import logging import new import os.path import shutil import tempfile from base.interactor import stage_data_in_history from .test_toolbox import ToolTestCase log = logging.getLogger(__name__) data_managers = None class DataManagerToolTestCase(ToolTestCase): """Test case that runs Data Manager tests based on a `galaxy.tools.test.ToolTest`""" def do_it(self, testdef): """ Run through a tool test case. """ shed_tool_id = self.shed_tool_id self._handle_test_def_errors(testdef) galaxy_interactor = self._galaxy_interactor(testdef) test_history = galaxy_interactor.new_history() # history where inputs will be put, if any stage_data_in_history(galaxy_interactor, testdef.test_data(), test_history, shed_tool_id) galaxy_interactor.run_tool(testdef, test_history) # test_history will have inputs only, outputs are placed in the specialized data manager history # FIXME: Move history determination and switching into the interactor data_manager_history = None for assoc in reversed(test_history.user.data_manager_histories): if not assoc.history.deleted: data_manager_history = assoc.history break self.switch_history(id=self.security.encode_id(data_manager_history.id)) data_list = self.get_history_as_data_list() # end self.assertTrue(data_list) self._verify_outputs(testdef, data_manager_history, shed_tool_id, data_list, galaxy_interactor) self.switch_history(id=self.security.encode_id(test_history.id)) galaxy_interactor.delete_history(test_history) def build_tests(tmp_dir=None, testing_shed_tools=False, master_api_key=None, user_api_key=None): """ If the module level variable `data_managers` is set, generate `DataManagerToolTestCase` classes for all of its tests and put them into this modules globals() so they can be discovered by nose. """ if data_managers is None: log.warning('data_managers was not set for Data Manager functional testing. Will not test.') return # Push all the data_managers tests to module level G = globals() # Eliminate all previous tests from G. for key, val in G.items(): if key.startswith('TestForDataManagerTool_'): del G[key] # first we will loop through data table loc files and copy them to temporary location, then swap out filenames: for data_table_name, data_table in data_managers.app.tool_data_tables.get_tables().items(): for filename, value in list(data_table.filenames.items()): new_filename = tempfile.NamedTemporaryFile(prefix=os.path.basename(filename), dir=tmp_dir).name try: shutil.copy(filename, new_filename) except IOError as e: log.warning("Failed to copy '%s' to '%s', will create empty file at '%s': %s", filename, new_filename, new_filename, e) open(new_filename, 'wb').close() if 'filename' in value: value['filename'] = new_filename del data_table.filenames[filename] # remove filename:value pair data_table.filenames[new_filename] = value # add new value by for i, (data_manager_id, data_manager) in enumerate(data_managers.data_managers.items()): tool = data_manager.tool if not tool: log.warning("No Tool has been specified for Data Manager: %s", data_manager_id) if tool.tests: # fixme data_manager.tool_shed_repository_info_dict should be filled when is toolshed based shed_tool_id = None if not testing_shed_tools else tool.id # Create a new subclass of ToolTestCase, dynamically adding methods # named test_tool_XXX that run each test defined in the tool config. name = "TestForDataManagerTool_" + data_manager_id.replace(' ', '_') baseclasses = (DataManagerToolTestCase, ) namespace = dict() for j, testdef in enumerate(tool.tests): def make_test_method(td): def test_tool(self): self.do_it(td) return test_tool test_method = make_test_method(testdef) test_method.__doc__ = "%s ( %s ) > %s" % (tool.name, tool.id, testdef.name) namespace['test_tool_%06d' % j] = test_method namespace['shed_tool_id'] = shed_tool_id namespace['master_api_key'] = master_api_key namespace['user_api_key'] = user_api_key # The new.classobj function returns a new class object, with name name, derived # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj(name, baseclasses, namespace) G[name] = new_class_obj