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Source code for galaxy.model.metadata
"""
Galaxy Metadata
"""
import copy
import json
import logging
import os
import sys
import tempfile
import weakref
from collections import OrderedDict
from collections.abc import Mapping
from os.path import abspath
from typing import (
Any,
Iterator,
Optional,
TYPE_CHECKING,
Union,
)
from sqlalchemy.orm import object_session
from sqlalchemy.orm.attributes import flag_modified
import galaxy.model
from galaxy.model.scoped_session import galaxy_scoped_session
from galaxy.security.object_wrapper import sanitize_lists_to_string
from galaxy.util import (
form_builder,
listify,
string_as_bool,
stringify_dictionary_keys,
unicodify,
)
from galaxy.util.json import safe_dumps
if TYPE_CHECKING:
from galaxy.model import DatasetInstance
from galaxy.model.none_like import NoneDataset
from galaxy.model.store import SessionlessContext
log = logging.getLogger(__name__)
STATEMENTS = "__galaxy_statements__" # this is the name of the property in a Datatype class where new metadata spec element Statements are stored
[docs]class Statement:
"""
This class inserts its target into a list in the surrounding
class. the data.Data class has a metaclass which executes these
statements. This is how we shove the metadata element spec into
the class.
"""
def __call__(self, *args, **kwargs):
# get the locals dictionary of the frame object one down in the call stack (i.e. the Datatype class calling MetadataElement)
class_locals = sys._getframe(1).f_locals
# get and set '__galaxy_statements__' to an empty list if not in locals dict
statements = class_locals.setdefault(STATEMENTS, [])
# add Statement containing info to populate a MetadataElementSpec
statements.append((self, args, kwargs))
[docs] @classmethod
def process(cls, element):
for statement, args, kwargs in getattr(element, STATEMENTS, []):
statement.target(
element, *args, **kwargs
) # statement.target is MetadataElementSpec, element is a Datatype class
[docs]class MetadataCollection(Mapping):
"""
MetadataCollection is not a collection at all, but rather a proxy
to the real metadata which is stored as a Dictionary. This class
handles processing the metadata elements when they are set and
retrieved, returning default values in cases when metadata is not set.
"""
[docs] def __init__(
self,
parent: Union["DatasetInstance", "NoneDataset"],
session: Optional[Union[galaxy_scoped_session, "SessionlessContext"]] = None,
) -> None:
self.parent = parent
self._session = session
# initialize dict if needed
if self.parent._metadata is None:
self.parent._metadata = {}
[docs] def get_parent(self):
if "_parent" in self.__dict__:
return self.__dict__["_parent"]()
return None
[docs] def set_parent(self, parent):
# use weakref to prevent a circular reference interfering with garbage
# collection: hda/lda (parent) <--> MetadataCollection (self) ; needs to be
# hashable, so cannot use proxy.
self.__dict__["_parent"] = weakref.ref(parent)
parent = property(get_parent, set_parent)
@property
def spec(self):
return self.parent.datatype.metadata_spec
def _object_session(self, item):
return self._session if self._session else object_session(item)
def __iter__(self) -> Iterator[Any]:
yield from self.spec.keys()
def __getitem__(self, key):
try:
self.__getattribute__(key)
except AttributeError:
try:
return self.__getattr__(key)
except Exception:
raise KeyError
# `key` is an attribute of this instance, not some metadata: raise
# KeyError to prevent e.g. `'items' in dataset.metadata` from returning
# True
# Not doing this would also break Cheetah's NameMapper._valueForName()
# since dataset.metadata['items'] would be None
raise KeyError
def __len__(self):
return len(self.spec)
def __str__(self):
return dict(self.items()).__str__()
def __bool__(self):
return bool(self.parent._metadata)
__nonzero__ = __bool__
def __getattr__(self, name):
if name in self.spec:
if name in self.parent._metadata:
return self.spec[name].wrap(self.parent._metadata[name], self._object_session(self.parent))
return self.spec[name].wrap(self.spec[name].default, self._object_session(self.parent))
if name in self.parent._metadata:
return self.parent._metadata[name]
# Instead of raising an AttributeError for non-existing metadata, we return None
return None
def __setattr__(self, name, value):
if name == "parent":
return self.set_parent(value)
elif name == "_session":
super().__setattr__(name, value)
else:
if name in self.spec:
self.parent._metadata[name] = self.spec[name].unwrap(value)
else:
self.parent._metadata[name] = value
flag_modified(self.parent, "_metadata")
[docs] def remove_key(self, name):
if name in self.parent._metadata:
del self.parent._metadata[name]
else:
log.info(f"Attempted to delete invalid key '{name}' from MetadataCollection")
[docs] def element_is_set(self, name) -> bool:
"""
check if the meta data with the given name is set, i.e.
- if the such a metadata actually exists and
- if its value differs from no_value
:param name: the name of the metadata element
:returns: True if the value differes from the no_value
False if its equal of if no metadata with the name is specified
"""
meta_val = self[name]
try:
meta_spec = self.parent.metadata.spec[name]
except KeyError:
log.debug(f"No metadata element with name '{name}' found")
return False
return meta_val != meta_spec.no_value
[docs] def get_metadata_parameter(self, name, **kwd):
if name in self.spec:
field = self.spec[name].param.get_field(getattr(self, name), self, None, **kwd)
field.value = getattr(self, name)
return field
[docs] def make_dict_copy(self, to_copy):
"""Makes a deep copy of input iterable to_copy according to self.spec"""
rval = {}
for key, value in to_copy.items():
if key in self.spec:
rval[key] = self.spec[key].param.make_copy(value, target_context=self, source_context=to_copy)
return rval
@property
def requires_dataset_id(self):
for key in self.spec:
if isinstance(self.spec[key].param, FileParameter):
return True
return False
[docs] def from_JSON_dict(self, filename=None, path_rewriter=None, json_dict=None):
dataset = self.parent
if filename is not None:
log.debug(f"loading metadata from file for: {dataset.__class__.__name__} {dataset.id}")
with open(filename) as fh:
JSONified_dict = json.load(fh)
elif json_dict is not None:
log.debug(f"loading metadata from dict for: {dataset.__class__.__name__} {dataset.id}")
if isinstance(json_dict, str):
JSONified_dict = json.loads(json_dict)
elif isinstance(json_dict, dict):
JSONified_dict = json_dict
else:
raise ValueError(f"json_dict must be either a dictionary or a string, got {type(json_dict)}.")
else:
raise ValueError("You must provide either a filename or a json_dict")
# We build a dictionary for metadata name / value pairs
# because when we copy MetadataTempFile objects we flush the datasets'
# session, but only include the newly created MetadataFile object.
# If we were to set the metadata elements in the first for loop we'd
# lose all previously set metadata elements
metadata_name_value = {}
for name, spec in self.spec.items():
if name in JSONified_dict:
from_ext_kwds = {}
external_value = JSONified_dict[name]
param = spec.param
if isinstance(param, FileParameter):
from_ext_kwds["path_rewriter"] = path_rewriter
value = param.from_external_value(external_value, dataset, **from_ext_kwds)
metadata_name_value[name] = value
elif name in dataset._metadata:
# if the metadata value is not found in our externally set metadata but it has a value in the 'old'
# metadata associated with our dataset, we'll delete it from our dataset's metadata dict
del dataset._metadata[name]
for name, value in metadata_name_value.items():
dataset._metadata[name] = value
if "__extension__" in JSONified_dict:
dataset.extension = JSONified_dict["__extension__"]
if "__validated_state__" in JSONified_dict:
dataset.validated_state = JSONified_dict["__validated_state__"]
if "__validated_state_message__" in JSONified_dict:
dataset.validated_state_message = JSONified_dict["__validated_state_message__"]
flag_modified(dataset, "_metadata")
[docs] def to_JSON_dict(self, filename=None):
meta_dict = {}
dataset_meta_dict = self.parent._metadata
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[name] = spec.param.to_external_value(dataset_meta_dict[name])
if "__extension__" in dataset_meta_dict:
meta_dict["__extension__"] = dataset_meta_dict["__extension__"]
if "__validated_state__" in dataset_meta_dict:
meta_dict["__validated_state__"] = dataset_meta_dict["__validated_state__"]
if "__validated_state_message__" in dataset_meta_dict:
meta_dict["__validated_state_message__"] = dataset_meta_dict["__validated_state_message__"]
try:
encoded_meta_dict = galaxy.model.custom_types.json_encoder.encode(meta_dict)
except Exception as e:
raise Exception(f"Failed encoding metadata dictionary: {meta_dict}") from e
if filename is None:
return encoded_meta_dict
with open(filename, "wt+") as fh:
fh.write(encoded_meta_dict)
def __getstate__(self):
# cannot pickle a weakref item (self._parent), when
# data._metadata_collection is None, it will be recreated on demand
return None
[docs]class MetadataSpecCollection(OrderedDict):
"""
A simple extension of OrderedDict which allows cleaner access to items
and allows the values to be iterated over directly as if it were a
list. append() is also implemented for simplicity and does not
"append".
"""
def __getattr__(self, name):
if name not in self:
raise AttributeError
return self.get(name)
def __repr__(self):
# force elements to draw with __str__ for sphinx-apidoc
return ", ".join(item.__str__() for item in self.values())
[docs]class MetadataParameter:
[docs] def get_field(self, value=None, context=None, other_values=None, **kwd):
context = context or {}
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=value)
[docs] def make_copy(self, value, target_context: MetadataCollection, source_context):
return copy.deepcopy(value)
[docs] @classmethod
def marshal(cls, value):
"""
This method should/can be overridden to convert the incoming
value to whatever type it is supposed to be.
"""
return value
[docs] def unwrap(self, form_value):
"""
Turns a value into its storable form.
"""
value = self.marshal(form_value)
self.validate(value)
return value
[docs] def from_external_value(self, value, parent):
"""
Turns a value read from an external dict into its value to be pushed directly into the metadata dict.
"""
return value
[docs] def to_external_value(self, value):
"""
Turns a value read from a metadata into its value to be pushed directly into the external dict.
"""
return value
[docs]class MetadataElementSpec:
"""
Defines a metadata element and adds it to the metadata_spec (which
is a MetadataSpecCollection) of datatype.
"""
[docs] def __init__(
self,
datatype,
name=None,
desc=None,
param=MetadataParameter,
default=None,
no_value=None,
visible=True,
set_in_upload=False,
**kwargs,
):
self.name = name
self.desc = desc or name
self.default = default
self.no_value = no_value
self.visible = visible
self.set_in_upload = set_in_upload
# Catch-all, allows for extra attributes to be set
self.__dict__.update(kwargs)
# set up param last, as it uses values set above
self.param = param(self)
# add spec element to the spec
datatype.metadata_spec.append(self)
# Should we validate that non-optional elements have been set ?
# (The answer is yes, but not all datatypes control optionality appropriately at this point.)
# This allows us to check that inherited MetadataElement instances from datatypes that set
# check_required_metadata have been reviewed and considered really required.
self.check_required_metadata = datatype.__dict__.get("check_required_metadata", False)
[docs] def wrap(self, value, session):
"""
Turns a stored value into its usable form.
"""
return self.param.wrap(value, session)
[docs] def unwrap(self, value):
"""
Turns an incoming value into its storable form.
"""
return self.param.unwrap(value)
def __str__(self):
# TODO??: assuming param is the class of this MetadataElementSpec - add the plain class name for that
spec_dict = dict(param_class=self.param.__class__.__name__)
spec_dict.update(self.__dict__)
return "{name} ({param_class}): {desc}, defaults to '{default}'".format(**spec_dict)
# create a statement class that, when called,
# will add a new MetadataElementSpec to a class's metadata_spec
MetadataElement = Statement(MetadataElementSpec)
"""
MetadataParameter sub-classes.
"""
[docs]class SelectParameter(MetadataParameter):
[docs] def __init__(self, spec):
MetadataParameter.__init__(self, spec)
self.values = self.spec.get("values")
self.multiple = string_as_bool(self.spec.get("multiple"))
[docs] def to_string(self, value):
if value in [None, []]:
return str(self.spec.no_value)
if not isinstance(value, list):
value = [value]
return ",".join(map(str, value))
[docs] def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
field = form_builder.SelectField(self.spec.name, multiple=self.multiple, display=self.spec.get("display"))
if self.values:
value_list = self.values
elif values:
value_list = values
elif value:
value_list = [(v, v) for v in listify(value)]
else:
value_list = []
for val, label in value_list:
try:
if (self.multiple and val in value) or (not self.multiple and val == value):
field.add_option(label, val, selected=True)
else:
field.add_option(label, val, selected=False)
except TypeError:
field.add_option(val, label, selected=False)
return field
[docs] def wrap(self, value, session):
# do we really need this (wasteful)? - yes because we are not sure that
# all existing selects have been stored previously as lists. Also this
# will handle the case where defaults/no_values are specified and are
# single non-list values.
value = self.marshal(value)
if self.multiple:
return value
elif value:
return value[0] # single select, only return the first value
return None
[docs] @classmethod
def marshal(cls, value):
# Store select as list, even if single item
if value is None:
return []
if not isinstance(value, list):
return [value]
return value
[docs]class DBKeyParameter(SelectParameter):
[docs] def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
try:
values = kwd["trans"].app.genome_builds.get_genome_build_names(kwd["trans"])
except KeyError:
pass
return super().get_field(value, context, other_values, values, **kwd)
[docs] def make_copy(self, value, target_context: MetadataCollection, source_context):
value = listify(value)
return super().make_copy(value, target_context, source_context)
[docs]class RangeParameter(SelectParameter):
[docs] def __init__(self, spec):
SelectParameter.__init__(self, spec)
# The spec must be set with min and max values
self.min = spec.get("min") or 1
self.max = spec.get("max") or 1
self.step = self.spec.get("step") or 1
[docs] def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
if values is None:
values = list(zip(range(self.min, self.max, self.step), range(self.min, self.max, self.step)))
return SelectParameter.get_field(
self, value=value, context=context, other_values=other_values, values=values, **kwd
)
[docs] @classmethod
def marshal(cls, value):
value = SelectParameter.marshal(value)
values = [int(x) for x in value]
return values
[docs]class ColumnParameter(RangeParameter):
[docs] def get_field(self, value=None, context=None, other_values=None, values=None, **kwd):
context = context or {}
other_values = other_values or {}
if values is None and context:
column_range = range(1, (context.columns or 0) + 1, 1)
values = list(zip(column_range, column_range))
return RangeParameter.get_field(
self, value=value, context=context, other_values=other_values, values=values, **kwd
)
[docs]class PythonObjectParameter(MetadataParameter):
[docs] def to_string(self, value):
if not value:
return self.spec._to_string(self.spec.no_value)
return self.spec._to_string(value)
[docs] def get_field(self, value=None, context=None, other_values=None, **kwd):
context = context or {}
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=self._to_string(value))
[docs]class FileParameter(MetadataParameter):
[docs] def to_string(self, value):
if not value:
return str(self.spec.no_value)
return value.file_name
[docs] def to_safe_string(self, value):
# We do not sanitize file names
return self.to_string(value)
[docs] def get_field(self, value=None, context=None, other_values=None, **kwd):
context = context or {}
other_values = other_values or {}
return form_builder.TextField(self.spec.name, value=str(value.id))
[docs] def wrap(self, value, session):
if value is None:
return None
if isinstance(value, galaxy.model.MetadataFile) or isinstance(value, MetadataTempFile):
return value
if isinstance(value, int):
return session.query(galaxy.model.MetadataFile).get(value)
else:
return session.query(galaxy.model.MetadataFile).filter_by(uuid=value).one()
[docs] def make_copy(self, value, target_context: MetadataCollection, source_context):
session = target_context._object_session(target_context.parent)
value = self.wrap(value, session=session)
target_dataset = target_context.parent.dataset
if value and not value.id:
# This is a new MetadataFile object, we're not copying to another dataset.
# Just use it.
return self.unwrap(value)
if value and target_dataset.object_store.exists(target_dataset):
# Only copy MetadataFile if the target dataset has been created in an object store.
# All current datatypes re-generate MetadataFile objects when setting metadata,
# so this would ultimately get overwritten anyway.
new_value = galaxy.model.MetadataFile(dataset=target_context.parent, name=self.spec.name)
session.add(new_value)
try:
new_value.update_from_file(value.file_name)
except AssertionError:
session(target_context.parent).flush()
new_value.update_from_file(value.file_name)
return self.unwrap(new_value)
return None
[docs] @classmethod
def marshal(cls, value):
if isinstance(value, galaxy.model.MetadataFile):
# We want to push value.id to the database, but need to skip this when no session is available,
# as in extended_metadata mode, so there we just accept MetadataFile.
# We will only serialize MetadataFile in this mode and not push to the database, so this is OK.
value = value.id or value
if not isinstance(value, int) and object_session(value):
value = str(value.uuid)
return value
[docs] def from_external_value(self, value, parent, path_rewriter=None):
"""
Turns a value read from a external dict into its value to be pushed directly into the metadata dict.
"""
if MetadataTempFile.is_JSONified_value(value):
value = MetadataTempFile.from_JSON(value)
if isinstance(value, MetadataTempFile):
mf = parent.metadata.get(self.spec.name, None)
if mf is None:
mf = self.new_file(dataset=parent, **value.kwds)
# Ensure the metadata file gets updated with content
file_name = value.file_name
if path_rewriter:
# Job may have run with a different (non-local) tmp/working
# directory. Correct.
file_name = path_rewriter(file_name)
mf.update_from_file(file_name)
os.unlink(file_name)
value = mf.id
return value
[docs] def to_external_value(self, value):
"""
Turns a value read from a metadata into its value to be pushed directly into the external dict.
"""
if isinstance(value, galaxy.model.MetadataFile):
value = value.id
elif isinstance(value, MetadataTempFile):
value = MetadataTempFile.to_JSON(value)
return value
[docs] def new_file(self, dataset=None, metadata_tmp_files_dir=None, **kwds):
# If there is a place to store the file (i.e. an object_store has been bound to
# Dataset) then use a MetadataFile and assume it is accessible. Otherwise use
# a MetadataTempFile.
if getattr(dataset.dataset, "object_store", False) and not metadata_tmp_files_dir:
mf = galaxy.model.MetadataFile(name=self.spec.name, dataset=dataset, **kwds)
sa_session = object_session(dataset)
if sa_session:
sa_session.add(mf)
sa_session.flush() # flush to assign id
return mf
else:
# we need to make a tmp file that is accessable to the head node,
# we will be copying its contents into the MetadataFile objects filename after restoring from JSON
# we do not include 'dataset' in the kwds passed, as from_JSON_value() will handle this for us
return MetadataTempFile(metadata_tmp_files_dir=metadata_tmp_files_dir, **kwds)
# This class is used when a database file connection is not available
[docs]class MetadataTempFile:
tmp_dir = "database/tmp" # this should be overwritten as necessary in calling scripts
[docs] def __init__(self, metadata_tmp_files_dir=None, **kwds):
self.kwds = kwds
if metadata_tmp_files_dir:
self.tmp_dir = metadata_tmp_files_dir
self._filename = None
@property
def file_name(self):
if self._filename is None:
# we need to create a tmp file, accessable across all nodes/heads, save the name, and return it
self._filename = abspath(tempfile.NamedTemporaryFile(dir=self.tmp_dir, prefix="metadata_temp_file_").name)
open(self._filename, "wb+") # create an empty file, so it can't be reused using tempfile
return self._filename
[docs] def to_JSON(self):
return {"__class__": self.__class__.__name__, "filename": self.file_name, "kwds": self.kwds}
[docs] @classmethod
def from_JSON(cls, json_dict):
# need to ensure our keywords are not unicode
rval = cls(**stringify_dictionary_keys(json_dict["kwds"]))
rval._filename = json_dict["filename"]
return rval
[docs] @classmethod
def is_JSONified_value(cls, value):
return isinstance(value, dict) and value.get("__class__", None) == cls.__name__
[docs] @classmethod
def cleanup_from_JSON_dict_filename(cls, filename):
try:
with open(filename) as fh:
for value in json.load(fh).values():
if cls.is_JSONified_value(value):
value = cls.from_JSON(value)
if isinstance(value, cls) and os.path.exists(value.file_name):
log.debug("Cleaning up abandoned MetadataTempFile file: %s", value.file_name)
os.unlink(value.file_name)
except Exception as e:
log.debug("Failed to cleanup MetadataTempFile temp files from %s: %s", filename, unicodify(e))
__all__ = (
"Statement",
"MetadataElement",
"MetadataCollection",
"MetadataSpecCollection",
"MetadataParameter",
"MetadataElementSpec",
"SelectParameter",
"DBKeyParameter",
"RangeParameter",
"ColumnParameter",
"ColumnTypesParameter",
"ListParameter",
"DictParameter",
"PythonObjectParameter",
"FileParameter",
"MetadataTempFile",
)