fixed trapi->dict to ignore nones

check_types.py

@@ -0,0 +1,10 @@
+import json
+
+types = set()
+with open("robokop_nodes.jsonl","r") as inf:
+    for line in inf:
+        s = json.loads(line)
+        type = s["category"][0]
+        if type not in types:
+            print(type, len(types))
+            types.add(type)

notebooks/ROBOKOP.ipynb

@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "id": "controlling-greek",
    "metadata": {},
    "outputs": [],
@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 2,
    "id": "psychological-sunrise",
    "metadata": {},
    "outputs": [
@@ -115,7 +115,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "id": "caring-invitation",
    "metadata": {},
    "outputs": [],
@@ -191,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 3,
    "id": "premier-myrtle",
    "metadata": {},
    "outputs": [
@@ -245,15 +245,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 9,
    "id": "directed-steel",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Returned 5062 in 0:02:09.111197\n"
+      "Returned 5062 in 0:01:37.274773\n"
      ]
     }
    ],

src/server.py

@@ -38,7 +38,7 @@
 @APP.post("/query", tags=["Query"], response_model=PDResponse, response_model_exclude_none=True, status_code=200)
 async def query_handler(request: PDResponse):
     """ Query operations. """
-    dict_request = request.to_dict()
+    dict_request = request.dict(exclude_unset=True, exclude_none=True)
     # Check the query graph for basic validity
     query_graph = dict_request['message']['query_graph']
     if len(query_graph['edges']) != 1:
@@ -91,9 +91,6 @@ async def query_handler(request: PDResponse):
         # edges.extend(edges_r)
 
     # Create edge identifiers
-    for eid, edge in enumerate(edges):
-        print(type(json.loads(edge)))
-        print(edge)
     edge_id_to_edge = { f"knowledge_edge_{i}":json.loads(edge) for i, edge in enumerate(edges)}
     # These edges are the ones that are going the same direction as the query
     forward_edge_ids = set(edge_id_to_edge.keys())

tests/test_trapi.py

@@ -49,6 +49,38 @@ def test_profile_asthma():
     }
     response = client.post("/query", json={"message": {"query_graph": query_graph}}).json()
 
+def test_500():
+    # This is giving a 500, seems like it's getting into the double ended query by mistake.
+    m = {
+      "message": {
+        "query_graph": {
+          "nodes": {
+            "chemical": {
+              "categories": ["biolink:ChemicalEntity"],
+              "is_set": False,
+              "constraints": []
+            },
+            "f": {
+              "ids": ["MONDO:0005737"],
+              "is_set": False,
+              "constraints": []
+            }
+          },
+          "edges": {
+            "edge_1": {
+              "subject": "chemical",
+              "object": "f",
+              "predicates": ["biolink:treats"],
+              "attribute_constraints": [],
+              "qualifier_constraints": []
+            }
+          }
+        }
+      }
+    }
+    response = client.post("/query", json=m)
+    assert response.status_code == 200
+
 def xtest_type_descendant_queries(rc, descender):
     # Given the edge defined in run_basic_tests, query for it by subject and object with super types
     run_basic_tests(rc, descender, subject_type = "biolink:NamedThing", object_type = "biolink:NamedThing")