def test_snippet_builder(self): import yaml from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'echo.cwl'])) as f: echo_workflow = f.read().splitlines() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"% snippet add\n{os.linesep.join(echo_workflow[:6])}") ) self.assertDictEqual( yaml.load(StringIO(os.linesep.join(echo_workflow[:6])), yaml.Loader), dict(responses[-1][0][2]['data']['application/json']) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"% snippet build\n{os.linesep.join(echo_workflow[6:])}") ) self.assertDictEqual( yaml.load(StringIO(os.linesep.join(echo_workflow)), yaml.Loader), dict(responses[-1][0][2]['data']['application/json']) ) self.assertDictEqual( yaml.load(StringIO(kernel._workflow_repository.__repo__.get_by_id("echo").to_yaml()), yaml.Loader), yaml.load(StringIO('\n'.join(echo_workflow)), yaml.Loader), )
def test_handle_input_data_files(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.data_directory, 'input_with_file.yml'])) as f: data = yaml.load(f, Loader=yaml.Loader) tmp_dir = tempfile.mkdtemp() data['example_file']['location'] = os.path.join(tmp_dir, 'file.txt') with open(data['example_file']['location'], 'w') as f: f.write('') data_stream = StringIO() yaml.dump(data, data_stream) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data_stream.getvalue(), False) ) with open(os.sep.join([self.cwl_directory, 'workflow_with_input_file.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str, False) ) import uuid input_with_missing_file = StringIO() yaml.dump({"missing_file": {"class": "File", "location": f"/{uuid.uuid4()}"}}, input_with_missing_file) response = kernel.do_execute(input_with_missing_file.getvalue()) self.assertDictEqual( {'status': 'error', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, response )
def test_logs_magic_command(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.extend(args[2]['data']['application/json']) exec_response = kernel.do_execute('% logs') self.assertDictEqual( {"status": "ok", "execution_count": 0, 'payload': [], 'user_expressions': {}}, exec_response ) exec_response = kernel.do_execute('% logs') self.assertDictEqual( {"status": "ok", "execution_count": 0, 'payload': [], 'user_expressions': {}}, exec_response ) number_of_responses = len(responses) self.assertEqual(number_of_responses, 2) exec_response = kernel.do_execute('% logs 1') self.assertDictEqual( {"status": "ok", "execution_count": 0, 'payload': [], 'user_expressions': {}}, exec_response ) self.assertEqual(len(responses), number_of_responses + 1) self.assertEqual( responses[0]['process_id']['process_id'], os.getpid() )
def test_get_past_results_from_kernel(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.data_directory, 'tar_job.yml'])) as f: data = f.read() tar_directory = kernel._cwl_executor.file_manager.ROOT_DIRECTORY with open(os.path.join(tar_directory, 'hello.txt'), 'w') as temp_hello_world_file: temp_hello_world_file.write("hello world") tar_full_name = os.path.join(tar_directory, 'tarfile.tar') print('create tar file:', tar_full_name) with tarfile.open(tar_full_name, 'w') as tar: tar.add(temp_hello_world_file.name) data = data.format(tar_directory=tar_directory) result = kernel.do_execute(data, False) self.assertEqual('ok', result['status'], f'execution returned an error') with open(os.sep.join([self.cwl_directory, 'extract_tar.cwl'])) as f: workflow_str = f.read().format(example_out=temp_hello_world_file.name[1:]) result = kernel.do_execute(workflow_str, False) self.assertEqual('ok', result['status'], f'execution returned an error') full_path, basename = [(f, os.path.basename(f)) for f in kernel.get_past_results()][0] self.assertTrue(full_path.startswith(kernel._results_manager.ROOT_DIRECTORY), 'output is in a wrong directory') self.assertTrue(basename, 'hello.txt')
def test_display_data_magic_command(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # monitor responses responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.data_directory, 'echo-job.yml'])) as f: data = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data, False) ) with open(os.sep.join([self.cwl_directory, 'echo_stdout.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str, False) ) kernel.do_execute('% display_data') self.assertEqual( 'ERROR: you must select an output to display. Correct format:\n % display_data [output name]', responses[-1][0][2]['text'] ) kernel.do_execute('% display_data echo_output') self.assertEqual( 'Hello world!\n', responses[-1][0][2]['text'] )
def test_send_workflow_without_id(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'without_id.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str) ) self.assertRegex( responses[-1][0][2]['text'], r"^tool '[a-zA-Z0-9-]+' registered" ) with open(os.sep.join([self.cwl_directory, 'echo.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str) ) self.assertTupleEqual( ((None, 'stream', {'name': 'stdout', 'text': "tool 'echo' registered"}), {}), responses[-1] )
def test_magics_magic_command(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) commands = [f'\t- {cmd}' for cmd in kernel._magic_commands.keys()] commands.sort() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% magics""") ) self.assertEqual( 'List of Available Magic commands\n' + os.linesep.join(commands), responses[-1][0][2]['text'] ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% magics data""") ) from cwlkernel.kernel_magics import data as data_magic_command import inspect self.assertEqual( inspect.getdoc(data_magic_command), responses[-1][0][2]['text'] ) self.assertIn(' '.join('Display all the data which are registered in the kernel session.'.split()), ' '.join(responses[-1][0][2]['text'].split()))
def test_viewTool(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'echo.cwl'])) as f: cwl_string = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""{cwl_string}""") ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% viewTool x""") ) self.assertEqual( "Tool 'x' is not registered", responses[-1][0][2]['text'] ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% viewTool echo""") ) self.assertDictEqual( yaml.load(StringIO(cwl_string), yaml.Loader), responses[-1][0][2]['data']['application/json'] )
def test_data_magic_command(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # monitor responses responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'echo_stdout.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str, False) ) with open(os.sep.join([self.data_directory, 'echo-job.yml'])) as f: data = f"% execute echo\n{f.read()}" self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data, False) ) from lxml import etree kernel.do_execute('% data') self.assertEqual( 1, len(etree.HTML(responses[-1][0][2]['data']['text/html']).xpath('//a')) )
def test_all_magic_commands_have_methods(self): kernel = CWLKernel() for magic in kernel._magic_commands: try: kernel.__getattribute__(f'_execute_magic_{magic}') except AttributeError as e: self.fail(f'Missing function for magic command: {magic}. \nAttribute error raises: {e}')
def test_display_json_output_after_execution(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) # prepare data with open(os.sep.join([self.data_directory, 'tar_job.yml'])) as f: data = f.read() tar_directory = kernel._cwl_executor.file_manager.ROOT_DIRECTORY with open(os.path.join(tar_directory, 'hello.txt'), 'w') as temp_hello_world_file: temp_hello_world_file.write("hello world") tar_full_name = os.path.join(tar_directory, 'tarfile.tar') print('create tar file:', tar_full_name) with tarfile.open(tar_full_name, 'w') as tar: tar.add(temp_hello_world_file.name) data = f"% execute extract-tar\n{data.format(tar_directory=tar_directory)}" # set workflow with open(os.sep.join([self.cwl_directory, 'extract_tar.cwl'])) as f: workflow_str = f.read().format(example_out=temp_hello_world_file.name[1:]) result = kernel.do_execute(workflow_str, False) self.assertEqual('ok', result['status'], f'execution returned an error') result = kernel.do_execute(data, False) self.assertEqual('ok', result['status'], f'execution returned an error') self.assertDictEqual( { 'example_out': { 'location': f'file://{tar_directory}/hello.txt', 'basename': 'hello.txt', 'nameroot': 'hello', 'nameext': '.txt', 'class': 'File', 'checksum': 'sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed', 'size': 11, 'http://commonwl.org/cwltool#generation': 0, 'id': 'example_out', "result_counter": 0, '_produced_by': 'extract-tar', } }, responses[-1][0][2]['data']['application/json'] ) self.assertDictEqual( { 'example_out': { 'location': f'file://{tar_directory}/hello.txt', 'basename': 'hello.txt', 'nameroot': 'hello', 'nameext': '.txt', 'class': 'File', 'checksum': 'sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed', 'size': 11, 'http://commonwl.org/cwltool#generation': 0, 'id': 'example_out', "result_counter": 0, '_produced_by': 'extract-tar', } }, json.loads(responses[-1][0][2]['data']['text/plain']) )
def test_execute_multiple_steps(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'head.cwl'])) as f: head_cwl = f.read() with open(os.sep.join([self.cwl_directory, 'tail.cwl'])) as f: tail = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(head_cwl) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(tail) ) execute_tail = os.linesep.join([ f"% execute tail", f"tailinput:", f" class: File", f" location: {os.sep.join([self.data_directory, 'data.csv'])}", f"number_of_lines: 15" ]) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(execute_tail) ) execute_head = os.linesep.join([ '% execute head', 'headinput:', ' class: File', ' $data: tailoutput', 'number_of_lines: 5', ]) self.assertDictEqual( {'status': 'error', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(execute_head) ) # execute by referencing id/output execute_head = os.linesep.join([ '% execute head', 'headinput:', ' class: File', ' $data: tail/tailoutput', 'number_of_lines: 5', ]) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(execute_head) )
def test_display_json_output_after_execution(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.data_directory, 'tar_job.yml'])) as f: data = f.read() tar_directory = kernel._cwl_executor.file_manager.ROOT_DIRECTORY with open(os.path.join(tar_directory, 'hello.txt'), 'w') as temp_hello_world_file: temp_hello_world_file.write("hello world") tar_full_name = os.path.join(tar_directory, 'tarfile.tar') print('create tar file:', tar_full_name) with tarfile.open(tar_full_name, 'w') as tar: tar.add(temp_hello_world_file.name) data = data.format(tar_directory=tar_directory) result = kernel.do_execute(data, False) self.assertEqual('ok', result['status'], f'execution returned an error') with open(os.sep.join([self.cwl_directory, 'extract_tar.cwl'])) as f: workflow_str = f.read().format(example_out=temp_hello_world_file.name[1:]) result = kernel.do_execute(workflow_str, False) self.assertEqual('ok', result['status'], f'execution returned an error') self.assertTupleEqual( (None, 'display_data', { 'data': { 'text/plain': '<IPython.core.display.JSON object>', 'application/json': { 'example_out': { 'location': f'file://{tar_directory}/hello.txt', 'basename': 'hello.txt', 'nameroot': 'hello', 'nameext': '.txt', 'class': 'File', 'checksum': 'sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed', 'size': 11, 'http://commonwl.org/cwltool#generation': 0, 'id': 'example_out' } } }, 'metadata': { 'application/json': { 'expanded': False, 'root': 'root' } } } ), responses[1][0] )
def test_get_past_results_without_input(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.cwl_directory, 'touched.cwl'])) as f: workflow_str = f.read() result = kernel.do_execute(workflow_str, False) full_path, basename = [(f, os.path.basename(f)) for f in kernel.get_past_results()][0] self.assertTrue(full_path.startswith(kernel._results_manager.ROOT_DIRECTORY), 'output is in a wrong directory') self.assertTrue(basename, 'touchedfile.txt')
def test_array_output(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.cwl_directory, 'array-outputs.cwl'])) as f: workflow_str = f.read() with open(os.sep.join([self.data_directory, 'array-outputs-job.yml'])) as f: data = f"% execute touch\n{f.read()}" self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data) )
def test_execute_echo_cwl(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.data_directory, 'echo-job.yml'])) as f: data = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data, False) ) with open(os.sep.join([self.cwl_directory, 'echo.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str, False) )
def test_send_invalid_yaml(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None invalid_yaml = """ this is an invalid yaml: fp ?: 1 ?: 2 ? """ exec_result = kernel.do_execute(invalid_yaml, False) self.assertDictEqual({ 'status': 'error', # The base class increments the execution count 'execution_count': 0, 'payload': [], 'user_expressions': {}, }, exec_result)
def test_display_data_csv(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% displayDataCSV no-existing""") ) self.assertEqual( 'Result not found', responses[-1][0][2]['text'] ) with open(os.sep.join([self.cwl_directory, 'head.cwl'])) as f: head = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(head) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% execute head headinput: class: File location: {os.sep.join([self.data_directory, 'data.csv'])} number_of_lines: 15""") ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("% displayDataCSV headoutput") ) self.assertListEqual( [-54, -85, -5, 47, 39, 20, -58, 24, 12, 13, 4, -22, -1, -70, 44, -30, 91, -6, 40, -24], list(pd.read_html(responses[-1][0][2]['data']['text/html'], header=None)[0].values[0]) )
def test_sample_csv(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% displayDataCSV no-existing""") ) self.assertEqual( 'Result not found', responses[-1][0][2]['text'] ) with open(os.sep.join([self.cwl_directory, 'head.cwl'])) as f: head = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(head) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% execute head headinput: class: File location: {os.sep.join([self.data_directory, 'data.csv'])} number_of_lines: 15""") ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("% sampleCSV headoutput 0.2") ) shape = pd.read_html(responses[-1][0][2]['data']['text/html'], header=None)[0].shape print('shape:', shape) self.assertAlmostEqual(shape[0], 4, delta=4) self.assertEqual(shape[1], 20)
def test_githubImport_without_id(self): when(requests) \ .get( "https://api.github.com/repos/giannisdoukas/CWLJNIKernel/contents/tests/cwl/without_id.cwl?ref=dev") \ .thenReturn(mock({ 'status_code': 200, 'json': lambda: { "name": "without_id.cwl", "path": "tests/cwl/without_id.cwl", "sha": "8dd9d522c666d469c75bac566957e78acdb4a5f6", "size": 129, "url": "https://api.github.com/repos/giannisdoukas/CWLJNIKernel/contents/tests/cwl/without_id.cwl?ref=dev", "html_url": "https://github.com/giannisdoukas/CWLJNIKernel/blob/dev/tests/cwl/without_id.cwl", "git_url": "https://api.github.com/repos/giannisdoukas/CWLJNIKernel/git/blobs/8dd9d522c666d469c75bac566957e78acdb4a5f6", "download_url": "https://raw.githubusercontent.com/giannisdoukas/CWLJNIKernel/dev/tests/cwl/without_id.cwl", "type": "file", "content": "Y3dsVmVyc2lvbjogdjEuMApjbGFzczogQ29tbWFuZExpbmVUb29sCmJhc2VD\nb21tYW5kOiBbZWNobywgImhlbGxvIHdvcmxkIl0KaW5wdXRzOiBbXQpvdXRw\ndXRzOgogIGV4YW1wbGVfb3V0cHV0OgogICAgdHlwZTogc3Rkb3V0\n", "encoding": "base64", "_links": { "self": "https://api.github.com/repos/giannisdoukas/CWLJNIKernel/contents/tests/cwl/without_id.cwl?ref=dev", "git": "https://api.github.com/repos/giannisdoukas/CWLJNIKernel/git/blobs/8dd9d522c666d469c75bac566957e78acdb4a5f6", "html": "https://github.com/giannisdoukas/CWLJNIKernel/blob/dev/tests/cwl/without_id.cwl" } }})) kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute( "% githubImport https://github.com/giannisdoukas/CWLJNIKernel/blob/dev/tests/cwl/without_id.cwl") ) self.assertRegex(responses[-1][0][2]['text'], r"^tool 'without_id' registered") self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"""% execute {responses[-1][0][2]['text'].split("'")[1]}""") )
def test_get_past_results_without_input(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.cwl_directory, 'touched.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str) ) self.assertEqual(0, len(kernel.get_past_results())) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% execute touch') ) full_path, basename = [(f, os.path.basename(f)) for f in kernel.get_past_results()][0] self.assertTrue(full_path.startswith(kernel._results_manager.ROOT_DIRECTORY), 'output is in a wrong directory') self.assertTrue(basename, 'touchedfile.txt')
def test_system_magic_command(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("% system echo 'Hello World'") ) self.assertDictEqual( {'name': 'stdout', 'text': 'Hello World\n'}, responses[-1][0][2], ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% system ls ERROR') ) self.assertEqual( 'stderr', responses[-1][0][2]['name'], )
def test_get_input_data(self): from cwlkernel.CWLKernel import CWLKernel kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None with open(os.sep.join([self.data_directory, 'data1.yml'])) as f: data = f.read() exec_response = kernel.do_execute(data, False) self.assertDictEqual( {"status": "ok", "execution_count": 0, 'payload': [], 'user_expressions': {}}, exec_response ) self.assertListEqual([data], kernel._yaml_input_data) exec_response = kernel.do_execute(data, False) # The base class increments the execution count. So, exec_count remains 0 self.assertDictEqual( {"status": "ok", "execution_count": 0, 'payload': [], 'user_expressions': {}}, exec_response ) self.assertListEqual([data, data], kernel._yaml_input_data)
def test_execute_with_provenance(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) yaml = YAML(typ='safe') with open(os.sep.join([self.cwl_directory, 'echo.cwl'])) as f: workflow_str = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(workflow_str, False) ) self.assertIsNotNone(kernel._workflow_repository.get_by_id(yaml.load(workflow_str)['id'])) with open(os.sep.join([self.data_directory, 'echo-job.yml'])) as f: data = '\n'.join(["% executeWithProvenance echo", f.read()]) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(data) ) provenance_directory = list(filter( lambda r: 'text' in r[0][2] and "Provenance stored in directory" in r[0][2]['text'], responses ))[0][0][2]['text'].split()[-1] print(provenance_directory) self.assertTrue(os.path.isdir(provenance_directory)) self.assertTrue(os.path.isdir(os.path.join(provenance_directory, 'data'))) self.assertTrue(os.path.isdir(os.path.join(provenance_directory, 'metadata'))) self.assertTrue(os.path.isdir(os.path.join(provenance_directory, 'snapshot'))) self.assertTrue(os.path.isfile(os.path.join(provenance_directory, 'snapshot', 'echo.cwl'))) self.assertTrue(os.path.isdir(os.path.join(provenance_directory, 'workflow'))) shutil.rmtree(provenance_directory)
def test_view_magic_command(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'head.cwl'])) as f: head = f.read() with open(os.sep.join([self.cwl_directory, 'tail.cwl'])) as f: tail = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(head) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(tail) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("""% newWorkflow main % newWorkflowAddStep tail tailstepid % newWorkflowAddStep head headstepid % newWorkflowAddInput headstepid headinput id: inputfile type: File % newWorkflowAddStepIn tailstepid headstepid headoutput tailinput: headstepid/headoutput % newWorkflowAddOutputSource tailstepid/tailoutput File % newWorkflowBuild""") ) self.assertDictEqual( { "cwlVersion": "v1.0", "class": "Workflow", "id": "main", "inputs": [{'id': 'inputfile', 'type': 'File'}], "outputs": [{'id': 'tailoutput', 'type': 'File', 'outputSource': "tailstepid/tailoutput"}], "steps": { "headstepid": { "run": "head.cwl", "in": {"headinput": "inputfile"}, "out": ['headoutput'] }, "tailstepid": { "run": "tail.cwl", "in": {"tailinput": "headstepid/headoutput"}, "out": ['tailoutput'] }, }, 'requirements': {} }, yaml.load(kernel._workflow_repository.get_by_id("main").to_yaml(), yaml.Loader), ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% view main') ) self.assertIn( 'text/html', responses[-1][0][2]['data']) # should not raise an exception tree = ET.fromstring(responses[-1][0][2]['data']['text/html']) self.assertEqual(len(tree.findall("./{http://www.w3.org/2000/svg}svg")), 1)
def test_scatter_tool(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.path.join(self.cwl_directory, 'echo_stdout.cwl')) as f: yaml_tool = f.read() expected_tool = { 'cwlVersion': 'v1.0', 'id': 'scattered_echo', 'class': 'Workflow', 'inputs': [{'id': 'message_scatter_array', 'type': 'string[]'}], 'outputs': [{'type': 'File[]', 'id': 'echo_output_scatter_array', 'outputSource': 'echo/echo_output'}], 'steps': {'echo': {'run': 'echo.cwl', 'scatter': 'message', 'in': {'message': 'message_scatter_array'}, 'out': ['echo_output']}}, 'requirements': {'ScatterFeatureRequirement': {}} } self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(yaml_tool) ) self.assertDictEqual( {'status': 'error', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% scatter echo') ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% scatter NOT-EXISTING-TOOL-ID message') ) self.assertEqual( responses[-1][0][2]['name'], 'stderr' ) self.assertEqual( responses[-1][0][2]['text'], "Tool 'NOT-EXISTING-TOOL-ID' not found" ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% scatter echo NOT-EXISTING-INPUT') ) self.assertEqual( responses[-1][0][2]['name'], 'stderr' ) self.assertEqual( responses[-1][0][2]['text'], "There is no input 'NOT-EXISTING-INPUT' in tool 'echo'" ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% scatter echo message') ) scattered_tool = dict(responses[-1][0][2]['data']['application/json']) self.assertListEqual( expected_tool['inputs'], scattered_tool['inputs'] ) self.assertListEqual( expected_tool['outputs'], scattered_tool['outputs'] ) expected_tool['steps']['echo']['run'] = os.path.join( os.path.dirname(scattered_tool['steps']['echo']['run']), expected_tool['steps']['echo']['run'] ) self.assertDictEqual( expected_tool['steps'], scattered_tool['steps'] ) self.assertDictEqual( expected_tool, scattered_tool ) self.assertIsNotNone(kernel.workflow_repository.get_instance().get_by_id(scattered_tool['id']))
def get_kernel(self) -> CWLKernel: kernel = CWLKernel() # cancel send_response kernel.send_response = lambda *args, **kwargs: None return kernel
def test_edit_magic(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.path.join(self.cwl_directory, 'echo_stdout.cwl')) as f: yaml_tool = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(yaml_tool) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("% edit ") ) self.assertEqual( responses[-1][0][2]['name'], 'stderr' ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute("% edit NOT-EXISTING") ) self.assertEqual( responses[-1][0][2]['name'], 'stderr' ) execute_response = kernel.do_execute("% edit echo") self.assertEqual('ok', execute_response['status']) self.assertListEqual( execute_response['payload'], [ { 'source': "set_next_input", 'replace': True, 'text': f'% edit echo\n{kernel.workflow_repository.get_instance().get_by_id("echo").to_yaml()}', } ] ) new_tool = yaml.safe_load(StringIO(yaml_tool)) new_tool['outputs'] = { 'new_echo_output': {'type': 'stdout'} } output = StringIO() yaml.safe_dump(new_tool, output) new_tool_yaml = output.getvalue() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(f"% edit echo\n{new_tool_yaml}") ) new_tool = kernel.workflow_repository.get_instance().get_by_id('echo') self.assertListEqual( new_tool.outputs, [{'id': 'new_echo_output', 'type': 'stdout'}] )
def test_compile_executed_steps(self): kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) with open(os.sep.join([self.cwl_directory, 'head-no-optional.cwl'])) as f: head_cwl = f.read() with open(os.sep.join([self.cwl_directory, 'tail-no-optional.cwl'])) as f: tail = f.read() self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(head_cwl) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(tail) ) execute_tail = os.linesep.join([ f"% execute tail", f"tailinput:", f" class: File", f" location: {os.sep.join([self.data_directory, 'data.csv'])}", ]) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(execute_tail) ) execute_head = os.linesep.join([ '% execute head', 'headinput:', ' class: File', ' $data: tail/tailoutput', ]) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(execute_head) ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute('% compile main') ) expected_workflow = { 'class': 'Workflow', 'cwlVersion': "v1.0", 'id': 'main', 'inputs': [ { 'id': 'tailinput', 'type': 'File' }, ], 'outputs': [ { 'id': 'headoutput', 'type': 'File', 'outputSource': "head/headoutput" } ], "steps": { "head": { "run": "head.cwl", "in": { "headinput": "tail/tailoutput" }, "out": ['headoutput'] }, "tail": { "run": "tail.cwl", "in": {"tailinput": "tailinput"}, "out": ['tailoutput'] }, }, 'requirements': {} } self.assertDictEqual( expected_workflow, responses[-1][0][2]['data']['application/json'] ) self.assertDictEqual( expected_workflow, kernel.workflow_repository.get_instance().get_by_id('main').to_dict() )
def test_githubImport_walk_paths(self): when(requests) \ .get( "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Workflows/pdf2wordcloud.cwl?ref=master") \ .thenReturn(mock({ 'status_code': 200, 'json': lambda: { "name": "pdf2wordcloud.cwl", "path": "CWL/Workflows/pdf2wordcloud.cwl", "sha": "a5227591046300bf2c86a4e159b4a7b3ef8dd131", "size": 1310, "url": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Workflows/pdf2wordcloud.cwl?ref=master", "html_url": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Workflows/pdf2wordcloud.cwl", "git_url": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/a5227591046300bf2c86a4e159b4a7b3ef8dd131", "download_url": "https://raw.githubusercontent.com/wilke/CWL-Quick-Start/master/CWL/Workflows/pdf2wordcloud.cwl", "type": "file", "content": 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"encoding": "base64", "_links": { "self": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Workflows/pdf2wordcloud.cwl?ref=master", "git": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/a5227591046300bf2c86a4e159b4a7b3ef8dd131", "html": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Workflows/pdf2wordcloud.cwl" } } })) when(requests) \ .get("https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/pdftotext.cwl?ref=master") \ .thenReturn(mock({ 'status_code': 200, 'json': lambda: { "name": "pdftotext.cwl", "path": "CWL/Tools/pdftotext.cwl", "sha": "a1e42933af7dd288ae77a6a7c52babbcbf5c0032", "size": 874, "url": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/pdftotext.cwl?ref=master", "html_url": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Tools/pdftotext.cwl", "git_url": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/a1e42933af7dd288ae77a6a7c52babbcbf5c0032", "download_url": "https://raw.githubusercontent.com/wilke/CWL-Quick-Start/master/CWL/Tools/pdftotext.cwl", "type": "file", "content": "IyEvdXNyL2Jpbi9lbnYgY3dsLXJ1bm5lcgpjd2xWZXJzaW9uOiB2MS4wCgoj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\nb2I6ICQoaW5wdXRzLnRleHQpCg==\n", "encoding": "base64", "_links": { "self": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/pdftotext.cwl?ref=master", "git": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/a1e42933af7dd288ae77a6a7c52babbcbf5c0032", "html": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Tools/pdftotext.cwl" } } })) when(requests) \ .get("https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/wordcloud.cwl?ref=master") \ .thenReturn(mock({ 'status_code': 200, 'json': lambda: { "name": "wordcloud.cwl", "path": "CWL/Tools/wordcloud.cwl", "sha": "3b43b020c5b3ba43bbb5d6d8335e57f30172916b", "size": 925, "url": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/wordcloud.cwl?ref=master", "html_url": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Tools/wordcloud.cwl", "git_url": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/3b43b020c5b3ba43bbb5d6d8335e57f30172916b", "download_url": "https://raw.githubusercontent.com/wilke/CWL-Quick-Start/master/CWL/Tools/wordcloud.cwl", "type": "file", "content": "IyEvdXNyL2Jpbi9lbnYgY3dsLXJ1bm5lcgpjd2xWZXJzaW9uOiB2MS4wCgoj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\nIGdsb2I6ICQoaW5wdXRzLm91dG5hbWUpCg==\n", "encoding": "base64", "_links": { "self": "https://api.github.com/repos/wilke/CWL-Quick-Start/contents/CWL/Tools/wordcloud.cwl?ref=master", "git": "https://api.github.com/repos/wilke/CWL-Quick-Start/git/blobs/3b43b020c5b3ba43bbb5d6d8335e57f30172916b", "html": "https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Tools/wordcloud.cwl" } } })) kernel = CWLKernel() # cancel send_response responses = [] kernel.send_response = lambda *args, **kwargs: responses.append((args, kwargs)) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute( "% githubImport https://github.com/wilke/CWL-Quick-Start/blob/master/CWL/Workflows/pdf2wordcloud.cwl") ) self.assertDictEqual( {'status': 'ok', 'execution_count': 0, 'payload': [], 'user_expressions': {}}, kernel.do_execute(os.linesep.join([ f"% execute pdf2wordcloud", f"pdf:", f" class: File", f" location: {os.sep.join([self.data_directory, 'text.pdf'])}" ])) ) self.assertIsNotNone(kernel.results_manager.get_last_result_by_id('words'))