diff --git a/ADC-API-Data-provenance/Repertoire_Tests/README.md b/ADC-API-Data-provenance/Repertoire_Tests/README.md index e09ca10..490d9ea 100644 --- a/ADC-API-Data-provenance/Repertoire_Tests/README.md +++ b/ADC-API-Data-provenance/Repertoire_Tests/README.md @@ -1,5 +1,26 @@ ### Running the script + +Ensure you run `generate_facet_json.py` first to generate the appropriate repertoire_id JSON input files. + + usage: generate_facet_json.py [-h] [-v] base_url entry_point path_to_json + + positional arguments: + base_url String containing URL to API server (e.g. https://airr- + api2.ireceptor.org) + entry_point Options: string 'rearragement' or string 'repertoire' + path_to_json Enter full path to JSON query containing repertoire ID's for + a given study - this must match the value given for study_id + + optional arguments: + -h, --help show this help message and exit + -v, --verbose Run the program in verbose mode. + +Example: + + python 3./generate_facet_json.py "http://covid19-2.ireceptor.org" "repertoire" "./JSON-Files/repertoire/nofilters.json" + +Once that has been completed, you can then run a repertoire sanity check with the facet JSON as well as the repertoire ID input JSON files. DATA PROVENANCE TEST usage: AIRR-repertoire-checks.py [-h] [-v]