def test_save_with_inline_tools(self, tmpdir):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wf.set_documentation('Counts words of a message via echo and wc')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wced = wf.wc(file2count=echoed)
wf.add_outputs(wfcount=wced)
wf_filename = tmpdir.join('echo-wc.cwl').strpath
wf.save(wf_filename, inline=True)
# Strip absolute paths from ids
actual = load_yaml(wf_filename)
expected_wf_filename = 'tests/data/workflows/echo-wc_inline.cwl'
expected = load_yaml(expected_wf_filename)
# Random id's will differ and that's ok, so just remove them
def remove_random_ids(step):
del(step['outputs'][0]['outputBinding']['glob'])
del(step['stdout'])
remove_random_ids(actual['steps']['wc']['run'])
remove_random_ids(actual['steps']['echo']['run'])
remove_random_ids(expected['steps']['wc']['run'])
remove_random_ids(expected['steps']['echo']['run'])
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_print_wf_absolute_paths(self, tmpdir):
wf = setup_workflowgenerator(tmpdir)
wf.load(steps_dir=tmpdir.join('tools').strpath)
wf.set_documentation('Counts words of a message via echo and wc')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wced = wf.wc(file2count=echoed)
wf.add_outputs(wfcount=wced)
actual = wf.__str__()
# make workflows contents relative to tests/data/tools directory
actual = yaml.safe_load(actual)
def fix_path(path):
res = path.rsplit(os.sep, 2)
res[0] = '..'
return (os.sep).join(res)
actual['steps']['echo']['run'] = \
fix_path(actual['steps']['echo']['run'])
actual['steps']['wc']['run'] = fix_path(actual['steps']['wc']['run'])
expected_wf_filename = 'tests/data/workflows/echo-wc.cwl'
expected = load_yaml(expected_wf_filename)
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_save_with_workflow(self, tmpdir):
wf = setup_workflowgenerator(tmpdir)
wf.load(tmpdir.join('workflows').strpath)
wfmessage = wf.add_input(wfmessage='string')
wced = wf.echo_wc(wfmessage=wfmessage)
wf.add_outputs(wfcount=wced)
wf_filename = tmpdir.join('echo-wc.cwl').strpath
wf.save(wf_filename, mode='rel')
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename)
expected_wf_filename = 'tests/data/echo-wc.workflowstep.cwl'
expected = load_yaml(expected_wf_filename)
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_save_with_wd(self, tmpdir):
wf = WorkflowGenerator(working_dir=tmpdir.join('wd').strpath)
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wced = wf.wc(file2count=echoed)
wf.add_outputs(wfcount=wced)
wf_filename = tmpdir.join('echo-wc.cwl').strpath
wf.save(wf_filename, mode='wd')
actual = load_yaml(wf_filename)
expected_wf_filename = 'tests/data/workflows/echo-wc_wd.cwl'
expected = load_yaml(expected_wf_filename)
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_save_with_tools(self, tmpdir):
wf = setup_workflowgenerator(tmpdir)
wf.load(steps_dir=tmpdir.join('tools').strpath)
wf.set_documentation('Counts words of a message via echo and wc')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wced = wf.wc(file2count=echoed)
wf.add_outputs(wfcount=wced)
wf_filename = tmpdir.join('workflows/echo-wc.cwl').strpath
wf.save(wf_filename, mode='rel')
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename)
expected_wf_filename = 'tests/data/workflows/echo-wc.cwl'
expected = load_yaml(expected_wf_filename)
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_save_with_scattered_step(self, tmpdir):
wf = setup_workflowgenerator(tmpdir)
wf.load(tmpdir.join('tools').strpath)
msgs = wf.add_input(wfmessages='string[]')
echoed = wf.echo(
message=msgs,
scatter='message',
scatter_method='nested_crossproduct')
wf.add_outputs(out_files=echoed)
wf_filename = tmpdir.join('echo-scattered.cwl').strpath
wf.save(wf_filename, mode='rel')
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename)
expected_wf_filename = 'tests/data/echo.scattered.cwl'
expected = load_yaml(expected_wf_filename)
print(' actual:', actual)
print('expected:', expected)
assert actual == expected
def test_load_yaml_packed(datafiles):
cwl_file = str(datafiles.listdir()[0])
assert {} == load_yaml(cwl_file)