Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.managers.cloud
"""
Manager and serializer for cloud-based storages.
"""
import json
import logging
from galaxy import model
from galaxy import util
from galaxy.exceptions import (
ItemAccessibilityException,
MessageException,
ObjectNotFound,
RequestParameterInvalidException,
RequestParameterMissingException
)
from galaxy.managers import sharable
from galaxy.util import Params
try:
from cloudbridge.factory import CloudProviderFactory, ProviderList
except ImportError:
CloudProviderFactory = None
ProviderList = None
log = logging.getLogger(__name__)
NO_CLOUDBRIDGE_ERROR_MESSAGE = (
"Cloud ObjectStore is configured, but no CloudBridge dependency available."
"Please install CloudBridge or modify ObjectStore configuration."
)
# Any change to this list, MUST be reflected in the SEND_TOOL wrapper
# (tools/cloud/send.xml).
SUPPORTED_PROVIDERS = {"aws": 0, "azure": 1}
SEND_TOOL = "send_to_cloud"
SEND_TOOL_VERSION = "0.1.0"
# TODO: this configuration should be set in a config file.
SINGED_URL_TTL = 3600
[docs]class CloudManager(sharable.SharableModelManager):
# This manager does not manage a history; however,
# some of its functions require operations
# on history objects using methods from the base
# manager class (e.g., get_accessible), which requires
# setting this property.
model_class = model.History
[docs] @staticmethod
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
@staticmethod
def _get_inputs(obj, key, input_args):
space_to_tab = None
if input_args.get('space_to_tab', "").lower() == "true":
space_to_tab = "Yes"
elif input_args.get('space_to_tab', "").lower() not in ["false", ""]:
raise RequestParameterInvalidException(
"The valid values for `space_to_tab` argument are `true` and `false`; received {}".format(
input_args.get('space_to_tab')))
to_posix_lines = None
if input_args.get('to_posix_lines', "").lower() == "true":
to_posix_lines = "Yes"
elif input_args.get('to_posix_lines', "").lower() not in ["false", ""]:
raise RequestParameterInvalidException(
"The valid values for `to_posix_lines` argument are `true` and `false`; received {}".format(
input_args.get('to_posix_lines')))
return {
'dbkey': input_args.get("dbkey", "?"),
'file_type': input_args.get("file_type", "auto"),
'files_0|type': 'upload_dataset',
'files_0|space_to_tab': space_to_tab,
'files_0|to_posix_lines': to_posix_lines,
'files_0|NAME': obj,
'files_0|url_paste': key.generate_url(expires_in=SINGED_URL_TTL),
}
[docs] def get(self, trans, history_id, bucket_name, objects, authz_id, input_args=None):
"""
Implements the logic of getting a file from a cloud-based storage (e.g., Amazon S3)
and persisting it as a Galaxy dataset.
This manager does NOT require use credentials, instead, it uses a more secure method,
which leverages CloudAuthz (https://github.com/galaxyproject/cloudauthz) and automatically
requests temporary credentials to access the defined resources.
:type trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
:param trans: Galaxy web transaction
:type history_id: string
:param history_id: the (decoded) id of history to which the object should be received to.
:type bucket_name: string
:param bucket_name: the name of a bucket from which data should be fetched (e.g., a bucket name on AWS S3).
:type objects: list of string
:param objects: the name of objects to be fetched.
:type authz_id: int
:param authz_id: the ID of CloudAuthz to be used for authorizing access to the resource provider. You may
get a list of the defined authorizations sending GET to `/api/cloud/authz`. Also, you can
POST to `/api/cloud/authz` to define a new authorization.
:type input_args: dict
:param input_args: a [Optional] a dictionary of input parameters:
dbkey, file_type, space_to_tab, to_posix_lines (see galaxy/webapps/galaxy/api/cloud.py)
:rtype: list of galaxy.model.Dataset
:return: a list of datasets created for the fetched files.
"""
if CloudProviderFactory is None:
raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
if input_args is None:
input_args = {}
if not hasattr(trans.app, 'authnz_manager'):
err_msg = "The OpenID Connect protocol, a required feature for getting data from cloud, " \
"is not enabled on this Galaxy instance."
log.debug(err_msg)
raise MessageException(err_msg)
cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
credentials = trans.app.authnz_manager.get_cloud_access_credentials(cloudauthz, trans.sa_session, trans.user.id, trans.request)
connection = self.configure_provider(cloudauthz.provider, credentials)
try:
bucket = connection.storage.buckets.get(bucket_name)
if bucket is None:
raise RequestParameterInvalidException(f"The bucket `{bucket_name}` not found.")
except Exception as e:
raise ItemAccessibilityException("Could not get the bucket `{}`: {}".format(bucket_name, util.unicodify(e)))
datasets = []
for obj in objects:
try:
key = bucket.objects.get(obj)
except Exception as e:
raise MessageException("The following error occurred while getting the object {}: {}".format(obj, util.unicodify(e)))
if key is None:
log.exception(
"Could not get object `{}` for user `{}`. Object may not exist, or the provided credentials are "
"invalid or not authorized to read the bucket/object.".format(obj, trans.user.id))
raise ObjectNotFound(
"Could not get the object `{}`. Please check if the object exists, and credentials are valid and "
"authorized to read the bucket and object. ".format(obj))
params = Params(self._get_inputs(obj, key, input_args), sanitize=False)
incoming = params.__dict__
history = trans.sa_session.query(trans.app.model.History).get(history_id)
if not history:
raise ObjectNotFound("History with ID `{}` not found.".format(trans.app.security.encode_id(history_id)))
output = trans.app.toolbox.get_tool('upload1').handle_input(trans, incoming, history=history)
job_errors = output.get('job_errors', [])
if job_errors:
raise ValueError('Following error occurred while getting the given object(s) from {}: {}'.format(
cloudauthz.provider, job_errors))
else:
for d in output['out_data']:
datasets.append(d[1].dataset)
return datasets
[docs] def send(self, trans, history_id, bucket_name, authz_id, dataset_ids=None, overwrite_existing=False):
"""
Implements the logic of sending dataset(s) from a given history to a given cloud-based storage
(e.g., Amazon S3).
:type trans: galaxy.webapps.base.webapp.GalaxyWebTransaction
:param trans: Galaxy web transaction
:type history_id: string
:param history_id: the (encoded) id of history from which the object should be sent.
:type bucket_name: string
:param bucket_name: the name of a bucket to which data should be sent (e.g., a bucket
name on AWS S3).
:type authz_id: int
:param authz_id: the ID of CloudAuthz to be used for authorizing access to the resource provider.
You may get a list of the defined authorizations via `/api/cloud/authz`. Also,
you can use `/api/cloud/authz/create` to define a new authorization.
:type dataset_ids: set
:param dataset_ids: [Optional] The list of (decoded) dataset ID(s) belonging to the given
history which should be sent to the given provider. If not provided,
Galaxy sends all the datasets belonging to the given history.
:type overwrite_existing: boolean
:param overwrite_existing: [Optional] If set to "True", and an object with same name of the
dataset to be sent already exist in the bucket, Galaxy replaces
the existing object with the dataset to be sent. If set to
"False", Galaxy appends datetime to the dataset name to prevent
overwriting the existing object.
:rtype: tuple
:return: A tuple of two lists of labels of the objects that were successfully and
unsuccessfully sent to cloud.
"""
if CloudProviderFactory is None:
raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
if not hasattr(trans.app, 'authnz_manager'):
err_msg = "The OpenID Connect protocol, a required feature for sending data to cloud, " \
"is not enabled on this Galaxy instance."
log.debug(err_msg)
raise MessageException(err_msg)
cloudauthz = trans.app.authnz_manager.try_get_authz_config(trans.sa_session, trans.user.id, authz_id)
history = trans.sa_session.query(trans.app.model.History).get(history_id)
if not history:
raise ObjectNotFound("History with ID `{}` not found.".format(trans.app.security.encode_id(history_id)))
sent = []
failed = []
for hda in history.datasets:
if hda.deleted or hda.purged or hda.state != "ok" or hda.creating_job.tool_id == SEND_TOOL:
continue
if dataset_ids is None or hda.dataset.id in dataset_ids:
try:
object_label = hda.name.replace(" ", "_")
args = {
# We encode ID here because the tool wrapper expects
# an encoded ID and attempts decoding it.
"authz_id": trans.security.encode_id(cloudauthz.id),
"bucket": bucket_name,
"object_label": object_label,
"filename": hda,
"overwrite_existing": overwrite_existing
}
incoming = (util.Params(args, sanitize=False)).__dict__
d2c = trans.app.toolbox.get_tool(SEND_TOOL, SEND_TOOL_VERSION)
if not d2c:
log.debug(f"Failed to get the `send` tool per user `{trans.user.id}` request.")
failed.append(json.dumps(
{
"object": object_label,
"error": "Unable to get the `send` tool."
}))
continue
res = d2c.execute(trans, incoming, history=history)
job = res[0]
sent.append(json.dumps(
{
"object": object_label,
"job_id": trans.app.security.encode_id(job.id)
}))
except Exception as e:
err_msg = "maybe invalid or unauthorized credentials. {}".format(util.unicodify(e))
log.debug("Failed to send the dataset `{}` per user `{}` request to cloud, {}".format(
object_label, trans.user.id, err_msg))
failed.append(json.dumps(
{
"object": object_label,
"error": err_msg
}))
return sent, failed