def validate_path_upload(trans):
if not trans.app.config.allow_library_path_paste:
raise ConfigDoesNotAllowException(
'"allow_path_paste" is not set to True in the Galaxy configuration file'
)
if not trans.user_is_admin:
raise AdminRequiredException(
'Uploading files via filesystem paths can only be performed by administrators'
)
def get_url_paste_urls_or_filename(group_incoming,
override_name=None,
override_info=None):
url_paste_file = group_incoming.get('url_paste', None)
if url_paste_file is not None:
url_paste = open(url_paste_file, 'r').read()
def start_of_url(content):
start_of_url_paste = content.lstrip()[0:8].lower()
looks_like_url = False
for url_prefix in [
"http://", "https://", "ftp://", "file://"
]:
if start_of_url_paste.startswith(url_prefix):
looks_like_url = True
break
return looks_like_url
if start_of_url(url_paste):
url_paste = url_paste.replace('\r', '').split('\n')
for line in url_paste:
line = line.strip()
if line:
if not start_of_url(line):
continue # non-url line, ignore
if "file://" in line:
if not trans.user_is_admin:
raise AdminRequiredException()
elif not trans.app.config.allow_path_paste:
raise ConfigDoesNotAllowException()
upload_path = line[len("file://"):]
dataset_name = os.path.basename(upload_path)
else:
dataset_name = line
if override_name:
dataset_name = override_name
yield Bunch(type='url',
path=line,
name=dataset_name)
else:
dataset_name = 'Pasted Entry' # we need to differentiate between various url pastes here
if override_name:
dataset_name = override_name
yield Bunch(type='file',
path=url_paste_file,
name=dataset_name)
def index(self, trans, deleted=False, **kwd):
"""
GET /api/groups
Return a list of dictionaries that contain information about each Group.
:param deleted: flag used to include deleted groups
Example: GET localhost:9009/api/groups
"""
group_dicts = []
deleted = util.asbool(deleted)
if deleted and not trans.user_is_admin:
raise AdminRequiredException('Only administrators can query deleted groups.')
for group in self.group_manager.list(trans, deleted):
group_dicts.append(self._populate(trans, group))
return group_dicts
def get_admin_user(trans: SessionRequestContext = DependsOnTrans):
if not trans.user_is_admin:
raise AdminRequiredException(
require_admin_message(trans.app.config, trans.user))
return trans.user