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Source code for galaxy.model.metadata
"""
Galaxy Metadata
"""
import copy
import json
import logging
import os
import shutil
import sys
import tempfile
import weakref
from collections import OrderedDict
from os.path import abspath
from six import string_types
from sqlalchemy.orm import object_session
import galaxy.model
from galaxy.util import (
form_builder,
listify,
string_as_bool,
stringify_dictionary_keys,
unicodify,
)
from galaxy.util.json import safe_dumps
from galaxy.util.object_wrapper import sanitize_lists_to_string
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(object):
"""
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_statments__' 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(object):
"""
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):
self.parent = parent
# 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 __iter__(self):
return self.parent._metadata.__iter__()
[docs] def get(self, key, default=None):
try:
return self.__getattr__(key) or default
except Exception:
return default
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], object_session(self.parent))
return self.spec[name].wrap(self.spec[name].default, object_session(self.parent))
if name in self.parent._metadata:
return self.parent._metadata[name]
def __setattr__(self, name, value):
if name == "parent":
return self.set_parent(value)
else:
if name in self.spec:
self.parent._metadata[name] = self.spec[name].unwrap(value)
else:
self.parent._metadata[name] = value
[docs] def remove_key(self, name):
if name in self.parent._metadata:
del self.parent._metadata[name]
else:
log.info("Attempted to delete invalid key '%s' from MetadataCollection" % name)
[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('loading metadata from file for: %s %s' % (dataset.__class__.__name__, dataset.id))
JSONified_dict = json.load(open(filename))
elif json_dict is not None:
log.debug('loading metadata from dict for: %s %s' % (dataset.__class__.__name__, dataset.id))
if isinstance(json_dict, string_types):
JSONified_dict = json.loads(json_dict)
elif isinstance(json_dict, dict):
JSONified_dict = json_dict
else:
raise ValueError("json_dict must be either a dictionary or a string, got %s." % (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__']
[docs] def to_JSON_dict(self, filename=None):
# galaxy.model.customtypes.json_encoder.encode()
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__']
if filename is None:
return json.dumps(meta_dict)
json.dump(meta_dict, open(filename, 'wt+'))
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".
"""
[docs] def __init__(self, *args, **kwds):
super(MetadataSpecCollection, self).__init__(*args, **kwds)
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(object):
[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=None, source_context=None):
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(object):
"""
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)
[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(DBKeyParameter, self).get_field(value, context, other_values, values, **kwd)
[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
mf = session.query(galaxy.model.MetadataFile).get(value)
return mf
[docs] def make_copy(self, value, target_context, source_context):
value = self.wrap(value, object_session(target_context.parent))
if value:
new_value = galaxy.model.MetadataFile(dataset=target_context.parent, name=self.spec.name)
object_session(target_context.parent).add(new_value)
object_session(target_context.parent).flush()
shutil.copy(value.file_name, new_value.file_name)
return self.unwrap(new_value)
return None
[docs] @classmethod
def marshal(cls, value):
if isinstance(value, galaxy.model.MetadataFile):
value = value.id
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)
parent.dataset.object_store.update_from_file(mf,
file_name=file_name,
extra_dir='_metadata_files',
extra_dir_at_root=True,
alt_name=os.path.basename(mf.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, **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):
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(**kwds)
# This class is used when a database file connection is not available
[docs]class MetadataTempFile(object):
tmp_dir = 'database/tmp' # this should be overwritten as necessary in calling scripts
@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:
for key, value in json.load(open(filename)).items():
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",
)