def __get__(self, instance, owner):
"""Descriptor to automatically dereference references."""
if instance is None:
# Document class being used rather than a document object
return self
ReferenceField = _import_class("ReferenceField")
GenericReferenceField = _import_class("GenericReferenceField")
EmbeddedDocumentListField = _import_class("EmbeddedDocumentListField")
auto_dereference = instance._fields[self.name]._auto_dereference
dereference = auto_dereference and (
self.field is None
or isinstance(self.field, (GenericReferenceField, ReferenceField))
)
if (
instance._initialised
and dereference
and instance._data.get(self.name)
and not getattr(instance._data[self.name], "_dereferenced", False)
):
ref_values = instance._data.get(self.name)
instance._data[self.name] = self._lazy_load_refs(
ref_values=ref_values, instance=instance, name=self.name, max_depth=1
)
if hasattr(instance._data[self.name], "_dereferenced"):
instance._data[self.name]._dereferenced = True
value = super().__get__(instance, owner)
# Convert lists / values so we can watch for any changes on them
if isinstance(value, (list, tuple)):
if issubclass(type(self), EmbeddedDocumentListField) and not isinstance(
value, EmbeddedDocumentList
):
value = EmbeddedDocumentList(value, instance, self.name)
elif not isinstance(value, BaseList):
value = BaseList(value, instance, self.name)
instance._data[self.name] = value
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, instance, self.name)
instance._data[self.name] = value
if (
auto_dereference
and instance._initialised
and isinstance(value, (BaseList, BaseDict))
and not value._dereferenced
):
value = self._lazy_load_refs(
ref_values=value, instance=instance, name=self.name, max_depth=1
)
value._dereferenced = True
instance._data[self.name] = value
return value
def __get__(self, instance, owner):
"""Descriptor to automatically dereference references."""
if instance is None:
# Document class being used rather than a document object
return self
ReferenceField = _import_class('ReferenceField')
GenericReferenceField = _import_class('GenericReferenceField')
EmbeddedDocumentListField = _import_class('EmbeddedDocumentListField')
auto_dereference = instance._fields[self.name]._auto_dereference
dereference = (auto_dereference and
(self.field is None or isinstance(self.field,
(GenericReferenceField, ReferenceField))))
_dereference = _import_class('DeReference')()
if (instance._initialised and
dereference and
instance._data.get(self.name) and
not getattr(instance._data[self.name], '_dereferenced', False)):
instance._data[self.name] = _dereference(
instance._data.get(self.name), max_depth=1, instance=instance,
name=self.name
)
if hasattr(instance._data[self.name], '_dereferenced'):
instance._data[self.name]._dereferenced = True
value = super(ComplexBaseField, self).__get__(instance, owner)
# Convert lists / values so we can watch for any changes on them
if isinstance(value, (list, tuple)):
if (issubclass(type(self), EmbeddedDocumentListField) and
not isinstance(value, EmbeddedDocumentList)):
value = EmbeddedDocumentList(value, instance, self.name)
elif not isinstance(value, BaseList):
value = BaseList(value, instance, self.name)
instance._data[self.name] = value
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, instance, self.name)
instance._data[self.name] = value
if (auto_dereference and instance._initialised and
isinstance(value, (BaseList, BaseDict)) and
not value._dereferenced):
value = _dereference(
value, max_depth=1, instance=instance, name=self.name
)
value._dereferenced = True
instance._data[self.name] = value
return value
def __get__(self, instance, owner):
"""Descriptor to automatically dereference references.
"""
if instance is None:
# Document class being used rather than a document object
return self
ReferenceField = _import_class('ReferenceField')
GenericReferenceField = _import_class('GenericReferenceField')
EmbeddedDocumentListField = _import_class('EmbeddedDocumentListField')
dereference = (self._auto_dereference
and (self.field is None or isinstance(
self.field,
(GenericReferenceField, ReferenceField))))
_dereference = _import_class("DeReference")()
self._auto_dereference = instance._fields[self.name]._auto_dereference
if instance._initialised and dereference and instance._data.get(
self.name):
instance._data[self.name] = _dereference(instance._data.get(
self.name),
max_depth=1,
instance=instance,
name=self.name)
value = super(ComplexBaseField, self).__get__(instance, owner)
# Convert lists / values so we can watch for any changes on them
if isinstance(value, (list, tuple)):
if (issubclass(type(self), EmbeddedDocumentListField)
and not isinstance(value, EmbeddedDocumentList)):
value = EmbeddedDocumentList(value, instance, self.name)
elif not isinstance(value, BaseList):
value = BaseList(value, instance, self.name)
instance._data[self.name] = value
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, instance, self.name)
instance._data[self.name] = value
if (self._auto_dereference and instance._initialised
and isinstance(value, (BaseList, BaseDict))
and not value._dereferenced):
value = _dereference(value,
max_depth=1,
instance=instance,
name=self.name)
value._dereferenced = True
instance._data[self.name] = value
return value
def __expand_dynamic_values(self, name, value):
"""Expand any dynamic values to their correct types / values."""
if not isinstance(value, (dict, list, tuple)):
return value
# If the value is a dict with '_cls' in it, turn it into a document
is_dict = isinstance(value, dict)
if is_dict and '_cls' in value:
cls = get_document(value['_cls'])
return cls(**value)
if is_dict:
value = {
k: self.__expand_dynamic_values(k, v)
for k, v in value.items()
}
else:
value = [self.__expand_dynamic_values(name, v) for v in value]
# Convert lists / values so we can watch for any changes on them
EmbeddedDocumentListField = _import_class('EmbeddedDocumentListField')
if (isinstance(value, (list, tuple))
and not isinstance(value, BaseList)):
if issubclass(type(self), EmbeddedDocumentListField):
value = EmbeddedDocumentList(value, self, name)
else:
value = BaseList(value, self, name)
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, self, name)
return value
def get_queryset(self):
"""Get the AnalysisJob Annotation corresponding property from Mongo.
"""
acc = self.kwargs['accession'].lstrip('MGYA')
job_query = Q(pk=acc)
if self.analysis_job_filters:
job_query &= self.analysis_job_filters
job = get_object_or_404(emg_models.AnalysisJob, job_query)
analysis = None
try:
analysis = self.annotation_model.objects \
.get(analysis_id=str(job.job_id))
except self.annotation_model.DoesNotExist:
# Return an empty EmbeddedDocumentList, the entity exists
# but it doesn't have annotations
return EmbeddedDocumentList([], self.annotation_model,
self.annotation_model_property)
if hasattr(self, "annotation_model_property_resolver"):
return self.annotation_model_property_resolver(analysis)
return getattr(analysis, self.annotation_model_property)
def _convert_value(self, instance, value):
if isinstance(value, (list, tuple)):
if (issubclass(type(self), fields.EmbeddedDocumentListField) and
not isinstance(value, fields.EmbeddedDocumentList)):
value = EmbeddedDocumentList(value, instance, self.name)
elif not isinstance(value, BaseList):
value = BaseList(value, instance, self.name)
instance._data[self.name] = value
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, instance, self.name)
instance._data[self.name] = value
return value
def __expand_dynamic_values(self, name, value):
"""expand any dynamic values to their correct types / values"""
if not isinstance(value, (dict, list, tuple)):
return value
EmbeddedDocumentListField = _import_class('EmbeddedDocumentListField')
is_list = False
if not hasattr(value, 'items'):
is_list = True
value = dict([(k, v) for k, v in enumerate(value)])
if not is_list and '_cls' in value:
cls = get_document(value['_cls'])
return cls(**value)
data = {}
for k, v in value.items():
key = name if is_list else k
data[k] = self.__expand_dynamic_values(key, v)
if is_list: # Convert back to a list
data_items = sorted(data.items(), key=operator.itemgetter(0))
value = [v for k, v in data_items]
else:
value = data
# Convert lists / values so we can watch for any changes on them
if (isinstance(value, (list, tuple))
and not isinstance(value, BaseList)):
if issubclass(type(self), EmbeddedDocumentListField):
value = EmbeddedDocumentList(value, self, name)
else:
value = BaseList(value, self, name)
elif isinstance(value, dict) and not isinstance(value, BaseDict):
value = BaseDict(value, self, name)
return value
def annotation_model_property_resolver(self, analysis):
"""Get the taxonomic annotations using the following order:
- SSU -> version <= 5.0 of pipeline
- SSU >= 5.0 of pipeline
- ITS OneDB {}
- ITS unite
- LSU
"""
alternatives = [
"taxonomy",
"taxonomy_ssu",
"taxonomy_itsonedb",
"taxonomy_unite"
"taxonomy_lsu",
]
for alt in alternatives:
try:
return getattr(analysis, alt)
except AttributeError:
pass
return EmbeddedDocumentList([], self.annotation_model, "taxonomy")
