vgardner-renci
commented
3 years ago https://arax.ncats.io/?source=ARS&id=c9c02a08-5574-45e2-836c-cf16f95fa964
{
"callback": "http://localhost:8000/ars/api/messages/290dd07d-71e2-42d4-a404-8fb041151ac4",
"description": "",
"logs": [
{
"code": null,
"level": "ERROR",
"message": "Exception 'logs'",
"timestamp": "2021-09-01 23:27:38.171649"
},
{
"code": "InvalidTRAPI",
"level": "ERROR",
"message": "TRAPI validator reported an error: Additional properties are not allowed ('negated' was unexpected)\n\nFailed validating 'additionalProperties' in schema[0]['items']:\n {'additionalProperties': False,\n 'description': 'Generic query constraint for a query node or query '\n 'edge',\n 'properties': {'id': {'allOf': [{'$ref': '#/components/schemas/CURIE'}],\n 'description': 'CURIE of the concept being '\n 'constrained. For properties '\n 'defined by the Biolink model '\n 'this SHOULD be a biolink CURIE. '\n 'otherwise, if possible, from '\n 'the EDAM ontology. If a '\n 'suitable CURIE does not exist, '\n 'enter a descriptive phrase here '\n 'and submit the new type for '\n 'consideration by the '\n 'appropriate authority.',\n 'example': 'EDAM:data_0844'},\n 'name': {'description': 'Human-readable name or label '\n 'for the constraint concept. '\n 'If appropriate, it SHOULD be '\n 'the term name of the CURIE '\n \"used as the 'id'. This is \"\n 'redundant but required for '\n 'human readability.',\n 'example': 'molecular mass',\n 'type': 'string'},\n 'not': {'default': False, 'type': 'boolean'},\n 'operator': {'description': 'Relationship between the '\n 'database value and the '\n 'constraint value for the '\n 'specified id. The '\n 'operators ==, >, and < '\n 'mean is exactly equal to, '\n 'is greater than, and is '\n 'less than, respectively. '\n \"The 'matches' operator \"\n 'indicates that the value '\n 'is a regular expression '\n 'to be evaluated. If value '\n 'is a list type, then at '\n 'least one evaluation must '\n 'be true (equivalent to '\n 'OR). This means that the '\n '== operator with a list '\n \"acts like a SQL 'IN' \"\n \"clause. The 'not' \"\n 'property negates the '\n 'operator such that not '\n \"and == means 'not equal \"\n \"to' (or 'not in' for a \"\n 'list), and not > means '\n '<=, and not < means >=, '\n 'and not matches means '\n \"does not match. The '==' \"\n 'operator SHOULD NOT be '\n 'used in a manner that '\n 'describes an \"is a\" '\n 'subclass relationship for '\n 'the parent QNode.',\n 'enum': ['==', '>', '<', 'matches'],\n 'type': 'string'},\n 'unit_id': {'description': 'CURIE of the units of the '\n 'value or list of values in '\n \"the 'value' property. The \"\n 'Units of Measurement '\n 'Ontology (UO) should be '\n 'used if possible. The '\n 'unit_id MUST be provided '\n 'for (lists of) numerical '\n 'values that correspond to '\n 'a quantity that has units.',\n 'example': 'UO:0000222'},\n 'unit_name': {'description': 'Term name that is '\n 'associated with the '\n 'CURIE of the units of '\n 'the value or list of '\n \"values in the 'value' \"\n 'property. The Units of '\n 'Measurement Ontology '\n '(UO) SHOULD be used if '\n 'possible. This property '\n 'SHOULD be provided if a '\n 'unit_id is provided. '\n 'This is redundant but '\n 'recommended for human '\n 'readability.',\n 'example': 'kilodalton'},\n 'value': {'description': 'Value of the attribute. May '\n 'be any data type, including '\n 'a list. If the value is a '\n 'list and there are multiple '\n 'items, at least one '\n 'comparison must be true '\n '(equivalent to OR). If '\n \"'value' is of data type \"\n \"'object', the keys of the \"\n 'object MAY be treated as a '\n \"list. A 'list' data type \"\n \"paired with the '>' or '<' \"\n 'operators will encode '\n 'extraneous comparisons, but '\n 'this is permitted as it is '\n 'in SQL and other languages.',\n 'example': 57.0}},\n 'required': ['name', 'id', 'operator', 'value'],\n 'type': 'object'}\n\nOn instance[0]:\n {'id': 'biolink:highest_FDA_approval_status',\n 'name': 'highest FDA approval status',\n 'negated': False,\n 'operator': '==',\n 'unit_id': None,\n 'unit_name': None,\n 'value': 'regular approval'}",
"timestamp": "2021-09-02T12:15:08.350362"
}
],
"message": {
"knowledge_graph": null,
"query_graph": {
"edges": {
"e0": {
"constraints": null,
"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"
],
"relation": null,
"subject": "n0"
}
},
"nodes": {
"n0": {
"categories": [
"biolink:SmallMolecule"
],
"constraints": [
{
"id": "biolink:highest_FDA_approval_status",
"name": "highest FDA approval status",
"negated": false,
"operator": "==",
"unit_id": null,
"unit_name": null,
"value": "regular approval"
}
],
"ids": null,
"is_set": false,
"name": "Small Molecule"
},
"n1": {
"categories": null,
"constraints": null,
"ids": [
"NCBIGene:1956"
],
"is_set": false,
"name": "EGFR"
}
}
},
"results": null
},
"status": null,
"validation_result": {
"message": "TRAPI validator reported an error: Additional properties are not allowed ('negated' was unexpected)\n\nFailed validating 'additionalProperties' in schema[0]['items']:\n {'additionalProperties': False,\n 'description': 'Generic query constraint for a query node or query '\n 'edge',\n 'properties': {'id': {'allOf': [{'$ref': '#/components/schemas/CURIE'}],\n 'description': 'CURIE of the concept being '\n 'constrained. For properties '\n 'defined by the Biolink model '\n 'this SHOULD be a biolink CURIE. '\n 'otherwise, if possible, from '\n 'the EDAM ontology. If a '\n 'suitable CURIE does not exist, '\n 'enter a descriptive phrase here '\n 'and submit the new type for '\n 'consideration by the '\n 'appropriate authority.',\n 'example': 'EDAM:data_0844'},\n 'name': {'description': 'Human-readable name or label '\n 'for the constraint concept. '\n 'If appropriate, it SHOULD be '\n 'the term name of the CURIE '\n \"used as the 'id'. This is \"\n 'redundant but required for '\n 'human readability.',\n 'example': 'molecular mass',\n 'type': 'string'},\n 'not': {'default': False, 'type': 'boolean'},\n 'operator': {'description': 'Relationship between the '\n 'database value and the '\n 'constraint value for the '\n 'specified id. The '\n 'operators ==, >, and < '\n 'mean is exactly equal to, '\n 'is greater than, and is '\n 'less than, respectively. '\n \"The 'matches' operator \"\n 'indicates that the value '\n 'is a regular expression '\n 'to be evaluated. If value '\n 'is a list type, then at '\n 'least one evaluation must '\n 'be true (equivalent to '\n 'OR). This means that the '\n '== operator with a list '\n \"acts like a SQL 'IN' \"\n \"clause. The 'not' \"\n 'property negates the '\n 'operator such that not '\n \"and == means 'not equal \"\n \"to' (or 'not in' for a \"\n 'list), and not > means '\n '<=, and not < means >=, '\n 'and not matches means '\n \"does not match. The '==' \"\n 'operator SHOULD NOT be '\n 'used in a manner that '\n 'describes an \"is a\" '\n 'subclass relationship for '\n 'the parent QNode.',\n 'enum': ['==', '>', '<', 'matches'],\n 'type': 'string'},\n 'unit_id': {'description': 'CURIE of the units of the '\n 'value or list of values in '\n \"the 'value' property. The \"\n 'Units of Measurement '\n 'Ontology (UO) should be '\n 'used if possible. The '\n 'unit_id MUST be provided '\n 'for (lists of) numerical '\n 'values that correspond to '\n 'a quantity that has units.',\n 'example': 'UO:0000222'},\n 'unit_name': {'description': 'Term name that is '\n 'associated with the '\n 'CURIE of the units of '\n 'the value or list of '\n \"values in the 'value' \"\n 'property. The Units of '\n 'Measurement Ontology '\n '(UO) SHOULD be used if '\n 'possible. This property '\n 'SHOULD be provided if a '\n 'unit_id is provided. '\n 'This is redundant but '\n 'recommended for human '\n 'readability.',\n 'example': 'kilodalton'},\n 'value': {'description': 'Value of the attribute. May '\n 'be any data type, including '\n 'a list. If the value is a '\n 'list and there are multiple '\n 'items, at least one '\n 'comparison must be true '\n '(equivalent to OR). If '\n \"'value' is of data type \"\n \"'object', the keys of the \"\n 'object MAY be treated as a '\n \"list. A 'list' data type \"\n \"paired with the '>' or '<' \"\n 'operators will encode '\n 'extraneous comparisons, but '\n 'this is permitted as it is '\n 'in SQL and other languages.',\n 'example': 57.0}},\n 'required': ['name', 'id', 'operator', 'value'],\n 'type': 'object'}\n\nOn instance[0]:\n {'id': 'biolink:highest_FDA_approval_status',\n 'name': 'highest FDA approval status',\n 'negated': False,\n 'operator': '==',\n 'unit_id': None,\n 'unit_name': None,\n 'value': 'regular approval'} --- ",
"size": "4 kB",
"status": "FAIL",
"version": "1.1.1"
},
"araxui_provider": "ARS",
"araxui_response": "290dd07d-71e2-42d4-a404-8fb041151ac4"
}
cbizon
https://github.com/NCATSTranslator/minihackathons/blob/main/2021-12_demo/workflowA/A.9_EGFR_advanced.json