def test_missing_scatter_argument(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_inputs(wfmessages='string[]')
with pytest.raises(ValueError):
wf.echo(message=msgs, scatter_method='nested_crossproduct')
def test_scatter_method_incorrect(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_inputs(wfmessages='string[]')
with pytest.raises(ValueError):
wf.echo(message=msgs, scatter='message', scatter_method='blah')
def test_scatter_variable_correct(self):
scatter_methods = [
'dotproduct', 'nested_crossproduct', 'flat_crossproduct'
]
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_inputs(wfmessages='string[]')
for method in scatter_methods:
echoed = wf.echo(message=msgs,
scatter='message',
scatter_method=method)
assert echoed == 'echo/echoed'
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_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_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
