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Source code for galaxy.objectstore.cloud

"""
Object Store plugin for Cloud storage.
"""

import logging
import multiprocessing
import os
import os.path
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,
    umask_fix_perms,
)
from galaxy.util.sleeper import Sleeper
from .s3 import parse_config_xml
from ..objectstore import convert_bytes, ObjectStore
try:
    from cloudbridge.factory import CloudProviderFactory, ProviderList
    from cloudbridge.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 CloudConfigMixin(object): def _config_to_dict(self): return { "provider": self.provider, "auth": self.credentials, "bucket": { "name": self.bucket_name, "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, } }
[docs]class Cloud(ObjectStore, CloudConfigMixin): """ 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. """ store_type = 'cloud'
[docs] def __init__(self, config, config_dict): super(Cloud, self).__init__(config, config_dict) self.transfer_progress = 0 bucket_dict = config_dict['bucket'] connection_dict = config_dict.get('connection', {}) cache_dict = config_dict['cache'] self.provider = config_dict["provider"] self.credentials = config_dict["auth"] self.bucket_name = 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', -1) self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path self._initialize()
def _initialize(self): if CloudProviderFactory is None: raise Exception(NO_CLOUDBRIDGE_ERROR_MESSAGE) self.conn = self._get_connection(self.provider, self.credentials) self.bucket = self._get_bucket(self.bucket_name) # 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 @staticmethod def _get_connection(provider, credentials): log.debug("Configuring `{}` Connection".format(provider)) if provider == "aws": config = {"aws_access_key": credentials["access_key"], "aws_secret_key": credentials["secret_key"]} connection = CloudProviderFactory().create_provider(ProviderList.AWS, config) elif provider == "azure": config = {"azure_subscription_id": credentials["subscription_id"], "azure_client_id": credentials["client_id"], "azure_secret": credentials["secret"], "azure_tenant": credentials["tenant"]} connection = CloudProviderFactory().create_provider(ProviderList.AZURE, config) elif provider == "google": config = {"gcp_service_creds_file": credentials["credentials_file"]} connection = CloudProviderFactory().create_provider(ProviderList.GCP, config) else: raise Exception("Unsupported provider `{}`.".format(provider)) # Ideally it would be better to assert if the connection is # authorized to perform operations required by ObjectStore # before returning it (and initializing ObjectStore); hence # any related issues can be handled properly here, and ObjectStore # can "trust" the connection is established. # # However, the mechanism implemented in Cloudbridge to assert if # a user/service is authorized to perform an operation, assumes # the user/service is granted with an elevated privileges, such # as admin/owner-level access to all resources. For a detailed # discussion see: # # https://github.com/CloudVE/cloudbridge/issues/135 # # Hence, if a resource owner wants to only authorize Galaxy to r/w # a bucket/container on the provider, but does not allow it to access # other resources, Cloudbridge may fail asserting credentials. # For instance, to r/w an Amazon S3 bucket, the resource owner # also needs to authorize full access to Amazon EC2, because Cloudbridge # leverages EC2-specific functions to assert the credentials. # # Therefore, to adhere with principle of least privilege, we do not # assert credentials; instead, we handle exceptions raised as a # result of signing API calls to cloud provider (e.g., GCP) using # incorrect, invalid, or unauthorized credentials. return connection
[docs] @classmethod def parse_xml(clazz, config_xml): # The following reads common cloud-based storage configuration # as implemented for the S3 backend. Hence, it also attempts to # parse S3-specific configuration (e.g., credentials); however, # such provider-specific configuration is overwritten in the # following. config = parse_config_xml(config_xml) try: provider = config_xml.attrib.get("provider") if provider is None: msg = "Missing `provider` attribute from the Cloud backend of the ObjectStore." log.error(msg) raise Exception(msg) provider = provider.lower() config["provider"] = provider # Read any provider-specific configuration. auth_element = config_xml.findall("auth")[0] missing_config = [] if provider == "aws": akey = auth_element.get("access_key") if akey is None: missing_config.append("access_key") skey = auth_element.get("secret_key") if skey is None: missing_config.append("secret_key") config["auth"] = { "access_key": akey, "secret_key": skey} elif provider == "azure": sid = auth_element.get("subscription_id") if sid is None: missing_config.append("subscription_id") cid = auth_element.get("client_id") if cid is None: missing_config.append("client_id") sec = auth_element.get("secret") if sec is None: missing_config.append("secret") ten = auth_element.get("tenant") if ten is None: missing_config.append("tenant") config["auth"] = { "subscription_id": sid, "client_id": cid, "secret": sec, "tenant": ten} elif provider == "google": cre = auth_element.get("credentials_file") if not os.path.isfile(cre): msg = "The following file specified for GCP credentials not found: {}".format(cre) log.error(msg) raise IOError(msg) if cre is None: missing_config.append("credentials_file") config["auth"] = { "credentials_file": cre} else: msg = "Unsupported provider `{}`.".format(provider) log.error(msg) raise Exception(msg) if len(missing_config) > 0: msg = "The following configuration required for {} cloud backend " \ "are missing: {}".format(provider, missing_config) log.error(msg) raise Exception(msg) else: return config except Exception: log.exception("Malformed ObjectStore Configuration XML -- unable to continue") raise
[docs] def to_dict(self): as_dict = super(Cloud, self).to_dict() as_dict.update(self._config_to_dict()) return as_dict
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: log.exception("Invalid bucket name -- unable to continue") raise except Exception: # 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)) 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
[docs] def get_store_usage_percent(self): return 0.0