Merge pull request #202 from ranking-agent/fix_rules_2

fixed some more affects rules

src/rules/Notes

@@ -9,5 +9,10 @@ The current rules have been created through a somewhat complicated process:
    * remove subclass rules
 5. By hand, I went into kara_typed_rules/rules_with_types_cleaned_finalized.json and changed "biolink:correlated_with"
      to "biolink:positively_correlated_with"
+6. For reasons unclear to me after all this, we still have a bunch of rules of this form:
+    ?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_biolink:affects  ?b
+    For these I go into hand and edit the rule to be
+    ?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_biolink:affects  ?b
+    Changing both the "Rule" and the edge in "template" by adding the correct qualifier
 
 This process is obviously roundabout and we are going to clarify it in the next round of rule minings.

src/rules/kara_typed_rules/check_rule_for_direction.py

@@ -0,0 +1,22 @@
+import json
+
+with open("rules_with_types_cleaned_finalized.json","r") as infile:
+    rules = json.load(infile)
+
+for key,ruleset in rules.items():
+    print(key)
+    for rule in ruleset:
+        trapi = rule["template"]
+        edges = trapi["query_graph"]["edges"]
+        for edge_id,edge in edges.items():
+            if edge["predicates"][0] == "biolink:affects":
+                try:
+                    qualifiers = edge["qualifier_constraints"][0]["qualifier_set"]
+                    found = False
+                    for qualifier in qualifiers:
+                        if qualifier["qualifier_type_id"] == "biolink:object_direction_qualifier":
+                            found = True
+                    if not found:
+                        print(" ",rule["Rule"])
+                except:
+                    print(" ", rule["Rule"])

src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json

@@ -4863,7 +4863,7 @@
             }
         },
         {
-            "Rule": "?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_biolink:affects  ?b",
+            "Rule": "?e  increased_activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_biolink:affects  ?b",
             "Head Coverage": "0.000698966",
             "Std Confidence": "0.192307692",
             "PCA Confidence": "0.3125",
@@ -4909,6 +4909,10 @@
                                         {
                                             "qualifier_type_id": "biolink:object_aspect_qualifier",
                                             "qualifier_value": "activity_or_abundance"
+                                        },
+                                        {
+                                            "qualifier_type_id": "biolink:object_direction_qualifier",
+                                            "qualifier_value": "increased"
                                         }
                                     ]
                                 }
@@ -7751,7 +7755,7 @@
             }
         },
         {
-            "Rule": "?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  decreased_activity_biolink:affects  ?b",
+            "Rule": "?e  decreased_activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  decreased_activity_biolink:affects  ?b",
             "Head Coverage": "0.000052801",
             "Std Confidence": "0.104395604",
             "PCA Confidence": "0.154471545",
@@ -7797,6 +7801,10 @@
                                         {
                                             "qualifier_type_id": "biolink:object_aspect_qualifier",
                                             "qualifier_value": "activity_or_abundance"
+                                        },
+                                        {
+                                            "qualifier_type_id": "biolink:object_direction_qualifier",
+                                            "qualifier_value": "decreased"
                                         }
                                     ]
                                 }
@@ -8832,7 +8840,7 @@
             }
         },
         {
-            "Rule": "?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_or_abundance_biolink:affects  ?b",
+            "Rule": "?e  increased_activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  increased_activity_or_abundance_biolink:affects  ?b",
             "Head Coverage": "0.000584971",
             "Std Confidence": "0.192307692",
             "PCA Confidence": "0.3125",
@@ -8878,6 +8886,10 @@
                                         {
                                             "qualifier_type_id": "biolink:object_aspect_qualifier",
                                             "qualifier_value": "activity_or_abundance"
+                                        },
+                                        {
+                                            "qualifier_type_id": "biolink:object_direction_qualifier",
+                                            "qualifier_value": "increased"
                                         }
                                     ]
                                 }
@@ -11779,7 +11791,7 @@
             }
         },
         {
-            "Rule": "?e  activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  decreased_activity_or_abundance_biolink:affects  ?b",
+            "Rule": "?e  decreased_activity_or_abundance_biolink:affects  ?b  ?e  biolink:similar_to  ?a   => ?a  decreased_activity_or_abundance_biolink:affects  ?b",
             "Head Coverage": "0.000051974",
             "Std Confidence": "0.104395604",
             "PCA Confidence": "0.154471545",
@@ -11825,6 +11837,10 @@
                                         {
                                             "qualifier_type_id": "biolink:object_aspect_qualifier",
                                             "qualifier_value": "activity_or_abundance"
+                                        },
+                                        {
+                                            "qualifier_type_id": "biolink:object_direction_qualifier",
+                                            "qualifier_value": "decreased"
                                         }
                                     ]
                                 }

src/service_aggregator.py

@@ -225,7 +225,7 @@ async def post_with_callback(host_url, query, guid, params=None):
         # check the response status.
         if post_response.status_code != 200:
             # queue isn't needed for failed service call
-            logger.warning(f"Deleting unneeded queue for {guid}")
+            logger.warning(f"{guid} POST status: {post_response.status_code}. Deleting unneeded queue.")
             await delete_queue(guid)
             # if there is an error this will return a <requests.models.Response> type
             return post_response
@@ -337,6 +337,8 @@ async def check_for_messages(guid, num_queries, num_previously_received=0):
                         num_responses += 1
                         logger.info(f"{guid}: Strider returned {num_responses} out of {num_queries}.")
                         jr = process_message(message)
+                        with open(f"{guid}_{num_responses}.json","w") as outf:
+                            json.dump(jr,outf,indent=2)
                         if is_end_message(jr):
                             logger.info(f"{guid}: Received complete message from multistrider")
                             complete = True
@@ -467,7 +469,6 @@ async def subservice_post(name, url, message, guid, asyncquery=False, params=Non
                 if len(response.json()):
                     #pass it through pydantic for validation and cleaning
                     ret_val = await to_jsonable_dict(PDResponse.parse_obj(response.json()).dict(exclude_none = True))
-
             except Exception as e:
                 status_code = 500
                 logger.exception(f"{guid}: ARAGORN Exception {e} translating json from post to {name}")
@@ -913,6 +914,10 @@ async def robokop_infer(input_message, guid, question_qnode, answer_qnode):
     max_conns = os.environ.get("MAX_CONNECTIONS", 5)
     nrules = int(os.environ.get("MAXIMUM_ROBOKOPKG_RULES", 101))
     messages = expand_query(input_message, {}, guid)
+    with open('robokop_infer.txt', 'w') as logfile:
+        json.dump(input_message, logfile, indent=2)
+        logfile.write("------\n")
+        json.dump(messages, logfile, indent=2)
     lookup_query_graph = messages[0]["message"]["query_graph"]
     logger.info(f"{guid}: {len(messages)} to send to {automat_url}")
     result_messages = []
@@ -926,6 +931,7 @@ async def robokop_infer(input_message, guid, question_qnode, answer_qnode):
 
         responses = await asyncio.gather(*tasks)
 
+    nr = 0
     for response in responses:
         if response.status_code == 200:
             #Validate and clean
@@ -934,6 +940,9 @@ async def robokop_infer(input_message, guid, question_qnode, answer_qnode):
             num_results = len(rmessage["message"].get("results",[]))
             logger.info(f"Returned {num_results} results")
             if num_results > 0 and num_results < 10000: #more than this number of results and you're into noise.
+                with (open(f"{guid}_r_{nr}.json", 'w')) as outf:
+                    json.dump(rmessage, outf, indent=2)
+                    nr += 1
                 result_messages.append(rmessage)
         else:
             logger.error(f"{guid}: {response.status_code} returned.")
@@ -1032,6 +1041,9 @@ async def omnicorp(message, params, guid) -> (dict, int):
     """
     url = f'{os.environ.get("RANKER_URL", "https://aragorn-ranker.renci.org/1.4/")}omnicorp_overlay'
 
+    with open("to_corp.json","w") as f:
+        f.write(json.dumps(message,indent=2))
+
     rval, omni_status =  await subservice_post("omnicorp", url, message, guid)
 
     # Omnicorp is not strictly necessary.  When we get something other than a 200,
@@ -1048,6 +1060,9 @@ async def score(message, params, guid) -> (dict, int):
     :param guid:
     :return:
     """
+    with open("to_score.json","w") as f:
+        f.write(json.dumps(message,indent=2))
+
     ranker_url = os.environ.get("RANKER_URL", "https://aragorn-ranker.renci.org/1.4/")
 
     score_url = f"{ranker_url}score"