cr-connect-workflow/crc/api/study.py

81 lines
2.9 KiB
Python

from connexion import NoContent
from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.api.workflow import __get_workflow_api_model
from crc.models.study import StudyModelSchema, StudyModel
from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
from crc.services.workflow_processor import WorkflowProcessor
def all_studies():
# todo: Limit returned studies to a user
schema = StudyModelSchema(many=True)
return schema.dump(session.query(StudyModel).all())
def add_study(body):
study = StudyModelSchema().load(body, session=session)
session.add(study)
session.commit()
# FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
for spec in session.query(WorkflowSpecModel).all():
WorkflowProcessor.create(study.id, spec.id)
return StudyModelSchema().dump(study)
def update_study(study_id, body):
if study_id is None:
error = ApiError('unknown_study', 'Please provide a valid Study ID.')
return ApiErrorSchema.dump(error), 404
study = session.query(StudyModel).filter_by(id=study_id).first()
if study is None:
error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
return ApiErrorSchema.dump(error), 404
study = StudyModelSchema().load(body, session=session)
session.add(study)
session.commit()
return StudyModelSchema().dump(study)
def get_study(study_id):
study = session.query(StudyModel).filter_by(id=study_id).first()
schema = StudyModelSchema()
if study is None:
return NoContent, 404
return schema.dump(study)
def update_from_protocol_builder():
"""Call the """
def post_update_study_from_protocol_builder(study_id):
"""This will update the list of known studies based on data received from
the protocol builder."""
# todo: Actually get data from an external service here
return NoContent, 304
def get_study_workflows(study_id):
workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
api_models = []
for workflow_model in workflow_models:
processor = WorkflowProcessor(workflow_model.workflow_spec_id,
workflow_model.bpmn_workflow_json)
api_models.append( __get_workflow_api_model(processor))
schema = WorkflowApiSchema(many=True)
return schema.dump(api_models)
def add_workflow_to_study(study_id, body):
workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
if workflow_spec_model is None:
error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
return ApiErrorSchema.dump(error), 404
processor = WorkflowProcessor.create(study_id, workflow_spec_model.id)
return WorkflowApiSchema().dump(__get_workflow_api_model(processor))