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Source code for galaxy.objectstore.s3
"""
Object Store plugin for the Amazon Simple Storage Service (S3)
"""
import logging
import multiprocessing
import os
import shutil
import subprocess
import time
from datetime import datetime
from typing import Optional
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.exceptions import (
ObjectInvalid,
ObjectNotFound,
)
from galaxy.util import (
directory_hash_id,
string_as_bool,
umask_fix_perms,
unlink,
which,
)
from galaxy.util.path import safe_relpath
from . import ConcreteObjectStore
from .caching import (
CacheTarget,
enable_cache_monitor,
InProcessCacheMonitor,
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", "/")
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]
return {
"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,
},
"cache": cache_dict,
"extra_dirs": extra_dirs,
"private": ConcreteObjectStore.parse_private_from_config_xml(config_xml),
}
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,
},
"cache": {
"size": self.cache_size,
"path": self.staging_path,
"cache_updated_data": self.cache_updated_data,
},
}
[docs]class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
"""
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.
"""
cache_monitor: Optional[InProcessCacheMonitor] = None
store_type = "aws_s3"
[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.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._configure_connection()
self._bucket = self._get_bucket(self.bucket)
self.start_cache_monitor()
# Test if 'axel' is available for parallel download and pull the key into cache
if which("axel"):
self.use_axel = True
else:
self.use_axel = False
[docs] def start_cache_monitor(self):
if self.enable_cache_monitor:
self.cache_monitor = InProcessCacheMonitor(self.cache_target, self.cache_monitor_interval)
def _configure_connection(self):
log.debug("Configuring S3 Connection")
# If access_key is empty use default credential chain
if self.access_key:
self.conn = S3Connection(self.access_key, self.secret_key)
else:
self.conn = S3Connection()
[docs] def to_dict(self):
as_dict = super().to_dict()
as_dict.update(self._config_to_dict())
return as_dict
@property
def cache_target(self) -> CacheTarget:
return CacheTarget(
self.staging_path,
self.cache_size,
0.9,
)
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."""
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:
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
raise S3ResponseError
def _fix_permissions(self, rel_path):
"""Set permissions on rel_path"""
for basedir, _, files in os.walk(rel_path):
umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
for filename in files:
path = os.path.join(basedir, filename)
# Ignore symlinks
if os.path.islink(path):
continue
umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
def _construct_path(
self,
obj,
base_dir=None,
dir_only=None,
extra_dir=None,
extra_dir_at_root=False,
alt_name=None,
obj_dir=False,
in_cache=False,
**kwargs,
):
# extra_dir should never be constructed from provided data but just
# make sure there are no shenannigans afoot
if extra_dir and extra_dir != os.path.normpath(extra_dir):
log.warning("extra_dir is not normalized: %s", extra_dir)
raise ObjectInvalid("The requested object is invalid")
# ensure that any parent directory references in alt_name would not
# result in a path not contained in the directory path constructed here
if alt_name:
if not safe_relpath(alt_name):
log.warning("alt_name would locate path outside dir: %s", alt_name)
raise ObjectInvalid("The requested object is invalid")
# alt_name can contain parent directory references, but S3 will not
# follow them, so if they are valid we normalize them out
alt_name = os.path.normpath(alt_name)
rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
if extra_dir is not None:
if extra_dir_at_root:
rel_path = os.path.join(extra_dir, rel_path)
else:
rel_path = os.path.join(rel_path, extra_dir)
# for JOB_WORK directory
if obj_dir:
rel_path = os.path.join(rel_path, str(self._get_object_id(obj)))
if base_dir:
base = self.extra_dirs.get(base_dir)
return os.path.join(base, rel_path)
# S3 folders are marked by having trailing '/' so add it now
rel_path = f"{rel_path}/"
if not dir_only:
rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
if in_cache:
return self._get_cache_path(rel_path)
return rel_path
def _get_cache_path(self, rel_path):
return os.path.abspath(os.path.join(self.staging_path, rel_path))
def _get_transfer_progress(self):
return self.transfer_progress
def _get_size_in_s3(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 _key_exists(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 _in_cache(self, rel_path):
"""Check if the given dataset is in the local cache and return True if so."""
# log.debug("------ Checking cache for rel_path %s" % rel_path)
cache_path = self._get_cache_path(rel_path)
return os.path.exists(cache_path)
# TODO: Part of checking if a file is in cache should be to ensure the
# size of the cached file matches that on S3. Once the upload tool explicitly
# creates, this check sould be implemented- in the mean time, it's not
# looking likely to be implementable reliably.
# if os.path.exists(cache_path):
# # print("***1 %s exists" % cache_path)
# if self._key_exists(rel_path):
# # print("***2 %s exists in S3" % rel_path)
# # Make sure the size in cache is available in its entirety
# # print("File '%s' cache size: %s, S3 size: %s" % (cache_path, os.path.getsize(cache_path), self._get_size_in_s3(rel_path)))
# if os.path.getsize(cache_path) == self._get_size_in_s3(rel_path):
# # print("***2.1 %s exists in S3 and the size is the same as in cache (in_cache=True)" % rel_path)
# exists = True
# else:
# # print("***2.2 %s exists but differs in size from cache (in_cache=False)" % cache_path)
# exists = False
# else:
# # Although not perfect decision making, this most likely means
# # that the file is currently being uploaded
# # print("***3 %s found in cache but not in S3 (in_cache=True)" % cache_path)
# exists = True
# else:
# return False
def _pull_into_cache(self, rel_path):
# Ensure the cache directory structure exists (e.g., dataset_#_files/)
rel_path_dir = os.path.dirname(rel_path)
if not os.path.exists(self._get_cache_path(rel_path_dir)):
os.makedirs(self._get_cache_path(rel_path_dir), exist_ok=True)
# Now pull in the file
file_ok = self._download(rel_path)
self._fix_permissions(self._get_cache_path(rel_path_dir))
return file_ok
def _transfer_cb(self, complete, total):
self.transfer_progress += 10
def _download(self, rel_path):
try:
log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
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)
# Test if cache is large enough to hold the new file
if not self.cache_target.fits_in_cache(key.size):
log.critical(
"File %s is larger (%s) than the configured cache allows (%s). Cannot download.",
rel_path,
key.size,
self.cache_target.log_description,
)
return False
if self.use_axel:
log.debug("Parallel pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
ncores = multiprocessing.cpu_count()
url = key.generate_url(7200)
ret_code = subprocess.call(["axel", "-a", "-n", str(ncores), url])
if ret_code == 0:
return True
else:
log.debug("Pulled key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
self.transfer_progress = 0 # Reset transfer progress counter
key.get_contents_to_filename(self._get_cache_path(rel_path), 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_os(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
[docs] def file_ready(self, obj, **kwargs):
"""
A helper method that checks if a file corresponding to a dataset is
ready and available to be used. Return ``True`` if so, ``False`` otherwise.
"""
rel_path = self._construct_path(obj, **kwargs)
# Make sure the size in cache is available in its entirety
if self._in_cache(rel_path):
if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path):
return True
log.debug(
"Waiting for dataset %s to transfer from OS: %s/%s",
rel_path,
os.path.getsize(self._get_cache_path(rel_path)),
self._get_size_in_s3(rel_path),
)
return False
def _exists(self, obj, **kwargs):
in_cache = in_s3 = False
rel_path = self._construct_path(obj, **kwargs)
# Check cache
if self._in_cache(rel_path):
in_cache = True
# Check S3
in_s3 = self._key_exists(rel_path)
# log.debug("~~~~~~ File '%s' exists in cache: %s; in s3: %s" % (rel_path, in_cache, in_s3))
# dir_only does not get synced so shortcut the decision
dir_only = kwargs.get("dir_only", False)
base_dir = kwargs.get("base_dir", None)
if dir_only:
if in_cache or in_s3:
return True
# for JOB_WORK directory
elif base_dir:
if not os.path.exists(rel_path):
os.makedirs(rel_path, exist_ok=True)
return True
else:
return False
# TODO: Sync should probably not be done here. Add this to an async upload stack?
if in_cache and not in_s3:
self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
return True
elif in_s3:
return True
else:
return False
def _create(self, obj, **kwargs):
if not self._exists(obj, **kwargs):
# Pull out locally used fields
extra_dir = kwargs.get("extra_dir", None)
extra_dir_at_root = kwargs.get("extra_dir_at_root", False)
dir_only = kwargs.get("dir_only", False)
alt_name = kwargs.get("alt_name", None)
# Construct hashed path
rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
# Optionally append extra_dir
if extra_dir is not None:
if extra_dir_at_root:
rel_path = os.path.join(extra_dir, rel_path)
else:
rel_path = os.path.join(rel_path, extra_dir)
# Create given directory in cache
cache_dir = os.path.join(self.staging_path, rel_path)
if not os.path.exists(cache_dir):
os.makedirs(cache_dir, exist_ok=True)
# Although not really necessary to create S3 folders (because S3 has
# flat namespace), do so for consistency with the regular file system
# S3 folders are marked by having trailing '/' so add it now
# s3_dir = '%s/' % rel_path
# self._push_to_os(s3_dir, from_string='')
# If instructed, create the dataset in cache & in S3
if not dir_only:
rel_path = os.path.join(rel_path, alt_name if alt_name else f"dataset_{self._get_object_id(obj)}.dat")
open(os.path.join(self.staging_path, rel_path), "w").close()
self._push_to_os(rel_path, from_string="")
return self
def _empty(self, obj, **kwargs):
if self._exists(obj, **kwargs):
return bool(self._size(obj, **kwargs) > 0)
else:
raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
def _size(self, obj, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
if self._in_cache(rel_path):
try:
return os.path.getsize(self._get_cache_path(rel_path))
except OSError as ex:
log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
elif self._exists(obj, **kwargs):
return self._get_size_in_s3(rel_path)
log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
return 0
def _delete(self, obj, entire_dir=False, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
extra_dir = kwargs.get("extra_dir", None)
base_dir = kwargs.get("base_dir", None)
dir_only = kwargs.get("dir_only", False)
obj_dir = kwargs.get("obj_dir", False)
try:
# Remove temparory data in JOB_WORK directory
if base_dir and dir_only and obj_dir:
shutil.rmtree(os.path.abspath(rel_path))
return True
# For the case of extra_files, because we don't have a reference to
# individual files/keys we need to remove the entire directory structure
# with all the files in it. This is easy for the local file system,
# but requires iterating through each individual key in S3 and deleing it.
if entire_dir and extra_dir:
shutil.rmtree(self._get_cache_path(rel_path), ignore_errors=True)
results = self._bucket.get_all_keys(prefix=rel_path)
for key in results:
log.debug("Deleting key %s", key.name)
key.delete()
return True
else:
# Delete from cache first
unlink(self._get_cache_path(rel_path), ignore_errors=True)
# Delete from S3 as well
if self._key_exists(rel_path):
key = Key(self._bucket, rel_path)
log.debug("Deleting key %s", key.name)
key.delete()
return True
except S3ResponseError:
log.exception("Could not delete key '%s' from S3", rel_path)
except OSError:
log.exception("%s delete error", self._get_filename(obj, **kwargs))
return False
def _get_data(self, obj, start=0, count=-1, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
# Check cache first and get file if not there
if not self._in_cache(rel_path) or os.path.getsize(self._get_cache_path(rel_path)) == 0:
self._pull_into_cache(rel_path)
# Read the file content from cache
data_file = open(self._get_cache_path(rel_path))
data_file.seek(start)
content = data_file.read(count)
data_file.close()
return content
def _get_filename(self, obj, **kwargs):
base_dir = kwargs.get("base_dir", None)
dir_only = kwargs.get("dir_only", False)
obj_dir = kwargs.get("obj_dir", False)
sync_cache = kwargs.get("sync_cache", True)
rel_path = self._construct_path(obj, **kwargs)
# for JOB_WORK directory
if base_dir and dir_only and obj_dir:
return os.path.abspath(rel_path)
cache_path = self._get_cache_path(rel_path)
if not sync_cache:
return cache_path
# S3 does not recognize directories as files so cannot check if those exist.
# So, if checking dir only, ensure given dir exists in cache and return
# the expected cache path.
# dir_only = kwargs.get('dir_only', False)
# if dir_only:
# if not os.path.exists(cache_path):
# os.makedirs(cache_path)
# return cache_path
# Check if the file exists in the cache first, always pull if file size in cache is zero
if self._in_cache(rel_path) and (dir_only or os.path.getsize(self._get_cache_path(rel_path)) > 0):
return cache_path
# Check if the file exists in persistent storage and, if it does, pull it into cache
elif self._exists(obj, **kwargs):
if dir_only:
download_directory(self._bucket, rel_path, cache_path)
return cache_path
else:
if self._pull_into_cache(rel_path):
return cache_path
# For the case of retrieving a directory only, return the expected path
# even if it does not exist.
# if dir_only:
# return cache_path
raise ObjectNotFound(f"objectstore.get_filename, no cache_path: {obj}, kwargs: {kwargs}")
# return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
if create:
self._create(obj, **kwargs)
if self._exists(obj, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
# Chose whether to use the dataset file itself or an alternate file
if file_name:
source_file = os.path.abspath(file_name)
# Copy into cache
cache_file = self._get_cache_path(rel_path)
try:
if source_file != cache_file and self.cache_updated_data:
# FIXME? Should this be a `move`?
shutil.copy2(source_file, cache_file)
self._fix_permissions(cache_file)
except OSError:
log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
else:
source_file = self._get_cache_path(rel_path)
# Update the file on S3
self._push_to_os(rel_path, source_file)
else:
raise ObjectNotFound(f"objectstore.update_from_file, object does not exist: {obj}, kwargs: {kwargs}")
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):
return 0.0
[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,
)