mirror of
https://github.com/sartography/cr-connect-workflow.git
synced 2025-02-22 20:58:28 +00:00
7e76639cf3
In api.study.update_study we test the study status and call the new WorkflowService method process_workflows_for_cancels. In services.workflow_service we added the new method process_workflows_for_cancels. It loops through workflows for a study, and resets them if they are in progress. In services.workflow_processor, we changed the reset method to be an instance method so we can call self.cancel_notify. In tests.test_lookup_service we changed the call to WorkflowProcessor.reset to reflect the change from class method to instance method
106 lines
4.2 KiB
Python
106 lines
4.2 KiB
Python
from datetime import datetime
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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
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from crc.api.common import ApiError, ApiErrorSchema
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from crc.models.protocol_builder import ProtocolBuilderStatus
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from crc.models.study import Study, StudyEvent, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, StudyStatus
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from crc.services.study_service import StudyService
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from crc.services.user_service import UserService
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from crc.services.workflow_service import WorkflowService
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def add_study(body):
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"""Or any study like object. Body should include a title, and primary_investigator_id """
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if 'primary_investigator_id' not in body:
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raise ApiError("missing_pi", "Can't create a new study without a Primary Investigator.")
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if 'title' not in body:
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raise ApiError("missing_title", "Can't create a new study without a title.")
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study_model = StudyModel(user_uid=UserService.current_user().uid,
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title=body['title'],
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primary_investigator_id=body['primary_investigator_id'],
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last_updated=datetime.now(),
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status=StudyStatus.in_progress)
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session.add(study_model)
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StudyService.add_study_update_event(study_model,
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status=StudyStatus.in_progress,
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event_type=StudyEventType.user,
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user_uid=g.user.uid)
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errors = StudyService._add_all_workflow_specs_to_study(study_model)
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session.commit()
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study = StudyService().get_study(study_model.id)
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study_data = StudySchema().dump(study)
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study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
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return study_data
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def update_study(study_id, body):
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"""Pretty limited, but allows manual modifications to the study status """
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if study_id is None:
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raise ApiError('unknown_study', 'Please provide a valid Study ID.')
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study_model = session.query(StudyModel).filter_by(id=study_id).first()
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if study_model is None:
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raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
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study: Study = StudyForUpdateSchema().load(body)
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status = StudyStatus(study.status)
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study_model.last_updated = datetime.now()
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if study_model.status != status:
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study_model.status = status
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StudyService.add_study_update_event(study_model, status, StudyEventType.user,
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user_uid=UserService.current_user().uid if UserService.has_user() else None,
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comment='' if not hasattr(study, 'comment') else study.comment,
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)
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if status == StudyStatus.open_for_enrollment:
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study_model.enrollment_date = study.enrollment_date
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session.add(study_model)
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session.commit()
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if status == StudyStatus.abandoned or status == StudyStatus.hold:
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WorkflowService.process_workflows_for_cancels(study_id)
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# Need to reload the full study to return it to the frontend
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study = StudyService.get_study(study_id)
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return StudySchema().dump(study)
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def get_study(study_id):
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study = StudyService.get_study(study_id)
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if (study is None):
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raise ApiError("unknown_study", 'The study "' + study_id + '" is not recognized.', status_code=404)
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return StudySchema().dump(study)
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def delete_study(study_id):
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try:
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StudyService.delete_study(study_id)
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except IntegrityError as ie:
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session.rollback()
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message = "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=message)
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def user_studies():
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"""Returns all the studies associated with the current user. """
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user = UserService.current_user(allow_admin_impersonate=True)
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StudyService.synch_with_protocol_builder_if_enabled(user)
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studies = StudyService.get_studies_for_user(user)
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results = StudySchema(many=True).dump(studies)
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return results
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def all_studies():
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"""Returns all studies (regardless of user) with submitted files"""
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studies = StudyService.get_all_studies_with_files()
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results = StudySchema(many=True).dump(studies)
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return results
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