feat!: update /search/studies endpoint

metakb/main.py

@@ -3,9 +3,7 @@
 from fastapi.openapi.utils import get_openapi
 from metakb.query import QueryHandler
 from metakb.version import __version__
-from metakb.schemas.app import SearchService, SearchIDService, \
-    SearchStatementsService
-from typing import Optional
+from typing import Dict, Optional
 
 app = FastAPI(
     docs_url='/api/v2',
@@ -15,7 +13,7 @@
 query = QueryHandler()
 
 
-def custom_openapi():
+def custom_openapi() -> Dict:
     """Generate custom fields for OpenAPI response."""
     if app.openapi_schema:
         return app.openapi_schema
@@ -38,76 +36,44 @@ def custom_openapi():
 
 
 app.openapi = custom_openapi
-search_summary = ("Given variation, disease, therapy, and/or gene, "
-                  "return associated statements and propositions.")
-search_response_description = "A response to a validly-formed query."
-search_description = ("Return statements and propositions associated"
-                      " to the queried concepts.")
-v_description = "Variation (subject) to search"
+search_studies_summary = (
+    "Get nested studies from queried concepts that match all conditions provided."
+)
+search_studies_descr = (
+    "Return nested studies associated to the queried concepts. For example, if "
+    "`variation` and `therapy` are provided, will return all studies that have both "
+    "the provided `variation` and `therapy`."
+)
+v_description = ("Variation (subject) to search. Can be free text or VRS Variation ID.")
 d_description = "Disease (object qualifier) to search"
 t_description = "Therapy (object) to search"
 g_description = "Gene to search"
-s_description = "Statement ID to search"
-detail_description = "Display all descriptors, methods, and documents."
+s_description = ("Study ID to search.")
+search_study_response_descr = "A response to a validly-formed query."
 
 
-@app.get('/api/v2/search',
-         summary=search_summary,
-         response_description=search_response_description,
-         response_model=SearchService,
-         description=search_description,
-         response_model_exclude_none=True)
-async def search(
+@app.get('/api/v2/search/studies',
+         summary=search_studies_summary,
+         response_description=search_study_response_descr,
+         description=search_studies_descr,)
+async def get_studies(
     variation: Optional[str] = Query(None, description=v_description),
     disease: Optional[str] = Query(None, description=d_description),
     therapy: Optional[str] = Query(None, description=t_description),
     gene: Optional[str] = Query(None, description=g_description),
-    statement_id: Optional[str] = Query(None, description=s_description),
-    detail: Optional[bool] = Query(False, description=detail_description)
-):
-    """Search endpoint"""
-    resp = await query.search(variation, disease, therapy, gene, statement_id, detail)
-    return resp
-
-
-search_statements_summary = (
-    "Given variation, disease, therapy, and/or gene, return associated "
-    "nested statements containing propositions and descriptors.")
-search_statement_response_descr = "A response to a validly-formed query."
-search_statements_descr = (
-    "Return nested statements associated to the queried concepts.")
-
-
-@app.get('/api/v2/search/statements',
-         summary=search_statements_summary,
-         response_description=search_statement_response_descr,
-         response_model=SearchStatementsService,
-         description=search_statements_descr,
-         response_model_exclude_none=True)
-async def get_statements(
-        variation: Optional[str] = Query(None, description=v_description),
-        disease: Optional[str] = Query(None, description=d_description),
-        therapy: Optional[str] = Query(None, description=t_description),
-        gene: Optional[str] = Query(None, description=g_description),
-        statement_id: Optional[str] = Query(None, description=s_description)):
-    """Return nested statements for queried concepts"""
-    resp = await query.search_statements(variation, disease, therapy, gene,
-                                         statement_id)
-    return resp
-
-
-id_query_desc = ("Given Meta-KB statement_id, proposition_id, descriptor_id,"
-                 " document_id, or method_id return the node content.")
-id_search_description = ("Return node of the queried node id.")
-id_description = "Node ID to search"
-
-
-@app.get('/api/v2/search/{id}',
-         summary=id_query_desc,
-         response_description=search_response_description,
-         response_model=SearchIDService,
-         description=id_search_description,
-         response_model_exclude_none=True)
-async def search_by_id(id: str = Query(None, description=id_description)):
-    """Search by ID endpoint"""
-    return query.search_by_id(id)
+    study_id: Optional[str] = Query(None, description=s_description)
+) -> dict:
+    """Get nested studies from queried concepts that match all conditions provided.
+    For example, if `variation` and `therapy` are provided, will return all studies
+    that have both the provided `variation` and `therapy`.
+
+    :param variation: Variation query (Free text or VRS Variation ID)
+    :param disease: Disease query
+    :param therapy: Therapy query
+    :param gene: Gene query
+    :param study_id: Study ID query.
+    :return: SearchStudiesService response containing nested studies and service
+        metadata
+    """
+    resp = await query.search_studies(variation, disease, therapy, gene, study_id)
+    return resp.model_dump(exclude_none=True)