feat: write JSON dataset summary in project methods (17b96a30) · Commits · HIP / DataHIPy

bids_tools/cli/run.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -81,9 +81,9 @@ def main():
		if command == "sub.delete.file":
		return phdl.sub_delete_file(input_data=input_data)
		if command == "project.create":
		create_project(input_data=input_data)
		create_project(input_data=input_data, output_file=output_file)
		if command == "project.sub.import":
		import_subject(input_data=input_data)
		import_subject(input_data=input_data, output_file=output_file)
		if command == "project.doc.import":
		import_document(input_data=input_data)

bids_tools/handlers/project.py

+21 −2

Original line number	Diff line number	Diff line
		@@ -11,6 +11,7 @@ from pathlib import Path
		from sre_constants import SUCCESS

		from bids_tools.bids.dataset import create_empty_bids_dataset
		from bids_tools.bids.dataset import get_bidsdataset_content


		PROJECT_FOLDERS = [
		@@ -52,7 +53,7 @@ def initialize_project_structure(
		f.writelines([f"# {project_title}\n\n", f"{project_description}"])


		def create_project(input_data: str):
		def create_project(input_data: str, output_file: str):
		"""Create a new Collaborative Project on the HIP initialized with directory/file structure.

		Parameters
		@@ -76,6 +77,9 @@ def create_project(input_data: str):
		"DatasetDOI": "10.18112/openneuro.ds000000.v1.0.0"
		}
		}

		output_file : str
		Path to output file that will contain the JSON summary of the BIDS dataset of the project.
		"""
		# Load input data
		with open(input_data, "r") as f:
		@@ -92,10 +96,16 @@ def create_project(input_data: str):
		bids_dir=(project_dir / "inputs" / "bids-dataset").absolute(),
		dataset_desc=input_data["datasetDescription"],
		)
		# Create output file with summary of BIDS dataset
		dataset_content = get_bidsdataset_content(
		bids_dir=str((project_dir / "inputs" / "bids-dataset").absolute()),
		)
		with open(output_file, "w") as f:
		json.dump(dataset_content, f, indent=4)
		print(SUCCESS)


		def import_subject(input_data: str):
		def import_subject(input_data: str, output_file: str):
		"""Import a new subject from a BIDS dataset of the HIP Center space to the BIDS dataset of the HIP Collaborative Project.

		Parameters
		@@ -109,6 +119,9 @@ def import_subject(input_data: str):
		"participantId": "sub-01",
		"targetDatasetPath": "/path/to/target/bids/dataset/directory",
		}

		output_file : str
		Path to output file that will contain the JSON summary of the BIDS dataset of the project.
		"""
		# Load input data
		with open(input_data, "r") as f:
		@@ -138,6 +151,12 @@ def import_subject(input_data: str):
		Path(input_data["targetDatasetPath"]) / "participants.tsv"
		).absolute(),
		)
		# Create output file with summary of BIDS dataset
		dataset_content = get_bidsdataset_content(
		bids_dir=str((Path(input_data["targetDatasetPath"])).absolute()),
		)
		with open(output_file, "w") as f:
		json.dump(dataset_content, f, indent=4)
		print(SUCCESS)