Merge pull request #61 from BioPack-team/fix_lookup_results

Fix lookup results

Author: maximusunc

shepherd_server/openapi-config.yaml

@@ -4,7 +4,7 @@ contact:
   x-id: https://github.com/maximusunc
   x-role: responsible developer
 description: '<img src="/static/favicon.png" width="200px"><br /><br />Shepherd: Translator Autonomous Relay Agent Platform'
-version: 0.5.2
+version: 0.5.3
 servers:
 - description: Default server
   url: https://shepherd.renci.org

workers/bte_lookup/template_groups.json

@@ -11,7 +11,6 @@
     "predicate": ["treats", "ameliorates"],
     "object": ["Disease", "PhenotypicFeature", "DiseaseOrPhenotypicFeature"],
     "templates": [
-      "Chem-treats-DoP.json",
       "Chem-treats-PhenoOfDisease.json",
       "Chem-regulates,affects-Gene-biomarker,associated_condition-DoP.json"
     ],
@@ -33,7 +32,6 @@
     },
     "object": ["Gene", "Protein"],
     "templates": [
-      "Chem-increasesGene.json",
       "Chem-IncreaseAnotherGeneThatUpregs-Gene.json",
       "Chem-DecreaseAnotherGeneThatDownregs-Gene.json",
       "Chem-physically_interacts-GeneThatUpregs-Gene.json",
@@ -56,7 +54,6 @@
     },
     "object": ["Gene", "Protein"],
     "templates": [
-      "Chem-decreasesGene.json",
       "Chem-IncreaseAnotherGeneThatDownregs-Gene.json",
       "Chem-DecreaseAnotherGeneThatUpregs-Gene.json",
       "Chem-physically_interacts-GeneThatDownregs-Gene.json",

workers/bte_lookup/templates/Chem-decreases-Gene/Chem-decreasesGene.json

@@ -397,8 +397,18 @@ def expand_bte_query(query_dict: dict[str, Any], logger: logging.Logger) -> list
         object_key,
         object_curie,
     )
+    for qedge in query_graph["edges"].values():
+        del qedge["knowledge_type"]
 
-    return filled_templates
+    expanded_queries = [
+        {
+            "message": {"query_graph": query_graph},
+            "parameters": query_dict["parameters"],
+        }
+    ]
+    expanded_queries.extend(filled_templates)
+
+    return expanded_queries
 
 
 async def process_task(task, parent_ctx, logger, limiter):

workers/bte_lookup/templates/Chem-increases-Gene/Chem-increasesGene.json

@@ -223,8 +223,16 @@ def queries_equivalent(query1, query2):
         for node in q["nodes"].values():
             if "is_set" in node and node["is_set"] is False:
                 del node["is_set"]
+            if (
+                "set_interpretation" in node and node["set_interpretation"] == "BATCH"
+            ) or ("set_interpretation" in node and node["set_interpretation"] is None):
+                del node["set_interpretation"]
             if "constraints" in node and len(node["constraints"]) == 0:
                 del node["constraints"]
+            if "member_ids" in node and len(node["member_ids"]) == 0:
+                del node["member_ids"]
+            if "ids" in node and node["ids"] is None:
+                del node["ids"]
         for edge in q["edges"].values():
             if (
                 "attribute_constraints" in edge
@@ -236,6 +244,14 @@ def queries_equivalent(query1, query2):
                 and len(edge["qualifier_constraints"]) == 0
             ):
                 del edge["qualifier_constraints"]
+            if "knowledge_type" in edge:
+                del edge["knowledge_type"]
+            # handle treats and treats_or_applied_or_studied_to_treat
+            for pred_indx, predicate in enumerate(edge["predicates"]):
+                if predicate == "biolink:treats":
+                    edge["predicates"][
+                        pred_indx
+                    ] = "biolink:treats_or_applied_or_studied_to_treat"
     return q1 == q2
 
 
@@ -350,17 +366,22 @@ def merge_messages(
                         aux_dict
                     )
     # The result with the direct lookup needs to be handled specially.   It's the one with the lookup query graph
-    lookup_results = []  # in case we don't have any
     lookup_results = (
         response["message"]["results"]
         if response["message"].get("results") is not None
         else []
     )
-    result["message"]["results"].extend(
-        new_response["message"]["results"]
-        if new_response["message"].get("results") is not None
-        else []
+    is_direct_lookup = queries_equivalent(
+        new_response["message"]["query_graph"], original_query_graph
     )
+    if is_direct_lookup:
+        lookup_results.extend(new_response["message"]["results"])
+    else:
+        result["message"]["results"].extend(
+            new_response["message"]["results"]
+            if new_response["message"].get("results") is not None
+            else []
+        )
 
     answer_node_id = get_answer_node(original_query_graph)
     merged_messages = merge_results_by_node(