def test_get_prefix_direct(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.direct_workflow_version)
prefix = loader.get_prefix()
# Does not use tmpdir
self.assertEqual(prefix, 'file:///direct/')
self.assertFalse(mock_mkdtemp.called)
def test__download_workflow(self, mock_urlretrieve, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.zipped_workflow_version)
loader._download_workflow()
self.assertEqual(
mock_urlretrieve.call_args,
call(self.zipped_workflow_version.url, loader.download_path))
def test__handle_download_zipped(self, mock_zipfile, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.zipped_workflow_version)
loader._handle_download()
self.assertTrue(mock_zipfile.called)
self.assertEqual(
mock_zipfile.return_value.__enter__.return_value.extractall.
call_args, call(loader.download_dir))
def test__get_tool_path_raises(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
self.workflow_version.workflow_type = 'other'
loader = BespinWorkflowLoader(self.workflow_version)
with self.assertRaises(InvalidWorkflowFileException) as context:
tool_path = loader._get_tool_path()
self.assertIn('Workflow type other is not supported',
str(context.exception))
def test__load_downloaded_workflow(self, mock_context, mock_get_tool_path,
mock_load_tool, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
mock_get_tool_path.return_value = 'tool-path'
loader = BespinWorkflowLoader(self.workflow_version)
loaded = loader._load_downloaded_workflow()
self.assertEqual(loaded, mock_load_tool.return_value)
self.assertEqual(mock_load_tool.call_args,
call('tool-path', mock_context.return_value))
def __init__(self, workflow_version):
loader = BespinWorkflowLoader(workflow_version)
parser = BespinWorkflowParser(loader.load())
prefix = loader.get_prefix()
builder = ToolDetailsBuilder(prefix)
builder.accept(parser.loaded_workflow)
self.version = parser.version
self.tag = parser.tag
self.contents = builder.build()
def test_init_direct(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.direct_workflow_version)
self.assertFalse(mock_mkdtemp.called)
self.assertEqual(loader.workflow_version, self.direct_workflow_version)
self.assertFalse(hasattr(loader, 'download_path'))
self.assertFalse(hasattr(loader, 'download_dir'))
def test_load(self, mock_cleanup, mock_load_downloaded_workflow,
mock_handle_download, mock_download_workflow, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.workflow_version)
manager = Mock()
manager.attach_mock(mock_download_workflow, 'download')
manager.attach_mock(mock_handle_download, 'handle')
manager.attach_mock(mock_load_downloaded_workflow, 'load_downloaded')
manager.attach_mock(mock_cleanup, 'cleanup')
loaded = loader.load()
self.assertEqual(manager.mock_calls, [
call.download(),
call.handle(),
call.load_downloaded(),
call.cleanup()
])
# Make sure we assert this check after the order, because it interferes with the calls
self.assertEqual(loaded, mock_load_downloaded_workflow.return_value)
def test_init_common(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.workflow_version)
self.assertEqual(loader.download_dir, mock_mkdtemp.return_value)
self.assertEqual(loader.workflow_version, self.workflow_version)
self.assertEqual(loader.download_path, '/tmpdir/workflow.cwl')
def test_get_prefix_zipped(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.zipped_workflow_version)
prefix = loader.get_prefix()
self.assertEqual(prefix, 'file:///tmpdir/unzipped/')
def test__cleanup_direct(self, mock_rmtree, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.direct_workflow_version)
loader._cleanup()
self.assertFalse(mock_rmtree.called)
def test__get_tool_path_direct(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.direct_workflow_version)
tool_path = loader._get_tool_path()
self.assertEqual(tool_path, 'file:///direct/direct.cwl')
def test__get_tool_path_zipped(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.zipped_workflow_version)
tool_path = loader._get_tool_path()
self.assertEqual(tool_path, '/tmpdir/unzipped/workflow.cwl')
def test__get_tool_path_packed(self, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.packed_workflow_version)
tool_path = loader._get_tool_path()
self.assertEqual(tool_path, '/tmpdir/packed.cwl#main')
def test__handle_download_packed(self, mock_zipfile, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.packed_workflow_version)
loader._handle_download()
self.assertFalse(mock_zipfile.called)
def test__no_download_direct(self, mock_urlretriefve, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.direct_workflow_version)
loader._download_workflow()
self.assertFalse(mock_mkdtemp.called)
self.assertFalse(mock_urlretriefve.called)
def test__cleanup_zipped(self, mock_rmtree, mock_mkdtemp):
self.setup_mkdtemp(mock_mkdtemp)
loader = BespinWorkflowLoader(self.zipped_workflow_version)
loader._cleanup()
self.assertEqual(mock_rmtree.call_args, call(loader.download_dir))