In processing some of the merged objects, I noticed that the community contributed datasets had out of date scpca-meta.json files that were missing the assay_ontology_term_id and the submitter_cell_types_file field. We already have a script that updates these files to include any new fields we have added later on, but this script currently updates all scpca-meta.json files for all libraries in the library metadata.
In case we need to make other updates to specific libraries in the future, I made this a bit more flexible to update only a specific set of library IDs. A comma-separated list of library IDs can be provided as an optional argument. If they are provided, the library metadata is filtered before going through each library and updating the json files. Otherwise, the whole metadata file is used.
Note that I ran this script today for the two community-contributed datasets, so they now have complete scpca-meta.json files.
In processing some of the merged objects, I noticed that the community contributed datasets had out of date
scpca-meta.jsonfiles that were missing theassay_ontology_term_idand thesubmitter_cell_types_filefield. We already have a script that updates these files to include any new fields we have added later on, but this script currently updates allscpca-meta.jsonfiles for all libraries in the library metadata.In case we need to make other updates to specific libraries in the future, I made this a bit more flexible to update only a specific set of library IDs. A comma-separated list of library IDs can be provided as an optional argument. If they are provided, the library metadata is filtered before going through each library and updating the json files. Otherwise, the whole metadata file is used.
Note that I ran this script today for the two community-contributed datasets, so they now have complete
scpca-meta.jsonfiles.