def show( self, trans, id, **kwd ):
"""
GET /api/repositories/{encoded_repository_id}
Returns information about a repository in the Tool Shed.
Example URL: http://localhost:9009/api/repositories/f9cad7b01a472135
:param id: the encoded id of the Repository object
:type id: encoded str
:returns: detailed repository information
:rtype: dict
:raises: ObjectNotFound, MalformedId
"""
try:
trans.security.decode_id( id )
except Exception:
raise MalformedId( 'The given id is invalid.' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
if repository is None:
raise ObjectNotFound( 'Unable to locate repository for the given id.' )
repository_dict = repository.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
# TODO the following property would be better suited in the to_dict method
repository_dict[ 'category_ids' ] = \
[ trans.security.encode_id( x.category.id ) for x in repository.categories ]
return repository_dict
def delete(self, trans, encoded_authz_id, **kwargs):
"""
* DELETE /api/cloud/authz/{encoded_authz_id}
Deletes the CloudAuthz record with the given ``encoded_authz_id`` from database.
:type trans: galaxy.web.framework.webapp.GalaxyWebTransaction
:param trans: Galaxy web transaction
:type encoded_authz_id: string
:param encoded_authz_id: The encoded ID of the CloudAuthz record to be marked deleted.
:rtype JSON
:return The cloudauthz record marked as deleted, serialized as a JSON object.
"""
msg_template = "Rejected user `" + str(trans.user.id) + "`'s request to delete cloudauthz config because of {}."
try:
authz_id = self.decode_id(encoded_authz_id)
except Exception:
log.debug(msg_template.format("cannot decode authz_id `" + str(encoded_authz_id) + "`"))
raise MalformedId('Invalid `authz_id`!')
try:
cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
trans.sa_session.delete(cloudauthz)
trans.sa_session.flush()
log.debug('Deleted a cloudauthz record with id `{}` for the user id `{}` '.format(authz_id, str(trans.user.id)))
view = self.cloudauthz_serializer.serialize_to_view(cloudauthz, trans=trans, **self._parse_serialization_params(kwargs, 'summary'))
trans.response.status = '200'
return view
except Exception as e:
log.exception(msg_template.format("exception while deleting the cloudauthz record with "
"ID: `{}`.".format(encoded_authz_id)))
raise InternalServerError('An unexpected error has occurred while responding to the DELETE request of the '
'cloudauthz API.' + str(e))
def update(self, trans, encoded_authz_id, payload, **kwargs):
"""
* PUT /api/cloud/authz/{encoded_authz_id}
Updates the values for the cloudauthz configuration with the given ``encoded_authz_id``.
With this API only the following attributes of a cloudauthz configuration
can be updated: `authn_id`, `provider`, `config`, `deleted`.
:type trans: galaxy.web.framework.webapp.GalaxyWebTransaction
:param trans: Galaxy web transaction
:type encoded_authz_id: string
:param encoded_authz_id: The encoded ID of the CloudAuthz record to be updated.
:type payload: dict
:param payload: A dictionary structure containing the attributes to modified with their new values.
It can contain any number of the following attributes:
* provider: the cloud-based resource provider
to which this configuration belongs to.
* authn_id: the (encoded) ID of a third-party authentication of a user.
To have this ID, user must have logged-in to this Galaxy server
using third-party identity (e.g., Google), or has associated
their Galaxy account with a third-party OIDC-based identity.
See this page: https://galaxyproject.org/admin/authentication/
Note: A user can associate a cloudauthz record with their own
authentications only. If the given authentication with authn_id
belongs to a different user, Galaxy will throw the
ItemAccessibilityException exception.
* config: a dictionary containing all the configuration required to
request temporary credentials from the provider.
See the following page for details:
https://galaxyproject.org/cloud/authnz/
* deleted: a boolean type marking the specified cloudauthz as (un)deleted.
"""
msg_template = "Rejected user `" + str(trans.user.id) + "`'s request to delete cloudauthz config because of {}."
try:
authz_id = self.decode_id(encoded_authz_id)
except Exception:
log.debug(msg_template.format("cannot decode authz_id `" + str(encoded_authz_id) + "`"))
raise MalformedId('Invalid `authz_id`!')
try:
cloudauthz_to_update = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
self.cloudauthz_deserializer.deserialize(cloudauthz_to_update, payload, trans=trans)
self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view='summary')
return self.cloudauthz_serializer.serialize_to_view(cloudauthz_to_update, view='summary')
except MalformedId as e:
raise e
except Exception as e:
log.exception(msg_template.format("exception while updating the cloudauthz record with "
"ID: `{}`.".format(encoded_authz_id)))
raise InternalServerError('An unexpected error has occurred while responding to the PUT request of the '
'cloudauthz API.' + str(e))
def _remap(container, line):
id_match = re.search(ENCODED_ID_PATTERN, line)
object_id = None
if id_match:
object_id = id_match.group(2)
try:
decoded_id = trans.security.decode_id(object_id)
except Exception:
raise MalformedId("Invalid encoded ID %s" % object_id)
line = line.replace(id_match.group(), "%s=%d" % (id_match.group(1), decoded_id))
return (line, False)
def decode_folder_id(self, trans, encoded_folder_id):
"""
Decode the folder id given that it has already lost the prefixed 'F'.
:param encoded_folder_id: encoded id of the Folder object
:type encoded_folder_id: string
:returns: decoded Folder id
:rtype: int
:raises: MalformedId
"""
try:
decoded_id = trans.security.decode_id(encoded_folder_id)
except ValueError:
raise MalformedId("Malformed folder id ( %s ) specified, unable to decode" % (str(encoded_folder_id)))
return decoded_id
def cut_the_prefix(self, encoded_folder_id):
"""
Remove the prefix from the encoded folder id.
:param encoded_folder_id: encoded id of the Folder object with 'F' prepended
:type encoded_folder_id: string
:returns: encoded Folder id without the 'F' prefix
:rtype: string
:raises: MalformedId
"""
if ((len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith('F')):
cut_id = encoded_folder_id[1:]
else:
raise MalformedId('Malformed folder id ( %s ) specified, unable to decode.' % str(encoded_folder_id))
return cut_id
def deserialize_and_validate_authn_id(self, item, key, val, **context):
"""
Deserializes an authentication ID (authn_id), and asserts if the
current user can assume that authentication.
:type item: galaxy.model.CloudAuthz
:param item: an instance of cloudauthz
:type key: string
:param key: `authn_id` attribute of the cloudauthz object (i.e., the `item` param).
:type val: string
:param val: the value of `authn_id` attribute of the cloudauthz object (i.e., the `item` param).
:type context: dict
:param context: a dictionary object containing Galaxy `trans`.
:rtype: string
:return: decoded authentication ID.
"""
try:
decoded_authn_id = self.app.security.decode_id(val)
except Exception:
log.debug("cannot decode authz_id `" + str(val) + "`")
raise MalformedId("Invalid `authz_id` {}!".format(val))
trans = context.get("trans")
if trans is None:
log.debug(
"Not found expected `trans` when deserializing CloudAuthz.")
raise InternalServerError
try:
trans.app.authnz_manager.can_user_assume_authn(
trans, decoded_authn_id)
except Exception as e:
raise e
return decoded_authn_id
def create(self, trans, payload, **kwargs):
"""
* POST /api/cloud/authz
Request to store the payload as a cloudauthz (cloud authorization) configuration for a user.
:type trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
:param trans: Galaxy web transaction
:type payload: dict
:param payload: A dictionary structure containing the following keys:
* provider: the cloud-based resource provider to which this configuration belongs to.
* config: a dictionary containing all the configuration required to request temporary credentials
from the provider. See the following page for details:
https://galaxyproject.org/cloud/authnz/
* authn_id: the (encoded) ID of a third-party authentication of a user. To have this ID, user must
have logged-in to this Galaxy server using third-party identity (e.g., Google), or has
associated his/her Galaxy account with a third-party OIDC-based identity. See this page:
https://galaxyproject.org/admin/authentication/
* description: [Optional] a brief description for this configuration.
:param kwargs: empty dict
:rtype: dict
:return: a dictionary with the following kvp:
* status: HTTP response code
* message: A message complementary to the response code.
"""
msg_template = "Rejected user `" + str(
trans.user.id
) + "`'s request to create cloudauthz config because of {}."
if not isinstance(payload, dict):
raise ActionInputError(
'Invalid payload data type. The payload is expected to be a dictionary, but '
'received data of type `{}`.'.format(str(type(payload))))
missing_arguments = []
provider = payload.get('provider', None)
if provider is None:
missing_arguments.append('provider')
config = payload.get('config', None)
if config is None:
missing_arguments.append('config')
authn_id = payload.get('authn_id', None)
if authn_id is None and provider.lower() not in ["azure", "gcp"]:
missing_arguments.append('authn_id')
if len(missing_arguments) > 0:
log.debug(
msg_template.format(
"missing required config {}".format(missing_arguments)))
raise RequestParameterMissingException(
'The following required arguments are missing in the payload: '
'{}'.format(missing_arguments))
description = payload.get("description", "")
if not isinstance(config, dict):
log.debug(
msg_template.format(
"invalid config type `{}`, expect `dict`".format(
type(config))))
raise RequestParameterInvalidException(
'Invalid type for the required `config` variable; expect `dict` '
'but received `{}`.'.format(type(config)))
if authn_id:
try:
authn_id = self.decode_id(authn_id)
except Exception:
log.debug(
msg_template.format("cannot decode authn_id `" +
str(authn_id) + "`"))
raise MalformedId('Invalid `authn_id`!')
try:
trans.app.authnz_manager.can_user_assume_authn(trans, authn_id)
except Exception as e:
raise e
# No two authorization configuration with
# exact same key/value should exist.
for ca in trans.user.cloudauthzs:
if ca.equals(trans.user.id, provider, authn_id, config):
log.debug(
"Rejected user `{}`'s request to create cloud authorization because a similar config "
"already exists.".format(trans.user.id))
raise ActionInputError(
"A similar cloud authorization configuration is already defined."
)
try:
new_cloudauthz = self.cloudauthz_manager.create(
user_id=trans.user.id,
provider=provider,
config=config,
authn_id=authn_id,
description=description)
view = self.cloudauthz_serializer.serialize_to_view(
new_cloudauthz,
trans=trans,
**self._parse_serialization_params(kwargs, 'summary'))
log.debug(
'Created a new cloudauthz record for the user id `{}` '.format(
str(trans.user.id)))
return view
except Exception as e:
log.exception(
msg_template.format(
"exception while creating the new cloudauthz record"))
raise InternalServerError(
'An unexpected error has occurred while responding to the create request of the '
'cloudauthz API.' + unicodify(e))