Loading bids_tools/handlers/project.py +101 −12 Original line number Diff line number Diff line Loading @@ -3,8 +3,48 @@ """Methods supporting the Collaborative Space of the HIP.""" import os import shutil import json import pandas as pd from pathlib import Path def create_project(input_data): from bids_tools.bids.dataset import create_empty_bids_dataset PROJECT_FOLDERS = ["code", "documents", "inputs/bids-dataset", "outputs"] PROJECT_DOCUMENTS = [ "README.md", ] def initialize_project_structure( project_dir: Path, project_title: str, project_description: str ): """Initialize the directory structure of a Collaborative Project on the HIP. Parameters ---------- project_dir : pathlib.Path Path to the project directory. project_title : str Title of the project. project_description : str Description of the project. """ # Create initial project directory structure for folder in PROJECT_FOLDERS: os.makedirs(project_dir / folder, exist_ok=True) # Create initial project README.md file with open(project_dir / "README.md", "w") as f: f.writelines([f"# {project_title}\n\n", f"{project_description}"]) def create_project(input_data: dict): """Create a new Collaborative Project on the HIP initialized with directory/file structure. Parameters Loading @@ -17,20 +57,37 @@ def create_project(input_data): "path": "/path/to/project/directory", "title": "Project Title", "description": "Project Description that would be put in the README.md file", "bids_dataset": { "path": "/path/to/bids/dataset/directory", "title": "BIDS Dataset Title", "description": "BIDS Dataset Description that would be put in the README.md file", "authors": ["Author 1", "Author 2"], "license": "CC-BY-4.0" "createBidsDatasetDto": { "owner": "username", "parent_path": "/path/to/project/directory/inputs", "dataset_dirname": "bids-dataset", "DatasetDescJSON": { "Name": "BIDS Dataset Title", "BIDSVersion": "1.6.0", "License": "CC-BY-4.0", "Authors": ["Author 1", "Author 2"], "Acknowledgements": "Acknowledgement 1", "Funding": ["Funding 1"], "ReferencesAndLinks": ["Reference 1", "Reference 2"], "DatasetDOI": "10.18112/openneuro.ds000000.v1.0.0" } } } """ # Extract input data project_dir = Path(input_data["path"]) project_title = input_data["title"] project_description = input_data["description"] # Initialize project directory structure with README.md file initialize_project_structure(project_dir, project_title, project_description) # Create initial BIDS dataset create_empty_bids_dataset( bids_dir=(project_dir / "inputs" / "bids-dataset").absolute(), dataset_desc=input_data["createBidsDatasetDto"], ) def import_subject(input_data): def import_subject(input_data: dict): """Import a new subject from a BIDS dataset of the HIP Center space to the BIDS dataset of the HIP Collaborative Project. Parameters Loading @@ -45,10 +102,38 @@ def import_subject(input_data): "targetDatasetPath": "/path/to/target/bids/dataset/directory", } """ # 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(), ) # Extract subject line from participants.tsv file of source dataset as dataframe source_participants_df = pd.read_csv( Path(input_data["sourceDatasetPath"] / "participants.tsv"), sep="\t" ) source_subject_df = source_participants_df[ source_participants_df["participant_id"] == input_data["subject"] ] # Extract participants.tsv file of target dataset as dataframe target_participants_df = pd.read_csv( Path(input_data["targetDatasetPath"] / "participants.tsv"), sep="\t" ) # Append subject row dataframe to target dataframe target_participants_df = pd.concat( [target_participants_df, source_subject_df], join="outer" ) # Replace any NaN values with 'n/a' following BIDS convention target_participants_df = target_participants_df.fillna("n/a") # Write updated participants.tsv file of target dataset target_participants_df.to_csv( Path(input_data["targetDatasetPath"] / "participants.tsv"), sep="\t", index=False, ) def import_document(input_data): """Import a new supporting document supporting to the `documents/` folder of the HIP Collaborative Project. def import_document(input_data: dict): """Import a new supporting document to the `documents/` folder of the HIP Collaborative Project. Parameters ---------- Loading @@ -61,3 +146,7 @@ def import_document(input_data): "targetDocumentPath": "/path/to/target/document/file", } """ source_document_path = Path(input_data["sourceDocumentPath"]) target_document_path = Path(input_data["targetDocumentPath"]) # Copy document from source to target shutil.copyfile(source_document_path, target_document_path) Loading
bids_tools/handlers/project.py +101 −12 Original line number Diff line number Diff line Loading @@ -3,8 +3,48 @@ """Methods supporting the Collaborative Space of the HIP.""" import os import shutil import json import pandas as pd from pathlib import Path def create_project(input_data): from bids_tools.bids.dataset import create_empty_bids_dataset PROJECT_FOLDERS = ["code", "documents", "inputs/bids-dataset", "outputs"] PROJECT_DOCUMENTS = [ "README.md", ] def initialize_project_structure( project_dir: Path, project_title: str, project_description: str ): """Initialize the directory structure of a Collaborative Project on the HIP. Parameters ---------- project_dir : pathlib.Path Path to the project directory. project_title : str Title of the project. project_description : str Description of the project. """ # Create initial project directory structure for folder in PROJECT_FOLDERS: os.makedirs(project_dir / folder, exist_ok=True) # Create initial project README.md file with open(project_dir / "README.md", "w") as f: f.writelines([f"# {project_title}\n\n", f"{project_description}"]) def create_project(input_data: dict): """Create a new Collaborative Project on the HIP initialized with directory/file structure. Parameters Loading @@ -17,20 +57,37 @@ def create_project(input_data): "path": "/path/to/project/directory", "title": "Project Title", "description": "Project Description that would be put in the README.md file", "bids_dataset": { "path": "/path/to/bids/dataset/directory", "title": "BIDS Dataset Title", "description": "BIDS Dataset Description that would be put in the README.md file", "authors": ["Author 1", "Author 2"], "license": "CC-BY-4.0" "createBidsDatasetDto": { "owner": "username", "parent_path": "/path/to/project/directory/inputs", "dataset_dirname": "bids-dataset", "DatasetDescJSON": { "Name": "BIDS Dataset Title", "BIDSVersion": "1.6.0", "License": "CC-BY-4.0", "Authors": ["Author 1", "Author 2"], "Acknowledgements": "Acknowledgement 1", "Funding": ["Funding 1"], "ReferencesAndLinks": ["Reference 1", "Reference 2"], "DatasetDOI": "10.18112/openneuro.ds000000.v1.0.0" } } } """ # Extract input data project_dir = Path(input_data["path"]) project_title = input_data["title"] project_description = input_data["description"] # Initialize project directory structure with README.md file initialize_project_structure(project_dir, project_title, project_description) # Create initial BIDS dataset create_empty_bids_dataset( bids_dir=(project_dir / "inputs" / "bids-dataset").absolute(), dataset_desc=input_data["createBidsDatasetDto"], ) def import_subject(input_data): def import_subject(input_data: dict): """Import a new subject from a BIDS dataset of the HIP Center space to the BIDS dataset of the HIP Collaborative Project. Parameters Loading @@ -45,10 +102,38 @@ def import_subject(input_data): "targetDatasetPath": "/path/to/target/bids/dataset/directory", } """ # 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(), ) # Extract subject line from participants.tsv file of source dataset as dataframe source_participants_df = pd.read_csv( Path(input_data["sourceDatasetPath"] / "participants.tsv"), sep="\t" ) source_subject_df = source_participants_df[ source_participants_df["participant_id"] == input_data["subject"] ] # Extract participants.tsv file of target dataset as dataframe target_participants_df = pd.read_csv( Path(input_data["targetDatasetPath"] / "participants.tsv"), sep="\t" ) # Append subject row dataframe to target dataframe target_participants_df = pd.concat( [target_participants_df, source_subject_df], join="outer" ) # Replace any NaN values with 'n/a' following BIDS convention target_participants_df = target_participants_df.fillna("n/a") # Write updated participants.tsv file of target dataset target_participants_df.to_csv( Path(input_data["targetDatasetPath"] / "participants.tsv"), sep="\t", index=False, ) def import_document(input_data): """Import a new supporting document supporting to the `documents/` folder of the HIP Collaborative Project. def import_document(input_data: dict): """Import a new supporting document to the `documents/` folder of the HIP Collaborative Project. Parameters ---------- Loading @@ -61,3 +146,7 @@ def import_document(input_data): "targetDocumentPath": "/path/to/target/document/file", } """ source_document_path = Path(input_data["sourceDocumentPath"]) target_document_path = Path(input_data["targetDocumentPath"]) # Copy document from source to target shutil.copyfile(source_document_path, target_document_path)
