cr-connect-workflow/crc/api/study.py

from connexion import NoContent

from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.api.workflow import __get_workflow_api_model
from crc.models.study import StudyModelSchema, StudyModel
from crc.models.workflow import WorkflowModel, WorkflowApiSchema, WorkflowSpecModel
from crc.workflow_processor import Workflow, WorkflowProcessor


def all_studies():
    # todo: Limit returned studies to a user
    schema = StudyModelSchema(many=True)
    return schema.dump(session.query(StudyModel).all())


def add_study(body):
    study = StudyModelSchema().load(body, session=session)
    session.add(study)
    session.commit()
    # FIXME: We need to ask the protocol builder what workflows to add to the study, not just add them all.
    for spec in session.query(WorkflowSpecModel).all():
        processor = WorkflowProcessor.create(spec.id)
        workflow = WorkflowModel(bpmn_workflow_json=processor.serialize(),
                                 status=processor.get_status(),
                                 study_id=study.id,
                                 workflow_spec_id=spec.id)
        session.add(workflow)
    session.commit()
    return StudyModelSchema().dump(study)


def update_study(study_id, body):
    if study_id is None:
        error = ApiError('unknown_study', 'Please provide a valid Study ID.')
        return ApiErrorSchema.dump(error), 404

    study = session.query(StudyModel).filter_by(id=study_id).first()

    if study is None:
        error = ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')
        return ApiErrorSchema.dump(error), 404

    study = StudyModelSchema().load(body, session=session)
    session.add(study)
    session.commit()
    return StudyModelSchema().dump(study)


def get_study(study_id):
    study = session.query(StudyModel).filter_by(id=study_id).first()
    schema = StudyModelSchema()
    if study is None:
        return NoContent, 404
    return schema.dump(study)


def post_update_study_from_protocol_builder(study_id):
    # todo: Actually get data from an external service here
    return NoContent, 304


def get_study_workflows(study_id):
    workflow_models = session.query(WorkflowModel).filter_by(study_id=study_id).all()
    api_models = []
    for workflow_model in workflow_models:
        processor = WorkflowProcessor(workflow_model.workflow_spec_id,
                                      workflow_model.bpmn_workflow_json)
        api_models.append( __get_workflow_api_model(workflow_model, processor))
    schema = WorkflowApiSchema(many=True)
    return schema.dump(api_models)


def add_workflow_to_study(study_id, body):
    workflow_spec_model = session.query(WorkflowSpecModel).filter_by(id=body["id"]).first()
    if workflow_spec_model is None:
        error = ApiError('unknown_spec', 'The specification "' + body['id'] + '" is not recognized.')
        return ApiErrorSchema.dump(error), 404
    processor = WorkflowProcessor.create(workflow_spec_model.id)
    workflow = WorkflowModel(bpmn_workflow_json=processor.serialize(),
                             status=processor.get_status(),
                             study_id=study_id,
                             workflow_spec_id=workflow_spec_model.id)
    session.add(workflow)
    session.commit()
    return WorkflowApiSchema().dump(__get_workflow_api_model(workflow, processor))