Closed vgardner-renci closed 3 years ago
https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.9_EGFR_advanced.json
{ "context": "https://raw.githubusercontent.com/biolink/biolink-model/master/context.jsonld", "datetime": "2021-08-12 15:57:38", "description": "Unsupported constraint(s) detected on qnode n0 for {'biolink:highest_FDA_approval_status'}. Don't know how to handle these!", "logs": [ { "code": "", "level": "INFO", "message": "ARAX Query launching on incoming Query", "timestamp": "2021-08-12T15:57:38.809167" }, { "code": "", "level": "INFO", "message": "Creating an empty template TRAPI Response", "timestamp": "2021-08-12T15:57:38.809227" }, { "code": "", "level": "INFO", "message": "Examine input Query for needed information for dispatch", "timestamp": "2021-08-12T15:57:38.809618" }, { "code": "", "level": "INFO", "message": "Validating the input query graph", "timestamp": "2021-08-12T15:57:38.809651" }, { "code": "", "level": "DEBUG", "message": "Deserializing message", "timestamp": "2021-08-12T15:57:38.809693" }, { "code": "", "level": "INFO", "message": "Found input query_graph. Interpreting it and generating ARAXi processing plan to answer it", "timestamp": "2021-08-12T15:57:38.809933" }, { "code": "", "level": "DEBUG", "message": "Assessing the QueryGraph for basic information", "timestamp": "2021-08-12T15:57:38.873067" }, { "code": "", "level": "DEBUG", "message": "Found 2 nodes and 1 edges", "timestamp": "2021-08-12T15:57:38.873121" }, { "code": "", "level": "DEBUG", "message": "canonical_curies={'NCBIGene:1956': {'preferred_curie': 'UniProtKB:P00533', 'preferred_name': 'EGFR', 'preferred_category': 'biolink:Protein', 'expanded_categories': {'biolink:Protein': True, 'biolink:Gene': True, 'biolink:Polypeptide': True, 'biolink:BiologicalEntity': True, 'biolink:NamedThing': True, 'biolink:GeneProductMixin': True, 'biolink:GeneOrGeneProduct': True, 'biolink:MacromolecularMachineMixin': True, 'biolink:ThingWithTaxon': True, 'biolink:ChemicalEntityOrGeneOrGeneProduct': True, 'biolink:ChemicalEntityOrProteinOrPolypeptide': True, 'biolink:GenomicEntity': True, 'biolink:PhysicalEssence': True, 'biolink:PhysicalEssenceOrOccurrent': True, 'biolink:OntologyClass': True}, 'all_categories': {'biolink:NucleicAcidEntity': 1, 'biolink:Gene': 8, 'biolink:Polypeptide': 7, 'biolink:NamedThing': 1, 'biolink:Protein': 4, 'biolink:GeneFamily': 1, 'biolink:MolecularEntity': 65}}}, curie=NCBIGene:1956", "timestamp": "2021-08-12T15:57:38.881362" }, { "code": "", "level": "DEBUG", "message": "The QueryGraph reference template is: n00(ids)-e00()-n01(categories=biolink:SmallMolecule)", "timestamp": "2021-08-12T15:57:38.881455" }, { "code": "", "level": "INFO", "message": "Found input processing plan. Sending to the ProcessingPlanExecutor", "timestamp": "2021-08-12T15:57:38.881679" }, { "code": "", "level": "DEBUG", "message": "Entering execute_processing_plan", "timestamp": "2021-08-12T15:57:38.881710" }, { "code": "", "level": "DEBUG", "message": "A single Message is ready and in hand", "timestamp": "2021-08-12T15:57:38.900962" }, { "code": "", "level": "DEBUG", "message": "Found actions", "timestamp": "2021-08-12T15:57:38.901023" }, { "code": "", "level": "INFO", "message": "Parsing input actions list", "timestamp": "2021-08-12T15:57:38.901057" }, { "code": "", "level": "DEBUG", "message": "Parsing action: expand()", "timestamp": "2021-08-12T15:57:38.901080" }, { "code": "", "level": "DEBUG", "message": "Parsing action: overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n1, object_qnode_key=n0)", "timestamp": "2021-08-12T15:57:38.901154" }, { "code": "", "level": "DEBUG", "message": "Parsing action: resultify()", "timestamp": "2021-08-12T15:57:38.901235" }, { "code": "", "level": "DEBUG", "message": "Parsing action: filter_results(action=limit_number_of_results, max_results=500)", "timestamp": "2021-08-12T15:57:38.901281" }, { "code": "", "level": "INFO", "message": "Processing action 'expand' with parameters {'': 'true'}", "timestamp": "2021-08-12T15:57:38.901743" }, { "code": "UnsupportedConstraint", "level": "ERROR", "message": "Unsupported constraint(s) detected on qnode n0 for {'biolink:highest_FDA_approval_status'}. Don't know how to handle these!", "timestamp": "2021-08-12T15:57:38.902297" } ], "message": { "knowledge_graph": { "edges": {}, "nodes": {} }, "query_graph": { "edges": { "e0": { "object": "n1", "predicates": [ "biolink:decreases_abundance_of", "biolink:decreases_activity_of", "biolink:decreases_expression_of", "biolink:decreases_synthesis_of", "biolink:increases_degradation_of", "biolink:disrupts", "biolink:entity_negatively_regulates_entity" ], "subject": "n0" } }, "nodes": { "n0": { "categories": [ "biolink:SmallMolecule" ], "constraints": [ { "id": "biolink:highest_FDA_approval_status", "name": "highest FDA approval status", "not": false, "operator": "==", "value": "regular approval" } ], "is_set": false }, "n1": { "ids": [ "NCBIGene:1956" ], "is_set": false } } }, "results": [] }, "operations": { "actions": [ "expand()", "overlay(action=compute_ngd, virtual_relation_label=N1, subject_qnode_key=n1, object_qnode_key=n0)", "resultify()", "filter_results(action=limit_number_of_results, max_results=500)" ] }, "reasoner_id": "ARAX", "schema_version": "1.1.0", "status": "UnsupportedConstraint", "tool_version": "ARAX 0.8.0", "type": "translator_reasoner_response", "validation_result": { "message": "", "n_edges": 0, "n_nodes": 0, "provenance_summary": { "n_sources": 0, "predicate_counts": {}, "provenance_counts": {} }, "size": "11 kB", "status": "PASS", "version": "1.1.1" }, "araxui_provider": "ARS", "araxui_response": "24a2c04c-1f78-49b1-a521-d116c9d24e58" }
Returning results
https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.9_EGFR_advanced.json