Trapi15

openapi-config.yaml

@@ -21,7 +21,7 @@ x-translator:
   - Ranking Agent
   infores: "infores:aragorn-ranker"
 x-trapi:
-  version: 1.4.0
+  version: 1.5.0
   operations:
   - Rank by OmniCorp overlay
   - Rank by score

ranker/modules/omnicorp_overlay.py

@@ -216,11 +216,10 @@ async def query(request: PDResponse):
 
         #Now we want to find the publication count for every pair.   But: we only want to do that for pairs that
         # are part of the same answer
-        #Note, this will be affected by TRAPI 1.4
         t1 = datetime.now()
         pair_to_answer = await generate_curie_pairs(answers, qgraph_setnodes, node_pub_counts, message)
         t2 = datetime.now()
-        logger.info(f"generate_curie_pairs time: {t2 - t1}")
+        logger.info(f"generate_curie_pairs time: {t2 - t1}. Number of pairs: {len(pair_to_answer)}")
 
         # get all pair supports
         keypairs = {make_key(x,node_indices):x for x in pair_to_answer.keys()}

ranker/server.py

@@ -16,7 +16,7 @@
 from ranker.util.omnicorp_get_node_pmids import get_node_pmids
 
 # set the app version
-APP_VERSION = '3.2.8'
+APP_VERSION = '3.3.0'
 
 APP = FastAPI(title='ARAGORN Ranker', version=APP_VERSION)
 

requirements.txt

@@ -1,15 +1,15 @@
-asyncpg==0.27.0
+asyncpg==0.29.0
 fastapi==0.63.0
 gunicorn==20.0.4
 httpx==0.16.1
 jsonschema==3.2.0
-lru-dict==1.1.8
+lru-dict==1.3.0
 pydantic>=1.8.1
 pyyaml==5.3.1
 redis==4.5.4
 uvicorn==0.17.6
-uvloop==0.17.0
-numpy==1.24.1
-httptools==0.5.0
-reasoner-pydantic==4.0.5
-yappi==1.4.0
+uvloop==0.19.0
+numpy==1.26.4
+httptools==0.6.0
+reasoner-pydantic==5.0.0
+yappi==1.6.0

tests/InputJson_15/UpdateJSON.py

@@ -0,0 +1,85 @@
+import os
+import json
+
+#TO run this, grab the jsons you want from earlier version, copy them into this directory (changing the names to
+#whatever_original.json) and then run it.  There some cleaner ways to do this...
+
+def get_originals():
+    files = os.listdir('.')
+    originals = []
+    for f in files:
+        if f.endswith("_original.json"):
+            originals.append(f)
+    return originals
+
+def go():
+    originals = get_originals()
+    for original in originals:
+        parse(original)
+
+def add_logs(trapi):
+    if "logs" not in trapi.keys():
+        trapi["logs"] = []
+
+def add_sources_and_attributes_to_edges(trapi):
+    for edge_id, edge in trapi["message"]["knowledge_graph"]["edges"].items():
+        if "sources" not in edge:
+            edge["sources"] =  [
+            {
+              "resource_id": "infores:madeup",
+              "resource_role": "primary_knowledge_source"
+            }
+            ]
+        if "attributes" not in edge:
+            edge["attributes"] = []
+
+def add_attributes_to_nodes(trapi):
+    for node_id, node in trapi["message"]["knowledge_graph"]["nodes"].items():
+        if "categories" not in node:
+            node["categories"] = ["biolink:NamedThing"]
+        if "attributes" not in node:
+            node["attributes"] = []
+
+def add_attributes_to_bindings(trapi):
+    for result in trapi["message"]["results"]:
+        for node_binding, nb in result["node_bindings"].items():
+            for nbx in nb:
+                if "attributes" not in nbx:
+                    nbx["attributes"] = []
+        for analysis in result["analyses"]:
+            for edge_binding ,eb in analysis["edge_bindings"].items():
+                for ebx in eb:
+                    if "attributes" not in ebx:
+                        ebx["attributes"] = []
+
+def add_attributes_to_auxgraphs(trapi):
+    if "auxiliary_graphs" not in trapi["message"]:
+        return
+    for auxid,auxgraph in trapi["message"]["auxiliary_graphs"].items():
+        if "attributes" not in auxgraph:
+            auxgraph["attributes"] = []
+
+def fix_analysis(trapi):
+    for result in trapi["message"]["results"]:
+        if "analysis" not in result:
+            result["analyses"] = []
+        if "edge_bindings" in result:
+            analysis = {"edge_bindings": result["edge_bindings"], "attributes": [], "resource_id": "fake:thing" }
+            result["analyses"].append(analysis)
+            del result["edge_bindings"]
+
+def parse(original):
+    with open(original,"r") as inf:
+        trapi = json.load(inf)
+    add_logs(trapi)
+    add_sources_and_attributes_to_edges(trapi)
+    add_attributes_to_nodes(trapi)
+    fix_analysis(trapi)
+    add_attributes_to_bindings(trapi)
+    add_attributes_to_auxgraphs(trapi)
+    newname = original[:-len("_original.json")]+".json"
+    with open(newname, "w") as outf:
+        json.dump(trapi,outf,indent=2)
+
+if __name__ == "__main__":
+    go()