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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,
NamedTuple,
Optional,
Tuple,
Type,
TYPE_CHECKING,
)
import yaml
from pydantic import BaseModel
from galaxy.exceptions import (
MalformedContents,
ObjectInvalid,
ObjectNotFound,
)
from galaxy.util import (
asbool,
directory_hash_id,
force_symlink,
in_directory,
parse_xml,
umask_fix_perms,
)
from galaxy.util.bunch import Bunch
from galaxy.util.path import (
safe_makedirs,
safe_relpath,
safe_walk,
)
from galaxy.util.sleeper import Sleeper
from .badges import (
BadgeDict,
read_badges,
serialize_badges,
StoredBadgeDict,
)
from .caching import CacheTarget
if TYPE_CHECKING:
from galaxy.model import DatasetInstance
NO_SESSION_ERROR_MESSAGE = (
"Attempted to 'create' object store entity in configuration with no database session present."
)
DEFAULT_PRIVATE = False
DEFAULT_QUOTA_SOURCE = None # Just track quota right on user object in Galaxy.
DEFAULT_QUOTA_ENABLED = True # enable quota tracking in object stores by default
DEFAULT_DEVICE_ID = None
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 construct_path(
self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None
):
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.
The method returns the concrete objectstore the supplied object is stored
in.
"""
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) -> int:
"""
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,
preserve_symlinks=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_concrete_store_badges(self, obj) -> List[BadgeDict]:
"""Return a list of dictified badges summarizing the object store configuration."""
[docs] @abc.abstractmethod
def is_private(self, obj):
"""Return True iff supplied object is stored in private ConcreteObjectStore."""
[docs] def object_store_ids(self, private=None):
"""Return IDs of all concrete object stores - either private ones or non-private ones.
This should just return an empty list for non-DistributedObjectStore object stores,
i.e. concrete objectstores and the HierarchicalObjectStore since these do not
use the object_store_id column for objects (Galaxy Datasets).
"""
return []
[docs] def object_store_allows_id_selection(self) -> bool:
"""Return True if this object store respects object_store_id and allow selection of this."""
return False
[docs] def object_store_ids_allowing_selection(self) -> List[str]:
"""Return a non-emtpy list of allowed selectable object store IDs during creation."""
return []
[docs] def get_concrete_store_by_object_store_id(self, object_store_id: str) -> Optional["ConcreteObjectStore"]:
"""If this is a distributed object store, get ConcreteObjectStore by object_store_id."""
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] @abc.abstractmethod
def cache_targets(self) -> List[CacheTarget]:
"""Return a list of CacheTargets used by this object store."""
raise NotImplementedError()
[docs] @abc.abstractmethod
def get_quota_source_map(self):
"""Return QuotaSourceMap describing mapping of object store IDs to quota sources."""
[docs] @abc.abstractmethod
def get_device_source_map(self) -> "DeviceSourceMap":
"""Return DeviceSourceMap describing mapping of object store IDs to device sources."""
[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
self.galaxy_enable_quotas = config.enable_quotas
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 start(self):
"""
Call all postfork function(s) here. These functions spawn a thread.
We register start(self) with app, so app starts the threads. Override
this function in subclasses, as needed.
"""
[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})
store_type = self.store_type
return {
"config": config_to_dict(self.config),
"extra_dirs": extra_dirs,
"type": 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 construct_path(self, obj, **kwargs):
return self._invoke("construct_path", 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_description_markdown(self, obj):
return self._invoke("get_concrete_store_description_markdown", obj)
[docs] def get_concrete_store_badges(self, obj) -> List[BadgeDict]:
return self._invoke("get_concrete_store_badges", obj)
[docs] @classmethod
def parse_private_from_config_xml(clazz, config_xml):
private = DEFAULT_PRIVATE
if config_xml is not None:
private = asbool(config_xml.attrib.get("private", DEFAULT_PRIVATE))
return private
[docs] @classmethod
def parse_badges_from_config_xml(clazz, badges_xml):
badges = []
for e in badges_xml:
type = e.tag
message = e.text
badges.append({"type": type, "message": message})
return badges
[docs] def get_quota_source_map(self):
# I'd rather keep this abstract... but register_singleton wants it to be instantiable...
raise NotImplementedError()
[docs]class ConcreteObjectStore(BaseObjectStore):
"""Subclass of ObjectStore for stores that don't delegate (non-nested).
Adds store_by and quota_source functionality. These attributes do not make
sense for the delegating object stores, they should describe files at actually
persisted, not how a file is routed to a persistence source.
"""
badges: List[StoredBadgeDict]
device_id: Optional[str] = None
[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)
# Annotate this as true to prevent sharing of data.
self.private = config_dict.get("private", DEFAULT_PRIVATE)
# short label describing the quota source or null to use default
# quota source right on user object.
quota_config = config_dict.get("quota", {})
self.quota_source = quota_config.get("source", DEFAULT_QUOTA_SOURCE)
self.quota_enabled = quota_config.get("enabled", DEFAULT_QUOTA_ENABLED)
self.device_id = config_dict.get("device", None)
self.badges = read_badges(config_dict)
[docs] def to_dict(self):
rval = super().to_dict()
rval["private"] = self.private
rval["store_by"] = self.store_by
rval["name"] = self.name
rval["description"] = self.description
rval["quota"] = {
"source": self.quota_source,
"enabled": self.quota_enabled,
}
rval["badges"] = self._get_concrete_store_badges(None)
rval["device"] = self.device_id
return rval
[docs] def to_model(self, object_store_id: str) -> "ConcreteObjectStoreModel":
return ConcreteObjectStoreModel(
object_store_id=object_store_id,
private=self.private,
name=self.name,
description=self.description,
quota=QuotaModel(source=self.quota_source, enabled=self.quota_enabled),
badges=self._get_concrete_store_badges(None),
device=self.device_id,
)
def _get_concrete_store_badges(self, obj) -> List[BadgeDict]:
return serialize_badges(
self.badges,
self.galaxy_enable_quotas and self.quota_enabled,
self.private,
)
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
def _is_private(self, obj):
return self.private
@property
def cache_target(self) -> Optional[CacheTarget]:
return None
[docs] def cache_targets(self) -> List[CacheTarget]:
cache_target = self.cache_target
return [cache_target] if cache_target is not None else []
[docs] def get_quota_source_map(self):
quota_source_map = QuotaSourceMap(
self.quota_source,
self.quota_enabled,
)
return quota_source_map
[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, enable_quotas=True), dict(files_dir=file_path))
>>> o = 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
device = config_xml.attrib.get("device", None)
config_dict["device"] = device
for e in config_xml:
if e.tag == "quota":
config_dict["quota"] = {
"source": e.get("source", DEFAULT_QUOTA_SOURCE),
"enabled": asbool(e.get("enabled", DEFAULT_QUOTA_ENABLED)),
}
elif e.tag == "files_dir":
config_dict["files_dir"] = e.get("path")
elif e.tag == "description":
config_dict["description"] = e.text
elif e.tag == "badges":
config_dict["badges"] = BaseObjectStore.parse_badges_from_config_xml(e)
else:
extra_dirs.append({"type": e.get("type"), "path": e.get("path")})
config_dict["extra_dirs"] = extra_dirs
config_dict["private"] = BaseObjectStore.parse_private_from_config_xml(config_xml)
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) or 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)
return self
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) -> int:
"""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:
# Likely a race condition in which we delete the job working directory
# and another process writes files into that directory.
# If the path doesn't exist anymore, another rmtree call was successful.
path = self.__get_filename(obj, **kwargs)
if path is None:
return True
else:
log.critical(f"{path} delete error {ex}", exc_info=True)
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."""
objectstore = random.choice(list(self.backends.values()))
return objectstore.create(obj, **kwargs)
[docs] def cache_targets(self) -> List[CacheTarget]:
cache_targets = []
for backend in self.backends.values():
cache_targets.extend(backend.cache_targets())
# TODO: merge more intelligently - de-duplicate paths and handle conflicting sizes/percents
return cache_targets
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_concrete_store_badges(self, obj) -> List[BadgeDict]:
return self._call_method("_get_concrete_store_badges", obj, [], False)
def _is_private(self, obj):
return self._call_method("_is_private", obj, ObjectNotFound, True)
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(
f"objectstore, _call_method failed: {method} on {self._repr_object_for_exception(obj)}, kwargs: {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._quota_source_map = None
self._device_source_map = None
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()
user_selection_allowed = []
for backend_def in config_dict["backends"]:
backened_id = backend_def["id"]
maxpctfull = backend_def.get("max_percent_full", 0)
weight = backend_def["weight"]
allow_selection = backend_def.get("allow_selection")
if allow_selection:
user_selection_allowed.append(backened_id)
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.user_selection_allowed = user_selection_allowed
self.allow_user_selection = bool(user_selection_allowed)
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)
allow_selection = asbool(b.get("allow_selection"))
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
backend_config_dict["allow_selection"] = allow_selection
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 _construct_path(self, obj, **kwargs):
return self.backends[obj.object_store_id].construct_path(obj, **kwargs)
def _create(self, obj, **kwargs):
"""The only method in which obj.object_store_id may be None."""
object_store_id = obj.object_store_id
if object_store_id is None or not self._exists(obj, **kwargs):
if object_store_id is None or object_store_id not in self.backends:
try:
object_store_id = random.choice(self.weighted_backend_ids)
obj.object_store_id = object_store_id
except IndexError:
raise ObjectInvalid(
f"objectstore.create, could not generate obj.object_store_id: {obj}, kwargs: {kwargs}"
)
log.debug(
"Selected backend '%s' for creation of %s %s", object_store_id, obj.__class__.__name__, obj.id
)
else:
log.debug(
"Using preferred backend '%s' for creation of %s %s",
object_store_id,
obj.__class__.__name__,
obj.id,
)
return self.backends[object_store_id].create(obj, **kwargs)
else:
return self.backends[object_store_id]
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(
f"objectstore, _call_method failed: {method} on {self._repr_object_for_exception(obj)}, kwargs: {kwargs}"
)
else:
return default
[docs] def get_quota_source_map(self):
if self._quota_source_map is None:
quota_source_map = QuotaSourceMap()
self._merge_quota_source_map(quota_source_map, self)
self._quota_source_map = quota_source_map
return self._quota_source_map
[docs] def get_device_source_map(self) -> "DeviceSourceMap":
if self._device_source_map is None:
device_source_map = DeviceSourceMap()
self._merge_device_source_map(device_source_map, self)
self._device_source_map = device_source_map
return self._device_source_map
@classmethod
def _merge_quota_source_map(clz, quota_source_map, object_store):
for backend_id, backend in object_store.backends.items():
if isinstance(backend, DistributedObjectStore):
clz._merge_quota_source_map(quota_source_map, backend)
else:
quota_source_map.backends[backend_id] = backend.get_quota_source_map()
@classmethod
def _merge_device_source_map(clz, device_source_map: "DeviceSourceMap", object_store):
for backend_id, backend in object_store.backends.items():
if isinstance(backend, DistributedObjectStore):
clz._merge_device_source_map(device_source_map, backend)
else:
device_source_map.backends[backend_id] = backend.get_device_source_map()
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] def object_store_ids(self, private=None):
object_store_ids = []
for backend_id, backend in self.backends.items():
object_store_ids.extend(backend.object_store_ids(private=private))
if backend.private is private or private is None:
object_store_ids.append(backend_id)
return object_store_ids
[docs] def object_store_allows_id_selection(self) -> bool:
"""Return True if this object store respects object_store_id and allow selection of this."""
return self.allow_user_selection
[docs] def object_store_ids_allowing_selection(self) -> List[str]:
"""Return a non-emtpy list of allowed selectable object store IDs during creation."""
return self.user_selection_allowed
[docs] def get_concrete_store_by_object_store_id(self, object_store_id: str) -> Optional["ConcreteObjectStore"]:
"""If this is a distributed object store, get ConcreteObjectStore by object_store_id."""
return self.backends[object_store_id]
[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] = {}
is_private = config_dict.get("private", DEFAULT_PRIVATE)
for order, backend_def in enumerate(config_dict["backends"]):
backend_is_private = backend_def.get("private")
if backend_is_private is not None:
assert (
is_private == backend_is_private
), "The private attribute must be defined on the HierarchicalObjectStore and not contained concrete objectstores."
backend_quota = backend_def.get("quota")
if backend_quota is not None:
# Make sure just was using defaults - because cannot override what is
# is setup by the HierarchicalObjectStore.
assert backend_quota.get("source", DEFAULT_QUOTA_SOURCE) == DEFAULT_QUOTA_SOURCE
assert backend_quota.get("enabled", DEFAULT_QUOTA_ENABLED) == DEFAULT_QUOTA_ENABLED
backends[order] = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
self.backends = backends
self.private = is_private
quota_config = config_dict.get("quota", {})
self.quota_source = quota_config.get("source", DEFAULT_QUOTA_SOURCE)
self.quota_enabled = quota_config.get("enabled", DEFAULT_QUOTA_ENABLED)
[docs] @classmethod
def parse_xml(clazz, config_xml):
backends_list = []
is_private = BaseObjectStore.parse_private_from_config_xml(config_xml)
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["private"] = is_private
backend_config_dict["type"] = store_type
backends_list.append(backend_config_dict)
config_dict = {"backends": backends_list}
config_dict["private"] = is_private
return config_dict
[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
as_dict["private"] = self.private
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 _construct_path(self, obj, **kwargs):
return self.backends[0].construct_path(obj, **kwargs)
def _create(self, obj, **kwargs):
"""Call the primary object store."""
return self.backends[0].create(obj, **kwargs)
def _is_private(self, obj):
# Unlink the DistributedObjectStore - the HierarchicalObjectStore does not use
# object_store_id - so all the contained object stores need to define is_private
# the same way.
return self.private
[docs] def get_quota_source_map(self):
quota_source_map = QuotaSourceMap(
self.quota_source,
self.quota_enabled,
)
return quota_source_map
[docs]class ConcreteObjectStoreModel(BaseModel):
object_store_id: Optional[str] = None
private: bool
name: Optional[str] = None
description: Optional[str] = None
quota: QuotaModel
badges: List[BadgeDict]
device: Optional[str] = None
[docs]def type_to_object_store_class(store: str, fsmon: bool = False) -> Tuple[Type[BaseObjectStore], Dict[str, Any]]:
objectstore_class: Type[BaseObjectStore]
objectstore_constructor_kwds = {}
if store == "disk":
objectstore_class = DiskObjectStore
elif store in ["s3", "aws_s3"]:
from .s3 import S3ObjectStore
objectstore_class = S3ObjectStore
elif store == "cloud":
from .cloud import Cloud
objectstore_class = Cloud
elif store in ["swift", "generic_s3"]:
from .s3 import GenericS3ObjectStore
objectstore_class = GenericS3ObjectStore
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, disable_process_management=False
):
"""
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 an application config object from to_dict of an ObjectStore.
config = Bunch(disable_process_management=disable_process_management, **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):
log.debug("Reading object store config from file: %s", 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")
elif config.object_store_config:
log.debug("Reading object store config from object_store_config option")
from_object = "dict"
config_dict = config.object_store_config
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 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,
"enable_quotas": config.enable_quotas,
"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 DeviceSourceMap:
[docs] def __init__(self, device_id=DEFAULT_DEVICE_ID):
self.default_device_id = device_id
self.backends = {}
[docs] def get_device_id(self, object_store_id: str) -> Optional[str]:
if object_store_id in self.backends:
device_map = self.backends.get(object_store_id)
if device_map:
print(device_map)
return device_map.get_device_id(object_store_id)
return self.default_device_id
[docs]class QuotaSourceMap:
[docs] def __init__(self, source=DEFAULT_QUOTA_SOURCE, enabled=DEFAULT_QUOTA_ENABLED):
self.default_quota_source = source
self.default_quota_enabled = enabled
self.info = QuotaSourceInfo(self.default_quota_source, self.default_quota_enabled)
self.backends = {}
self._labels = None
[docs] def get_quota_source_info(self, object_store_id):
if object_store_id in self.backends:
return self.backends[object_store_id].get_quota_source_info(object_store_id)
else:
return self.info
[docs] def get_quota_source_label(self, object_store_id):
if object_store_id in self.backends:
return self.backends[object_store_id].get_quota_source_label(object_store_id)
else:
return self.default_quota_source
[docs] def get_quota_source_labels(self):
if self._labels is None:
labels = set()
if self.default_quota_source:
labels.add(self.default_quota_source)
for backend in self.backends.values():
labels = labels.union(backend.get_quota_source_labels())
self._labels = labels
return self._labels
[docs] def default_usage_excluded_ids(self):
exclude_object_store_ids = []
for backend_id, backend_source_map in self.backends.items():
if backend_source_map.default_quota_source is not None:
exclude_object_store_ids.append(backend_id)
elif not backend_source_map.default_quota_enabled:
exclude_object_store_ids.append(backend_id)
return exclude_object_store_ids
[docs] def get_id_to_source_pairs(self, include_default_quota_source=False):
pairs = []
for backend_id, backend_source_map in self.backends.items():
if (
backend_source_map.default_quota_source is not None or include_default_quota_source
) and backend_source_map.default_quota_enabled:
pairs.append((backend_id, backend_source_map.default_quota_source))
return pairs
[docs] def ids_per_quota_source(self, include_default_quota_source=False):
quota_sources: Dict[Optional[str], List[str]] = {}
for object_id, quota_source_label in self.get_id_to_source_pairs(
include_default_quota_source=include_default_quota_source
):
if quota_source_label not in quota_sources:
quota_sources[quota_source_label] = []
quota_sources[quota_source_label].append(object_id)
return quota_sources
# Calling these client_message to make it clear they should use the language of the
# Galaxy UI/UX - for instance "storage location" not "objectstore".
[docs]class ObjectCreationProblemSharingDisabled(ObjectCreationProblem):
client_message = "Job attempted to create sharable output datasets in a storage location with sharing disabled"
[docs]class ObjectCreationProblemStoreFull(ObjectCreationProblem):
client_message = (
"Job attempted to create output datasets in a full storage location, please contact your admin for more details"
)
[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, require_shareable=False):
self.set_dataset_object_store_id(data.dataset, require_shareable=require_shareable)
[docs] def set_dataset_object_store_id(self, dataset, require_shareable=True):
# 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:
ensure_non_private = require_shareable
concrete_store = self.object_store.create(dataset, ensure_non_private=ensure_non_private)
if concrete_store.private and require_shareable:
raise ObjectCreationProblemSharingDisabled()
except ObjectInvalid:
raise ObjectCreationProblemStoreFull()
self.object_store_id = dataset.object_store_id # these will be the same thing after the first output
[docs]def persist_extra_files(
object_store: ObjectStore,
src_extra_files_path: str,
primary_data: "DatasetInstance",
extra_files_path_name: Optional[str] = None,
) -> None:
if not primary_data.dataset.purged and os.path.exists(src_extra_files_path):
assert primary_data.dataset
if not extra_files_path_name:
extra_files_path_name = primary_data.dataset.extra_files_path_name_from(object_store)
assert extra_files_path_name
for root, _dirs, files in safe_walk(src_extra_files_path):
extra_dir = os.path.join(extra_files_path_name, os.path.relpath(root, src_extra_files_path))
extra_dir = os.path.normpath(extra_dir)
for f in files:
if not in_directory(f, src_extra_files_path):
# Unclear if this can ever happen if we use safe_walk ... probably not ?
raise MalformedContents(f"Invalid dataset path: {f}")
object_store.update_from_file(
primary_data.dataset,
extra_dir=extra_dir,
alt_name=f,
file_name=os.path.join(root, f),
create=True,
preserve_symlinks=True,
)