NCATSTranslator / minihackathons

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ARAX error 400 on Workflow A.9 #208

Closed vgardner-renci closed 3 years ago

vgardner-renci commented 3 years ago

https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.9_EGFR_advanced.json

image


{
  "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"
}
vgardner-renci commented 3 years ago

Returning results