien Tourbier
Browse files

fix(handlers.project): changes to make all tests passed

parent d387507b

bids_tools/handlers/project.py

+31 −17
Original line number Diff line number Diff line
@@ -52,13 +52,13 @@ def initialize_project_structure( 
        f.writelines([f"# {project_title}\n\n", f"{project_description}"])





def create_project(input_data: dict):

def create_project(input_data: str):

    """Create a new Collaborative Project on the HIP initialized with directory/file structure.



    Parameters

    ----------

    input_data : dict

        Dictionary sent by the HIP that contains all information

    input_data : str

        Path to input data JSON file sent by the HIP that contains all information

        about Project and corresponding BIDS dataset in the form::



            {
@@ -82,7 +82,10 @@ def create_project(input_data: dict): 
                }

            }

    """

    print(f"Creating new collaborative project at {input_data['path']}...")

    # Load input data

    with open(input_data, "r") as f:

        input_data = json.load(f)

    print(f'Creating new collaborative project at {input_data["path"]}...')

    # Extract input data

    project_dir = Path(input_data["path"])

    project_title = input_data["title"]
@@ -92,18 +95,18 @@ def create_project(input_data: dict): 
    # Create initial BIDS dataset

    create_empty_bids_dataset(

        bids_dir=(project_dir / "inputs" / "bids-dataset").absolute(),

        dataset_desc=input_data["createBidsDatasetDto"],

        dataset_desc=input_data["createBidsDatasetDto"]["DatasetDescJSON"],

    )

    print(SUCCESS)





def import_subject(input_data: dict):

def import_subject(input_data: str):

    """Import a new subject from a BIDS dataset of the HIP Center space to the BIDS dataset of the HIP Collaborative Project.



    Parameters

    ----------

    input_data : dict

        Dictionary sent by the HIP that contains all information

    input_data : str

        Path to input data JSON file sent by the HIP that contains all information

        about the subject and files to import in the form::



            {
@@ -112,6 +115,9 @@ def import_subject(input_data: dict): 
                "targetDatasetPath": "/path/to/target/bids/dataset/directory",

            }

    """

    # Load input data

    with open(input_data, "r") as f:

        input_data = json.load(f)

    print(

        f"Importing subject {input_data['subject']} "

        f"from {input_data['sourceDatasetPath']} "
@@ -119,17 +125,18 @@ def import_subject(input_data: dict): 
    )

    # Copy subject directory from source to target

    shutil.copytree(

        Path(input_data["sourceDatasetPath"] / input_data["subject"]).absolute(),

        Path(input_data["targetDatasetPath"] / input_data["subject"]).absolute(),

        (Path(input_data["sourceDatasetPath"]) / input_data["subject"]).absolute(),

        (Path(input_data["targetDatasetPath"]) / input_data["subject"]).absolute(),

        dirs_exist_ok=True,

    )

    # Update participants.tsv file of target dataset with subject row from source dataset

    transfer_subject_participants_tsv_row(

        participant_id=input_data["subject"],

        source_participant_tsv=Path(

            input_data["sourceDatasetPath"] / "participants.tsv"

        source_participant_tsv=(

            Path(input_data["sourceDatasetPath"]) / "participants.tsv"

        ).absolute(),

        target_participants_tsv=Path(

            input_data["targetDatasetPath"] / "participants.tsv"

        target_participants_tsv=(

            Path(input_data["targetDatasetPath"]) / "participants.tsv"

        ).absolute(),

    )

    print(SUCCESS)
@@ -168,13 +175,13 @@ def transfer_subject_participants_tsv_row( 
    target_participants_df.to_csv(target_participants_tsv, sep="\t", index=False)





def import_document(input_data: dict):

def import_document(input_data: str):

    """Import a new supporting document to the `documents/` folder of the HIP Collaborative Project.



    Parameters

    ----------

    input_data : dict

        Dictionary sent by the HIP that contains all information

    iinput_data : str

        Path to input data JSON file sent by the HIP that contains all information

        about the document to import in the form::



            {
@@ -182,12 +189,19 @@ def import_document(input_data: dict): 
                "targetDocumentPath": "/path/to/target/document/file",

            }

    """

    # Load input data

    with open(input_data, "r") as f:

        input_data = json.load(f)

    print(

        f'Importing document {input_data["sourceDocumentPath"]} from HIP Center space '

        f'to HIP Collaborative Project at {input_data["targetDocumentPath"]}... '

    )

    source_document_path = Path(input_data["sourceDocumentPath"])

    target_document_path = Path(input_data["targetDocumentPath"])

    # Remove target document if it already exists

    if target_document_path.exists():

        print(f"WARNING: Overwriting target document at {target_document_path}...")

        os.remove(target_document_path)

    # Copy document from source to target

    shutil.copyfile(source_document_path, target_document_path)

    print(SUCCESS)