def refresh(self):
label_response = requests.get(
f'{COMPUTESERVER}/api/workflows/v1/{self.id}/labels')
if label_response.status_code == 404 or label_response.status_code == 400:
raise NotFoundException(
f'No job with id {self.id} found on jobserver.')
label_response.raise_for_status()
label_data = label_response.json()['labels']
job_response = requests.get(
f'{COMPUTESERVER}/api/workflows/v1/query?id={self.id}')
job_data = job_response.json()['results'][0] if len(
job_response.json()['results']) else {}
job_data.update(label_data)
self.owner_id = job_data['owner_id'] if 'owner_id' in job_data else None
self.owner = User.query.filter_by(id=job_data['owner_id']).first(
) if 'owner_id' in job_data else None
self.user_group = self.owner.primary_user_group if 'owner_id' in job_data else None
self.type = job_data['type'] if 'type' in job_data else None
self.submission = datetime.strptime(
job_data['submission'],
'%Y-%m-%dT%H:%M:%S.%fZ') if 'submission' in job_data else None
self.start = datetime.strptime(
job_data['start'],
'%Y-%m-%dT%H:%M:%S.%fZ') if 'start' in job_data else None
self.end = datetime.strptime(
job_data['end'],
'%Y-%m-%dT%H:%M:%S.%fZ') if 'end' in job_data else None
self.status = job_data['status'] if 'status' in job_data else None
self.active = True
def get_user_password_hash(email: str) -> str:
"""
Get the password hash for a user based on their email address
:param email:
:return:
"""
user = User.query.filter_by(email=email).first()
if user is None:
raise NotFoundException(f'No user with email {email}.')
return user.password
def get_user_by_email(email: str) -> User:
"""
Get the user record for a user based on their email address
:param email:
:return:
"""
user = User.query.filter_by(email=email).first()
if user is None:
raise NotFoundException(f'No user with email {email}')
return user
def get_user_group(user: User, user_group_id: int) -> UserGroup:
"""
Get a user group.
:param user
:param user_group_id:
:return:
"""
user_group = UserGroup.query.filter_by(id=user_group_id).first()
if user_group is None:
raise NotFoundException(f'No user group with id {user_group_id}')
if user_group.all_can_read or user in user_group.members:
return user_group
def get_collection(user: User, collection_id: int) -> Collection:
"""
Get the attributes and dataset information of a collection
:param user:
:param collection_id:
:return:
"""
collection = Collection.query.filter_by(id=collection_id).first()
if collection is None:
raise NotFoundException(f'No collection with id {collection_id}')
if is_read_permitted(user, collection):
return collection
raise AuthException(f'User {user.email} is not authorized to view collection {collection.id}')
def get_sample_group(user: User, group_id: int) -> SampleGroup:
"""
Get a sample group.
:param user:
:param group_id:
:return:
"""
sample_group = SampleGroup.query.filter_by(id=group_id).first()
if sample_group is None:
raise NotFoundException(f'Sample group with id {group_id} not found.')
if is_read_permitted(user, sample_group):
return sample_group
raise AuthException(f'User {user.email} is not authorized to view sample group {group_id}')
def get_workflow(user: User, workflow_id: int) -> Workflow:
"""
Get workflow metadata.
:param user:
:param workflow_id:
:return:
"""
workflow = Workflow.query.filter_by(id=workflow_id).first()
if workflow is None:
raise NotFoundException(f'No workflow with id {workflow_id}.')
if is_read_permitted(user, workflow):
return workflow
raise AuthException(
f'User {user.email} is not permitted to access workflow {workflow_id}')
def get_sample(user: User, sample_id: int) -> Sample:
"""
Get the attributes and dataset paths of the sample with sample_id
:param user:
:param sample_id:
:return:
"""
sample = Sample.query.filter_by(id=sample_id).first()
if sample is None:
raise NotFoundException(f'No sample with id {sample_id}')
if is_read_permitted(user, sample):
return sample
raise AuthException(
f'User {user.email} is not permitted to access sample {sample_id}')
def get_user(user: User, target_user_id: int) -> User:
"""
Get the record for one user
:param user:
:param target_user_id:
:return:
"""
target_user = User.query.filter_by(id=target_user_id).first()
if target_user is None:
raise NotFoundException(f'No user with id {target_user_id}.')
if is_read_permitted(user, target_user):
return target_user
raise AuthException(
f'User with id {target_user_id} does not exist or is not visible to {user.email}'
)
def get_external_file(user: User, external_file_id: int) -> ExternalFile:
"""
Get a record corresponding to an external file
:param user:
:param external_file_id:
:return:
"""
external_file = ExternalFile.query.filter_by(id=external_file_id).first()
if external_file is None:
raise NotFoundException(f'No external file with id {external_file_id}')
if is_read_permitted(user, external_file):
return external_file
raise AuthException(
f'User {user.id} is not authorized to view external file {external_file.id}'
)
def get_external_file_by_path(user: User, filename: str) -> ExternalFile:
"""
Get the external file record for the file with path filename
:param user:
:param filename:
:return:
"""
external_file = ExternalFile.query.filter_by(filename=filename).first()
if external_file is None:
raise NotFoundException(
f'No external file record exists for {filename}')
if is_read_permitted(user, external_file):
return external_file
raise AuthException(
f'User {user.id} is not authorized to view external file record for {filename}'
)
def render_submit_job():
try:
if request.args.get('workflow_id') is None:
raise NotFoundException(f'No workflow id provided')
current_user = get_current_user()
workflow = get_workflow(current_user, request.args.get('workflow_id'))
workflow_data = workflow.get_file_info()
if request.method == 'POST':
job_params, workflow_data, labels, options = prepare_job_params(workflow_data,
process_input_dict(request.form),
current_user, workflow.id)
job = start_job(workflow_data, job_params, current_user, 'analysis', labels, options)
return redirect(url_for('jobs.render_job', job_id=job.id))
page_data = SubmitFormData(current_user, workflow_data, f'Workflow {workflow.id}')
return render_template('pages/submit_job.html', page_data=page_data)
except Exception as e:
return handle_exception_browser(e)