93 lines
3.2 KiB
Python
93 lines
3.2 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 sqlalchemy.exc import IntegrityError
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from crc import session, 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 StudySchema, StudyModel, Study
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from crc.models.workflow import WorkflowModel, WorkflowSpecModel
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from crc.services.protocol_builder import ProtocolBuilderService
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from crc.services.study_service import StudyService
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from crc.services.workflow_processor import WorkflowProcessor
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def add_study(body):
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"""This should never get called, and is subject to deprication. Studies
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should be added through the protocol builder only."""
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study: Study = StudySchema().load(body)
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study_model = StudyModel(**study.model_args())
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session.add(study_model)
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errors = StudyService._add_all_workflow_specs_to_study(study)
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session.commit()
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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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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 = StudySchema().load(body)
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study.update_model(study_model)
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session.add(study_model)
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session.commit()
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return StudySchema().dump(study)
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def get_study(study_id):
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study_service = StudyService()
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study = study_service.get_study(study_id)
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if(study is None):
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raise ApiError("Study not found", status_code=404)
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schema = StudySchema()
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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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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 all_studies():
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"""Returns all the studies associated with the current user. Assures we are
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in sync with values read in from the protocol builder. """
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StudyService.synch_all_studies_with_protocol_builder(g.user)
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studies = StudyService.get_studies_for_user(g.user)
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results = StudySchema(many=True).dump(studies)
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return results
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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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db_study = session.query(StudyModel).filter_by(study_id=study_id).all()
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pb_studies: List[ProtocolBuilderStudy] = ProtocolBuilderService.get_studies(g.user.uid)
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pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study_id), None)
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if pb_study:
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db_study.update_from_protocol_builder(pb_study)
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else:
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db_study.inactive = True
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db_study.protocol_builder_status = ProtocolBuilderStatus.ABANDONED
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return NoContent, 304
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