def __init__( self, **kwargs ):
self.config = MockAppConfig( **kwargs )
self.security = self.config.security
self.object_store = objectstore.build_object_store_from_config( self.config )
self.model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True, object_store=self.object_store )
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagManager( self )
self.quota_agent = quota.QuotaAgent( self.model )
def __init__(self, app):
self.type_registry = DatasetCollectionTypesRegistry(app)
self.collection_type_descriptions = CollectionTypeDescriptionFactory(self.type_registry)
self.model = app.model
self.security = app.security
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.tag_manager = tags.GalaxyTagManager(app.model.context)
self.ldda_manager = lddas.LDDAManager(app)
def __init__(self, config=None, **kwargs):
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.security
self.name = kwargs.get('name', 'galaxy')
self.object_store = objectstore.build_object_store_from_config(self.config)
self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=self.object_store)
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagManager(self.model.context)
self.quota_agent = quota.QuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(
dynamic_params=None,
)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.genome_builds = GenomeBuilds(self)
self.job_manager = Bunch(job_queue=NoopQueue())
self.application_stack = ApplicationStack()
def __new_library_upload(trans,
cntrller,
uploaded_dataset,
library_bunch,
state=None):
current_user_roles = trans.get_current_user_roles()
if not ((trans.user_is_admin() and cntrller in ['library_admin', 'api'])
or trans.app.security_agent.can_add_library_item(
current_user_roles, library_bunch.folder)):
# This doesn't have to be pretty - the only time this should happen is if someone's being malicious.
raise Exception(
"User is not authorized to add datasets to this library.")
folder = library_bunch.folder
if uploaded_dataset.get('in_folder', False):
# Create subfolders if desired
for name in uploaded_dataset.in_folder.split(os.path.sep):
trans.sa_session.refresh(folder)
matches = [
x for x in active_folders(trans, folder) if x.name == name
]
if matches:
folder = matches[0]
else:
new_folder = trans.app.model.LibraryFolder(
name=name,
description='Automatically created by upload tool')
new_folder.genome_build = trans.app.genome_builds.default_value
folder.add_folder(new_folder)
trans.sa_session.add(new_folder)
trans.sa_session.flush()
trans.app.security_agent.copy_library_permissions(
trans, folder, new_folder)
folder = new_folder
if library_bunch.replace_dataset:
ld = library_bunch.replace_dataset
else:
ld = trans.app.model.LibraryDataset(folder=folder,
name=uploaded_dataset.name)
trans.sa_session.add(ld)
trans.sa_session.flush()
trans.app.security_agent.copy_library_permissions(trans, folder, ld)
ldda = trans.app.model.LibraryDatasetDatasetAssociation(
name=uploaded_dataset.name,
extension=uploaded_dataset.file_type,
dbkey=uploaded_dataset.dbkey,
library_dataset=ld,
user=trans.user,
create_dataset=True,
sa_session=trans.sa_session)
if uploaded_dataset.get('tag_using_filenames', False):
tag_from_filename = os.path.splitext(
os.path.basename(uploaded_dataset.name))[0]
tag_manager = tags.GalaxyTagManager(trans.sa_session)
tag_manager.apply_item_tag(item=ldda,
user=trans.user,
name='name',
value=tag_from_filename)
trans.sa_session.add(ldda)
if state:
ldda.state = state
else:
ldda.state = ldda.states.QUEUED
ldda.message = library_bunch.message
trans.sa_session.flush()
# Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
trans.app.security_agent.copy_library_permissions(trans, ld, ldda)
if library_bunch.replace_dataset:
# Copy the Dataset level permissions from replace_dataset to the new LibraryDatasetDatasetAssociation.dataset
trans.app.security_agent.copy_dataset_permissions(
library_bunch.replace_dataset.library_dataset_dataset_association.
dataset, ldda.dataset)
else:
# Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset
trans.app.security_agent.set_all_dataset_permissions(
ldda.dataset,
trans.app.security_agent.user_get_default_permissions(trans.user))
folder.add_library_dataset(ld, genome_build=uploaded_dataset.dbkey)
trans.sa_session.add(folder)
trans.sa_session.flush()
ld.library_dataset_dataset_association_id = ldda.id
trans.sa_session.add(ld)
trans.sa_session.flush()
# Handle template included in the upload form, if any. If the upload is not asynchronous ( e.g., URL paste ),
# then the template and contents will be included in the library_bunch at this point. If the upload is
# asynchronous ( e.g., uploading a file ), then the template and contents will be included in the library_bunch
# in the get_uploaded_datasets() method below.
if library_bunch.template and library_bunch.template_field_contents:
# Since information templates are inherited, the template fields can be displayed on the upload form.
# If the user has added field contents, we'll need to create a new form_values and info_association
# for the new library_dataset_dataset_association object.
# Create a new FormValues object, using the template we previously retrieved
form_values = trans.app.model.FormValues(
library_bunch.template, library_bunch.template_field_contents)
trans.sa_session.add(form_values)
trans.sa_session.flush()
# Create a new info_association between the current ldda and form_values
# TODO: Currently info_associations at the ldda level are not inheritable to the associated LibraryDataset,
# we need to figure out if this is optimal
info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation(
ldda, library_bunch.template, form_values)
trans.sa_session.add(info_association)
trans.sa_session.flush()
# If roles were selected upon upload, restrict access to the Dataset to those roles
if library_bunch.roles:
for role in library_bunch.roles:
dp = trans.app.model.DatasetPermissions(
trans.app.security_agent.permitted_actions.DATASET_ACCESS.
action, ldda.dataset, role)
trans.sa_session.add(dp)
trans.sa_session.flush()
return ldda
def __init__(self, app):
self.app = app
self.tag_manager = tags.GalaxyTagManager(app.model.context)
