diff --git a/src/jazayeri_lab_to_nwb/another_conversion/__init__.py b/src/jazayeri_lab_to_nwb/another_conversion/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/jazayeri_lab_to_nwb/watters/watters_convert_session.py b/src/jazayeri_lab_to_nwb/watters/watters_convert_session.py index 2a32d1e..cc50b95 100644 --- a/src/jazayeri_lab_to_nwb/watters/watters_convert_session.py +++ b/src/jazayeri_lab_to_nwb/watters/watters_convert_session.py @@ -1,5 +1,5 @@ """Primary script to run to convert an entire session for of data using the NWBConverter.""" - +import os import datetime import glob import json @@ -9,6 +9,7 @@ from uuid import uuid4 from zoneinfo import ZoneInfo +from neuroconv.tools.data_transfers import automatic_dandi_upload from neuroconv.utils import load_dict_from_file, dict_deep_update from jazayeri_lab_to_nwb.watters import WattersNWBConverter @@ -34,8 +35,39 @@ def session_to_nwb( data_dir: Union[str, Path], output_dir_path: Union[str, Path], stub_test: bool = False, - overwrite: bool = False, + overwrite: bool = True, + dandiset_id: Union[str, None] = None, ): + """ + Convert a single session to an NWB file. + + Parameters + ---------- + data_dir : string or Path + Source data directory. + output_dir_path : string or Path + Output data directory. + stub_test : boolean + Whether or not to generate a preview file by limiting data write to a few MB. + Default is False. + overwrite : boolean + If the file exists already, True will delete and replace with a new file, False will append the contents. + Default is True. + dandiset_id : string, optional + If you want to upload the file to the DANDI archive, specify the six-digit ID here. + Requires the DANDI_API_KEY environment variable to be set. + To set this in your bash terminal in Linux or macOS, run + export DANDI_API_KEY=... + or in Windows + set DANDI_API_KEY=... + Default is None. + """ + if dandiset_id is not None: + import dandi # check importability + assert os.getenv("DANDI_API_KEY"), ( + "Unable to find environment variable 'DANDI_API_KEY'. " + "Please retrieve your token from DANDI and set this environment variable." + ) logging.info("") logging.info(f"data_dir = {data_dir}") @@ -201,6 +233,7 @@ def session_to_nwb( conversion_options=raw_conversion_options, overwrite=overwrite, ) + automatic_dandi_upload(dandiset_id=dandiset_id) if __name__ == "__main__": @@ -216,4 +249,5 @@ def session_to_nwb( output_dir_path=output_dir_path, stub_test=stub_test, overwrite=overwrite, + # dandiset_id = "000620", )