From 4792b156104343eacd07c0076714add13b9e2309 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 13 Dec 2024 17:24:56 -0500 Subject: [PATCH] A fix for assigning ids to Individuals --- src/ontogpt/templates/phenopackets.py | 2 +- src/ontogpt/templates/phenopackets.yaml | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/templates/phenopackets.py b/src/ontogpt/templates/phenopackets.py index da54e5c32..1963ce7fe 100644 --- a/src/ontogpt/templates/phenopackets.py +++ b/src/ontogpt/templates/phenopackets.py @@ -1561,7 +1561,7 @@ class Individual(ConfiguredBaseModel): 'gender identity; nobinary ' 'gender identity; agendered'}}, 'domain_of': ['Individual']} }) - id: str = Field(..., description="""An identifier for the individual. This must be unique within the record. ARGO mapping donor::submitter_donor_id""", json_schema_extra = { "linkml_meta": {'alias': 'id', + id: Optional[str] = Field(None, description="""An identifier for the individual. This must be unique within the record. ARGO mapping donor::submitter_donor_id""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'annotations': {'prompt': {'tag': 'prompt', 'value': 'The identifier for the individual. These ' 'may also be present in the ' diff --git a/src/ontogpt/templates/phenopackets.yaml b/src/ontogpt/templates/phenopackets.yaml index 9ba914b63..8bc71eef4 100644 --- a/src/ontogpt/templates/phenopackets.yaml +++ b/src/ontogpt/templates/phenopackets.yaml @@ -1272,13 +1272,17 @@ classes: female gender identity; male gender identity; nobinary gender identity; agendered id: + # This does not always get assigned, so it isn't + # considered a true identifier. + # TODO: assign after phenopacket creation, along + # with other metadata, as necessary. description: >- An identifier for the individual. This must be unique within the record. ARGO mapping donor::submitter_donor_id exact_mappings: - ARGO:donor.submitter_donor_id range: string - identifier: true + # identifier: true annotations: prompt: >- The identifier for the individual. These may also be present