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_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_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')