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_multiline_output(tmpdir):
wf = WorkflowGenerator()
wf.set_documentation('Testing a multiline\ndocumentation string')
tmpfile = os.path.join(str(tmpdir), 'test.cwl')
wf.save(tmpfile, mode='abs')
with open(tmpfile) as f:
contents = f.readlines()
assert len(contents) > 7
def test_save_with_relative_url(self, tmpdir):
wf = WorkflowGenerator()
url = 'https://raw.githubusercontent.com/NLeSC/scriptcwl/master/' \
'tests/data/tools/echo.cwl'
wf.load(step_file=url)
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wf.add_outputs(echoed=echoed)
wf_filename = tmpdir.join('echo-wf.cwl').strpath
wf.save(wf_filename, mode='rel')
def test_add_shebang_to_saved_cwl_file(self, tmpdir):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_inputs(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)
with open(wf_filename) as f:
shebang = f.readline()
assert shebang == '#!/usr/bin/env cwl-runner\n'
def test_save_with_wd_no_wd(self, tmpdir):
wf = WorkflowGenerator()
assert wf.get_working_dir() is None
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
with pytest.raises(ValueError):
wf.save(wf_filename, mode='wd')
def test_save_with_workflow(self, tmpdir):
wf = WorkflowGenerator()
wf.load('tests/data/workflows')
wfmessage = wf.add_inputs(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)
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename, os.getcwd() + '/tests/data/workflows')
expected_wf_filename = 'tests/data/echo-wc.workflowstep.cwl'
expected = load_yaml(expected_wf_filename, '../workflows')
assert actual == expected
def test_save_with_pack(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, mode='pack')
with WorkflowGenerator() as wf2:
wf2.load(wf_filename)
# wf_filename shouldn't be in the steps library, because it is a
# packed workflow
assert len(wf2.steps_library.steps.keys()) == 0
def test_save_with_scattered_step(self, tmpdir):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_inputs(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)
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename, os.getcwd() + '/tests/data/tools')
expected_wf_filename = 'tests/data/echo.scattered.cwl'
expected = load_yaml(expected_wf_filename, '../tools')
assert actual == expected
def test_save_with_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_inputs(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)
# make workflows contents relative to tests/data/tools directory
actual = load_yaml(wf_filename, os.getcwd() + '/tests/data/tools')
expected_wf_filename = 'tests/data/workflows/echo-wc.cwl'
expected = load_yaml(expected_wf_filename, '../tools')
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_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
with pytest.warns(DeprecationWarning):
wf.save(wf_filename, mode='inline')
# save with inline=True should result in a packed workflow (that isn't
# loaded).
with WorkflowGenerator() as wf2:
wf2.load(wf_filename)
# wf_filename shouldn't be in the steps library, because it is a
# packed workflow
assert len(wf2.steps_library.steps.keys()) == 0
