hubmapconsortium / ingest-validation-tools

HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.
MIT License
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Add "PA" to valid sample_id in the sample metadata & tissue_id in assay metadata #616

Closed cebriggs7135 closed 3 years ago

cebriggs7135 commented 3 years ago

PA is pancreas, a new organ type. Please add this to constraint "pattern" for both sample_id and tissueid. Currently, only these are allowed: "([A-Z]+[0-9]+)-(BL|BR|LB|RB|HT|LK|RK|LI|LV|LL|RL|LY\d\d|SI|SP|TH|TR|UR|OT)(-\d+)+(\d+)?"

@cebriggs7135 will evaluate this request, and if it can move forward, will file a PR for @ngehlenborg to review, and @mccalluc will make sure tests pass before merging.

mccalluc commented 3 years ago

@cebriggs7135 : Looking in to this, this regex has already been simplified in all_assays.yaml:

  constraints:
    pattern: '([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?'

I don't think there is any argument for Sample to be different from Dataset.