def get(self, trans, decoded_group_id=None, name=None):
"""
Get the group from the DB based on its ID or name.
:param decoded_group_id: decoded group id
:type decoded_group_id: int
:returns: the requested group
:rtype: Group
"""
if decoded_group_id is None and name is None:
raise RequestParameterInvalidException(
'You must supply either ID or a name of the group.')
name_query = trans.sa_session.query(trans.app.model.Group).filter(
trans.app.model.Group.table.c.name == name)
id_query = trans.sa_session.query(trans.app.model.Group).filter(
trans.app.model.Group.table.c.id == decoded_group_id)
try:
group = id_query.one() if decoded_group_id else name_query.one()
except MultipleResultsFound:
raise InconsistentDatabase(
'Multiple groups found with the same identifier.')
except NoResultFound:
raise ObjectNotFound(
'No group found with the identifier provided.')
except Exception:
raise InternalServerError('Error loading from the database.')
return group
def get(self, trans, decoded_folder_id, check_manageable=False, check_accessible=True):
"""
Get the folder from the DB.
:param decoded_folder_id: decoded folder id
:type decoded_folder_id: int
:param check_manageable: flag whether the check that user can manage item
:type check_manageable: bool
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
:returns: the requested folder
:rtype: LibraryFolder
:raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
"""
try:
folder = trans.sa_session.query(trans.app.model.LibraryFolder).filter(trans.app.model.LibraryFolder.table.c.id == decoded_folder_id).one()
except MultipleResultsFound:
raise InconsistentDatabase('Multiple folders found with the same id.')
except NoResultFound:
raise RequestParameterInvalidException('No folder found with the id provided.')
except Exception as e:
raise InternalServerError('Error loading from the database.' + unicodify(e))
folder = self.secure(trans, folder, check_manageable, check_accessible)
return folder
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.webapps.base.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 = f"Rejected user `{str(trans.user.id)}`'s request to delete cloudauthz config because of {{}}."
try:
authz_id = self.decode_id(encoded_authz_id)
except MalformedId as e:
log.debug(msg_template.format(f"cannot decode authz_id `{encoded_authz_id}`"))
raise e
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(f'Deleted a cloudauthz record with id `{authz_id}` for the user 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.' + unicodify(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 index(self, trans, **kwds):
"""
GET /api/tools: returns a list of tools defined by parameters::
parameters:
in_panel - if true, tools are returned in panel structure,
including sections and labels
trackster - if true, only tools that are compatible with
Trackster are returned
q - if present search on the given query will be performed
tool_id - if present the given tool_id will be searched for
all installed versions
"""
# Read params.
in_panel = util.string_as_bool(kwds.get('in_panel', 'True'))
trackster = util.string_as_bool(kwds.get('trackster', 'False'))
q = kwds.get('q', '')
tool_id = kwds.get('tool_id', '')
# Find whether to search.
if q:
hits = self._search(q)
results = []
if hits:
for hit in hits:
tool = self._get_tool(hit)
if tool:
results.append(tool.id)
return results
# Find whether to detect.
if tool_id:
detected_versions = self._detect(trans, tool_id)
return detected_versions
# Return everything.
try:
return self.app.toolbox.to_dict(trans,
in_panel=in_panel,
trackster=trackster)
except Exception:
raise InternalServerError(
"Error: Could not convert toolbox to dictionary")
def get(self, trans, decoded_library_dataset_id, check_accessible=True):
"""
Get the library dataset from the DB.
:param decoded_library_dataset_id: decoded library dataset id
:type decoded_library_dataset_id: int
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
:returns: the requested library dataset
:rtype: galaxy.model.LibraryDataset
"""
try:
ld = trans.sa_session.query(trans.app.model.LibraryDataset).filter(trans.app.model.LibraryDataset.table.c.id == decoded_library_dataset_id).one()
except Exception as e:
raise InternalServerError('Error loading from the database.' + util.unicodify(e))
ld = self.secure(trans, ld, check_accessible)
return ld
def get(self, trans, decoded_repo_id):
"""
Get the repo from the DB.
:param decoded_repo_id: decoded repo id
:type decoded_repo_id: int
:returns: the requested repo
:rtype: Repository
"""
try:
repo = trans.sa_session.query(trans.app.model.Repository).filter(trans.app.model.Repository.table.c.id == decoded_repo_id).one()
except MultipleResultsFound:
raise InconsistentDatabase('Multiple repositories found with the same id.')
except NoResultFound:
raise RequestParameterInvalidException('No repository found with the id provided.')
except Exception:
raise InternalServerError('Error loading from the database.')
return repo
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))