def __populate_non_job_params(self, param_dict):
# -- Add useful attributes/functions for use in creating command line.
# Function for querying a data table.
def get_data_table_entry(table_name, query_attr, query_val, return_attr):
"""
Queries and returns an entry in a data table.
"""
if table_name in self.app.tool_data_tables:
return self.app.tool_data_tables[table_name].get_entry(query_attr, query_val, return_attr)
param_dict['__tool_directory__'] = self.compute_environment.tool_directory()
param_dict['__get_data_table_entry__'] = get_data_table_entry
param_dict['__local_working_directory__'] = self.local_working_directory
# We add access to app here, this allows access to app.config, etc
param_dict['__app__'] = RawObjectWrapper(self.app)
# More convienent access to app.config.new_file_path; we don't need to
# wrap a string, but this method of generating additional datasets
# should be considered DEPRECATED
param_dict['__new_file_path__'] = self.compute_environment.new_file_path()
# The following points to location (xxx.loc) files which are pointers
# to locally cached data
param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
# For the upload tool, we need to know the root directory and the
# datatypes conf path, so we can load the datatypes registry
param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath(self.app.config.root)
param_dict['__admin_users__'] = self.app.config.admin_users
param_dict['__user__'] = RawObjectWrapper(param_dict.get('__user__', None))
def test_raw_object_wrapper():
obj = Bunch(x=4)
wrapper = RawObjectWrapper(obj)
assert wrapper.x == 4
assert wrapper
false_wrapper = RawObjectWrapper(False)
assert not false_wrapper