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

from datetime import datetime

from flask import g
from sqlalchemy.exc import IntegrityError

from crc import session
from crc.api.common import ApiError, ApiErrorSchema
from crc.models.protocol_builder import ProtocolBuilderStatus
from crc.models.study import Study, StudyEvent, StudyEventType, StudyModel, StudySchema, StudyForUpdateSchema, StudyStatus
from crc.services.study_service import StudyService
from crc.services.user_service import UserService


def add_study(body):
    """Or any study like object. Body should include a title, and primary_investigator_id """
    if 'primary_investigator_id' not in body:
        raise ApiError("missing_pi", "Can't create a new study without a Primary Investigator.")
    if 'title' not in body:
        raise ApiError("missing_title", "Can't create a new study without a title.")

    study_model = StudyModel(user_uid=UserService.current_user().uid,
                             title=body['title'],
                             primary_investigator_id=body['primary_investigator_id'],
                             last_updated=datetime.now(),
                             status=StudyStatus.in_progress)
    session.add(study_model)
    StudyService.add_study_update_event(study_model,
                                        status=StudyStatus.in_progress,
                                        event_type=StudyEventType.user,
                                        user_uid=g.user.uid)

    errors = StudyService._add_all_workflow_specs_to_study(study_model)
    session.commit()
    study = StudyService().get_study(study_model.id)
    study_data = StudySchema().dump(study)
    study_data["errors"] = ApiErrorSchema(many=True).dump(errors)
    return study_data


def update_study(study_id, body):
    """Pretty limited, but allows manual modifications to the study status """
    if study_id is None:
        raise ApiError('unknown_study', 'Please provide a valid Study ID.')

    study_model = session.query(StudyModel).filter_by(id=study_id).first()
    if study_model is None:
        raise ApiError('unknown_study', 'The study "' + study_id + '" is not recognized.')

    study: Study = StudyForUpdateSchema().load(body)

    status = StudyStatus(study.status)
    study_model.last_updated = datetime.now()

    if study_model.status != status:
        study_model.status = status
        StudyService.add_study_update_event(study_model, status, StudyEventType.user,
                                            user_uid=UserService.current_user().uid if UserService.has_user() else None,
                                            comment='' if not hasattr(study, 'comment') else study.comment,
                                            )

    if status == StudyStatus.open_for_enrollment:
        study_model.enrollment_date = study.enrollment_date

    session.add(study_model)
    session.commit()
    # Need to reload the full study to return it to the frontend
    study = StudyService.get_study(study_id)
    return StudySchema().dump(study)


def get_study(study_id):
    study = StudyService.get_study(study_id)
    if (study is None):
        raise ApiError("unknown_study",  'The study "' + study_id + '" is not recognized.', status_code=404)
    return StudySchema().dump(study)


def delete_study(study_id):
    try:
        StudyService.delete_study(study_id)
    except IntegrityError as ie:
        session.rollback()
        message = "Failed to delete Study #%i due to an Integrity Error: %s" % (study_id, str(ie))
        raise ApiError(code="study_integrity_error", message=message)


def user_studies():
    """Returns all the studies associated with the current user. """
    user = UserService.current_user(allow_admin_impersonate=True)
    StudyService.synch_with_protocol_builder_if_enabled(user)
    studies = StudyService.get_studies_for_user(user)
    results = StudySchema(many=True).dump(studies)
    return results


def all_studies():
    """Returns all studies (regardless of user) with submitted files"""
    studies = StudyService.get_all_studies_with_files()
    results = StudySchema(many=True).dump(studies)
    return results