def submit(req):
"""Query submission"""
if req.method != 'POST':
return HttpResponse('Only POST is permitted!', status=405)
try:
data = json.loads(req.body)
# if 'message' not in data:
# return HttpResponse('Not a valid Translator query json', status=400)
# create a head message
try:
validate_Query(data)
except ValidationError as ve:
logger.debug("Warning! Input query failed TRAPI validation " +
str(data))
logger.debug(ve)
return HttpResponse('Input query failed TRAPI validation',
status=400)
message = Message.create(code=200,
status='Running',
data=data,
actor=get_default_actor())
if 'name' in data:
message.name = data['name']
# save and broadcast
message.save()
data = message.to_dict()
return HttpResponse(json.dumps(data, indent=2),
content_type='application/json',
status=201)
except:
logger.debug("Unexpected error: %s" % sys.exc_info())
return HttpResponse('Content is not JSON', status=400)
def validateRequestBody(self):
"""
Verify its a valid TRAPI request
:return: None
:raises: Will raise if not valid
"""
# todo, Multiomics provider is sending bad TRAPI format!
reasoner_validator.validate_Query(self.requestBody)
def userRequestBodyValidation(self):
"""
A function to evaluate whether the JSON body received from the client conforms to the proper input standard.
:return: Boolean: True meaning the body is valid, False meaning the body is not valid
"""
try:
reasoner_validator.validate_Query(self.userRequestBody)
return {"isValid": True, "error": None}
except ValidationError as e:
return {"isValid": False, "error": e}
def userRequestBodyValidate(body: dict):
"""
A function to evaluate whether the JSON body received from the client conforms to the proper input standard.
:param body: A dictionary representing a JSON body
:return: Boolean: True meaning the body is valid, False meaning the body is not valid
"""
try:
reasoner_validator.validate_Query(body)
return None
except ValidationError as e:
return e
def knowledgeProviderResponseBodyIsValid(body: dict):
"""
A function to evaluate whether the JSON body received from the knowledge provider conforms to our assumptions.
:param body: A dictionary representing a JSON body
:return: Boolean: True meaning the body is valid, False meaning the body is not valid (the knowledge provider has changed their api!)
"""
try:
reasoner_validator.validate_Query(body)
return True
except Exception as e:
return False
def query(self, query: dict):
"""
Sends a query to MolePro.
:param query: TRAPI Message JSON object to send to the Genetics Provider
:return: Query object of the response.
"""
try:
response = requests.post(url=MolecularDataProvider.url, json=query)
response.raise_for_status()
except Exception as e:
raise e
# verify it is a TRAPI response
try:
trapi_response = response.json()
reasoner_validator.validate_Query(trapi_response)
except Exception as e:
raise e
return trapi_response
def buildOneHopRequestBody(node1: dict, node2: dict, edge: dict):
"""
Builds a TRAPI one hop query message.
:param node1: node1 dictionary
:param node2: node2 dictioanry
:param edge: edge dictionary
:return:
"""
requestBody = {
"message": {
"query_graph": {
"edges": {
"e0": {
"subject": "n0",
"predicate": edge["predicate"],
"object": "n1"
}
},
"nodes": {
"n0": {
"category": node1["category"]
},
"n1": {
"category": node2["category"]
}
}
}
}
}
if "id" in node1:
requestBody["message"]["query_graph"]["nodes"]["n0"]["id"] = node1[
"id"]
if "id" in node2:
requestBody["message"]["query_graph"]["nodes"]["n0"]["id"] = node2[
"id"]
# ensure the message is valid before returning it
reasoner_validator.validate_Query(requestBody)
return requestBody
def build_one_hop_query(node_1, node_2, edge):
"""
Builds a TRAPI one hop query message.
"""
message = {
"message": {
"query_graph": {
"edges": {
"e0": {
"subject": "n0",
"predicate": edge["predicate"],
"object": "n1"
}
},
"nodes": {
"n0": {
"category": node_1["category"]
},
"n1": {
"category": node_2["category"]
}
}
}
}
}
if "id" in node_1:
message["message"]["query_graph"]["nodes"]["n0"]["id"] = node_1[
"id"]
if "id" in node_2:
message["message"]["query_graph"]["nodes"]["n0"]["id"] = node_2[
"id"]
# ensure the message is valid before returning it
reasoner_validator.validate_Query(message)
return message
import reasoner_validator
nominal = {
"message": {
"query_graph": {
"edges": {
"e00": {
"subject": "n00",
"object": "n01",
"type": "biolink:associated"
}
},
"nodes": {
"n00": {
"curie": "MONDO:0004981",
"type": "biolink:Disease"
},
"n01": {
"type": "biolink:Gene"
}
}
}
}
}
reasoner_validator.validate_Query(nominal)
x = 5
