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.objectstore.cloud
"""
Object Store plugin for Cloud storage.
"""
import logging
import multiprocessing
import os
import shutil
import subprocess
import threading
import time
from datetime import datetime
from galaxy.exceptions import ObjectInvalid, ObjectNotFound
from galaxy.util import (
directory_hash_id,
safe_relpath,
string_as_bool,
umask_fix_perms,
)
from galaxy.util.sleeper import Sleeper
from ..objectstore import convert_bytes, ObjectStore
try:
from cloudbridge.cloud.factory import CloudProviderFactory, ProviderList
from cloudbridge.cloud.interfaces.exceptions import InvalidNameException
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."
)
[docs]class Cloud(ObjectStore):
"""
Object store that stores objects as items in an cloud storage. A local
cache exists that is used as an intermediate location for files between
Galaxy and the cloud storage.
"""
[docs] def __init__(self, config, config_xml):
super(Cloud, self).__init__(config)
if CloudProviderFactory is None:
raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE)
self.staging_path = self.config.file_path
self.transfer_progress = 0
self._parse_config_xml(config_xml)
self._configure_connection()
self.bucket = self._get_bucket(self.bucket)
# Clean cache only if value is set in galaxy.ini
if self.cache_size != -1:
# Convert GBs to bytes for comparison
self.cache_size = self.cache_size * 1073741824
# Helper for interruptable sleep
self.sleeper = Sleeper()
self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
self.cache_monitor_thread.start()
log.info("Cache cleaner manager started")
# Test if 'axel' is available for parallel download and pull the key into cache
try:
subprocess.call('axel')
self.use_axel = True
except OSError:
self.use_axel = False
def _configure_connection(self):
log.debug("Configuring AWS-S3 Connection")
aws_config = {'aws_access_key': self.access_key,
'aws_secret_key': self.secret_key}
self.conn = CloudProviderFactory().create_provider(ProviderList.AWS, aws_config)
def _parse_config_xml(self, config_xml):
try:
a_xml = config_xml.findall('auth')[0]
self.access_key = a_xml.get('access_key')
self.secret_key = a_xml.get('secret_key')
b_xml = config_xml.findall('bucket')[0]
self.bucket = b_xml.get('name')
self.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]
self.host = cn_xml.get('host', None)
self.port = int(cn_xml.get('port', 6000))
self.multipart = string_as_bool(cn_xml.get('multipart', 'True'))
self.is_secure = string_as_bool(cn_xml.get('is_secure', 'True'))
self.conn_path = cn_xml.get('conn_path', '/')
c_xml = config_xml.findall('cache')[0]
self.cache_size = float(c_xml.get('size', -1))
self.staging_path = c_xml.get('path', self.config.object_store_cache_path)
for d_xml in config_xml.findall('extra_dir'):
self.extra_dirs[d_xml.get('type')] = d_xml.get('path')
log.debug("Object cache dir: %s", self.staging_path)
log.debug(" job work dir: %s", self.extra_dirs['job_work'])
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
def __cache_monitor(self):
time.sleep(2) # Wait for things to load before starting the monitor
while self.running:
total_size = 0
# Is this going to be too expensive of an operation to be done frequently?
file_list = []
for dirpath, _, filenames in os.walk(self.staging_path):
for filename in filenames:
filepath = os.path.join(dirpath, filename)
file_size = os.path.getsize(filepath)
total_size += file_size
# Get the time given file was last accessed
last_access_time = time.localtime(os.stat(filepath)[7])
# Compose a tuple of the access time and the file path
file_tuple = last_access_time, filepath, file_size
file_list.append(file_tuple)
# Sort the file list (based on access time)
file_list.sort()
# Initiate cleaning once within 10% of the defined cache size?
cache_limit = self.cache_size * 0.9
if total_size > cache_limit:
log.info("Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
convert_bytes(total_size), convert_bytes(cache_limit))
# How much to delete? If simply deleting up to the cache-10% limit,
# is likely to be deleting frequently and may run the risk of hitting
# the limit - maybe delete additional #%?
# For now, delete enough to leave at least 10% of the total cache free
delete_this_much = total_size - cache_limit
self.__clean_cache(file_list, delete_this_much)
self.sleeper.sleep(30) # Test cache size every 30 seconds?
def __clean_cache(self, file_list, delete_this_much):
""" Keep deleting files from the file_list until the size of the deleted
files is greater than the value in delete_this_much parameter.
:type file_list: list
:param file_list: List of candidate files that can be deleted. This method
will start deleting files from the beginning of the list so the list
should be sorted accordingly. The list must contains 3-element tuples,
positioned as follows: position 0 holds file last accessed timestamp
(as time.struct_time), position 1 holds file path, and position 2 has
file size (e.g., (<access time>, /mnt/data/dataset_1.dat), 472394)
:type delete_this_much: int
:param delete_this_much: Total size of files, in bytes, that should be deleted.
"""
# Keep deleting datasets from file_list until deleted_amount does not
# exceed delete_this_much; start deleting from the front of the file list,
# which assumes the oldest files come first on the list.
deleted_amount = 0
for entry in enumerate(file_list):
if deleted_amount < delete_this_much:
deleted_amount += entry[2]
os.remove(entry[1])
# Debugging code for printing deleted files' stats
# folder, file_name = os.path.split(f[1])
# file_date = time.strftime("%m/%d/%y %H:%M:%S", f[0])
# log.debug("%s. %-25s %s, size %s (deleted %s/%s)" \
# % (i, file_name, convert_bytes(f[2]), file_date, \
# convert_bytes(deleted_amount), convert_bytes(delete_this_much)))
else:
log.debug("Cache cleaning done. Total space freed: %s", convert_bytes(deleted_amount))
return
def _get_bucket(self, bucket_name):
try:
bucket = self.conn.storage.buckets.get(bucket_name)
if bucket is None:
log.debug("Bucket not found, creating a bucket with handle '%s'", bucket_name)
bucket = self.conn.storage.buckets.create(bucket_name)
log.debug("Using cloud ObjectStore with bucket '%s'", bucket.name)
return bucket
except InvalidNameException as e:
log.exception("Invalid bucket name -- unable to continue. {}".format(e.message))
raise
except Exception as e:
# These two generic exceptions will be replaced by specific exceptions
# once proper exceptions are exposed by CloudBridge.
log.exception("Could not get bucket '{}'. {}".format(bucket_name, e.message))
raise Exception
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, **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(obj.id))
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(obj.id))
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 = '%s/' % rel_path
if not dir_only:
rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
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_cloud(self, rel_path):
try:
obj = self.bucket.objects.get(rel_path)
if obj:
return obj.size
except Exception:
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.objects.list(prefix=rel_path)
if len(keyresult) > 0:
exists = True
else:
exists = False
else:
exists = True if self.bucket.objects.get(rel_path) is not None else False
except Exception:
log.exception("Trouble checking existence of S3 key '%s'", rel_path)
return False
if rel_path[0] == '/':
raise
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)
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))
# 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.objects.get(rel_path)
# Test if cache is large enough to hold the new file
if self.cache_size > 0 and key.size > self.cache_size:
log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
rel_path, key.size, self.cache_size)
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 %s '%s'" % (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
with open(self._get_cache_path(rel_path), "w+") as downloaded_file_handle:
key.save_content(downloaded_file_handle)
return True
except Exception:
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):
if os.path.getsize(source_file) == 0 and (self.bucket.objects.get(rel_path) is not None):
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:
if not self.bucket.objects.get(rel_path):
created_obj = self.bucket.objects.create(rel_path)
created_obj.upload(source_file)
else:
self.bucket.objects.get(rel_path).upload(source_file)
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)
self.transfer_progress = 0 # Reset transfer progress counter
if not self.bucket.objects.get(rel_path):
created_obj = self.bucket.objects.create(rel_path)
created_obj.upload_from_file(source_file)
else:
self.bucket.objects.get(rel_path).upload_from_file(source_file)
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 Exception:
log.exception("Trouble pushing S3 key '%s' from file '%s'", rel_path, source_file)
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_cloud(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_cloud(rel_path))
return False
[docs] def exists(self, obj, **kwargs):
in_cache = False
rel_path = self._construct_path(obj, **kwargs)
# Check cache
if self._in_cache(rel_path):
in_cache = True
# Check cloud
in_cloud = 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_cloud:
return True
# for JOB_WORK directory
elif base_dir:
if not os.path.exists(rel_path):
os.makedirs(rel_path)
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_cloud:
self._push_to_os(rel_path, source_file=self._get_cache_path(rel_path))
return True
elif in_cloud:
return True
else:
return False
[docs] 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(obj.id))
# 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)
if not dir_only:
rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
open(os.path.join(self.staging_path, rel_path), 'w').close()
self._push_to_os(rel_path, from_string='')
[docs] def empty(self, obj, **kwargs):
if self.exists(obj, **kwargs):
return bool(self.size(obj, **kwargs) > 0)
else:
raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
% (str(obj), str(kwargs)))
[docs] 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 cloud. Error: %s", rel_path, ex)
elif self.exists(obj, **kwargs):
return self._get_size_in_cloud(rel_path)
log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
return 0
[docs] 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))
results = self.bucket.objects.list(prefix=rel_path)
for key in results:
log.debug("Deleting key %s", key.name)
key.delete()
return True
else:
# Delete from cache first
os.unlink(self._get_cache_path(rel_path))
# Delete from S3 as well
if self._key_exists(rel_path):
key = self.bucket.objects.get(rel_path)
log.debug("Deleting key %s", key.name)
key.delete()
return True
except Exception:
log.exception("Could not delete key '%s' from cloud", rel_path)
except OSError:
log.exception('%s delete error', self.get_filename(obj, **kwargs))
return False
[docs] 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):
self._pull_into_cache(rel_path)
# Read the file content from cache
data_file = open(self._get_cache_path(rel_path), 'r')
data_file.seek(start)
content = data_file.read(count)
data_file.close()
return content
[docs] 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)
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)
# 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
if self._in_cache(rel_path):
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: # Directories do not get pulled into cache
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('objectstore.get_filename, no cache_path: %s, kwargs: %s'
% (str(obj), str(kwargs)))
# return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
[docs] 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:
# 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 cloud
self._push_to_os(rel_path, source_file)
else:
raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
% (str(obj), str(kwargs)))
[docs] def get_object_url(self, obj, **kwargs):
if self.exists(obj, **kwargs):
rel_path = self._construct_path(obj, **kwargs)
try:
key = self.bucket.objects.get(rel_path)
return key.generate_url(expires_in=86400) # 24hrs
except Exception:
log.exception("Trouble generating URL for dataset '%s'", rel_path)
return None