117 lines
4.8 KiB
Python
117 lines
4.8 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, \
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StudyStatus, StudyAssociatedSchema
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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.utcnow(),
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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, do_status=True)
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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.utcnow()
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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, update_status=False):
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study = StudyService.get_study(study_id, do_status=update_status)
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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 get_study_associates(study_id):
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return StudyAssociatedSchema(many=True).dump(StudyService.get_study_associates(study_id))
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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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if len(studies) == 0:
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studies = StudyService().get_studies_for_user(user, include_invalid=True)
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if len(studies) > 0:
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message = f"All studies associated with User: {user.display_name} failed study validation"
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raise ApiError(code="study_integrity_error", message=message)
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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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