Source code for galaxy.objectstore.s3

"""
Object Store plugin for the Amazon Simple Storage Service (S3)
"""

import logging
import os
import time
from datetime import datetime

try:
    # Imports are done this way to allow objectstore code to be used outside of Galaxy.
    import boto
    from boto.exception import S3ResponseError
    from boto.s3.connection import S3Connection
    from boto.s3.key import Key
except ImportError:
    boto = None  # type: ignore[assignment]

from galaxy.util import string_as_bool
from ._caching_base import CachingConcreteObjectStore
from ._util import UsesAxel
from .caching import (
    enable_cache_monitor,
    parse_caching_config_dict_from_xml,
)
from .s3_multipart_upload import multipart_upload

NO_BOTO_ERROR_MESSAGE = (
    "S3/Swift object store configured, but no boto dependency available."
    "Please install and properly configure boto or modify object store configuration."
)

log = logging.getLogger(__name__)
logging.getLogger("boto").setLevel(logging.INFO)  # Otherwise boto is quite noisy


[docs]def download_directory(bucket, remote_folder, local_path): # List objects in the specified S3 folder objects = bucket.list(prefix=remote_folder) for obj in objects: remote_file_path = obj.key local_file_path = os.path.join(local_path, os.path.relpath(remote_file_path, remote_folder)) # Create directories if they don't exist os.makedirs(os.path.dirname(local_file_path), exist_ok=True) # Download the file obj.get_contents_to_filename(local_file_path)
[docs]def parse_config_xml(config_xml): try: a_xml = config_xml.findall("auth")[0] access_key = a_xml.get("access_key") secret_key = a_xml.get("secret_key") b_xml = config_xml.findall("bucket")[0] bucket_name = b_xml.get("name") use_rr = string_as_bool(b_xml.get("use_reduced_redundancy", "False")) max_chunk_size = int(b_xml.get("max_chunk_size", 250)) cn_xml = config_xml.findall("connection") if not cn_xml: cn_xml = {} else: cn_xml = cn_xml[0] host = cn_xml.get("host", None) port = int(cn_xml.get("port", 6000)) multipart = string_as_bool(cn_xml.get("multipart", "True")) is_secure = string_as_bool(cn_xml.get("is_secure", "True")) conn_path = cn_xml.get("conn_path", "/") region = cn_xml.get("region", None) 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] config_dict = { "auth": { "access_key": access_key, "secret_key": secret_key, }, "bucket": { "name": bucket_name, "use_reduced_redundancy": use_rr, "max_chunk_size": max_chunk_size, }, "connection": { "host": host, "port": port, "multipart": multipart, "is_secure": is_secure, "conn_path": conn_path, "region": region, }, "cache": cache_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 CloudConfigMixin: def _config_to_dict(self): return { "auth": { "access_key": self.access_key, "secret_key": self.secret_key, }, "bucket": { "name": self.bucket, "use_reduced_redundancy": self.use_rr, }, "connection": { "host": self.host, "port": self.port, "multipart": self.multipart, "is_secure": self.is_secure, "conn_path": self.conn_path, "region": self.region, }, "cache": { "size": self.cache_size, "path": self.staging_path, "cache_updated_data": self.cache_updated_data, }, }
[docs]class S3ObjectStore(CachingConcreteObjectStore, CloudConfigMixin, UsesAxel): """ Object store that stores objects as items in an AWS S3 bucket. A local cache exists that is used as an intermediate location for files between Galaxy and S3. """ store_type = "aws_s3" cloud = True
[docs] def __init__(self, config, config_dict): super().__init__(config, config_dict) self.cache_monitor = None self.transfer_progress = 0 auth_dict = config_dict["auth"] bucket_dict = config_dict["bucket"] connection_dict = config_dict.get("connection", {}) cache_dict = config_dict.get("cache") or {} self.enable_cache_monitor, self.cache_monitor_interval = enable_cache_monitor(config, config_dict) self.access_key = auth_dict.get("access_key") self.secret_key = auth_dict.get("secret_key") self.bucket = bucket_dict.get("name") self.use_rr = bucket_dict.get("use_reduced_redundancy", False) self.max_chunk_size = bucket_dict.get("max_chunk_size", 250) self.host = connection_dict.get("host", None) self.port = connection_dict.get("port", 6000) self.multipart = connection_dict.get("multipart", True) self.is_secure = connection_dict.get("is_secure", True) self.conn_path = connection_dict.get("conn_path", "/") self.region = connection_dict.get("region", None) 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) extra_dirs = {e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])} self.extra_dirs.update(extra_dirs) self._initialize()
def _initialize(self): if boto is None: raise Exception(NO_BOTO_ERROR_MESSAGE) # for multipart upload self.s3server = { "access_key": self.access_key, "secret_key": self.secret_key, "is_secure": self.is_secure, "max_chunk_size": self.max_chunk_size, "host": self.host, "port": self.port, "use_rr": self.use_rr, "conn_path": self.conn_path, } self._ensure_staging_path_writable() self._configure_connection() self._bucket = self._get_bucket(self.bucket) self._start_cache_monitor_if_needed() self._init_axel() def _configure_connection(self): log.debug("Configuring S3 Connection") # If access_key is empty use default credential chain if self.access_key: if self.region: # If specify a region we can infer a host and turn on SIGV4. # https://stackoverflow.com/questions/26744712/s3-using-boto-and-sigv4-missing-host-parameter # Turning on SIGV4 is needed for AWS regions created after 2014... from # https://docs.aws.amazon.com/AmazonS3/latest/API/sig-v4-authenticating-requests.html: # # "Amazon S3 supports Signature Version 4, a protocol for authenticating inbound API requests to AWS services, # in all AWS Regions. At this time, AWS Regions created before January 30, 2014 will continue to support the # previous protocol, Signature Version 2. Any new Regions after January 30, 2014 will support only Signature # Version 4 and therefore all requests to those Regions must be made with Signature Version 4." os.environ["S3_USE_SIGV4"] = "True" self.conn = S3Connection(self.access_key, self.secret_key, host=f"s3.{self.region}.amazonaws.com") else: # See notes above, this path through the code will not work for # newer regions. self.conn = S3Connection(self.access_key, self.secret_key) else: self.conn = S3Connection()
[docs] @classmethod def parse_xml(clazz, config_xml): return parse_config_xml(config_xml)
[docs] def to_dict(self): as_dict = super().to_dict() as_dict.update(self._config_to_dict()) return as_dict
def _get_bucket(self, bucket_name): """Sometimes a handle to a bucket is not established right away so try it a few times. Raise error is connection is not established.""" last_error = None for i in range(5): try: bucket = self.conn.get_bucket(bucket_name) log.debug("Using cloud object store with bucket '%s'", bucket.name) return bucket except S3ResponseError as e: last_error = e try: log.debug("Bucket not found, creating s3 bucket with handle '%s'", bucket_name) self.conn.create_bucket(bucket_name) except S3ResponseError: log.exception("Could not get bucket '%s', attempt %s/5", bucket_name, i + 1) time.sleep(2) # All the attempts have been exhausted and connection was not established, # raise error if last_error: raise last_error else: raise Exception("Failed to connect to target object store.") def _get_transfer_progress(self): return self.transfer_progress def _get_remote_size(self, rel_path): try: key = self._bucket.get_key(rel_path) return key.size except (S3ResponseError, AttributeError): log.exception("Could not get size of key '%s' from S3", rel_path) return -1 def _exists_remotely(self, rel_path): exists = False try: # A hackish way of testing if the rel_path is a folder vs a file is_dir = rel_path[-1] == "/" if is_dir: keyresult = self._bucket.get_all_keys(prefix=rel_path) if len(keyresult) > 0: exists = True else: exists = False else: key = Key(self._bucket, rel_path) exists = key.exists() except S3ResponseError: log.exception("Trouble checking existence of S3 key '%s'", rel_path) return False return exists def _transfer_cb(self, complete, total): self.transfer_progress += 10 def _download(self, rel_path): local_destination = self._get_cache_path(rel_path) try: log.debug("Pulling key '%s' into cache to %s", rel_path, local_destination) key = self._bucket.get_key(rel_path) if key is None: message = f"Attempting to download an invalid key for path {rel_path}." log.critical(message) raise Exception(message) remote_size = key.size if not self._caching_allowed(rel_path, remote_size): return False if self.use_axel: log.debug("Parallel pulled key '%s' into cache to %s", rel_path, local_destination) url = key.generate_url(7200) return self._axel_download(url, local_destination) else: log.debug("Pulled key '%s' into cache to %s", rel_path, local_destination) self.transfer_progress = 0 # Reset transfer progress counter key.get_contents_to_filename(local_destination, cb=self._transfer_cb, num_cb=10) return True except S3ResponseError: log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self._bucket.name) return False def _push_to_storage(self, rel_path, source_file=None, from_string=None): """ Push the file pointed to by ``rel_path`` to the object store naming the key ``rel_path``. If ``source_file`` is provided, push that file instead while still using ``rel_path`` as the key name. If ``from_string`` is provided, set contents of the file to the value of the string. """ try: source_file = source_file if source_file else self._get_cache_path(rel_path) if os.path.exists(source_file): key = Key(self._bucket, rel_path) if os.path.getsize(source_file) == 0 and key.exists(): log.debug( "Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path ) return True if from_string: key.set_contents_from_string(from_string, reduced_redundancy=self.use_rr) log.debug("Pushed data from string '%s' to key '%s'", from_string, rel_path) else: start_time = datetime.now() log.debug( "Pushing cache file '%s' of size %s bytes to key '%s'", source_file, os.path.getsize(source_file), rel_path, ) mb_size = os.path.getsize(source_file) / 1e6 if mb_size < 10 or (not self.multipart): self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename( source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10 ) else: multipart_upload(self.s3server, self._bucket, key.name, source_file, mb_size) end_time = datetime.now() log.debug( "Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)", source_file, rel_path, os.path.getsize(source_file), end_time - start_time, ) return True else: log.error( "Tried updating key '%s' from source file '%s', but source file does not exist.", rel_path, source_file, ) except S3ResponseError: log.exception("Trouble pushing S3 key '%s' from file '%s'", rel_path, source_file) raise return False def _delete_remote_all(self, rel_path: str) -> bool: try: results = self._bucket.get_all_keys(prefix=rel_path) for key in results: log.debug("Deleting key %s", key.name) key.delete() return True except S3ResponseError: log.exception("Could not delete blob '%s' from S3", rel_path) return False def _delete_existing_remote(self, rel_path: str) -> bool: try: key = Key(self._bucket, rel_path) log.debug("Deleting key %s", key.name) key.delete() return True except S3ResponseError: log.exception("Could not delete blob '%s' from S3", rel_path) return False def _download_directory_into_cache(self, rel_path, cache_path): download_directory(self._bucket, rel_path, cache_path) def _get_object_url(self, obj, **kwargs): if self._exists(obj, **kwargs): rel_path = self._construct_path(obj, **kwargs) try: key = Key(self._bucket, rel_path) return key.generate_url(expires_in=86400) # 24hrs except S3ResponseError: log.exception("Trouble generating URL for dataset '%s'", rel_path) return None def _get_store_usage_percent(self, obj): return 0.0
[docs] def shutdown(self): self._shutdown_cache_monitor()
[docs]class GenericS3ObjectStore(S3ObjectStore): """ Object store that stores objects as items in a generic S3 (non AWS) bucket. A local cache exists that is used as an intermediate location for files between Galaxy and the S3 storage service. """ store_type = "generic_s3" def _configure_connection(self): log.debug("Configuring generic S3 Connection") self.conn = boto.connect_s3( aws_access_key_id=self.access_key, aws_secret_access_key=self.secret_key, is_secure=self.is_secure, host=self.host, port=self.port, calling_format=boto.s3.connection.OrdinaryCallingFormat(), path=self.conn_path, )