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.pithos

# This work originally developed by Stavros Sachtouris <saxtouri@grnet.gr>
# as part of the effort committed GRNET S.A. (Greek Research and Technology
# Network) in the context of the OpenMinTeD project (openminted.eu)

import logging
import os
import shutil

    from kamaki.clients import (
        Client as KamakiClient,
except ImportError:
    KamakiClient = None

from galaxy.exceptions import (
from galaxy.util import (
from galaxy.util.path import safe_relpath
from ..objectstore import ObjectStore

    "ObjectStore configured, but no kamaki.clients dependency available."
    "Please install and properly configure kamaki.clients or modify Object "
    "Store configuration.")

log = logging.getLogger(__name__)

[docs]def parse_config_xml(config_xml): """Parse and validate config_xml, return dict for convenience :param config_xml: (xml.etree.ElementTree.Element) root of XML subtree :returns: (dict) according to syntax :raises: various XML parse errors """ r = dict() try: for tag, required_attrs, optional_attrs in ( ('auth', ('url', 'token', ), ('ca_certs', 'ignore_ssl', )), ('container', ('name', ), ('project', )), ): element = config_xml.findall(tag)[0] required = tuple((k, element.get(k)) for k in required_attrs) for k, v in required: if not v: msg = 'No value for {tag}:{k} in XML tree'.format( tag=tag, k=k) log.error(msg) raise Exception(msg) optional = tuple((k, element.get(k)) for k in optional_attrs) r[tag] = dict(required + optional) # Extract extra_dir tag, attrs = 'extra_dir', ('type', 'path') extra_dirs = config_xml.findall(tag) if not extra_dirs: msg = 'No {tag} element in XML tree'.format(tag=tag) log.error(msg) raise Exception(msg) r['extra_dirs'] = [ dict(((k, e.get(k)) for k in attrs)) for e in extra_dirs] if 'job_work' not in (d['type'] for d in r['extra_dirs']): msg = 'No value for {0}:type="job_work" in XML tree'.format(tag) log.error(msg) raise Exception(msg) except Exception: log.exception( "Malformed PithosObjectStore Configuration XML -- " "unable to continue") raise return r
[docs]class PithosObjectStore(ObjectStore): """ Object store that stores objects as items in a Pithos+ container. Cache is ignored for the time being. """ store_type = 'pithos'
[docs] def __init__(self, config, config_dict): super(PithosObjectStore, self).__init__(config, config_dict) self.staging_path = self.config.file_path log.info('Parse config_xml for pithos object store') self.config_dict = config_dict log.debug(self.config_dict) self._initialize()
def _initialize(self): if KamakiClient is None: raise Exception(NO_KAMAKI_ERROR_MESSAGE) log.info('Authenticate Synnefo account') self._authenticate() log.info('Initialize Pithos+ client') self._init_pithos()
[docs] @classmethod def parse_xml(clazz, config_xml): return parse_config_xml(config_xml)
[docs] def to_dict(self): as_dict = super(PithosObjectStore, self).to_dict() as_dict.update(self.config_dict) return as_dict
def _authenticate(self): auth = self.config_dict['auth'] url, token = auth['url'], auth['token'] ca_certs = auth.get('ca_certs') if ca_certs: utils.https.patch_with_certs(ca_certs) elif auth.get('ignore_ssl').lower() in ('true', 'yes', 'on'): utils.https.patch_ignore_ssl() self.astakos = astakos.AstakosClient(url, token) def _init_pithos(self): uuid, token = self.astakos.user_term('id'), self.astakos.token service_type = pithos.PithosClient.service_type pithos_url = self.astakos.get_endpoint_url(service_type) container = self.config_dict['container']['name'] self.pithos = pithos.PithosClient(pithos_url, token, uuid, container) # Create container if not exist, or reassign to named project project = self.config_dict['container'].get('project', None) try: c = self.pithos.get_container_info() except ClientError as ce: if ce.status not in (404, ): raise c = self.pithos.create_container(project_id=project) return if project and c.get('x-container-policy-project') != project: self.pithos.reassign_container(project) 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): """Construct path from object and parameters""" # param 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: {0}'.format(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: {0}'.format( 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) # Pithos+ folders are marked by having trailing '/' so add it now rel_path = '{0}/'.format(rel_path) if not dir_only: an = alt_name if alt_name else 'dataset_{0}.dat'.format(obj.id) rel_path = os.path.join(rel_path, an) return rel_path def _get_cache_path(self, rel_path): return os.path.abspath(os.path.join(self.staging_path, rel_path)) def _in_cache(self, rel_path): """Check if the given dataset is in the local cache and return True if so. """ cache_path = self._get_cache_path(rel_path) return os.path.exists(cache_path) 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 _pull_into_cache(self, rel_path): # Ensure the cache directory structure exists (e.g., dataset_#_files/) rel_path_dir = os.path.dirname(rel_path) rel_cache_path_dir = self._get_cache_path(rel_path_dir) if not os.path.exists(rel_cache_path_dir): os.makedirs(self._get_cache_path(rel_path_dir)) # Now pull in the file cache_path = self._get_cache_path(rel_path_dir) self.pithos.download_object(rel_path, cache_path) self._fix_permissions(cache_path) return cache_path # No need to overwrite "shutdown"
[docs] def exists(self, obj, **kwargs): """Check if file exists, fix if file in cache and not on Pithos+ :returns: weather the file exists remotely or in cache """ path = self._construct_path(obj, **kwargs) try: self.pithos.get_object_info(path) return True except ClientError as ce: if ce.status not in (404, ): raise in_cache = self._in_cache(path) dir_only = kwargs.get('dir_only', False) if dir_only: base_dir = kwargs.get('base_dir', None) if in_cache: return True elif base_dir: # for JOB_WORK directory if not os.path.exists(path): os.makedirs(path) return True return False if in_cache: cache_path = self._get_cache_path(path) # Maybe the upload should have happened in some thread elsewhere? with open(cache_path) as f: self.pithos.upload_object(path, f) return True return False
[docs] def create(self, obj, **kwargs): """Touch a file (aka create empty), if it doesn't exist""" 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 dir_only: self.pithos.upload_from_string( rel_path, '', content_type='application/directory') else: rel_path = os.path.join( rel_path, alt_name if alt_name else 'dataset_{0}.dat'.format(obj.id)) new_file = os.path.join(self.staging_path, rel_path) open(new_file, 'w').close() self.pithos.upload_from_string(rel_path, '')
[docs] def empty(self, obj, **kwargs): """ :returns: weather the object has content :raises ObjectNotFound: """ if not self.exists(obj, **kwargs): raise ObjectNotFound( 'objectstore.empty, object does not exist: {obj}, ' 'kwargs: {kwargs}'.format(obj=obj, kwargs=kwargs)) return bool(self.size(obj, **kwargs))
[docs] def size(self, obj, **kwargs): """ :returns: The size of the object, or 0 if it doesn't exist (sorry for that, not our fault, the ObjectStore interface is like that some times) """ path = self._construct_path(obj, **kwargs) if self._in_cache(path): try: return os.path.getsize(self._get_cache_path(path)) except OSError as ex: log.warning( 'Could not get size of file {path} in local cache,' 'will try Pithos. Error: {err}'.format(path=path, err=ex)) try: file = self.pithos.get_object_info(path) except ClientError as ce: if ce.status not in (404, ): raise return 0 return int(file['content-length'])
[docs] def delete(self, obj, **kwargs): """Delete the object :returns: weather the object was deleted """ path = self._construct_path(obj, **kwargs) base_dir = kwargs.get('base_dir', None) dir_only = kwargs.get('dir_only', False) obj_dir = kwargs.get('obj_dir', False) try: if all((base_dir, dir_only, obj_dir)): shutil.rmtree(os.path.abspath(path)) return True cache_path = self._get_cache_path(path) entire_dir = kwargs.get('entire_dir', False) extra_dir = kwargs.get('extra_dir', False) if entire_dir and extra_dir: shutil.rmtree(cache_path) log.debug('On Pithos: delete -r {path}/'.format(path=path)) self.pithos.del_object(path, delimiter='/') return True else: os.unlink(cache_path) self.pithos.del_object(path) except OSError: log.exception( '{0} delete error'.format(self.get_filename(obj, **kwargs))) except ClientError as ce: log.exception('Could not delete {path} from Pithos, {err}'.format( path=path, err=ce)) return False
[docs] def get_data(self, obj, start=0, count=-1, **kwargs): """Fetch (e.g., download) data :param start: Chunk of data starts here :param count: Fetch at most as many data, fetch all if negative """ path = self._construct_path(obj, **kwargs) if self._in_cache(path): cache_path = self._pull_into_cache(path) else: cache_path = self._get_cache_path(path) data_file = open(cache_path, 'r') data_file.seek(start) content = data_file.read(count) data_file.close() return content
[docs] def get_filename(self, obj, **kwargs): """Get the expected filename with absolute path""" base_dir = kwargs.get('base_dir', None) dir_only = kwargs.get('dir_only', False) obj_dir = kwargs.get('obj_dir', False) path = self._construct_path(obj, **kwargs) # for JOB_WORK directory if base_dir and dir_only and obj_dir: return os.path.abspath(path) cache_path = self._get_cache_path(path) if dir_only: if not os.path.exists(cache_path): os.makedirs(cache_path) return cache_path if self._in_cache(path): return cache_path elif self.exists(obj, **kwargs): if not dir_only: self._pull_into_cache(path) return cache_path raise ObjectNotFound( 'objectstore.get_filename, no cache_path: {obj}, ' 'kwargs: {kwargs}'.format(obj, kwargs))
[docs] def update_from_file(self, obj, **kwargs): """Update the store when a file is updated""" if kwargs.get('create'): self.create(obj, **kwargs) if not self.exists(obj, **kwargs): raise ObjectNotFound( 'objectstore.update_from_file, object does not exist: {obj}, ' 'kwargs: {kwargs}'.format(obj, kwargs)) path = self._construct_path(obj, **kwargs) cache_path = self._get_cache_path(path) file_name = kwargs.get('file_name') if file_name: source_path = os.path.abspath(file_name) try: if source_path != cache_path: shutil.copy2(source_path, cache_path) self._fix_permissions(cache_path) except OSError: log.exception( 'Trouble copying source file "{source}" to cache "{cache}"' ''.format(source=source_path, cache=cache_path)) else: with open(cache_path) as f: self.pithos.upload_object(obj, f)
[docs] def get_object_url(self, obj, **kwargs): """ :returns: URL for direct access, None if no object """ if self.exists(obj, **kwargs): path = self._construct_path(obj, **kwargs) try: return self.pithos.publish_object(path) except ClientError as ce: log.exception( 'Trouble generating URL for dataset "{}"'.format(path)) log.exception('Kamaki: {0}'.format(ce)) return None
[docs] def get_store_usage_percent(self): """ :returns: percentage indicating how full the store is """ quotas = self.astakos.get_quotas() project = self.config_dict['container']['project'] pithos_quotas = quotas[project]['pithos.diskspace'] usage = pithos_quotas['usage'] limit = min(pithos_quotas['limit'], pithos_quotas['project_limit']) return (100.0 * usage) / limit