196 lines
6.9 KiB
Python
196 lines
6.9 KiB
Python
import logging
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from typing import List, Optional, Union, Tuple, Dict
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from connexion import NoContent
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from flask import g
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from sqlalchemy.exc import IntegrityError
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from crc import session, auth, app
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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.api_models import WorkflowApiSchema
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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, 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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return update_from_protocol_builder()
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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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schema = StudyModelSchema()
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study = schema.load(body, session=session, instance=study, partial=True)
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session.add(study)
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session.commit()
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return schema.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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def delete_study(study_id):
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try:
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session.query(StudyModel).filter_by(id=study_id).delete()
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except IntegrityError as ie:
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session.rollback()
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app.logger.error("Failed to delete Study #%i due to an Integrity Error: %s" % (study_id, str(ie)))
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raise ApiError(code="study_integrity_error", message="This study contains running workflows that is "
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"preventing deletion. Please delete the workflows " +
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"before proceeding.")
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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] = get_user_pb_studies()
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# Get studies from the database
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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['STUDYID'], pb_studies))
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for pb_study in pb_studies:
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# Update studies with latest data from Protocol Builder
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if pb_study['STUDYID'] in db_study_ids:
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update_study(pb_study['STUDYID'], map_pb_study_to_study(pb_study))
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# Add studies from Protocol Builder that aren't in the database yet
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else:
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new_study = map_pb_study_to_study(pb_study)
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add_study(new_study)
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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(
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study_id=study_id,
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body={
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'inactive': True,
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'protocol_builder_status': ProtocolBuilderStatus.INACTIVE.name
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}
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)
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# Return updated studies
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updated_studies = session.query(StudyModel).filter_by(user_uid=user.uid).all()
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results = StudyModelSchema(many=True).dump(updated_studies)
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return results
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@auth.login_required
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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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pb_studies: List[ProtocolBuilderStudy] = get_user_pb_studies()
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for pb_study in pb_studies:
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if pb_study['STUDYID'] == study_id:
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return update_study(study_id, map_pb_study_to_study(pb_study))
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return NoContent, 304
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@auth.login_required
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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,
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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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@auth.login_required
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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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@auth.login_required
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def get_user_pb_studies() -> List[ProtocolBuilderStudy]:
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"""Get studies from Protocol Builder matching the given user"""
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user = g.user
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""":type: crc.models.user.UserModel"""
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return ProtocolBuilderService.get_studies(user.uid)
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def map_pb_study_to_study(pb_study):
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"""Translates the given dict of ProtocolBuilderStudy properties to dict of StudyModel attributes"""
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prop_map = {
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'STUDYID': 'id',
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'HSRNUMBER': 'hsr_number',
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'TITLE': 'title',
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'NETBADGEID': 'user_uid',
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'DATE_MODIFIED': 'last_updated',
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}
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study_info = {}
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# Translate Protocol Builder property names to Study attributes
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for k, v in pb_study.items():
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if k in prop_map:
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study_info[prop_map[k]] = v
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# Translate Protocol Builder states to enum values
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status = ProtocolBuilderStatus.DRAFT
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pb_details = ProtocolBuilderService.get_study_details(pb_study['STUDYID'])
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if 'Q_COMPLETE' in pb_study and pb_study['Q_COMPLETE']:
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if 'UPLOAD_COMPLETE' in pb_details and pb_details['UPLOAD_COMPLETE']:
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if 'HSRNUMBER' in pb_study and pb_study['HSRNUMBER']:
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status = ProtocolBuilderStatus.REVIEW_COMPLETE
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else:
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status = ProtocolBuilderStatus.IN_REVIEW
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else:
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status = ProtocolBuilderStatus.IN_PROCESS
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study_info['protocol_builder_status'] = status.name
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study_info['inactive'] = False
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return study_info
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