Source code for galaxy.objectstore

"""
objectstore package, abstraction for storing blobs of data for use in Galaxy.

all providers ensure that data can be accessed on the filesystem for running
tools
"""

import abc
import logging
import os
import random
import shutil
import threading
import time
from typing import (
    Any,
    Dict,
    List,
    Type,
)

import yaml

from galaxy.exceptions import (
    ObjectInvalid,
    ObjectNotFound,
)
from galaxy.util import (
    asbool,
    directory_hash_id,
    force_symlink,
    parse_xml,
    umask_fix_perms,
)
from galaxy.util.bunch import Bunch
from galaxy.util.path import (
    safe_makedirs,
    safe_relpath,
)
from galaxy.util.sleeper import Sleeper

NO_SESSION_ERROR_MESSAGE = (
    "Attempted to 'create' object store entity in configuration with no database session present."
)

log = logging.getLogger(__name__)


[docs]class ObjectStore(metaclass=abc.ABCMeta): """ObjectStore interface. FIELD DESCRIPTIONS (these apply to all the methods in this class): :type obj: StorableObject :param obj: A Galaxy object with an assigned database ID accessible via the .id attribute. :type base_dir: string :param base_dir: A key in `self.extra_dirs` corresponding to the base directory in which this object should be created, or `None` to specify the default directory. :type dir_only: boolean :param dir_only: If `True`, check only the path where the file identified by `obj` should be located, not the dataset itself. This option applies to `extra_dir` argument as well. :type extra_dir: string :param extra_dir: Append `extra_dir` to the directory structure where the dataset identified by `obj` should be located. (e.g., 000/extra_dir/obj.id). Valid values include 'job_work' (defaulting to config.jobs_directory = '$GALAXY_ROOT/database/jobs_directory'); 'temp' (defaulting to config.new_file_path = '$GALAXY_ROOT/database/tmp'). :type extra_dir_at_root: boolean :param extra_dir_at_root: Applicable only if `extra_dir` is set. If True, the `extra_dir` argument is placed at root of the created directory structure rather than at the end (e.g., extra_dir/000/obj.id vs. 000/extra_dir/obj.id) :type alt_name: string :param alt_name: Use this name as the alternative name for the created dataset rather than the default. :type obj_dir: boolean :param obj_dir: Append a subdirectory named with the object's ID (e.g. 000/obj.id) """
[docs] @abc.abstractmethod def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """Return True if the object identified by `obj` exists, False otherwise.""" raise NotImplementedError()
[docs] @abc.abstractmethod def create( self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False ): """ Mark the object (`obj`) as existing in the store, but with no content. This method will create a proper directory structure for the file if the directory does not already exist. """ raise NotImplementedError()
[docs] @abc.abstractmethod def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False): """ Test if the object identified by `obj` has content. If the object does not exist raises `ObjectNotFound`. """ raise NotImplementedError()
[docs] @abc.abstractmethod def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False): """ Return size of the object identified by `obj`. If the object does not exist, return 0. """ raise NotImplementedError()
[docs] @abc.abstractmethod def delete( self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, ): """ Delete the object identified by `obj`. :type entire_dir: boolean :param entire_dir: If True, delete the entire directory pointed to by extra_dir. For safety reasons, this option applies only for and in conjunction with the extra_dir or obj_dir options. """ raise NotImplementedError()
[docs] @abc.abstractmethod def get_data( self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, ): """ Fetch `count` bytes of data offset by `start` bytes using `obj.id`. If the object does not exist raises `ObjectNotFound`. :type start: int :param start: Set the position to start reading the dataset file :type count: int :param count: Read at most `count` bytes from the dataset """ raise NotImplementedError()
[docs] @abc.abstractmethod def get_filename( self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False ): """ Get the expected filename with absolute path for object with id `obj.id`. This can be used to access the contents of the object. """ raise NotImplementedError()
[docs] @abc.abstractmethod def update_from_file( self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False, ): """ Inform the store that the file associated with `obj.id` has been updated. If `file_name` is provided, update from that file instead of the default. If the object does not exist raises `ObjectNotFound`. :type file_name: string :param file_name: Use file pointed to by `file_name` as the source for updating the dataset identified by `obj` :type create: boolean :param create: If True and the default dataset does not exist, create it first. """ raise NotImplementedError()
[docs] @abc.abstractmethod def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False): """ Return the URL for direct access if supported, otherwise return None. Note: need to be careful to not bypass dataset security with this. """ raise NotImplementedError()
[docs] @abc.abstractmethod def get_concrete_store_name(self, obj): """Return a display name or title of the objectstore corresponding to obj. To accommodate nested objectstores, obj is passed in so this metadata can be returned for the ConcreteObjectStore corresponding to the object. If the dataset is in a new or discarded state and an object_store_id has not yet been set, this may return ``None``. """
[docs] @abc.abstractmethod def get_concrete_store_description_markdown(self, obj): """Return a longer description of how data 'obj' is stored. To accommodate nested objectstores, obj is passed in so this metadata can be returned for the ConcreteObjectStore corresponding to the object. If the dataset is in a new or discarded state and an object_store_id has not yet been set, this may return ``None``. """
[docs] @abc.abstractmethod def get_store_usage_percent(self): """Return the percentage indicating how full the store is.""" raise NotImplementedError()
[docs] @abc.abstractmethod def get_store_by(self, obj): """Return how object is stored (by 'uuid', 'id', or None if not yet saved). Certain Galaxy remote data features aren't available if objects are stored by 'id'. """ raise NotImplementedError()
[docs]class BaseObjectStore(ObjectStore): store_by: str store_type: str
[docs] def __init__(self, config, config_dict=None, **kwargs): """ :type config: object :param config: An object, most likely populated from `galaxy/config.ini`, having the following attributes: * object_store_check_old_style (only used by the :class:`DiskObjectStore` subclass) * jobs_directory -- Each job is given a unique empty directory as its current working directory. This option defines in what parent directory those directories will be created. * new_file_path -- Used to set the 'temp' extra_dir. """ if config_dict is None: config_dict = {} self.running = True self.config = config self.check_old_style = config.object_store_check_old_style extra_dirs = {} extra_dirs["job_work"] = config.jobs_directory extra_dirs["temp"] = config.new_file_path extra_dirs.update({e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])}) self.extra_dirs = extra_dirs
[docs] def shutdown(self): """Close any connections for this ObjectStore.""" self.running = False
[docs] def file_ready( self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False ): """ Check if a file corresponding to a dataset is ready to be used. Return True if so, False otherwise """ return True
[docs] @classmethod def parse_xml(clazz, config_xml): """Parse an XML description of a configuration for this object store. Return a configuration dictionary (such as would correspond to the YAML configuration) for the object store. """ raise NotImplementedError()
[docs] @classmethod def from_xml(clazz, config, config_xml, **kwd): config_dict = clazz.parse_xml(config_xml) return clazz(config, config_dict, **kwd)
[docs] def to_dict(self): extra_dirs = [] for extra_dir_type, extra_dir_path in self.extra_dirs.items(): extra_dirs.append({"type": extra_dir_type, "path": extra_dir_path}) return { "config": config_to_dict(self.config), "extra_dirs": extra_dirs, "type": self.store_type, }
def _get_object_id(self, obj): if hasattr(obj, self.store_by): obj_id = getattr(obj, self.store_by) if obj_id is None: obj.flush() return obj.id return obj_id else: # job's don't have uuids, so always use ID in this case when creating # job working directories. return obj.id def _invoke(self, delegate, obj=None, **kwargs): return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
[docs] def exists(self, obj, **kwargs): return self._invoke("exists", obj, **kwargs)
[docs] def create(self, obj, **kwargs): return self._invoke("create", obj, **kwargs)
[docs] def empty(self, obj, **kwargs): return self._invoke("empty", obj, **kwargs)
[docs] def size(self, obj, **kwargs): return self._invoke("size", obj, **kwargs)
[docs] def delete(self, obj, **kwargs): return self._invoke("delete", obj, **kwargs)
[docs] def get_data(self, obj, **kwargs): return self._invoke("get_data", obj, **kwargs)
[docs] def get_filename(self, obj, **kwargs): return self._invoke("get_filename", obj, **kwargs)
[docs] def update_from_file(self, obj, **kwargs): return self._invoke("update_from_file", obj, **kwargs)
[docs] def get_object_url(self, obj, **kwargs): return self._invoke("get_object_url", obj, **kwargs)
[docs] def get_concrete_store_name(self, obj): return self._invoke("get_concrete_store_name", obj)
[docs] def get_concrete_store_description_markdown(self, obj): return self._invoke("get_concrete_store_description_markdown", obj)
[docs] def get_store_usage_percent(self): return self._invoke("get_store_usage_percent")
[docs] def get_store_by(self, obj, **kwargs): return self._invoke("get_store_by", obj, **kwargs)
[docs]class ConcreteObjectStore(BaseObjectStore): """Subclass of ObjectStore for stores that don't delegate (non-nested). Currently only adds store_by functionality. Which doesn't make sense for the delegating object stores. """
[docs] def __init__(self, config, config_dict=None, **kwargs): """ :type config: object :param config: An object, most likely populated from `galaxy/config.ini`, having the following attributes: * object_store_check_old_style (only used by the :class:`DiskObjectStore` subclass) * jobs_directory -- Each job is given a unique empty directory as its current working directory. This option defines in what parent directory those directories will be created. * new_file_path -- Used to set the 'temp' extra_dir. """ if config_dict is None: config_dict = {} super().__init__(config=config, config_dict=config_dict, **kwargs) self.store_by = config_dict.get("store_by", None) or getattr(config, "object_store_store_by", "id") self.name = config_dict.get("name", None) self.description = config_dict.get("description", None)
[docs] def to_dict(self): rval = super().to_dict() rval["store_by"] = self.store_by rval["name"] = self.name rval["description"] = self.description return rval
def _get_concrete_store_name(self, obj): return self.name def _get_concrete_store_description_markdown(self, obj): return self.description def _get_store_by(self, obj): return self.store_by
[docs]class DiskObjectStore(ConcreteObjectStore): """ Standard Galaxy object store. Stores objects in files under a specific directory on disk. >>> from galaxy.util.bunch import Bunch >>> import tempfile >>> file_path=tempfile.mkdtemp() >>> obj = Bunch(id=1) >>> s = DiskObjectStore(Bunch(umask=0o077, jobs_directory=file_path, new_file_path=file_path, object_store_check_old_style=False), dict(files_dir=file_path)) >>> s.create(obj) >>> s.exists(obj) True >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat' """ store_type = "disk"
[docs] def __init__(self, config, config_dict): """ :type config: object :param config: An object, most likely populated from `galaxy/config.ini`, having the same attributes needed by :class:`ObjectStore` plus: * file_path -- Default directory to store objects to disk in. * umask -- the permission bits for newly created files. :type file_path: str :param file_path: Override for the `config.file_path` value. :type extra_dirs: dict :param extra_dirs: Keys are string, values are directory paths. """ super().__init__(config, config_dict) self.file_path = os.path.abspath(config_dict.get("files_dir") or config.file_path)
[docs] @classmethod def parse_xml(clazz, config_xml): extra_dirs = [] config_dict = {} if config_xml is not None: store_by = config_xml.attrib.get("store_by", None) if store_by is not None: config_dict["store_by"] = store_by name = config_xml.attrib.get("name", None) if name is not None: config_dict["name"] = name for e in config_xml: if e.tag == "files_dir": config_dict["files_dir"] = e.get("path") elif e.tag == "description": config_dict["description"] = e.text else: extra_dirs.append({"type": e.get("type"), "path": e.get("path")}) config_dict["extra_dirs"] = extra_dirs return config_dict
[docs] def to_dict(self): as_dict = super().to_dict() as_dict["files_dir"] = self.file_path return as_dict
def __get_filename( self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False ): """ Return the absolute path for the file corresponding to the `obj.id`. This is regardless of whether or not the file exists. """ path = self._construct_path( obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, obj_dir=False, old_style=True, ) # For backward compatibility: check the old style root path first; # otherwise construct hashed path. if not os.path.exists(path): return self._construct_path( obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, ) # TODO: rename to _disk_path or something like that to avoid conflicts with # children that'll use the local_extra_dirs decorator, e.g. S3 def _construct_path( self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs, ): """ Construct the absolute path for accessing the object identified by `obj.id`. :type base_dir: string :param base_dir: A key in self.extra_dirs corresponding to the base directory in which this object should be created, or None to specify the default directory. :type dir_only: boolean :param dir_only: If True, check only the path where the file identified by `obj` should be located, not the dataset itself. This option applies to `extra_dir` argument as well. :type extra_dir: string :param extra_dir: Append the value of this parameter to the expected path used to access the object identified by `obj` (e.g., /files/000/<extra_dir>/dataset_10.dat). :type alt_name: string :param alt_name: Use this name as the alternative name for the returned dataset rather than the default. :type old_style: boolean param old_style: This option is used for backward compatibility. If `True` then the composed directory structure does not include a hash id (e.g., /files/dataset_10.dat (old) vs. /files/000/dataset_10.dat (new)) """ base = os.path.abspath(self.extra_dirs.get(base_dir, self.file_path)) # 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 and not safe_relpath(alt_name): log.warning("alt_name would locate path outside dir: %s", alt_name) raise ObjectInvalid("The requested object is invalid") obj_id = self._get_object_id(obj) if old_style: if extra_dir is not None: path = os.path.join(base, extra_dir) else: path = base else: # Construct hashed path rel_path = os.path.join(*directory_hash_id(obj_id)) # Create a subdirectory for the object ID if obj_dir: rel_path = os.path.join(rel_path, str(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) path = os.path.join(base, rel_path) if not dir_only: assert ( obj_id is not None ), f"The effective dataset identifier consumed by object store [{self.store_by}] must be set before a path can be constructed." path = os.path.join(path, alt_name if alt_name else f"dataset_{obj_id}.dat") return os.path.abspath(path) def _exists(self, obj, **kwargs): """Override `ObjectStore`'s stub and check on disk.""" if self.check_old_style: path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility: check root path first; otherwise # construct and check hashed path. if os.path.exists(path): return True return os.path.exists(self._construct_path(obj, **kwargs)) def _create(self, obj, **kwargs): """Override `ObjectStore`'s stub by creating any files and folders on disk.""" if not self._exists(obj, **kwargs): path = self._construct_path(obj, **kwargs) dir_only = kwargs.get("dir_only", False) # Create directory if it does not exist dir = path if dir_only else os.path.dirname(path) safe_makedirs(dir) # Create the file if it does not exist if not dir_only: open(path, "w").close() # Should be rb? umask_fix_perms(path, self.config.umask, 0o666) def _empty(self, obj, **kwargs): """Override `ObjectStore`'s stub by checking file size on disk.""" return self.size(obj, **kwargs) == 0 def _size(self, obj, **kwargs): """Override `ObjectStore`'s stub by return file size on disk. Returns 0 if the object doesn't exist yet or other error. """ if self._exists(obj, **kwargs): try: filepath = self._get_filename(obj, **kwargs) for _ in range(0, 2): size = os.path.getsize(filepath) if size != 0: break # May be legitimately 0, or there may be an issue with the FS / kernel, so we try again time.sleep(0.01) return size except OSError: return 0 else: return 0 def _delete(self, obj, entire_dir=False, **kwargs): """Override `ObjectStore`'s stub; delete the file or folder on disk.""" path = self._get_filename(obj, **kwargs) extra_dir = kwargs.get("extra_dir", None) obj_dir = kwargs.get("obj_dir", False) try: if entire_dir and (extra_dir or obj_dir): shutil.rmtree(path) return True os.remove(path) return True except FileNotFoundError: # Absolutely possible that a delete request races, but that's "fine". return True except OSError as ex: log.critical(f"{self.__get_filename(obj, **kwargs)} delete error {ex}") return False def _get_data(self, obj, start=0, count=-1, **kwargs): """Override `ObjectStore`'s stub; retrieve data directly from disk.""" data_file = open(self._get_filename(obj, **kwargs)) # Should be rb? data_file.seek(start) content = data_file.read(count) data_file.close() return content def _get_filename(self, obj, **kwargs): """ Override `ObjectStore`'s stub. If `object_store_check_old_style` is set to `True` in config then the root path is checked first. """ if self.check_old_style: path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility, check root path first; otherwise, # construct and return hashed path if os.path.exists(path): return path path = self._construct_path(obj, **kwargs) if not os.path.exists(path): raise ObjectNotFound return path def _update_from_file(self, obj, file_name=None, create=False, **kwargs): """`create` parameter is not used in this implementation.""" preserve_symlinks = kwargs.pop("preserve_symlinks", False) # FIXME: symlinks and the object store model may not play well together # these should be handled better, e.g. registering the symlink'd file # as an object if create: self._create(obj, **kwargs) if file_name and self._exists(obj, **kwargs): try: if preserve_symlinks and os.path.islink(file_name): force_symlink(os.readlink(file_name), self._get_filename(obj, **kwargs)) else: path = self._get_filename(obj, **kwargs) shutil.copy(file_name, path) umask_fix_perms(path, self.config.umask, 0o666) except shutil.SameFileError: # That's ok, we need to ignore this so that remote object stores can update # the remote object from the cache file path pass except OSError as ex: log.critical(f"Error copying {file_name} to {self.__get_filename(obj, **kwargs)}: {ex}") raise ex def _get_object_url(self, obj, **kwargs): """ Override `ObjectStore`'s stub. Returns `None`, we have no URLs. """ return None def _get_store_usage_percent(self, **kwargs): """Override `ObjectStore`'s stub by return percent storage used.""" st = os.statvfs(self.file_path) return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100
[docs]class NestedObjectStore(BaseObjectStore): """ Base for ObjectStores that use other ObjectStores. Example: DistributedObjectStore, HierarchicalObjectStore """
[docs] def __init__(self, config, config_xml=None): """Extend `ObjectStore`'s constructor.""" super().__init__(config) self.backends = {}
[docs] def shutdown(self): """For each backend, shuts them down.""" for store in self.backends.values(): store.shutdown() super().shutdown()
def _exists(self, obj, **kwargs): """Determine if the `obj` exists in any of the backends.""" return self._call_method("_exists", obj, False, False, **kwargs)
[docs] def file_ready(self, obj, **kwargs): """Determine if the file for `obj` is ready to be used by any of the backends.""" return self._call_method("file_ready", obj, False, False, **kwargs)
def _create(self, obj, **kwargs): """Create a backing file in a random backend.""" random.choice(list(self.backends.values())).create(obj, **kwargs) def _empty(self, obj, **kwargs): """For the first backend that has this `obj`, determine if it is empty.""" return self._call_method("_empty", obj, True, False, **kwargs) def _size(self, obj, **kwargs): """For the first backend that has this `obj`, return its size.""" return self._call_method("_size", obj, 0, False, **kwargs) def _delete(self, obj, **kwargs): """For the first backend that has this `obj`, delete it.""" return self._call_method("_delete", obj, False, False, **kwargs) def _get_data(self, obj, **kwargs): """For the first backend that has this `obj`, get data from it.""" return self._call_method("_get_data", obj, ObjectNotFound, True, **kwargs) def _get_filename(self, obj, **kwargs): """For the first backend that has this `obj`, get its filename.""" return self._call_method("_get_filename", obj, ObjectNotFound, True, **kwargs) def _update_from_file(self, obj, **kwargs): """For the first backend that has this `obj`, update it from the given file.""" if kwargs.get("create", False): self._create(obj, **kwargs) kwargs["create"] = False return self._call_method("_update_from_file", obj, ObjectNotFound, True, **kwargs) def _get_object_url(self, obj, **kwargs): """For the first backend that has this `obj`, get its URL.""" return self._call_method("_get_object_url", obj, None, False, **kwargs) def _get_concrete_store_name(self, obj): return self._call_method("_get_concrete_store_name", obj, None, False) def _get_concrete_store_description_markdown(self, obj): return self._call_method("_get_concrete_store_description_markdown", obj, None, False) def _get_store_by(self, obj): return self._call_method("_get_store_by", obj, None, False) def _repr_object_for_exception(self, obj): try: # there are a few objects in python that don't have __class__ obj_id = self._get_object_id(obj) return f"{obj.__class__.__name__}({self.store_by}={obj_id})" except AttributeError: return str(obj) def _call_method(self, method, obj, default, default_is_exception, **kwargs): """Check all children object stores for the first one with the dataset.""" for store in self.backends.values(): if store.exists(obj, **kwargs): return store.__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( "objectstore, _call_method failed: %s on %s, kwargs: %s" % (method, self._repr_object_for_exception(obj), str(kwargs)) ) else: return default
[docs]class DistributedObjectStore(NestedObjectStore): """ ObjectStore that defers to a list of backends. When getting objects the first store where the object exists is used. When creating objects they are created in a store selected randomly, but with weighting. """ store_type = "distributed"
[docs] def __init__(self, config, config_dict, fsmon=False): """ :type config: object :param config: An object, most likely populated from `galaxy/config.ini`, having the same attributes needed by :class:`NestedObjectStore` plus: * distributed_object_store_config_file :type config_xml: ElementTree :type fsmon: bool :param fsmon: If True, monitor the file system for free space, removing backends when they get too full. """ super().__init__(config, config_dict) self.backends = {} self.weighted_backend_ids = [] self.original_weighted_backend_ids = [] self.max_percent_full = {} self.global_max_percent_full = config_dict.get("global_max_percent_full", 0) self.search_for_missing = config_dict.get("search_for_missing", True) random.seed() for backend_def in config_dict["backends"]: backened_id = backend_def["id"] maxpctfull = backend_def.get("max_percent_full", 0) weight = backend_def["weight"] backend = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon) self.backends[backened_id] = backend self.max_percent_full[backened_id] = maxpctfull for _ in range(0, weight): # The simplest way to do weighting: add backend ids to a # sequence the number of times equalling weight, then randomly # choose a backend from that sequence at creation self.weighted_backend_ids.append(backened_id) self.original_weighted_backend_ids = self.weighted_backend_ids self.sleeper = None if fsmon and (self.global_max_percent_full or [_ for _ in self.max_percent_full.values() if _ != 0.0]): self.sleeper = Sleeper() self.filesystem_monitor_thread = threading.Thread(target=self.__filesystem_monitor, args=[self.sleeper]) self.filesystem_monitor_thread.daemon = True self.filesystem_monitor_thread.start() log.info("Filesystem space monitor started")
[docs] @classmethod def parse_xml(clazz, config_xml, legacy=False): if legacy: backends_root = config_xml else: backends_root = config_xml.find("backends") backends: List[Dict[str, Any]] = [] config_dict = { "search_for_missing": asbool(backends_root.get("search_for_missing", True)), "global_max_percent_full": float(backends_root.get("maxpctfull", 0)), "backends": backends, } for b in [e for e in backends_root if e.tag == "backend"]: store_id = b.get("id") store_weight = int(b.get("weight", 1)) store_maxpctfull = float(b.get("maxpctfull", 0)) store_type = b.get("type", "disk") store_by = b.get("store_by", None) objectstore_class, _ = type_to_object_store_class(store_type) backend_config_dict = objectstore_class.parse_xml(b) backend_config_dict["id"] = store_id backend_config_dict["weight"] = store_weight backend_config_dict["max_percent_full"] = store_maxpctfull backend_config_dict["type"] = store_type if store_by is not None: backend_config_dict["store_by"] = store_by backends.append(backend_config_dict) return config_dict
[docs] @classmethod def from_xml(clazz, config, config_xml, fsmon=False): legacy = False if config_xml is None: distributed_config = config.distributed_object_store_config_file assert distributed_config is not None, ( "distributed object store ('object_store = distributed') " "requires a config file, please set one in " "'distributed_object_store_config_file')" ) log.debug("Loading backends for distributed object store from %s", distributed_config) config_xml = parse_xml(distributed_config).getroot() legacy = True else: log.debug("Loading backends for distributed object store from %s", config_xml.get("id")) config_dict = clazz.parse_xml(config_xml, legacy=legacy) return clazz(config, config_dict, fsmon=fsmon)
[docs] def to_dict(self) -> Dict[str, Any]: as_dict = super().to_dict() as_dict["global_max_percent_full"] = self.global_max_percent_full as_dict["search_for_missing"] = self.search_for_missing backends: List[Dict[str, Any]] = [] for backend_id, backend in self.backends.items(): backend_as_dict = backend.to_dict() backend_as_dict["id"] = backend_id backend_as_dict["max_percent_full"] = self.max_percent_full[backend_id] backend_as_dict["weight"] = len([i for i in self.original_weighted_backend_ids if i == backend_id]) backends.append(backend_as_dict) as_dict["backends"] = backends return as_dict
[docs] def shutdown(self): """Shut down. Kill the free space monitor if there is one.""" super().shutdown() if self.sleeper is not None: self.sleeper.wake()
def __filesystem_monitor(self, sleeper: Sleeper): while self.running: new_weighted_backend_ids = self.original_weighted_backend_ids for id, backend in self.backends.items(): maxpct = self.max_percent_full[id] or self.global_max_percent_full pct = backend.get_store_usage_percent() if pct > maxpct: new_weighted_backend_ids = [_ for _ in new_weighted_backend_ids if _ != id] self.weighted_backend_ids = new_weighted_backend_ids sleeper.sleep(120) # Test free space every 2 minutes def _create(self, obj, **kwargs): """The only method in which obj.object_store_id may be None.""" if obj.object_store_id is None or not self._exists(obj, **kwargs): if obj.object_store_id is None or obj.object_store_id not in self.backends: try: obj.object_store_id = random.choice(self.weighted_backend_ids) except IndexError: raise ObjectInvalid( "objectstore.create, could not generate " "obj.object_store_id: %s, kwargs: %s" % (str(obj), str(kwargs)) ) log.debug( "Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id) ) else: log.debug( "Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id) ) self.backends[obj.object_store_id].create(obj, **kwargs) def _call_method(self, method, obj, default, default_is_exception, **kwargs): object_store_id = self.__get_store_id_for(obj, **kwargs) if object_store_id is not None: return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs) if default_is_exception: raise default( "objectstore, _call_method failed: %s on %s, kwargs: %s" % (method, self._repr_object_for_exception(obj), str(kwargs)) ) else: return default def __get_store_id_for(self, obj, **kwargs): if obj.object_store_id is not None: if obj.object_store_id in self.backends: return obj.object_store_id else: log.warning( "The backend object store ID (%s) for %s object with ID %s is invalid" % (obj.object_store_id, obj.__class__.__name__, obj.id) ) elif self.search_for_missing: # if this instance has been switched from a non-distributed to a # distributed object store, or if the object's store id is invalid, # try to locate the object for id, store in self.backends.items(): if store.exists(obj, **kwargs): log.warning( f"{obj.__class__.__name__} object with ID {obj.id} found in backend object store with ID {id}" ) obj.object_store_id = id return id return None
[docs]class HierarchicalObjectStore(NestedObjectStore): """ ObjectStore that defers to a list of backends. When getting objects the first store where the object exists is used. When creating objects only the first store is used. """ store_type = "hierarchical"
[docs] def __init__(self, config, config_dict, fsmon=False): """The default constructor. Extends `NestedObjectStore`.""" super().__init__(config, config_dict) backends: Dict[int, ObjectStore] = {} for order, backend_def in enumerate(config_dict["backends"]): backends[order] = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon) self.backends = backends
[docs] @classmethod def parse_xml(clazz, config_xml): backends_list = [] for backend in sorted(config_xml.find("backends"), key=lambda b: int(b.get("order"))): store_type = backend.get("type") objectstore_class, _ = type_to_object_store_class(store_type) backend_config_dict = objectstore_class.parse_xml(backend) backend_config_dict["type"] = store_type backends_list.append(backend_config_dict) return {"backends": backends_list}
[docs] def to_dict(self): as_dict = super().to_dict() backends = [] for backend in self.backends.values(): backend_as_dict = backend.to_dict() backends.append(backend_as_dict) as_dict["backends"] = backends return as_dict
def _exists(self, obj, **kwargs): """Check all child object stores.""" for store in self.backends.values(): if store.exists(obj, **kwargs): return True return False def _create(self, obj, **kwargs): """Call the primary object store.""" self.backends[0].create(obj, **kwargs)
[docs]def type_to_object_store_class(store, fsmon=False): objectstore_class: Type[ObjectStore] objectstore_constructor_kwds = {} if store == "disk": objectstore_class = DiskObjectStore elif store == "s3": from .s3 import S3ObjectStore objectstore_class = S3ObjectStore elif store == "cloud": from .cloud import Cloud objectstore_class = Cloud elif store == "swift": from .s3 import SwiftObjectStore objectstore_class = SwiftObjectStore elif store == "distributed": objectstore_class = DistributedObjectStore objectstore_constructor_kwds["fsmon"] = fsmon elif store == "hierarchical": objectstore_class = HierarchicalObjectStore objectstore_constructor_kwds["fsmon"] = fsmon elif store == "irods": from .irods import IRODSObjectStore objectstore_class = IRODSObjectStore elif store == "azure_blob": from .azure_blob import AzureBlobObjectStore objectstore_class = AzureBlobObjectStore elif store == "pithos": from .pithos import PithosObjectStore objectstore_class = PithosObjectStore else: raise Exception(f"Unrecognized object store definition: {store}") # Disable the Pulsar object store for now until it receives some attention # elif store == 'pulsar': # from .pulsar import PulsarObjectStore # return PulsarObjectStore(config=config, config_xml=config_xml) return objectstore_class, objectstore_constructor_kwds
[docs]def build_object_store_from_config(config, fsmon=False, config_xml=None, config_dict=None): """ Invoke the appropriate object store. Will use the `object_store_config_file` attribute of the `config` object to configure a new object store from the specified XML file. Or you can specify the object store type in the `object_store` attribute of the `config` object. Currently 'disk', 's3', 'swift', 'distributed', 'hierarchical', 'irods', and 'pulsar' are supported values. """ from_object = "xml" if config is None and config_dict is not None and "config" in config_dict: # Build a config object from to_dict of an ObjectStore. config = Bunch(**config_dict["config"]) elif config is None: raise Exception( "build_object_store_from_config sent None as config parameter and one cannot be recovered from config_dict" ) if config_xml is None and config_dict is None: config_file = config.object_store_config_file if os.path.exists(config_file): if config_file.endswith(".xml") or config_file.endswith(".xml.sample"): # This is a top level invocation of build_object_store_from_config, and # we have an object_store_conf.xml -- read the .xml and build # accordingly config_xml = parse_xml(config.object_store_config_file).getroot() store = config_xml.get("type") else: with open(config_file) as f: config_dict = yaml.safe_load(f) from_object = "dict" store = config_dict.get("type") else: store = config.object_store elif config_xml is not None: store = config_xml.get("type") elif config_dict is not None: from_object = "dict" store = config_dict.get("type") objectstore_class, objectstore_constructor_kwds = type_to_object_store_class(store, fsmon=fsmon) if from_object == "xml": return objectstore_class.from_xml(config=config, config_xml=config_xml, **objectstore_constructor_kwds) else: return objectstore_class(config=config, config_dict=config_dict, **objectstore_constructor_kwds)
[docs]def local_extra_dirs(func): """Non-local plugin decorator using local directories for the extra_dirs (job_work and temp).""" def wraps(self, *args, **kwargs): if kwargs.get("base_dir", None) is None: return func(self, *args, **kwargs) else: for c in self.__class__.__mro__: if c.__name__ == "DiskObjectStore": return getattr(c, func.__name__)(self, *args, **kwargs) raise Exception( "Could not call DiskObjectStore's %s method, does your " "Object Store plugin inherit from DiskObjectStore?" % func.__name__ ) return wraps
[docs]def convert_bytes(bytes): """A helper function used for pretty printing disk usage.""" if bytes is None: bytes = 0 bytes = float(bytes) if bytes >= 1099511627776: terabytes = bytes / 1099511627776 size = f"{terabytes:.2f}TB" elif bytes >= 1073741824: gigabytes = bytes / 1073741824 size = f"{gigabytes:.2f}GB" elif bytes >= 1048576: megabytes = bytes / 1048576 size = f"{megabytes:.2f}MB" elif bytes >= 1024: kilobytes = bytes / 1024 size = f"{kilobytes:.2f}KB" else: size = f"{bytes:.2f}b" return size
[docs]def config_to_dict(config): """Dict-ify the portion of a config object consumed by the ObjectStore class and its subclasses.""" return { "object_store_check_old_style": config.object_store_check_old_style, "file_path": config.file_path, "umask": config.umask, "jobs_directory": config.jobs_directory, "new_file_path": config.new_file_path, "object_store_cache_path": config.object_store_cache_path, "gid": config.gid, }
[docs]class ObjectStorePopulator: """Small helper for interacting with the object store and making sure all datasets from a job end up with the same object_store_id. """
[docs] def __init__(self, has_object_store, user): if hasattr(has_object_store, "object_store"): object_store = has_object_store.object_store else: object_store = has_object_store self.object_store = object_store self.object_store_id = None self.user = user
[docs] def set_object_store_id(self, data): self.set_dataset_object_store_id(data.dataset)
[docs] def set_dataset_object_store_id(self, dataset): # Create an empty file immediately. The first dataset will be # created in the "default" store, all others will be created in # the same store as the first. dataset.object_store_id = self.object_store_id try: self.object_store.create(dataset) except ObjectInvalid: raise Exception("Unable to create output dataset: object store is full") self.object_store_id = dataset.object_store_id # these will be the same thing after the first output