125 lines
4.5 KiB
Python
125 lines
4.5 KiB
Python
from typing import List
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from connexion import NoContent
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from flask import g
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from crc import session, auth
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.api.workflow import __get_workflow_api_model
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from crc.models.protocol_builder import ProtocolBuilderStatus, ProtocolBuilderStudy
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from crc.models.study import StudyModelSchema, StudyModel
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from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
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from crc.services.workflow_processor import WorkflowProcessor
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from crc.services.protocol_builder import ProtocolBuilderService
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@auth.login_required
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def all_studies():
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user = g.user
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""":type: crc.models.user.UserModel"""
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update_from_protocol_builder()
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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return StudyModelSchema(many=True).dump(db_studies)
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@auth.login_required
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def add_study(body):
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study = StudyModelSchema().load(body, session=session)
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session.add(study)
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session.commit()
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# FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
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for spec in session.query(WorkflowSpecModel).all():
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WorkflowProcessor.create(study.id, spec.id)
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return StudyModelSchema().dump(study)
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@auth.login_required
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def update_study(study_id, body):
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if study_id is None:
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error = ApiError('unknown_study', 'Please provide a valid Study ID.')
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return ApiErrorSchema.dump(error), 404
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study = session.query(StudyModel).filter_by(id=study_id).first()
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if study is None:
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error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
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return ApiErrorSchema.dump(error), 404
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study = StudyModelSchema().load(body, session=session, instance=study)
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session.add(study)
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session.commit()
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return StudyModelSchema().dump(study)
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@auth.login_required
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def get_study(study_id):
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study = session.query(StudyModel).filter_by(id=study_id).first()
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schema = StudyModelSchema()
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if study is None:
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return NoContent, 404
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return schema.dump(study)
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@auth.login_required
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def update_from_protocol_builder():
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"""Updates the list of known studies for a given user based on data received from
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the protocol builder."""
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user = g.user
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""":type: crc.models.user.UserModel"""
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# Get studies matching this user from Protocol Builder
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pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(user.uid)
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db_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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db_study_ids = list(map(lambda s: s.id, db_studies))
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pb_study_ids = list(map(lambda s: s.id, pb_studies))
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# Add studies from Protocol Builder that aren't in the database yet
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for pb_study in pb_studies:
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if pb_study['HSRNUMBER'] not in db_study_ids:
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status = ProtocolBuilderStatus.complete._value_ if pb_study[
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'Q_COMPLETE'] else ProtocolBuilderStatus.in_process._value_
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add_study({
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'id': pb_study['HSRNUMBER'],
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'title': pb_study['TITLE'],
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'protocol_builder_status': status,
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'user_uid': pb_study['NETBADGEID'],
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'last_updated': pb_study['DATE_MODIFIED']
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})
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# Mark studies as inactive that are no longer in Protocol Builder
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for study_id in db_study_ids:
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if study_id not in pb_study_ids:
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update_study(study_id=study_id, body={'inactive': True})
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def post_update_study_from_protocol_builder(study_id):
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"""Update a single study based on data received from
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the protocol builder."""
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# todo: Actually get data from an external service here
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return NoContent, 304
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def get_study_workflows(study_id):
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workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
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api_models = []
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for workflow_model in workflow_models:
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processor = WorkflowProcessor(workflow_model.workflow_spec_id,
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workflow_model.bpmn_workflow_json)
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api_models.append(__get_workflow_api_model(processor))
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schema = WorkflowApiSchema(many=True)
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return schema.dump(api_models)
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def add_workflow_to_study(study_id, body):
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workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
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if workflow_spec_model is None:
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error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
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return ApiErrorSchema.dump(error), 404
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processor = WorkflowProcessor.create(study_id, workflow_spec_model.id)
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return WorkflowApiSchema().dump(__get_workflow_api_model(processor))
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