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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 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,
    which,
)
from galaxy.util.sleeper import Sleeper

from .s3_multipart_upload import multipart_upload
from ..objectstore import convert_bytes, ObjectStore

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.key import Key
    from boto.s3.connection import S3Connection
except ImportError:
    boto = None

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]class S3ObjectStore(ObjectStore): """ 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. """
[docs] def __init__(self, config, config_xml): if boto is None: raise Exception(NO_BOTO_ERROR_MESSAGE) super(S3ObjectStore, self).__init__(config) 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 if which('axel'): self.use_axel = True else: self.use_axel = False
def _configure_connection(self): log.debug("Configuring S3 Connection") self.conn = S3Connection(self.access_key, self.secret_key) 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.use_rr = string_as_bool(b_xml.get('use_reduced_redundancy', "False")) 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']) # 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} 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 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): """ 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, **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_s3(self, rel_path): try: key = self.bucket.get_key(rel_path) if key: return key.size except S3ResponseError: 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 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) # 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)) # 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) # 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', 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) 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
[docs] 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) 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
[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) # 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 "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 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
[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.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 os.unlink(self._get_cache_path(rel_path)) # 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
[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 S3 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 = 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
[docs] def get_store_usage_percent(self): return 0.0
[docs]class SwiftObjectStore(S3ObjectStore): """ Object store that stores objects as items in a Swift bucket. A local cache exists that is used as an intermediate location for files between Galaxy and Swift. """ def _configure_connection(self): log.debug("Configuring Swift 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)