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Source code for galaxy.objectstore.azure_blob
"""
Object Store plugin for the Microsoft Azure Block Blob Storage system
"""
import logging
import os
from datetime import (
datetime,
timedelta,
)
try:
from azure.common import AzureHttpError
from azure.storage.blob import (
BlobSasPermissions,
BlobServiceClient,
generate_blob_sas,
)
except ImportError:
BlobServiceClient = None # type: ignore[assignment,unused-ignore,misc]
from ._caching_base import CachingConcreteObjectStore
from .caching import (
enable_cache_monitor,
parse_caching_config_dict_from_xml,
)
NO_BLOBSERVICE_ERROR_MESSAGE = (
"ObjectStore configured, but no azure.storage.blob dependency available."
"Please install and properly configure azure.storage.blob or modify Object Store configuration."
)
log = logging.getLogger(__name__)
[docs]
def parse_config_xml(config_xml):
try:
auth_xml = config_xml.findall("auth")[0]
account_name = auth_xml.get("account_name")
account_key = auth_xml.get("account_key")
account_url = auth_xml.get("account_url")
container_xml = config_xml.find("container")
container_name = container_xml.get("name")
transfer_xml = config_xml.findall("transfer")
if not transfer_xml:
transfer_xml = {}
else:
transfer_xml = transfer_xml[0]
transfer_dict = {}
for key in [
"max_concurrency",
"download_max_concurrency",
"upload_max_concurrency",
"max_single_put_size",
"max_single_get_size",
"max_block_size",
]:
value = transfer_xml.get(key)
if transfer_xml.get(key) is not None:
transfer_dict[key] = value
cache_dict = parse_caching_config_dict_from_xml(config_xml)
tag, attrs = "extra_dir", ("type", "path")
extra_dirs = config_xml.findall(tag)
if not extra_dirs:
msg = f"No {tag} element in XML tree"
log.error(msg)
raise Exception(msg)
extra_dirs = [{k: e.get(k) for k in attrs} for e in extra_dirs]
auth = {
"account_name": account_name,
"account_key": account_key,
}
if account_url:
auth["account_url"] = account_url
config_dict = {
"auth": auth,
"container": {
"name": container_name,
},
"cache": cache_dict,
"transfer": transfer_dict,
"extra_dirs": extra_dirs,
"private": CachingConcreteObjectStore.parse_private_from_config_xml(config_xml),
}
name = config_xml.attrib.get("name", None)
if name is not None:
config_dict["name"] = name
device = config_xml.attrib.get("device", None)
config_dict["device"] = device
return config_dict
except Exception:
# Toss it back up after logging, we can't continue loading at this point.
log.exception("Malformed ObjectStore Configuration XML -- unable to continue")
raise
[docs]
class AzureBlobObjectStore(CachingConcreteObjectStore):
"""
Object store that stores objects as blobs in an Azure Blob Container. A local
cache exists that is used as an intermediate location for files between
Galaxy and Azure.
"""
store_type = "azure_blob"
cloud = True
[docs]
def __init__(self, config, config_dict):
super().__init__(config, config_dict)
auth_dict = config_dict["auth"]
container_dict = config_dict["container"]
cache_dict = config_dict.get("cache") or {}
self.enable_cache_monitor, self.cache_monitor_interval = enable_cache_monitor(config, config_dict)
self.account_name = auth_dict.get("account_name")
self.account_url = auth_dict.get("account_url")
self.account_key = auth_dict.get("account_key")
self.container_name = container_dict.get("name")
raw_transfer_dict = config_dict.get("transfer", {})
typed_transfer_dict = {}
for key in [
"max_concurrency",
"download_max_concurrency",
"upload_max_concurrency",
"max_single_put_size",
"max_single_get_size",
"max_block_size",
]:
value = raw_transfer_dict.get(key)
if value is not None:
typed_transfer_dict[key] = int(value)
self.transfer_dict = typed_transfer_dict
self.cache_size = cache_dict.get("size") or self.config.object_store_cache_size
self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
self.cache_updated_data = cache_dict.get("cache_updated_data", True)
self._initialize()
def _initialize(self):
if BlobServiceClient is None:
raise Exception(NO_BLOBSERVICE_ERROR_MESSAGE)
self._configure_connection()
self._ensure_staging_path_writable()
self._start_cache_monitor_if_needed()
[docs]
def to_dict(self):
as_dict = super().to_dict()
auth = {
"account_name": self.account_name,
"account_key": self.account_key,
}
if self.account_url:
auth["account_url"] = self.account_url
as_dict.update(
{
"auth": auth,
"container": {
"name": self.container_name,
},
"transfer": self.transfer_dict,
"cache": {
"size": self.cache_size,
"path": self.staging_path,
"cache_updated_data": self.cache_updated_data,
},
}
)
return as_dict
# config_xml is an ElementTree object.
def _configure_connection(self):
log.debug("Configuring Connection")
extra_kwds = {}
for key in [
"max_single_put_size",
"max_single_get_size",
"max_block_size",
]:
if key in self.transfer_dict:
extra_kwds[key] = self.transfer_dict[key]
if self.account_url:
# https://pypi.org/project/azure-storage-blob/
service = BlobServiceClient(
account_url=self.account_url,
credential={"account_name": self.account_name, "account_key": self.account_key},
**extra_kwds,
)
else:
service = BlobServiceClient(
account_url=f"https://{self.account_name}.blob.core.windows.net",
credential=self.account_key,
**extra_kwds,
)
self.service = service
def _get_remote_size(self, rel_path):
try:
properties = self._blob_client(rel_path).get_blob_properties()
size_in_bytes = properties.size
return size_in_bytes
except AzureHttpError:
log.exception("Could not get size of blob '%s' from Azure", rel_path)
return -1
def _blobs_from(self, rel_path):
return self.service.get_container_client(self.container_name).list_blobs(name_starts_with=rel_path)
def _exists_remotely(self, rel_path: str):
try:
is_dir = rel_path[-1] == "/"
if is_dir:
blobs = self._blobs_from(rel_path)
if blobs:
return True
else:
return False
else:
exists = self._blob_client(rel_path).exists()
except AzureHttpError:
log.exception("Trouble checking existence of Azure blob '%s'", rel_path)
return False
return exists
def _blob_client(self, rel_path: str):
return self.service.get_blob_client(self.container_name, rel_path)
def _download(self, rel_path):
local_destination = self._get_cache_path(rel_path)
try:
log.debug("Pulling '%s' into cache to %s", rel_path, local_destination)
if not self._caching_allowed(rel_path):
return False
else:
self._download_to_file(rel_path, local_destination)
return True
except AzureHttpError:
log.exception("Problem downloading '%s' from Azure", rel_path)
return False
def _download_to_file(self, rel_path, local_destination):
kwd = {}
max_concurrency = self.transfer_dict.get("download_max_concurrency") or self.transfer_dict.get(
"max_concurrency"
)
if max_concurrency is not None:
kwd["max_concurrency"] = max_concurrency
with open(local_destination, "wb") as f:
self._blob_client(rel_path).download_blob().download_to_stream(f, **kwd)
def _download_directory_into_cache(self, rel_path, cache_path):
blobs = self._blobs_from(rel_path)
for blob in blobs:
key = blob.name
local_file_path = os.path.join(cache_path, os.path.relpath(key, rel_path))
# Create directories if they don't exist
os.makedirs(os.path.dirname(local_file_path), exist_ok=True)
# Download the file
self._download_to_file(key, local_file_path)
def _push_string_to_path(self, rel_path: str, from_string: str) -> bool:
try:
self._blob_client(rel_path).upload_blob(from_string, overwrite=True)
return True
except AzureHttpError:
log.exception("Trouble pushing to Azure Blob '%s' from string", rel_path)
return False
def _push_file_to_path(self, rel_path: str, source_file: str) -> bool:
try:
with open(source_file, "rb") as f:
kwd = {}
max_concurrency = self.transfer_dict.get("upload_max_concurrency") or self.transfer_dict.get(
"max_concurrency"
)
if max_concurrency is not None:
kwd["max_concurrency"] = max_concurrency
self._blob_client(rel_path).upload_blob(f, overwrite=True, **kwd)
return True
except AzureHttpError:
log.exception("Trouble pushing to Azure Blob '%s' from file '%s'", rel_path, source_file)
return False
def _delete_remote_all(self, rel_path: str) -> bool:
try:
blobs = self._blobs_from(rel_path)
for blob in blobs:
log.debug("Deleting from Azure: %s", blob)
self._blob_client(blob.name).delete_blob()
return True
except AzureHttpError:
log.exception("Could not delete blob '%s' from Azure", rel_path)
return False
def _delete_existing_remote(self, rel_path: str) -> bool:
try:
self._blob_client(rel_path).delete_blob()
return True
except AzureHttpError:
log.exception("Could not delete blob '%s' from Azure", rel_path)
return False
def _get_object_url(self, obj, **kwargs):
if self._exists(obj, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
try:
url = self._blob_client(rel_path).url
# https://learn.microsoft.com/en-us/azure/storage/blobs/sas-service-create-python
token = generate_blob_sas(
account_name=self.account_name,
account_key=self.account_key,
container_name=self.container_name,
blob_name=rel_path,
permission=BlobSasPermissions(read=True),
expiry=datetime.utcnow() + timedelta(hours=1),
)
return f"{url}?{token}"
except AzureHttpError:
log.exception("Trouble generating URL for dataset '%s'", rel_path)
return None
def _get_store_usage_percent(self, obj):
# Percent used for Azure blob containers is effectively zero realistically.
# https://learn.microsoft.com/en-us/azure/storage/blobs/scalability-targets
return 0.0