161 lines
6.2 KiB
Python
161 lines
6.2 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
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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.protocol_builder import ProtocolBuilderService
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from crc.services.workflow_processor import WorkflowProcessor
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def add_study(body):
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study: StudyModel = StudyModelSchema().load(body, session=session)
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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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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 = session.query(StudyModel).filter_by(id=study_id).first()
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if study is None:
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raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
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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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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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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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""":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(g.user.id)
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# Get studies from the database
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db_studies = session.query(StudyModel).filter_by(user_uid=g.user.uid).all()
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# Update all studies from the protocol builder, create new studies as needed.
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for pb_study in pb_studies:
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db_study = next((s for s in db_studies if s.id == pb_study.STUDYID), None)
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if not db_study:
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db_study = StudyModel(id=pb_study.STUDYID)
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session.add(db_study)
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db_studies.append(db_study)
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db_study.update_from_protocol_builder(pb_study)
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# Mark studies as inactive that are no longer in Protocol Builder
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for study in db_studies:
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pb_study = next((pbs for pbs in pb_studies if pbs.STUDYID == study.id), None)
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if not pb_study:
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study.inactive = True
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study.protocol_builder_status = ProtocolBuilderStatus.INACTIVE
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session.commit()
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# Return updated studies
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results = StudyModelSchema(many=True).dump(db_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.id)
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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.INACTIVE
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return NoContent, 304
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def get_study_workflows(study_id):
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"""Returns all the workflows related to this study"""
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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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def get_study_workflows_with_refresh(study_id):
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"""Returns all the workflows related to this study, assuring that the status of
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these workflows is up to date. """
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# Get study
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study: StudyModel = session.query(StudyModel).filter_by(id=study_id).first()
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current_workflows = session.query(WorkflowModel).filter_by(study_id=study_id).all()
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all_specs = session.query(WorkflowSpecModel).filter_by(is_status=False).first()
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api_models = []
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status_spec = session.query(WorkflowSpecModel).filter_by(is_status=True).first()
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if status_spec is not None:
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# Run status spec to get list of workflow specs applicable to this study
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status_processor = WorkflowProcessor.create(study.id, status_spec)
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status_processor.do_engine_steps()
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status_data = status_processor.next_task().data
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# Only add workflow specs listed in status spec
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for spec in all_specs:
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if spec.id in status_data and status_data[spec.id]:
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processor = WorkflowProcessor.create(study.id, spec.id)
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api_models.append(__get_workflow_api_model(processor, status_data))
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else:
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# No status spec. Just add all workflows.
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for spec in all_specs:
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processor = WorkflowProcessor.create(study.id, spec.id)
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api_models.append(__get_workflow_api_model(processor, status_data))
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def add_workflow_to_study(study_id, body):
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workflow_spec_model: WorkflowSpecModel = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
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if workflow_spec_model is None:
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raise ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
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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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