Adds frequency_quantifier mixin fields as defined by biolink-model (#606

)

Required for #329

backend/src/monarch_py/api/semsim.py

@@ -1,5 +1,4 @@
 from fastapi import APIRouter, Path, Query
-from typing import List
 
 from monarch_py.api.additional_models import (
     SemsimCompareRequest,
@@ -10,7 +9,7 @@
 from monarch_py.api.config import semsimian, solr
 from monarch_py.api.utils.similarity_utils import parse_similarity_prefix
 from monarch_py.datamodels.category_enums import AssociationPredicate, EntityCategory
-from monarch_py.datamodels.model import SearchResults, SemsimSearchResult
+from monarch_py.datamodels.model import SearchResults
 
 router = APIRouter(tags=["semsim"], responses={404: {"description": "Not Found"}})
 

backend/src/monarch_py/datamodels/model.py

@@ -79,6 +79,13 @@ class Association(ConfiguredBaseModel):
     has_evidence_links: Optional[List[ExpandedCurie]] = Field(
         default_factory=list, description="""List of ExpandedCuries with id and url for evidence"""
     )
+    has_count: Optional[int] = Field(None, description="""count of out of has_total representing a frequency""")
+    has_total: Optional[int] = Field(None, description="""total, devided by has_count, representing a frequency""")
+    has_percentage: Optional[float] = Field(
+        None,
+        description="""percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level""",
+    )
+    has_quotient: Optional[float] = Field(None, description="""quotient, which should be 1/100 of has_percentage""")
     grouping_key: Optional[str] = Field(
         None,
         description="""A concatenation of fields used to group associations with the same essential/defining properties""",
@@ -264,6 +271,13 @@ class DirectionalAssociation(Association):
     has_evidence_links: Optional[List[ExpandedCurie]] = Field(
         default_factory=list, description="""List of ExpandedCuries with id and url for evidence"""
     )
+    has_count: Optional[int] = Field(None, description="""count of out of has_total representing a frequency""")
+    has_total: Optional[int] = Field(None, description="""total, devided by has_count, representing a frequency""")
+    has_percentage: Optional[float] = Field(
+        None,
+        description="""percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level""",
+    )
+    has_quotient: Optional[float] = Field(None, description="""quotient, which should be 1/100 of has_percentage""")
     grouping_key: Optional[str] = Field(
         None,
         description="""A concatenation of fields used to group associations with the same essential/defining properties""",

backend/src/monarch_py/datamodels/model.yaml

@@ -53,6 +53,10 @@ classes:
       - evidence_count
       - has_evidence
       - has_evidence_links
+      - has_count
+      - has_total
+      - has_percentage
+      - has_quotient
       - grouping_key
       - provided_by
       - provided_by_link
@@ -389,6 +393,18 @@ slots:
   grouping_key:
     description: A concatenation of fields used to group associations with the same essential/defining properties
     range: string
+  has_count:
+    description: count of out of has_total representing a frequency
+    range: integer
+  has_total:
+    description: total, devided by has_count, representing a frequency
+    range: integer
+  has_percentage:
+    description: percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level
+    range: float
+  has_quotient:
+    description: quotient, which should be 1/100 of has_percentage
+    range: float
   has_evidence:
     range: string
     multivalued: true

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

@@ -82,6 +82,7 @@ def build_association_table_query(
 ) -> SolrQuery:
     if sort is None:
         sort = [
+            "frequency_computed_sortable_float desc",
             "evidence_count desc",
             "subject_label asc",
             "predicate asc",

backend/tests/fixtures/association_counts.py

@@ -5,8 +5,8 @@
 def association_counts():
     return {
         "items": [
-            {"label": "Phenotypes", "count": 3875, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
-            {"label": "Causal Genes", "count": 125, "category": "biolink:CausalGeneToDiseaseAssociation"},
+            {"label": "Phenotypes", "count": 3873, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"},
+            {"label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation"},
             {"label": "Correlated Genes", "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation"},
         ]
     }