Merge remote-tracking branch 'origin/features/phenov2-1394' into feat…

…ures/katsu-permissions
bento-platform · Oct 23, 2023 · 3d81d5d · 3d81d5d
2 parents 1d1132f + 40c2440
commit 3d81d5d
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Showing 14 changed files with 62 additions and 29 deletions.
diff --git a/chord_metadata_service/chord/ingest/phenopackets.py b/chord_metadata_service/chord/ingest/phenopackets.py
@@ -60,7 +60,7 @@ def get_or_create_phenotypic_feature(pf: dict) -> pm.PhenotypicFeature:
         description=pf.get("description", ""),
         pftype=pf["type"],
         excluded=pf.get("excluded", False),
-        modifier=pf.get("modifier", []),  # TODO: Validate ontology term in schema...
+        modifiers=pf.get("modifiers", []),  # TODO: Validate ontology term in schema...
         severity=pf.get("severity"),
         onset=pf.get("onset"),
         evidence=pf.get("evidence"),  # TODO: Separate class for evidence?
@@ -208,11 +208,22 @@ def get_or_create_genomic_interpretation(gen_interp: dict) -> pm.GenomicInterpre
     gene_descriptor = _get_or_create_opt("gene_descriptor", gen_interp, get_or_create_gene_descriptor)
     variant_interpretation = _get_or_create_opt("variant_interpretation", gen_interp, get_or_create_variant_interp)
 
+    # Check if a Biosample or Individual with subject_or_biosample_id exists
+    subject_or_biosample_id = gen_interp["subject_or_biosample_id"]
+    is_biosample = pm.Biosample.objects.filter(id=subject_or_biosample_id).exists()
+    is_subject = pm.Individual.objects.filter(id=subject_or_biosample_id).exists()
+
+    # Store the type the ID refers to in extra_properties
+    element_type = "biosample" if is_biosample and not is_subject else "subject"
+    extra_properties = gen_interp.get("extra_properties", {})
+    extra_properties["related_type"] = element_type
+
     gen_obj, _ = pm.GenomicInterpretation.objects.get_or_create(
-        subject_or_biosample_id=gen_interp["subject_or_biosample_id"],
+        subject_or_biosample_id=subject_or_biosample_id,
         interpretation_status=gen_interp["interpretation_status"],
         gene_descriptor=gene_descriptor,
-        variant_interpretation=variant_interpretation
+        variant_interpretation=variant_interpretation,
+        extra_properties=extra_properties,
     )
     return gen_obj
 

diff --git a/chord_metadata_service/chord/tests/example_invalid_phenopacket.json b/chord_metadata_service/chord/tests/example_invalid_phenopacket.json
@@ -14,7 +14,7 @@
                 "label": "Hematuria"
             },
             "negated": false,
-            "modifier": []
+            "modifiers": []
         },
         {
             "description": "",
@@ -27,7 +27,7 @@
                 "id": "HP:0012828",
                 "label": "Severe"
             },
-            "modifier": []
+            "modifiers": []
         }
     ],
     "diseases": [
@@ -229,4 +229,4 @@
             "is_control_sample": false
         }
     ]
-}
+}
diff --git a/chord_metadata_service/chord/tests/test_ingest.py b/chord_metadata_service/chord/tests/test_ingest.py
@@ -54,7 +54,7 @@ def test_create_pf(self):
                 "label": "Hematuria"
             },
             "excluded": False,
-            "modifier": [],
+            "modifiers": [],
             "evidence": []
         })
 

diff --git a/chord_metadata_service/patients/filters.py b/chord_metadata_service/patients/filters.py
@@ -86,7 +86,7 @@ def filter_search(self, qs, name, value):
                                 "phenopackets__phenotypic_features__description",
                                 Cast("phenopackets__phenotypic_features__pftype", TextField()),
                                 Cast("phenopackets__phenotypic_features__severity", TextField()),
-                                Cast("phenopackets__phenotypic_features__modifier", TextField()),
+                                Cast("phenopackets__phenotypic_features__modifiers", TextField()),
                                 Cast("phenopackets__phenotypic_features__onset", TextField()),
                                 Cast("phenopackets__phenotypic_features__evidence", TextField()),
                                 Cast("phenopackets__phenotypic_features__extra_properties", TextField()),

diff --git a/chord_metadata_service/phenopackets/descriptions.py b/chord_metadata_service/phenopackets/descriptions.py
@@ -111,7 +111,7 @@ def phenotypic_feature(subject="a subject or biosample"):
             "type": ontology_class("which describes the phenotype"),
             "negated": "Whether the feature is present (false) or absent (true, feature is negated); default is false.",
             "severity": ontology_class("that describes the severity of the condition"),
-            "modifier": {  # TODO: Plural?
+            "modifiers": {
                 "description": "A list of ontology terms that provide more expressive / precise descriptions of a "
                                "phenotypic feature, including e.g. positionality or external factors.",
                 "items": ontology_class("that expounds on the phenotypic feature")

diff --git a/...adata_service/phenopackets/migrations/0009_rename_modifier_phenotypicfeature_modifiers.py b/...adata_service/phenopackets/migrations/0009_rename_modifier_phenotypicfeature_modifiers.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.6 on 2023-10-16 18:02
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('phenopackets', '0008_alter_biosample_procedure_delete_procedure'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='phenotypicfeature',
+            old_name='modifier',
+            new_name='modifiers',
+        ),
+    ]
diff --git a/chord_metadata_service/phenopackets/models.py b/chord_metadata_service/phenopackets/models.py
@@ -86,8 +86,8 @@ class PhenotypicFeature(BaseTimeStamp, IndexableMixin):
     excluded = models.BooleanField(default=False, help_text=rec_help(d.PHENOTYPIC_FEATURE, "negated"))
     severity = JSONField(blank=True, null=True, validators=[ontology_validator],
                          help_text=rec_help(d.PHENOTYPIC_FEATURE, "severity"))
-    modifier = JSONField(blank=True, null=True, validators=[ontology_list_validator],
-                         help_text=rec_help(d.PHENOTYPIC_FEATURE, "modifier"))
+    modifiers = JSONField(blank=True, null=True, validators=[ontology_list_validator],
+                         help_text=rec_help(d.PHENOTYPIC_FEATURE, "modifiers"))
     onset = JSONField(blank=True, null=True, validators=[JsonSchemaValidator(schema=TIME_ELEMENT_SCHEMA)])
     resolution = JSONField(blank=True, null=True, validators=[
         JsonSchemaValidator(schema=TIME_ELEMENT_SCHEMA)])

diff --git a/chord_metadata_service/phenopackets/search_schemas.py b/chord_metadata_service/phenopackets/search_schemas.py
@@ -2,6 +2,7 @@
 from chord_metadata_service.patients.schemas import INDIVIDUAL_SCHEMA
 from chord_metadata_service.resources.search_schemas import RESOURCE_SEARCH_SCHEMA
 from chord_metadata_service.restapi.schema_utils import (
+    array_of,
     merge_schema_dictionaries,
     search_db_fk,
     search_db_pk,
@@ -176,13 +177,11 @@ def _tag_with_database_attrs(schema: dict, db_attrs: dict):
                 }
             }
         }),
-        "negated": {
+        "excluded": {
             "search": search_optional_eq(1),
         },
         "severity": ONTOLOGY_SEARCH_SCHEMA,
-        "modifier": {  # TODO: Plural?
-            "items": ONTOLOGY_SEARCH_SCHEMA
-        },
+        "modifiers": array_of(ONTOLOGY_SEARCH_SCHEMA),
         "onset": TIME_ELEMENT_SEARCH_SCHEMA,
         "resolution": TIME_ELEMENT_SEARCH_SCHEMA,
         "evidence": EVIDENCE_SEARCH_SCHEMA,
@@ -301,11 +300,11 @@ def _tag_with_database_attrs(schema: dict, db_attrs: dict):
         "onset": DISEASE_ONSET_SEARCH_SCHEMA,
         "disease_stage": {
             "items": ONTOLOGY_SEARCH_SCHEMA,
-            "search": {"database": {"type": "array"}}
+            "search": {"database": {"type": "jsonb"}}
         },
-        "tnm_finding": {
+        "clinical_tnm_finding": {
             "items": ONTOLOGY_SEARCH_SCHEMA,
-            "search": {"database": {"type": "array"}}
+            "search": {"database": {"type": "jsonb"}}
         },
     },
     "search": {

diff --git a/chord_metadata_service/phenopackets/serializers.py b/chord_metadata_service/phenopackets/serializers.py
@@ -177,10 +177,15 @@ class Meta:
 
     def to_representation(self, instance):
         response = super().to_representation(instance)
-        response["gene_descriptor"] = GeneDescriptorSerializer(
-            instance.gene_descriptor, many=False, required=False).data
-        response["variant_interpretation"] = VariantInterpretationSerializer(
-            instance.variant_interpretation, many=False, required=False).data
+
+        # May contain a gene_descriptor or a variant_interpretation, not both
+        if instance.gene_descriptor:
+            response["gene_descriptor"] = GeneDescriptorSerializer(
+                instance.gene_descriptor, many=False, required=False).data
+        elif instance.variant_interpretation:
+            response["variant_interpretation"] = VariantInterpretationSerializer(
+                instance.variant_interpretation, many=False, required=False).data
+
         return response
 
 

diff --git a/chord_metadata_service/phenopackets/tests/constants.py b/chord_metadata_service/phenopackets/tests/constants.py
@@ -538,7 +538,7 @@ def valid_phenotypic_feature(biosample=None, phenopacket=None):
             "id": "HP: 0012825",
             "label": "Mild"
         },
-        modifier=[
+        modifiers=[
             {
                 "id": "HP: 0012825 ",
                 "label": "Mild"
@@ -581,7 +581,7 @@ def invalid_phenotypic_feature():
             "id": "HP: 0012825",
             "label": "Mild"
         },
-        modifier=[
+        modifiers=[
             {
                 "label": "Mild"
             },

diff --git a/chord_metadata_service/restapi/fhir_utils.py b/chord_metadata_service/restapi/fhir_utils.py
@@ -182,7 +182,7 @@ def fhir_observation(obj):
         )
     observation.extension = []
     concept_extensions = codeable_concepts_fields(
-        ['severity', 'modifier', 'onset'], 'phenotypic_feature', obj
+        ['severity', 'modifiers', 'onset'], 'phenotypic_feature', obj
     )
     for ce in concept_extensions:
         observation.extension.append(ce)

diff --git a/chord_metadata_service/restapi/semantic_mappings/phenopackets_on_fhir_mapping.py b/chord_metadata_service/restapi/semantic_mappings/phenopackets_on_fhir_mapping.py
@@ -81,7 +81,7 @@
         "title": "Phenotypic Feature",
         "url": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/PhenotypicFeature",
         "severity": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-severity",
-        "modifier": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-modifier",
+        "modifiers": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-modifier",
         "onset": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-onset",
         "evidence": {
             "url": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/evidence",

diff --git a/examples/fhir-mapping.json b/examples/fhir-mapping.json
@@ -33,7 +33,7 @@
           }
         ]
       },
-      "modifier": {
+      "modifiers": {
         "url": "http://ga4gh.org/fhir/phenopackets/StructureDefinition/phenotypic-feature-modifier",
          "coding": [
           {

diff --git a/examples/single.json b/examples/single.json
@@ -13,7 +13,7 @@
         "label": "Hematuria"
       },
       "negated": false,
-      "modifier": [],
+      "modifiers": [],
       "evidence": []
     },
     {
@@ -27,7 +27,7 @@
         "id": "HP:0012828",
         "label": "Severe"
       },
-      "modifier": [],
+      "modifiers": [],
       "evidence": []
     }
   ],