Add direct only option to association table on node pages (#766)

fixes #763

Adds support for viewing direct associations only using a select box
after the association table "sentence" giving the options of "directly"
or "including sub-classes", and this select-box only appears if the node
actually has subclasses. I think this also sets up a nice pattern to
solve #626, since it can show as a select box in the exact same spot,
but will show on genes, which won't have subclasses.

(Not really deploy previewable, since it relies on a backend change as
well)

backend/src/monarch_py/api/entity.py

@@ -81,6 +81,11 @@ def _association_table(
         title="Download the results as a file",
         examples=[True, False],
     ),
+    direct: bool = Query(
+        default=False,
+        title="Only return direct associations",
+        examples=[True, False],
+    ),
 ) -> Union[AssociationTableResults, str]:
     """
     Retrieves association table data for a given entity and association type
@@ -99,6 +104,7 @@ def _association_table(
         category=category,
         q=query,
         traverse_orthologs=traverse_orthologs,
+        direct=direct,
         sort=sort,
         offset=pagination.offset,
         limit=pagination.limit,

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

@@ -463,6 +463,7 @@ def get_association_table(
         entity: str,
         category: AssociationCategory,
         traverse_orthologs: bool = False,
+        direct: bool = False,
         q: Optional[str] = None,
         sort: Optional[List[str]] = None,
         offset: int = 0,
@@ -480,6 +481,7 @@ def get_association_table(
         query = build_association_table_query(
             entity=entities,
             category=category.value,
+            direct=direct,
             q=q,
             sort=sort,
             offset=offset,

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

@@ -75,7 +75,13 @@ def build_association_query(
 
 
 def build_association_table_query(
-    entity: List[str], category: str, q: Optional[str] = None, offset: int = 0, limit: int = 5, sort: List[str] = None
+    entity: List[str],
+    category: str,
+    direct: bool = False,
+    q: Optional[str] = None,
+    offset: int = 0,
+    limit: int = 5,
+    sort: List[str] = None,
 ) -> SolrQuery:
     if sort is None:
         sort = [
@@ -88,7 +94,7 @@ def build_association_table_query(
         ]
 
     query = build_association_query(
-        entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=False
+        entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=direct
     )
     return query
 

backend/tests/api/test_entity_router.py

@@ -25,6 +25,7 @@ def test_association_table(mock_get_assoc_table):
         category=AssociationCategory.DISEASE_TO_PHENOTYPIC_FEATURE_ASSOCIATION,
         q=None,
         traverse_orthologs=False,
+        direct=False,
         sort=None,
         offset=0,
         limit=20,

backend/tests/fixtures/association_counts_response.py

@@ -5,7 +5,7 @@
 def association_counts_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 2,
             "params": {
                 "facet.query": [
                     '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',

backend/tests/fixtures/association_table_response.py

@@ -5,7 +5,7 @@
 def association_table_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 1,
             "params": {
                 "mm": "100%",
                 "q": "*:*",

backend/tests/fixtures/autocomplete_response.py

@@ -5,7 +5,7 @@
 def autocomplete_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 1,
             "params": {
                 "mm": "100%",
                 "q": "fanc",

backend/tests/fixtures/search_response.py

@@ -5,7 +5,7 @@
 def search_response():
     return {
         "responseHeader": {
-            "QTime": 0,
+            "QTime": 4,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",

frontend/fixtures/phenotype-explorer-compare.json

@@ -1,12 +1,12 @@
 {
   "subject_termset": {
-    "MP:0010771": {
-      "id": "MP:0010771",
-      "label": "integument phenotype"
-    },
     "MP:0002169": {
       "id": "MP:0002169",
       "label": "no abnormal phenotype detected"
+    },
+    "MP:0010771": {
+      "id": "MP:0010771",
+      "label": "integument phenotype"
     }
   },
   "object_termset": {
@@ -77,16 +77,16 @@
     "HP:0004325": {
       "match_source": "HP:0004325",
       "match_source_label": "Decreased body weight",
-      "match_target": "MP:0010771",
-      "match_target_label": "integument phenotype",
+      "match_target": "MP:0002169",
+      "match_target_label": "no abnormal phenotype detected",
       "score": 1.5518735174643892,
       "match_subsumer": null,
       "match_subsumer_label": null,
       "similarity": {
         "subject_id": "HP:0004325",
         "subject_label": null,
         "subject_source": null,
-        "object_id": "MP:0010771",
+        "object_id": "MP:0002169",
         "object_label": null,
         "object_source": null,
         "ancestor_id": "UPHENO:0001003",
@@ -95,10 +95,10 @@
         "object_information_content": null,
         "subject_information_content": null,
         "ancestor_information_content": 1.5518735174643892,
-        "jaccard_similarity": 0.24,
+        "jaccard_similarity": 0.23076923076923078,
         "cosine_similarity": null,
         "dice_similarity": null,
-        "phenodigm_score": 0.6102865263066631
+        "phenodigm_score": 0.5984351743308522
       },
       "score_metric": "ancestor_information_content"
     }