Semantic Search UI (#514)

Adds support for search back to the UI, using the new built-in phenogrid --------- Co-authored-by: Vincent Rubinetti <[email protected]>
monarch-initiative · Dec 19, 2023 · 4ac1886 · 4ac1886
1 parent 7a25f67
commit 4ac1886
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Showing 29 changed files with 2,433 additions and 1,888 deletions.
diff --git a/backend/src/monarch_py/api/additional_models.py b/backend/src/monarch_py/api/additional_models.py
@@ -14,7 +14,7 @@ class Config:
         arbitrary_types_allowed = True
 
 
-class SemsimSearchCategory(Enum):
+class SemsimSearchGroup(Enum):
     HGNC = "Human Genes"
     MGI = "Mouse Genes"
     RGD = "Rat Genes"
@@ -30,7 +30,7 @@ class SemsimCompareRequest(BaseModel):
 
 class SemsimSearchRequest(BaseModel):
     termset: List[str] = Field(..., title="Termset to search")
-    category: SemsimSearchCategory = Field(..., title="Category to search for")
+    group: SemsimSearchGroup = Field(..., title="Group of entities to search within (e.g. Human Genes)")
     limit: Optional[int] = Field(10, title="Limit the number of results", ge=1, le=50)
 
 

diff --git a/backend/src/monarch_py/api/semsim.py b/backend/src/monarch_py/api/semsim.py
@@ -1,6 +1,6 @@
 from fastapi import APIRouter, Path, Query
 
-from monarch_py.api.additional_models import SemsimCompareRequest, SemsimSearchRequest, SemsimSearchCategory
+from monarch_py.api.additional_models import SemsimCompareRequest, SemsimSearchRequest, SemsimSearchGroup
 from monarch_py.api.config import semsimian
 from monarch_py.api.utils.similarity_utils import parse_similarity_prefix
 
@@ -54,14 +54,14 @@ def _post_compare(request: SemsimCompareRequest):
 @router.get("/search/{termset}/{category}")
 def _search(
     termset: str = Path(..., title="Termset to search"),
-    category: SemsimSearchCategory = Path(..., title="Category of entities to search for"),
+    group: SemsimSearchGroup = Path(..., title="Group of entities to search within (e.g. Human Genes)"),
     limit: int = Query(default=10, ge=1, le=50),
 ):
     """Search for terms in a termset
 
     <b>Args:</b> <br>
         termset (str, optional): Comma separated list of term IDs to find matches for. <br>
-        category (str, optional): Category of entities to search for. <br>
+        group (str, optional): Group of entities to search within (e.g. Human Genes) <br>
         limit (int, optional): Limit the number of results. Defaults to 10.
 
     <b>Returns:</b> <br>
@@ -72,11 +72,11 @@ def _search(
         f"""
     Running semsim search:
         termset: {termset}
-        category: {category}
+        group: {group}
     """
     )
 
-    results = semsimian().search(termset=termset.split(","), prefix=parse_similarity_prefix(category), limit=limit)
+    results = semsimian().search(termset=termset.split(","), prefix=parse_similarity_prefix(group), limit=limit)
     return results
 
 
@@ -89,9 +89,9 @@ def _post_search(request: SemsimSearchRequest):
     <pre>
     {
       "termset": ["HP:0002104", "HP:0012378", "HP:0012378", "HP:0012378"],
-      "category": "Human Diseases",
+      "group": "Human Diseases",
       "limit": 5
     }
     </pre>
     """
-    return semsimian().search(request.termset, parse_similarity_prefix(request.category.value), request.limit)
+    return semsimian().search(request.termset, parse_similarity_prefix(request.group.value), request.limit)
diff --git a/backend/src/monarch_py/api/utils/similarity_utils.py b/backend/src/monarch_py/api/utils/similarity_utils.py
@@ -5,7 +5,7 @@
 
 from fastapi import HTTPException
 
-from monarch_py.api.additional_models import SemsimSearchCategory
+from monarch_py.api.additional_models import SemsimSearchGroup
 
 IS_A = omd.slots.subClassOf.curie
 HP_DB_URL = "https://s3.amazonaws.com/bbop-sqlite/hp.db.gz"
@@ -25,10 +25,10 @@ def compare_termsets(
 
 
 def parse_similarity_prefix(prefix: str):
-    if prefix in SemsimSearchCategory._member_names_:
+    if prefix in SemsimSearchGroup._member_names_:
         prefix = prefix
-    elif SemsimSearchCategory(prefix):
-        prefix = SemsimSearchCategory(prefix).name
+    elif SemsimSearchGroup(prefix):
+        prefix = SemsimSearchGroup(prefix).name
     else:
         raise HTTPException(status_code=404, detail="Prefix not found")
     return prefix
diff --git a/backend/tests/fixtures/association_counts_response.py b/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")',

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": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "*:*",

diff --git a/backend/tests/fixtures/association_table_response.py b/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": "*:*",