Merge pull request #24 from TranslatorSRI/better_query_runner

Better query runner

requirements-runners.txt

@@ -1,3 +1,3 @@
-ARS_Test_Runner==0.1.9
+ARS_Test_Runner==0.2.3
 # benchmarks-runner==0.1.3
 # ui-test-runner==0.0.2

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name="sri-test-harness",
-    version="0.2.3",
+    version="0.2.4",
     author="Max Wang",
     author_email="max@covar.com",
     url="https://github.com/TranslatorSRI/TestHarness",

test_harness/result_collector.py

@@ -69,11 +69,12 @@ def collect_result(
 
         # add result to csv
         agent_results = ",".join(
-            get_tag(report[agent]) for agent in self.agents if agent in report
+            get_tag(report.get(agent, {"status": "Not queried"}))
+            for agent in self.agents
         )
         pk_url = (
             f"https://arax.ncats.io/?r={parent_pk}" if parent_pk is not None else ""
         )
         self.csv += (
-            f"""{asset.name},{url},{pk_url},{test.id},{asset.id},{agent_results}\n"""
+            f""""{asset.name}",{url},{pk_url},{test.id},{asset.id},{agent_results}\n"""
         )

test_harness/run.py

@@ -101,7 +101,7 @@ async def run_tests(
                                     f"Status code: {response['status_code']}"
                                 )
                         elif (
-                            response["response"]["message"]["results"] is None
+                            response["response"]["message"].get("results") is None
                             or len(response["response"]["message"]["results"]) == 0
                         ):
                             agent_report["status"] = "DONE"

test_harness/runner/generate_query.py

@@ -1,5 +1,6 @@
 """Given a Test Asset, generate a TRAPI query."""
 
+import copy
 from translator_testing_model.datamodel.pydanticmodel import TestAsset
 
 from test_harness.utils import get_qualifier_constraints
@@ -61,7 +62,7 @@ def generate_query(test_asset: TestAsset) -> dict:
     query = {}
     if test_asset.predicate_id == "biolink:treats":
         # MVP1
-        query = MVP1
+        query = copy.deepcopy(MVP1)
         # add id to node
         if test_asset.input_category == "biolink:Disease":
             query["message"]["query_graph"]["nodes"]["ON"]["ids"] = [
@@ -76,7 +77,7 @@ def generate_query(test_asset: TestAsset) -> dict:
             ] = "inferred"
     elif test_asset.predicate_id == "biolink:affects":
         # MVP2
-        query = MVP2
+        query = copy.deepcopy(MVP2)
         # add id to corresponding node
         if test_asset.input_category == "biolink:ChemicalEntity":
             query["message"]["query_graph"]["nodes"]["SN"]["ids"] = [

test_harness/runner/query_runner.py

@@ -251,7 +251,7 @@ async def get_ars_responses(
                 else:
                     self.logger.info("ARS merging not done, waiting...")
                     current_time = time.time()
-                    await asyncio.sleep(5)
+                    await asyncio.sleep(10)
         else:
             self.logger.warning(
                 f"ARS merging took greater than {MAX_QUERY_TIME / 60} minutes."