diff --git a/openapi-config.yaml b/openapi-config.yaml index 9d7ad19..779be6d 100644 --- a/openapi-config.yaml +++ b/openapi-config.yaml @@ -11,7 +11,7 @@ servers: # url: http://127.0.0.1:5000 termsOfService: http://robokop.renci.org:7055/tos?service_long=ARAGORN&provider_long=RENCI title: ARAGORN -version: 2.4.14 +version: 2.4.15 tags: - name: translator - name: ARA diff --git a/src/rules/Notes b/src/rules/Notes index ace808b..4a799c7 100644 --- a/src/rules/Notes +++ b/src/rules/Notes @@ -14,5 +14,20 @@ The current rules have been created through a somewhat complicated process: 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 +7. Also hand removed several rules: +x ?a biolink:interacts_with ?b ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b" +x ?b activity_or_abundance_biolink:affects ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b +x ?b biolink:affects_response_to ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b +x ?a decreased_activity_or_abundance_biolink:affects ?b ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b +x ?b activity_or_abundance_biolink:affects ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b" +x ?b biolink:increases_response_to ?a ?a increased_activity_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b +x ?a biolink:interacts_with ?b ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b +x ?b activity_or_abundance_biolink:affects ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b +x ?b biolink:affects_response_to ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b +x ?a decreased_molecular_interaction_biolink:affects ?b ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b +x ?b activity_or_abundance_biolink:affects ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b +x ?b biolink:affects_response_to ?a ?a increased_activity_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b +"?b biolink:increases_response_to ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b + This process is obviously roundabout and we are going to clarify it in the next round of rule minings. diff --git a/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json b/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json index a013f8b..ec4f30d 100644 --- a/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json +++ b/src/rules/kara_typed_rules/rules_with_types_cleaned_finalized.json @@ -4991,68 +4991,6 @@ } } }, - { - "Rule": "?a biolink:interacts_with ?b ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b", - "Head Coverage": "0.005132404", - "Std Confidence": "0.157668712", - "PCA Confidence": "0.375730994", - "Positive Examples": "257", - "Body size": "1630", - "PCA Body size": "684", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:interacts_with" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b activity_or_abundance_biolink:affects ?a ?a biolink:directly_physically_interacts_with ?b => ?a increased_activity_biolink:affects ?b", "Head Coverage": "0.003534769", @@ -5111,78 +5049,6 @@ } } }, - { - "Rule": "?b activity_or_abundance_biolink:affects ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b", - "Head Coverage": "0.00091864", - "Std Confidence": "0.096842105", - "PCA Confidence": "0.156462585", - "Positive Examples": "46", - "Body size": "475", - "PCA Body size": "294", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?e biolink:similar_to ?a ?e decreased_degradation_biolink:affects ?b => ?a increased_activity_biolink:affects ?b", "Head Coverage": "0.000279586", @@ -5250,68 +5116,6 @@ } } }, - { - "Rule": "?b biolink:affects_response_to ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_biolink:affects ?b", - "Head Coverage": "0.000539202", - "Std Confidence": "0.086261981", - "PCA Confidence": "0.099264706", - "Positive Examples": "27", - "Body size": "313", - "PCA Body size": "272", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?f biolink:affects_response_to ?a ?b biolink:contributes_to ?f => ?a increased_activity_biolink:affects ?b", "Head Coverage": "0.000219675", @@ -6323,82 +6127,6 @@ } } }, - { - "Rule": "?a decreased_activity_or_abundance_biolink:affects ?b ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.002703949", - "Std Confidence": "0.98982706", - "PCA Confidence": "0.98982706", - "Positive Examples": "973", - "Body size": "983", - "PCA Body size": "983", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b biolink:contributes_to ?f ?a decreased_activity_or_abundance_biolink:affects ?f => ?a decreased_activity_biolink:affects ?b", "Head Coverage": "0.020258779", @@ -7407,85 +7135,13 @@ } }, { - "Rule": "?b activity_or_abundance_biolink:affects ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000116717", - "Std Confidence": "0.1875", - "PCA Confidence": "0.211055276", - "Positive Examples": "42", - "Body size": "224", - "PCA Body size": "199", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?b decreased_metabolic_processing_biolink:affects ?a => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000058359", - "Std Confidence": "0.156716418", - "PCA Confidence": "0.238636364", - "Positive Examples": "21", - "Body size": "134", - "PCA Body size": "88", + "Rule": "?b decreased_metabolic_processing_biolink:affects ?a => ?a decreased_activity_biolink:affects ?b", + "Head Coverage": "0.000058359", + "Std Confidence": "0.156716418", + "PCA Confidence": "0.238636364", + "Positive Examples": "21", + "Body size": "134", + "PCA Body size": "88", "Functional variable": "?a", "template": { "query_graph": { @@ -7692,68 +7348,6 @@ } } }, - { - "Rule": "?b biolink:increases_response_to ?a ?a increased_activity_biolink:affects ?b => ?a decreased_activity_biolink:affects ?b", - "Head Coverage": "0.000063917", - "Std Confidence": "0.112195122", - "PCA Confidence": "0.121693122", - "Positive Examples": "23", - "Body size": "205", - "PCA Body size": "189", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:increases_response_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?e decreased_activity_or_abundance_biolink:affects ?b ?e biolink:similar_to ?a => ?a decreased_activity_biolink:affects ?b", "Head Coverage": "0.000052801", @@ -8968,68 +8562,6 @@ } } }, - { - "Rule": "?a biolink:interacts_with ?b ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.00429536", - "Std Confidence": "0.157668712", - "PCA Confidence": "0.373004354", - "Positive Examples": "257", - "Body size": "1630", - "PCA Body size": "689", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:interacts_with" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b activity_or_abundance_biolink:affects ?a ?a biolink:directly_physically_interacts_with ?b => ?a increased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.002974997", @@ -9237,144 +8769,10 @@ ] } }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "metabolic_processing" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?b activity_or_abundance_biolink:affects ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000768819", - "Std Confidence": "0.096842105", - "PCA Confidence": "0.153333333", - "Positive Examples": "46", - "Body size": "475", - "PCA Body size": "300", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?b biolink:affects_response_to ?a ?a decreased_activity_or_abundance_biolink:affects ?b => ?a increased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000467977", - "Std Confidence": "0.089456869", - "PCA Confidence": "0.101083032", - "Positive Examples": "28", - "Body size": "313", - "PCA Body size": "277", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", + "edges": { + "edge_0": { + "subject": "$target", + "object": "$source", "predicates": [ "biolink:affects" ], @@ -9383,7 +8781,7 @@ "qualifier_set": [ { "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" + "qualifier_value": "metabolic_processing" }, { "qualifier_type_id": "biolink:object_direction_qualifier", @@ -11129,82 +10527,6 @@ } } }, - { - "Rule": "?a decreased_molecular_interaction_biolink:affects ?b ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000051974", - "Std Confidence": "0.25", - "PCA Confidence": "0.292307692", - "Positive Examples": "19", - "Body size": "76", - "PCA Body size": "65", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "molecular_interaction" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "decreased" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?a biolink:binds ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.01039749", @@ -11380,78 +10702,6 @@ } } }, - { - "Rule": "?b activity_or_abundance_biolink:affects ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000125831", - "Std Confidence": "0.205357143", - "PCA Confidence": "0.231155779", - "Positive Examples": "46", - "Body size": "224", - "PCA Body size": "199", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - } - ] - } - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "Rule": "?b decreased_metabolic_processing_biolink:affects ?a => ?a decreased_activity_or_abundance_biolink:affects ?b", "Head Coverage": "0.000057445", @@ -11666,130 +10916,6 @@ } } }, - { - "Rule": "?b biolink:affects_response_to ?a ?a increased_activity_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000073857", - "Std Confidence": "0.108433735", - "PCA Confidence": "0.119469027", - "Positive Examples": "27", - "Body size": "249", - "PCA Body size": "226", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:affects_response_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, - { - "Rule": "?b biolink:increases_response_to ?a ?a increased_activity_or_abundance_biolink:affects ?b => ?a decreased_activity_or_abundance_biolink:affects ?b", - "Head Coverage": "0.000087535", - "Std Confidence": "0.108108108", - "PCA Confidence": "0.113879004", - "Positive Examples": "32", - "Body size": "296", - "PCA Body size": "281", - "Functional variable": "?a", - "template": { - "query_graph": { - "nodes": { - "$source": { - "ids": [ - "$source_id" - ], - "categories": [ - "biolink:ChemicalEntity" - ] - }, - "$target": { - "ids": [ - "$target_id" - ], - "categories": [ - "biolink:Gene" - ] - } - }, - "edges": { - "edge_0": { - "subject": "$target", - "object": "$source", - "predicates": [ - "biolink:increases_response_to" - ] - }, - "edge_1": { - "subject": "$source", - "object": "$target", - "predicates": [ - "biolink:affects" - ], - "qualifier_constraints": [ - { - "qualifier_set": [ - { - "qualifier_type_id": "biolink:object_aspect_qualifier", - "qualifier_value": "activity_or_abundance" - }, - { - "qualifier_type_id": "biolink:object_direction_qualifier", - "qualifier_value": "increased" - } - ] - } - ] - } - } - } - } - }, { "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", diff --git a/src/service_aggregator.py b/src/service_aggregator.py index d869b08..cd7068c 100644 --- a/src/service_aggregator.py +++ b/src/service_aggregator.py @@ -642,10 +642,10 @@ async def normalize_qgraph_ids(m): nnresult = nnresult.json() for qid, qnode in qnodes.items(): if 'ids' in qnode and qnode['ids'] is not None: - new_ids = [ nnresult[i]["id"]["identifier"] for i in qnode["ids"]] - qnode["ids"] = new_ids + normalized_ids = [nnresult[i]["id"]["identifier"] if nnresult[i] else i for i in qnode["ids"]] + qnode["ids"] = normalized_ids else: - logger.error("Error reaching node normalizer: {nnresult.status_code}") + logger.error(f"Error reaching node normalizer: {nnresult.status_code}") return m @@ -659,7 +659,6 @@ async def robokop_lookup(message, params, guid, infer, question_qnode, answer_qn # It's an infer, just look it up rokres = await robokop_infer(message, guid, question_qnode, answer_qnode) return rokres - # return await normalize(rokres,params,guid) def get_key(predicate, qualifiers): keydict = {'predicate': predicate} @@ -940,20 +939,16 @@ 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 + 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.") if len(result_messages) > 0: - #with open(f"{guid}_r_individual_answers.json", 'w') as outf: - # json.dump(result_messages, outf, indent=2) # We have to stitch stuff together again mergedresults = await combine_messages(answer_qnode, input_message["message"]["query_graph"], lookup_query_graph, result_messages) - #with open(f"{guid}_r_merged.json", 'w') as outf: - # json.dump(result_messages, outf, indent=2) else: mergedresults = {"message": {"knowledge_graph": {"nodes": {}, "edges": {}}, "results": []}} # The merged results will have some expanded query, we want the original query.