def create(self, trans, parent, name, collection_type, element_identifiers=None,
elements=None, implicit_collection_info=None, trusted_identifiers=None,
hide_source_items=False, tags=None, copy_elements=False):
"""
PRECONDITION: security checks on ability to add to parent
occurred during load.
"""
# Trust embedded, newly created objects created by tool subsystem.
if trusted_identifiers is None:
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers(element_identifiers)
dataset_collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
)
implicit_inputs = []
if implicit_collection_info:
implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
implicit_output_name = None
if implicit_collection_info:
implicit_output_name = implicit_collection_info["implicit_output_name"]
return self._create_instance_for_collection(
trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags
)
def create(self, trans, parent, name, collection_type, element_identifiers=None,
elements=None, implicit_collection_info=None, trusted_identifiers=None,
hide_source_items=False, tags=None, copy_elements=False, history=None):
"""
PRECONDITION: security checks on ability to add to parent
occurred during load.
"""
# Trust embedded, newly created objects created by tool subsystem.
if trusted_identifiers is None:
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers(element_identifiers)
dataset_collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
hide_source_items=hide_source_items,
copy_elements=copy_elements,
history=history,
)
implicit_inputs = []
if implicit_collection_info:
implicit_inputs = implicit_collection_info.get('implicit_inputs', [])
implicit_output_name = None
if implicit_collection_info:
implicit_output_name = implicit_collection_info["implicit_output_name"]
return self._create_instance_for_collection(
trans, parent, name, dataset_collection, implicit_inputs=implicit_inputs, implicit_output_name=implicit_output_name, tags=tags
)
def create(
self,
trans,
parent, # PRECONDITION: security checks on ability to add to parent occurred during load.
name,
collection_type,
element_identifiers=None,
elements=None,
implicit_collection_info=None,
):
"""
"""
# Trust embedded, newly created objects created by tool subsystem.
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers( element_identifiers )
dataset_collection = self.__create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
)
if isinstance( parent, model.History ):
dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_collection_info:
for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]:
dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
for output_dataset in implicit_collection_info.get( "outputs" ):
if isinstance( output_dataset, model.HistoryDatasetCollectionAssociation ):
dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
else:
# dataset collection, don't need to do anything...
pass
trans.sa_session.add( output_dataset )
dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ]
log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) )
# Handle setting hid
parent.add_dataset_collection( dataset_collection_instance )
elif isinstance( parent, model.LibraryFolder ):
dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type( parent )
log.exception( message )
raise MessageException( message )
return self.__persist( dataset_collection_instance )
def create(
self,
trans,
parent, # PRECONDITION: security checks on ability to add to parent occurred during load.
name,
collection_type,
element_identifiers=None,
elements=None,
implicit_collection_info=None,
):
"""
"""
# Trust embedded, newly created objects created by tool subsystem.
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers( element_identifiers )
dataset_collection = self.__create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
)
if isinstance( parent, model.History ):
dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_collection_info:
for input_name, input_collection in implicit_collection_info[ "implicit_inputs" ]:
dataset_collection_instance.add_implicit_input_collection( input_name, input_collection )
for output_dataset in implicit_collection_info.get( "outputs" ):
output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
trans.sa_session.add( output_dataset )
dataset_collection_instance.implicit_output_name = implicit_collection_info[ "implicit_output_name" ]
log.debug("Created collection with %d elements" % ( len( dataset_collection_instance.collection.elements ) ) )
# Handle setting hid
parent.add_dataset_collection( dataset_collection_instance )
elif isinstance( parent, model.LibraryFolder ):
dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type( parent )
log.exception( message )
raise MessageException( message )
return self.__persist( dataset_collection_instance )
def create(self, trans, parent, name, collection_type, element_identifiers=None,
elements=None, implicit_collection_info=None, trusted_identifiers=None,
hide_source_items=False, tags=None):
"""
PRECONDITION: security checks on ability to add to parent
occurred during load.
"""
# Trust embedded, newly created objects created by tool subsystem.
if trusted_identifiers is None:
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers(element_identifiers)
dataset_collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
hide_source_items=hide_source_items,
)
if isinstance(parent, model.History):
dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_collection_info:
for input_name, input_collection in implicit_collection_info["implicit_inputs"]:
dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
for output_dataset in implicit_collection_info.get("outputs"):
if output_dataset not in trans.sa_session:
output_dataset = trans.sa_session.query(type(output_dataset)).get(output_dataset.id)
if isinstance(output_dataset, model.HistoryDatasetAssociation):
output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
elif isinstance(output_dataset, model.HistoryDatasetCollectionAssociation):
dataset_collection_instance.add_implicit_input_collection(input_name, input_collection)
else:
# dataset collection, don't need to do anything...
pass
trans.sa_session.add(output_dataset)
dataset_collection_instance.implicit_output_name = implicit_collection_info["implicit_output_name"]
log.debug("Created collection with %d elements" % (len(dataset_collection_instance.collection.elements)))
# Handle setting hid
parent.add_dataset_collection(dataset_collection_instance)
elif isinstance(parent, model.LibraryFolder):
dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type(parent)
log.exception(message)
raise MessageException(message)
tags = tags or {}
if implicit_collection_info:
for k, v in implicit_collection_info.get('implicit_inputs', []):
for tag in [t for t in v.tags if t.user_tname == 'name']:
tags[tag.value] = tag
for _, tag in tags.items():
dataset_collection_instance.tags.append(tag.copy())
return self.__persist(dataset_collection_instance)
def create(self,
trans,
parent,
name,
collection_type,
element_identifiers=None,
elements=None,
implicit_collection_info=None,
trusted_identifiers=None,
hide_source_items=False,
tags=None):
"""
PRECONDITION: security checks on ability to add to parent
occurred during load.
"""
# Trust embedded, newly created objects created by tool subsystem.
if trusted_identifiers is None:
trusted_identifiers = implicit_collection_info is not None
if element_identifiers and not trusted_identifiers:
validate_input_element_identifiers(element_identifiers)
dataset_collection = self.create_dataset_collection(
trans=trans,
collection_type=collection_type,
element_identifiers=element_identifiers,
elements=elements,
hide_source_items=hide_source_items,
)
if isinstance(parent, model.History):
dataset_collection_instance = self.model.HistoryDatasetCollectionAssociation(
collection=dataset_collection,
name=name,
)
if implicit_collection_info:
for input_name, input_collection in implicit_collection_info[
"implicit_inputs"]:
dataset_collection_instance.add_implicit_input_collection(
input_name, input_collection)
for output_dataset in implicit_collection_info.get("outputs"):
if output_dataset not in trans.sa_session:
output_dataset = trans.sa_session.query(
type(output_dataset)).get(output_dataset.id)
if isinstance(output_dataset,
model.HistoryDatasetAssociation):
output_dataset.hidden_beneath_collection_instance = dataset_collection_instance
elif isinstance(output_dataset,
model.HistoryDatasetCollectionAssociation):
dataset_collection_instance.add_implicit_input_collection(
input_name, input_collection)
else:
# dataset collection, don't need to do anything...
pass
trans.sa_session.add(output_dataset)
dataset_collection_instance.implicit_output_name = implicit_collection_info[
"implicit_output_name"]
log.debug("Created collection with %d elements" %
(len(dataset_collection_instance.collection.elements)))
# Handle setting hid
parent.add_dataset_collection(dataset_collection_instance)
elif isinstance(parent, model.LibraryFolder):
dataset_collection_instance = self.model.LibraryDatasetCollectionAssociation(
collection=dataset_collection,
folder=parent,
name=name,
)
else:
message = "Internal logic error - create called with unknown parent type %s" % type(
parent)
log.exception(message)
raise MessageException(message)
tags = tags or {}
if implicit_collection_info:
for k, v in implicit_collection_info.get('implicit_inputs', []):
for tag in [t for t in v.tags if t.user_tname == 'name']:
tags[tag.value] = tag
for _, tag in tags.items():
dataset_collection_instance.tags.append(tag.copy())
return self.__persist(dataset_collection_instance)
