def __init__(self, wf_input, current_user):
if wf_input['id'] in ('omics_url', 'omics_auth_token'):
self.editable = False
self.value = 'Set by Omics Dashboard'
else:
self.editable = True
self.value = wf_input['default'] if 'default' in wf_input else ''
self.id = wf_input['id']
if wf_input['type'].endswith('[]'):
self.input_type = wf_input['type'][:-2]
self.select_multiple = True
else:
self.input_type = wf_input['type']
self.select_multiple = False
self.label = wf_input['label'] if 'label' in wf_input else wf_input[
'id']
self.doc = wf_input['doc'] if 'doc' in wf_input else ''
self.select_options = []
if wf_input['type'].startswith('File'):
for collection in get_all_read_permitted_records(
current_user, Collection):
self.select_options.append(
SelectOption(
collection.filename,
f'Collection {collection.id}: {collection.name}'))
for external_file in get_all_read_permitted_records(
current_user, ExternalFile):
if external_file.file_exists():
self.select_options.append(
SelectOption(
external_file.filename,
f'External File {external_file.id}: {external_file.name}'
))
def render_create_user_group():
try:
current_user = get_current_user()
if request.method == 'POST':
data = {
'admin_ids':
[int(val) for val in request.form.getlist('admin_ids')],
'member_ids':
[int(val) for val in request.form.getlist('member_ids')],
'name':
request.form.get('name'),
'description':
request.form.get('description')
}
user_group = create_user_group(current_user, data)
return redirect(
url_for('user_groups.render_user_group',
user_group_id=user_group.id))
if request.method == 'GET':
selected_user_ids = {int(token) for token in request.args.get('sample_ids').strip('"').split(',')} \
if request.args.get('user_ids', '') else {}
selected_users = get_all_read_permitted_records(current_user, User)
return render_template('pages/create.html',
page_data=UserGroupCreateFormData(
current_user, selected_users))
except Exception as e:
return handle_exception_browser(e)
def get_samples(user: User, filter_by: Dict[str, Any] = None) -> List[Sample]:
"""
Get the attributes and dataset paths of all the samples to which the user with user_id has read access
:param user:
:return:
"""
return get_all_read_permitted_records(user, Sample, filter_by)
def get_workflows(user: User,
filter_by: Dict[str, Any] = None) -> List[Workflow]:
"""
Get a list of available saved workflows.
:param user:
:return:
"""
return get_all_read_permitted_records(user, Workflow, filter_by)
def get_all_collection_metadata(user: User) -> List[Dict[str, Any]]:
"""
Get the attributes of all collections a user is allowed to read.
:param user:
:return:
"""
return [get_collection_metadata(user, collection)
for collection in get_all_read_permitted_records(user, Collection)]
def get_collections(user: User, filter_by: Dict[str, Any] = None) -> List[Collection]:
"""
Get the attributes and dataset information of all collections a user is allowed to read.
:param user:
:param filter_by:
:return:
"""
return get_all_read_permitted_records(user, Collection, filter_by)
def get_sample_groups(user: User, filter_by: Dict[str, Any] = None) -> List[SampleGroup]:
"""
Get all sample groups visible to a user.
:param user:
:param filter_by:
:return:
"""
return get_all_read_permitted_records(user, SampleGroup, filter_by)
def get_analyses(user: User,
filter_by: Dict[str, Any] = None) -> List[Analysis]:
"""
Get all the analyses the user is allowed to view
:param user:
:param filter_by:
:return:
"""
return get_all_read_permitted_records(user, Analysis, filter_by)
def get_external_files(user: User,
filter_by: Dict[str, Any] = None) -> List[ExternalFile]:
"""
Get all the external files a user is permitted to read
:param user: A user (usually the currently authenticated user)
:param filter_by:
:return: All the external files the user is permitted to read
"""
return get_all_read_permitted_records(user, ExternalFile, filter_by)
def get_all_sample_metadata(user: User) -> List[Dict]:
"""
Get the attributes of all the samples to which the user with user_id has read access
:param user:
:return:
"""
return [
get_sample_metadata(user, sample)
for sample in get_all_read_permitted_records(user, Sample)
]
def get_attached_analyses(user: User,
collection: Collection) -> List[Analysis]:
"""
Get all analysis that a collection belongs to
:param user:
:param collection:
:return:
"""
if is_read_permitted(user, collection):
return get_all_read_permitted_records(user, collection.analyses)
raise AuthException(
f'User {user.email} not permitted to access collection {collection.id}'
)
def get_user_groups(user: User, filter_by: Dict[str, Any] = None) -> List[UserGroup]:
"""
Get a list of all user groups readable by user.
:return:
"""
return get_all_read_permitted_records(user, UserGroup, filter_by)
