111 lines
4.5 KiB
Python
Executable File
111 lines
4.5 KiB
Python
Executable File
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, StudyAssociatedSchema
|
|
from crc.services.study_service import StudyService
|
|
from crc.services.user_service import UserService
|
|
from crc.services.workflow_service import WorkflowService
|
|
|
|
|
|
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.utcnow(),
|
|
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, do_status=True)
|
|
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.utcnow()
|
|
|
|
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()
|
|
|
|
if status == StudyStatus.abandoned or status == StudyStatus.hold:
|
|
WorkflowService.process_workflows_for_cancels(study_id)
|
|
|
|
# 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, update_status=False):
|
|
study = StudyService.get_study(study_id, do_status=update_status)
|
|
if (study is None):
|
|
raise ApiError("unknown_study", 'The study "' + study_id + '" is not recognized.', status_code=404)
|
|
return StudySchema().dump(study)
|
|
|
|
|
|
def get_study_associates(study_id):
|
|
return StudyAssociatedSchema(many=True).dump(StudyService.get_study_associates(study_id))
|
|
|
|
|
|
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
|