"""
Get list of tasks (queued and completed)
---
tags: [tasks]
responses:
200:
description: tasks
type: array
items:
$ref: '#/definitions/Task'
"""
tasks = get_tasks()
return tasks
api.add_resource(Tasks, '/tasks/')
class TaskStatus(Resource):
def get(self, task_id):
"""Get status for task
---
tags: [tasks]
parameters:
- in: path
name: task_id
description: "task id"
type: string
required: true
responses:
200:
content:
application/json:
schema:
type: array
items:
type: string
"""
r = requests.get(f"http://{os.environ['BUILDER_HOST']}:{os.environ['BUILDER_PORT']}/api/concepts")
concepts = r.json()
bad_concepts =['NAME.DISEASE', 'NAME.PHENOTYPE', 'NAME.DRUG']
concepts = [c for c in concepts if not c in bad_concepts]
concepts.sort()
return concepts
api.add_resource(Concepts, '/concepts/')
class Omnicorp(Resource):
def get(self, id1, id2):
"""
Get publications for a pair of identifiers
---
tags: [util]
parameters:
- in: path
name: id1
description: "curie of first term"
schema:
type: string
required: true
answers = [json.loads(answer['body']) for answer in answers]
message = {
'question_graph': question_graph,
'answers': answers
}
if include_kg:
url = f'http://{os.environ["RANKER_HOST"]}:{os.environ["RANKER_PORT"]}/api/knowledge_graph'
response = requests.post(url, json=message)
if response.status_code >= 300:
return 'Trouble contacting the ranker, there is probably a problem with the neo4j database', 500
message['knowledge_graph'] = response.json()
return message, 200
api.add_resource(AnswersetAPI, '/a/<qid_aid>/')
class QuestionVisibilityAPI(Resource):
@auth_required('session', 'basic')
def post(self, question_id):
"""
Set Question Visiblity.
---
tags: [questions]
parameters:
- in: path
name: question_id
description: "question id"
schema:
# New Feedback Submission
class FeedbackAPI(Resource):
@auth_required('session', 'basic')
def post(self):
"""Create new feedback
---
tags: [feedback]
parameters:
- in: body
name: feedback
description: "new feedback"
schema:
$ref: '#/definitions/Feedback'
responses:
201:
description: "confirmation"
type: string
"""
f = Feedback(user_id=current_user.id,
question_id=request.json['question_id'],
answer_id=request.json['answer_id'],
accuracy=request.json['accuracy'],
impact=request.json['impact'],
notes=request.json['notes'])
return "Feedback created", 201
api.add_resource(FeedbackAPI, '/feedback/')
)
ug_task = update_kg.signature(args=[question_id],
kwargs={'user_email': user_email},
immutable=True)
as_task = answer_question.signature(
args=[question_id],
kwargs={'user_email': user_email},
immutable=True)
task = answer_question.apply_async(
args=[question_id],
kwargs={'user_email': user_email},
link_error=ug_task | as_task)
logger.info(
f'Update task for question {question_id} for user {user_email} to the queue has recieved task_id {task.id}'
)
elif request.headers.get('AnswerNow', default='true') == 'true':
logger.info(
f'Adding answer task for question {question_id} for user {user_email} to the queue'
)
task = answer_question.apply_async(
args=[question_id], kwargs={'user_email': user_email})
logger.info(
f'Answer task for question {question_id} for user {user_email} to the queue has recieved task_id {task.id}'
)
return question_id, 201
api.add_resource(QuestionsAPI, '/questions/')
max_results = parse_args_max_results(request.args)
output_format = parse_args_output_format(request.args)
max_connectivity = parse_args_max_connectivity(request.args)
# Ger rebuild from request args
question['rebuild'] = parse_args_rebuild(request.args)
response = requests.post(
f'http://manager:{os.environ["MANAGER_PORT"]}/api/simple/quick/?max_results={max_results}&max_connectivity={max_connectivity}&output_format={output_format}',
json=question)
answerset = response.json()
return answerset
api.add_resource(Expand, '/simple/expand/<type1>/<id1>/<type2>/')
class Quick(Resource):
def post(self):
"""
Get answers to a question without caching
---
tags: [simple]
requestBody:
name: question
description: The machine-readable question graph.
content:
application/json:
schema:
$ref: '#/definitions/Question'
$ref: '#/components/schemas/Message'
required: true
responses:
200:
description: A URL for further viewing
"""
logger.info('Recieving Answerset for storage and later viewing')
message = request.json
# Save the message to archive folder
for _ in range(25):
try:
uid = str(uuid4())
this_file = os.path.join(view_storage_dir, f'{uid}.json')
with open(this_file, 'x') as answerset_file:
logger.info('Saving Message')
json.dump(message, answerset_file)
break
except:
logger.info('Error encountered writting file. Retrying')
pass
else:
logger.info('Error encountered writting file')
return "Failed to save resource. Internal server error", 500
return uid, 200
api.add_resource(View, '/simple/view/')
if not answerset in answersets:
raise AssertionError()
except Exception as err:
return "Invalid answerset key.", 404
user = getAuthData()
feedback = list_feedback_by_question_answerset(question, answerset)
return {'question': question.toJSON(),\
'answerset': answerset.toStandard(),\
'feedback': [f.toJSON() for f in feedback],\
'other_answersets': [],
'other_questions': []}, 200
api.add_resource(AnswersetAPI, '/a/<qa_id>/')
class AnswerAPI(Resource):
def get(self, qa_id, answer_id):
"""
Get answer
---
tags: [answer]
parameters:
- in: path
name: qa_id
description: "<question_id>_<answerset_id>"
type: string
required: true
- in: path
name: answer_id
request_url = ''
if task['type'] == TASK_TYPES['answer']:
request_url = f"http://{os.environ['RANKER_HOST']}:{os.environ['RANKER_PORT']}/api/task/{task['remote_task_id']}"
response = requests.delete(request_url)
# We could check the reponses, but there is nothing we would tell the user either way
# elif task['type'] == TASK_TYPES['update']:
# request_url = f"http://{os.environ['BUILDER_HOST']}:{os.environ['BUILDER_PORT']}/api/task/{task['remote_task_id']}/log"
# else:
# raise Exception('Invalid task type')
# except:
# return 'Task not found', 404
return '', 204
api.add_resource(TaskStatus, '/t/<task_id>/')
class NLP(Resource):
def post(self):
"""
Parse Question
---
tags: [util]
summary: "Convert a natural-language question into machine-readable form."
consumes:
- text/plain
requestBody:
name: "question"
description: "Natural-language question"
required: true
user_email = auth.username
user = get_user_by_email(user_email)
else:
user = current_user
logger.info('Deleting question %s', question_id)
try:
question = get_question_by_id(question_id)
except Exception as err:
return "Invalid question key.", 404
if not (user == question.user or user.has_role('admin')):
return "UNAUTHORIZED", 401 # not authorized
db.session.delete(question)
db.session.commit()
return "SUCCESS", 200
api.add_resource(QuestionAPI, '/q/<question_id>/')
# get feedback by question
class GetFeedbackByQuestion(Resource):
def get(self, question_id):
"""
Create new feedback
---
tags: [feedback]
parameters:
- in: path
name: question_id
description: "question id"
type: string
required: true
responses: