Adds a full entity to the semsim search response (#504)

monarch-initiative · Dec 13, 2023 · fe5ec25 · fe5ec25
1 parent 456725f
commit fe5ec25
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Showing 12 changed files with 445 additions and 57 deletions.
diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py
@@ -92,8 +92,12 @@ def search(self, termset: List[str], prefix: str, limit: int):
         response = rq.get(url=url)
         data = response.json()
         results = [
-            SemsimSearchResult(score=i[0], similarity=self.convert_tsps_data(i[1]), subject_id=i[2]) for i in data
+            SemsimSearchResult(
+                subject=solr().get_entity(i[2], extra=False), score=i[0], similarity=self.convert_tsps_data(i[1])
+            )
+            for i in data
         ]
+
         return results
 
 

diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
@@ -646,7 +646,7 @@ class BestMatch(ConfiguredBaseModel):
 
 class SemsimSearchResult(ConfiguredBaseModel):
 
-    subject_id: str = Field(...)
+    subject: Entity = Field(...)
     score: Optional[float] = Field(None)
     similarity: Optional[TermSetPairwiseSimilarity] = Field(None)
 

diff --git a/backend/src/monarch_py/datamodels/similarity.yaml b/backend/src/monarch_py/datamodels/similarity.yaml
@@ -80,9 +80,13 @@ classes:
 
   SemsimSearchResult:
     slots:
-      - subject_id
+      - subject
       - score
       - similarity
+    slot_usage:
+      subject:
+        range: Entity
+        inlined: true
 
 types:
   ZeroToOne:

diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py
@@ -5,7 +5,7 @@
 def association_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 1,
             "params": {
                 "mm": "100%",
                 "q": "*:*",

diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
@@ -5,7 +5,7 @@
 def autocomplete_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanc",

diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
@@ -5,7 +5,7 @@
 def histopheno_response():
     return {
         "responseHeader": {
-            "QTime": 2,
+            "QTime": 1,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',

diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py
@@ -5,8 +5,8 @@
 def phenotype_explorer_compare():
     return {
         "subject_termset": {
-            "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"},
             "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"},
+            "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"},
         },
         "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}},
         "subject_best_matches": {
@@ -69,16 +69,16 @@ def phenotype_explorer_compare():
             "HP:0004325": {
                 "match_source": "HP:0004325",
                 "match_source_label": "Decreased body weight (HPO)",
-                "match_target": "MP:0010771",
-                "match_target_label": "integument phenotype (MPO)",
+                "match_target": "MP:0002169",
+                "match_target_label": "no abnormal phenotype detected (MPO)",
                 "score": 1.5540019332516637,
                 "match_subsumer": None,
                 "match_subsumer_label": None,
                 "similarity": {
                     "subject_id": "HP:0004325",
                     "subject_label": None,
                     "subject_source": None,
-                    "object_id": "MP:0010771",
+                    "object_id": "MP:0002169",
                     "object_label": None,
                     "object_source": None,
                     "ancestor_id": "UPHENO:0001003",
@@ -87,10 +87,10 @@ def phenotype_explorer_compare():
                     "object_information_content": None,
                     "subject_information_content": None,
                     "ancestor_information_content": 1.5540019332516637,
-                    "jaccard_similarity": 0.24,
+                    "jaccard_similarity": 0.23076923076923078,
                     "cosine_similarity": None,
                     "dice_similarity": None,
-                    "phenodigm_score": 0.61070489107293,
+                    "phenodigm_score": 0.5988454147360435,
                 },
             }
         },