Closed alyssadai closed 1 year ago
Related to #20
Currently when CLI is run using bagel pheno, the value passed for the --name argument is the OpenNeuro dataset ID instead of the human-readable name.
bagel pheno
--name
https://github.com/neurobagel/bulk_annotations/blob/e4a94909a2fc636ed4340acf1331b9beec028beb/run_bagel_cli.sh#L22
To remedy this, a script should first be run as part of https://github.com/neurobagel/bulk_annotations/blob/main/parallel_bagel.sh which checks if a dataset_description.json file exists in the dataset and if so, whether there is a "name" key (both should be required according to https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset-description), & then prints that name to stdout to be echoed. The shell script should echo the dataset ID instead if no name exists.
Related to #20
Currently when CLI is run using
bagel pheno, the value passed for the--nameargument is the OpenNeuro dataset ID instead of the human-readable name.https://github.com/neurobagel/bulk_annotations/blob/e4a94909a2fc636ed4340acf1331b9beec028beb/run_bagel_cli.sh#L22
To remedy this, a script should first be run as part of https://github.com/neurobagel/bulk_annotations/blob/main/parallel_bagel.sh which checks if a dataset_description.json file exists in the dataset and if so, whether there is a "name" key (both should be required according to https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset-description), & then prints that name to stdout to be echoed. The shell script should echo the dataset ID instead if no name exists.