def update(self, trans, encoded_folder_id, payload: dict):
"""
Update the folder defined by an ``encoded_folder_id``
with the data in the payload.
.. note:: Currently, only admin users can update library folders. Also the folder must not be `deleted`.
:param id: the encoded id of the folder
:type id: an encoded id string
:param payload: (required) dictionary structure containing::
'name': new folder's name, cannot be empty
'description': new folder's description
:type payload: dict
:returns: detailed folder information
:rtype: dict
:raises: RequestParameterMissingException
"""
decoded_folder_id = self.folder_manager.cut_and_decode(
trans, encoded_folder_id)
folder = self.folder_manager.get(trans, decoded_folder_id)
name = payload.get('name', None)
if not name:
raise RequestParameterMissingException(
"Parameter 'name' of library folder is required. You cannot remove it."
)
description = payload.get('description', None)
updated_folder = self.folder_manager.update(trans, folder, name,
description)
folder_dict = self.folder_manager.get_folder_dict(
trans, updated_folder)
return folder_dict
def create(self, trans, payload, **kwd):
"""
POST /api/groups
Return a dictionary of information about the created group.
The following parameters are included in the payload:
:param name (required): the name of the group
:param description (optional): the description of the group
Example: POST /api/groups/?key=XXXYYYXXXYYY
Content-Disposition: form-data; name="name" Group_Name
Content-Disposition: form-data; name="description" Group_Description
"""
group_dict = dict(message='', status='ok')
name = payload.get('name', '')
if name:
description = payload.get('description', '')
if not description:
description = ''
else:
# TODO add description field to the model
group_dict = self.group_manager.create(
trans, name=name).to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
else:
raise RequestParameterMissingException(
'Missing required parameter "name".')
return group_dict
def create(self, trans, encoded_parent_folder_id, payload: dict):
"""
Create a new folder object underneath the one specified in the parameters.
:param encoded_parent_folder_id: (required) the parent folder's id
:type encoded_parent_folder_id: an encoded id string (should be prefixed by 'F')
:param payload: dictionary structure containing:
:param name: (required) the name of the new folder
:type name: str
:param description: the description of the new folder
:type description: str
:type dictionary
:returns: information about newly created folder, notably including ID
:rtype: dictionary
:raises: RequestParameterMissingException
"""
name = payload.get('name', None)
if name is None:
raise RequestParameterMissingException(
"Missing required parameter 'name'.")
description = payload.get('description', '')
decoded_parent_folder_id = self.folder_manager.cut_and_decode(
trans, encoded_parent_folder_id)
parent_folder = self.folder_manager.get(trans,
decoded_parent_folder_id)
new_folder = self.folder_manager.create(trans, parent_folder.id, name,
description)
return self.folder_manager.get_folder_dict(trans, new_folder)
def _parse_dependency_info(self, kwds):
extra_kwds = kwds.copy()
name = extra_kwds.pop("name", None)
if name is None:
raise RequestParameterMissingException("Missing 'name' parameter required for resolution.")
version = extra_kwds.pop("version", None)
type = extra_kwds.pop("type", "package")
return name, version, type, extra_kwds
def update( self, trans, id, **kwd ):
"""
PATCH /api/repositories/{encoded_repository_id}
Updates information about a repository in the Tool Shed.
:param id: the encoded id of the Repository object
:param payload: dictionary structure containing::
'name': repo's name (optional)
'synopsis': repo's synopsis (optional)
'description': repo's description (optional)
'remote_repository_url': repo's remote repo (optional)
'homepage_url': repo's homepage url (optional)
'category_ids': list of existing encoded TS category ids
the updated repo should be associated with (optional)
:type payload: dict
:returns: detailed repository information
:rtype: dict
:raises: RequestParameterInvalidException, InsufficientPermissionsException
"""
payload = kwd.get( 'payload', None )
if not payload:
raise RequestParameterMissingException( "You did not specify any payload." )
name = payload.get( 'name', None )
synopsis = payload.get( 'synopsis', None )
description = payload.get( 'description', None )
remote_repository_url = payload.get( 'remote_repository_url', None )
homepage_url = payload.get( 'homepage_url', None )
category_ids = payload.get( 'category_ids', None )
if category_ids is not None:
# We need to know if it was actually passed, and listify turns None into []
category_ids = util.listify( category_ids )
update_kwds = dict(
name=name,
description=synopsis,
long_description=description,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url,
category_ids=category_ids,
)
repo, message = repository_util.update_repository( app=trans.app, trans=trans, id=id, **update_kwds )
if repo is None:
if "You are not the owner" in message:
raise InsufficientPermissionsException( message )
else:
raise ActionInputError( message )
repository_dict = repo.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) )
repository_dict[ 'category_ids' ] = \
[ trans.security.encode_id( x.category.id ) for x in repo.categories ]
return repository_dict
def replace_file_srcs(request_part):
if isinstance(request_part, dict):
if request_part.get("src", None) == "files":
path_def = next(files_iter)
if path_def is None or path_def["file_data"] is None:
raise RequestParameterMissingException("Failed to find uploaded file matching target with src='files'")
request_part["path"] = path_def["file_data"]["local_filename"]
if "name" not in request_part:
request_part["name"] = path_def["file_data"]["filename"]
request_part["src"] = "path"
else:
for key, value in request_part.items():
replace_file_srcs(value)
elif isinstance(request_part, list):
for value in request_part:
replace_file_srcs(value)
def validation_error_to_message_exception(e):
invalid_found = False
missing_found = False
for error in e.errors():
if error["type"] == "value_error.missing" or error[
"type"] == "type_error.none.not_allowed":
missing_found = True
elif error["type"].startswith("type_error"):
invalid_found = True
if missing_found and not invalid_found:
return RequestParameterMissingException(str(e),
validation_errors=loads(
e.json()))
else:
return RequestParameterInvalidException(str(e),
validation_errors=loads(
e.json()))
def configure_provider(provider, credentials):
"""
Given a provider name and required credentials, it configures and returns a cloudbridge
connection to the provider.
:type provider: string
:param provider: the name of cloud-based resource provided. A list of supported providers is given in
`SUPPORTED_PROVIDERS` variable.
:type credentials: dict
:param credentials: a dictionary containing all the credentials required to authenticated to the
specified provider.
:rtype: provider specific, e.g., `cloudbridge.cloud.providers.aws.provider.AWSCloudProvider` for AWS.
:return: a cloudbridge connection to the specified provider.
"""
missing_credentials = []
if provider == 'aws':
access = credentials.get('access_key', None)
if access is None:
access = credentials.get("AccessKeyId", None)
if access is None:
missing_credentials.append('access_key')
secret = credentials.get('secret_key', None)
if secret is None:
secret = credentials.get("SecretAccessKey", None)
if secret is None:
missing_credentials.append('secret_key')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
session_token = credentials.get("SessionToken")
config = {
'aws_access_key': access,
'aws_secret_key': secret,
"aws_session_token": session_token
}
connection = CloudProviderFactory().create_provider(
ProviderList.AWS, config)
elif provider == "azure":
subscription = credentials.get('subscription_id', None)
if subscription is None:
missing_credentials.append('subscription_id')
client = credentials.get('client_id', None)
if client is None:
missing_credentials.append('client_id')
secret = credentials.get('secret', None)
if secret is None:
missing_credentials.append('secret')
tenant = credentials.get('tenant', None)
if tenant is None:
missing_credentials.append('tenant')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
config = {
'azure_subscription_id': subscription,
'azure_client_id': client,
'azure_secret': secret,
'azure_tenant': tenant
}
storage_account = credentials.get("storage_account")
if storage_account:
config["azure_storage_account"] = storage_account
resource_group = credentials.get("resource_group")
if resource_group:
config["azure_resource_group"] = resource_group
connection = CloudProviderFactory().create_provider(
ProviderList.AZURE, config)
elif provider == "openstack":
username = credentials.get('username', None)
if username is None:
missing_credentials.append('username')
password = credentials.get('password', None)
if password is None:
missing_credentials.append('password')
auth_url = credentials.get('auth_url', None)
if auth_url is None:
missing_credentials.append('auth_url')
prj_name = credentials.get('project_name', None)
if prj_name is None:
missing_credentials.append('project_name')
prj_domain_name = credentials.get('project_domain_name', None)
if prj_domain_name is None:
missing_credentials.append('project_domain_name')
user_domain_name = credentials.get('user_domain_name', None)
if user_domain_name is None:
missing_credentials.append('user_domain_name')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
config = {
'os_username': username,
'os_password': password,
'os_auth_url': auth_url,
'os_project_name': prj_name,
'os_project_domain_name': prj_domain_name,
'os_user_domain_name': user_domain_name
}
connection = CloudProviderFactory().create_provider(
ProviderList.OPENSTACK, config)
elif provider == "gcp":
config = {"gcp_service_creds_dict": credentials}
connection = CloudProviderFactory().create_provider(
ProviderList.GCP, config)
else:
raise RequestParameterInvalidException(
"Unrecognized provider '{}'; the following are the supported "
"providers: {}.".format(provider, SUPPORTED_PROVIDERS.keys()))
# The authorization-assertion mechanism of Cloudbridge assumes a user has an elevated privileges,
# such as Admin-level access to all resources (see https://github.com/CloudVE/cloudbridge/issues/135).
# As a result, a user who wants to authorize Galaxy to read/write an Amazon S3 bucket, need to
# also authorize Galaxy with full permission to Amazon EC2 (because Cloudbridge leverages EC2-specific
# operation to assert credentials). While the EC2 authorization is not required by Galaxy to
# read/write a S3 bucket, it can cause this exception.
#
# Until Cloudbridge implements an authorization-specific credentials assertion, we are not asserting
# the authorization/validity of the credentials, in order to avoid asking users to grant Galaxy with an
# elevated, yet unnecessary, privileges.
#
# Note, if user's credentials are invalid/expired to perform the authorized action, that can cause
# exceptions which we capture separately in related read/write attempts.
return connection
def create( self, trans, **kwd ):
"""
create( self, trans, payload, **kwd )
* POST /api/repositories:
Creates a new repository.
Only ``name`` and ``synopsis`` parameters are required.
:param payload: dictionary structure containing::
'name': new repo's name (required)
'synopsis': new repo's synopsis (required)
'description': new repo's description (optional)
'remote_repository_url': new repo's remote repo (optional)
'homepage_url': new repo's homepage url (optional)
'category_ids[]': list of existing encoded TS category ids
the new repo should be associated with (optional)
'type': new repo's type, defaults to ``unrestricted`` (optional)
:type payload: dict
:returns: detailed repository information
:rtype: dict
:raises: RequestParameterMissingException, RequestParameterInvalidException
"""
payload = kwd.get( 'payload', None )
if not payload:
raise RequestParameterMissingException( "You did not specify any payload." )
name = payload.get( 'name', None )
if not name:
raise RequestParameterMissingException( "Missing required parameter 'name'." )
synopsis = payload.get( 'synopsis', None )
if not synopsis:
raise RequestParameterMissingException( "Missing required parameter 'synopsis'." )
description = payload.get( 'description', '' )
remote_repository_url = payload.get( 'remote_repository_url', '' )
homepage_url = payload.get( 'homepage_url', '' )
category_ids = util.listify( payload.get( 'category_ids[]', '' ) )
selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
repo_type = payload.get( 'type', rt_util.UNRESTRICTED )
if repo_type not in rt_util.types:
raise RequestParameterInvalidException( 'This repository type is not valid' )
invalid_message = repository_util.validate_repository_name( trans.app, name, trans.user )
if invalid_message:
raise RequestParameterInvalidException( invalid_message )
repo, message = repository_util.create_repository( app=trans.app,
name=name,
type=repo_type,
description=synopsis,
long_description=description,
user_id = trans.user.id,
category_ids=category_ids,
remote_repository_url=remote_repository_url,
homepage_url=homepage_url )
repository_dict = repo.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) )
repository_dict[ 'category_ids' ] = \
[ trans.security.encode_id( x.category.id ) for x in repo.categories ]
return repository_dict
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))
def set_permissions(self, trans, encoded_folder_id: EncodedDatabaseIdField,
payload: dict) -> LibraryFolderCurrentPermissions:
"""
Set permissions of the given folder to the given role ids.
:param encoded_folder_id: the encoded id of the folder to set the permissions of
:type encoded_folder_id: an encoded id string
:param payload: dictionary structure containing:
:param action: (required) describes what action should be performed
:type action: string
:param add_ids[]: list of Role.id defining roles that should have add item permission on the folder
:type add_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder
:type modify_ids[]: string or list
:type dictionary
:returns: dict of current roles for all available permission types.
:rtype: dictionary
:raises: RequestParameterInvalidException, InsufficientPermissionsException, RequestParameterMissingException
"""
is_admin = trans.user_is_admin
current_user_roles = trans.get_current_user_roles()
decoded_folder_id = self.folder_manager.cut_and_decode(
trans, encoded_folder_id)
folder = self.folder_manager.get(trans, decoded_folder_id)
if not (is_admin or trans.app.security_agent.can_manage_library_item(
current_user_roles, folder)):
raise InsufficientPermissionsException(
'You do not have proper permission to modify permissions of this folder.'
)
new_add_roles_ids = util.listify(payload.get('add_ids[]', None))
new_manage_roles_ids = util.listify(payload.get('manage_ids[]', None))
new_modify_roles_ids = util.listify(payload.get('modify_ids[]', None))
action = payload.get('action', None)
if action is None:
raise RequestParameterMissingException(
'The mandatory parameter "action" is missing.')
elif action == 'set_permissions':
# ADD TO LIBRARY ROLES
valid_add_roles = []
invalid_add_roles_names = []
for role_id in new_add_roles_ids:
role = self.role_manager.get(
trans, trans.security.decode_id(role_id,
object_name='role'))
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles(
trans, folder)
if role in valid_roles:
valid_add_roles.append(role)
else:
invalid_add_roles_names.append(role_id)
if len(invalid_add_roles_names) > 0:
log.warning(
f"The following roles could not be added to the add library item permission: {str(invalid_add_roles_names)}"
)
# MANAGE FOLDER ROLES
valid_manage_roles = []
invalid_manage_roles_names = []
for role_id in new_manage_roles_ids:
role = self.role_manager.get(
trans, trans.security.decode_id(role_id,
object_name='role'))
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles(
trans, folder)
if role in valid_roles:
valid_manage_roles.append(role)
else:
invalid_manage_roles_names.append(role_id)
if len(invalid_manage_roles_names) > 0:
log.warning(
f"The following roles could not be added to the manage folder permission: {str(invalid_manage_roles_names)}"
)
# MODIFY FOLDER ROLES
valid_modify_roles = []
invalid_modify_roles_names = []
for role_id in new_modify_roles_ids:
role = self.role_manager.get(
trans, trans.security.decode_id(role_id,
object_name='role'))
# Check whether role is in the set of allowed roles
valid_roles, total_roles = trans.app.security_agent.get_valid_roles(
trans, folder)
if role in valid_roles:
valid_modify_roles.append(role)
else:
invalid_modify_roles_names.append(role_id)
if len(invalid_modify_roles_names) > 0:
log.warning(
f"The following roles could not be added to the modify folder permission: {str(invalid_modify_roles_names)}"
)
permissions = {
trans.app.security_agent.permitted_actions.LIBRARY_ADD:
valid_add_roles
}
permissions.update({
trans.app.security_agent.permitted_actions.LIBRARY_MANAGE:
valid_manage_roles
})
permissions.update({
trans.app.security_agent.permitted_actions.LIBRARY_MODIFY:
valid_modify_roles
})
trans.app.security_agent.set_all_library_permissions(
trans, folder, permissions)
else:
raise RequestParameterInvalidException(
'The mandatory parameter "action" has an invalid value.'
'Allowed values are: "set_permissions"')
current_permissions = self.folder_manager.get_current_roles(
trans, folder)
return LibraryFolderCurrentPermissions.parse_obj(current_permissions)
def _configure_provider(provider, credentials):
"""
Given a provider name and required credentials, it configures and returns a cloudbridge
connection to the provider.
:type provider: string
:param provider: the name of cloud-based resource provided. A list of supported providers is given in
`SUPPORTED_PROVIDERS` variable.
:type credentials: dict
:param credentials: a dictionary containing all the credentials required to authenticated to the
specified provider.
:rtype: provider specific, e.g., `cloudbridge.cloud.providers.aws.provider.AWSCloudProvider` for AWS.
:return: a cloudbridge connection to the specified provider.
"""
missing_credentials = []
if provider == 'aws':
access = credentials.get('access_key', None)
if access is None:
missing_credentials.append('access_key')
secret = credentials.get('secret_key', None)
if secret is None:
missing_credentials.append('secret_key')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
config = {'aws_access_key': access, 'aws_secret_key': secret}
connection = CloudProviderFactory().create_provider(
ProviderList.AWS, config)
elif provider == "azure":
subscription = credentials.get('subscription_id', None)
if subscription is None:
missing_credentials.append('subscription_id')
client = credentials.get('client_id', None)
if client is None:
missing_credentials.append('client_id')
secret = credentials.get('secret', None)
if secret is None:
missing_credentials.append('secret')
tenant = credentials.get('tenant', None)
if tenant is None:
missing_credentials.append('tenant')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
config = {
'azure_subscription_id': subscription,
'azure_client_id': client,
'azure_secret': secret,
'azure_tenant': tenant
}
connection = CloudProviderFactory().create_provider(
ProviderList.AZURE, config)
elif provider == "openstack":
username = credentials.get('username', None)
if username is None:
missing_credentials.append('username')
password = credentials.get('password', None)
if password is None:
missing_credentials.append('password')
auth_url = credentials.get('auth_url', None)
if auth_url is None:
missing_credentials.append('auth_url')
prj_name = credentials.get('project_name', None)
if prj_name is None:
missing_credentials.append('project_name')
prj_domain_name = credentials.get('project_domain_name', None)
if prj_domain_name is None:
missing_credentials.append('project_domain_name')
user_domain_name = credentials.get('user_domain_name', None)
if user_domain_name is None:
missing_credentials.append('user_domain_name')
if len(missing_credentials) > 0:
raise RequestParameterMissingException(
"The following required key(s) are missing from the provided "
"credentials object: {}".format(missing_credentials))
config = {
'os_username': username,
'os_password': password,
'os_auth_url': auth_url,
'os_project_name': prj_name,
'os_project_domain_name': prj_domain_name,
'os_user_domain_name': user_domain_name
}
connection = CloudProviderFactory().create_provider(
ProviderList.OPENSTACK, config)
else:
raise RequestParameterInvalidException(
"Unrecognized provider '{}'; the following are the supported "
"providers: {}.".format(provider, SUPPORTED_PROVIDERS))
try:
if connection.authenticate():
return connection
except ProviderConnectionException as e:
raise AuthenticationFailed(
"Could not authenticate to the '{}' provider. {}".format(
provider, e))