Adds causal_gene and causes_disease properties to the node page respo…

…nse (#341)

Addresses #332

Shows causal g2d associations as a top level node property for genes and
diseases

backend/src/monarch_py/datamodels/model.py

@@ -384,6 +384,14 @@ class Node(Entity):
         description="""The label of the biolink taxon that the entity is in the closure of.""",
     )
     inheritance: Optional[Entity] = Field(None)
+    causal_gene: Optional[List[Entity]] = Field(
+        default_factory=list,
+        description="""A list of genes that are known to be causally associated with a disease""",
+    )
+    causes_disease: Optional[List[Entity]] = Field(
+        default_factory=list,
+        description="""A list of diseases that are known to be causally associated with a gene""",
+    )
     external_links: Optional[List[ExpandedCurie]] = Field(
         default_factory=list, description="""ExpandedCurie with id and url for xrefs"""
     )

backend/src/monarch_py/datamodels/model.yaml

@@ -203,6 +203,8 @@ classes:
       - in_taxon
       - in_taxon_label
       - inheritance
+      - causal_gene
+      - causes_disease
       - external_links
       - provided_by_link
       - association_counts
@@ -248,6 +250,18 @@ slots:
     required: true
   category:
     multivalued: false
+  causal_gene:
+    description: >-
+      A list of genes that are known to be causally associated with a disease
+    range: Entity
+    multivalued: true
+    inlined_as_list: true
+  causes_disease:
+    description: >-
+      A list of diseases that are known to be causally associated with a gene
+    range: Entity
+    multivalued: true
+    inlined_as_list: true
   count:
     description: count of documents
     range: integer

backend/src/monarch_py/implementations/solr/solr_implementation.py

@@ -86,6 +86,28 @@ def get_entity(self, id: str, extra: bool) -> Optional[Union[Node, Entity]]:
             )
             if mode_of_inheritance_associations is not None and len(mode_of_inheritance_associations.items) == 1:
                 node.inheritance = self._get_associated_entity(mode_of_inheritance_associations.items[0], node)
+
+        if "biolink:Disease" == node.category:
+            node.causal_gene = [
+                self._get_associated_entity(association, node)
+                for association in self.get_associations(
+                    object=id,
+                    direct=True,
+                    predicate="biolink:causes",
+                    category="biolink:CausalGeneToDiseaseAssociation",
+                ).items
+            ]
+        if "biolink:Gene" == node.category:
+            node.causes_disease = [
+                self._get_associated_entity(association, node)
+                for association in self.get_associations(
+                    subject=id,
+                    direct=True,
+                    predicate="biolink:causes",
+                    category="biolink:CausalGeneToDiseaseAssociation",
+                ).items
+            ]
+
         node.node_hierarchy = self._get_node_hierarchy(node)
         node.association_counts = self.get_association_counts(id).items
         node.external_links = (

backend/tests/fixtures/association_counts.py

@@ -7,18 +7,13 @@ def association_counts():
         "items": [
             {
                 "label": "Phenotypes",
-                "count": 4011,
+                "count": 2166,
                 "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
             },
             {
                 "label": "Causal Genes",
-                "count": 121,
+                "count": 124,
                 "category": "biolink:CausalGeneToDiseaseAssociation",
             },
-            {
-                "label": "Correlated Genes",
-                "count": 147,
-                "category": "biolink:CorrelatedGeneToDiseaseAssociation",
-            },
         ]
     }