A fix for assigning ids to Individuals

monarch-initiative · Dec 13, 2024 · 4792b15 · 4792b15
1 parent a62741f
commit 4792b15
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git 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
@@ -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