def test_detect_wrong_type(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
x = wf.add_input(msg='string')
x = 3
with pytest.raises(ValueError):
wf.echo(message=x)
def setup_workflowgenerator(tmpdir):
toolsdir = tmpdir.join('tools').strpath
workflows = tmpdir.join('workflows').strpath
copytree('tests/data/tools', toolsdir)
copytree('tests/data/workflows', workflows)
wf = WorkflowGenerator()
return wf
def test_step_with_compatible_step_output(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wced = wf.wc(file2count=echoed)
def test_step_with_incompatible_input(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
with pytest.raises(ValueError):
wced = wf.wc(file2count=wfmessage)
def test_default_value_for_workflow_input(self):
wf = WorkflowGenerator()
wf.add_input(input1='string', default='test')
obj = wf.to_obj()['inputs']['input1']
assert obj['type'] == 'string'
assert obj['default'] == 'test'
def test_combine_enum_with_label(self):
wf = WorkflowGenerator()
wf.add_input(input1='enum', symbols=['one', 'two', 'three'],
label='test label')
obj = wf.to_obj()['inputs']['input1']
assert obj['label'] == 'test label'
def test_convert_symbols_to_list_of_strings(self):
wf = WorkflowGenerator()
wf.add_input(input1='enum', symbols=[1, 2, 3])
obj = wf.to_obj()['inputs']['input1']
assert obj['type']['symbols'] == ['1', '2', '3']
def test_load(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
step_keys = wf.steps_library.keys()
step_keys.sort()
assert step_keys == ['echo', 'wc']
def test_load(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
step_keys = wf.steps_library.steps.keys()
step_keys = sorted(step_keys)
assert step_keys == ['echo', 'multiple-out-args', 'wc']
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_optional_type(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
# This could work, if you pass a string for input, even if
# the echo step requires an input. So we expect it to work.
wfmessage = wf.add_input(message='string?')
echod = wf.echo(message=wfmessage)
def test_step_with_incompatible_step_output(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
infile = wf.add_input(infile='File')
wced = wf.wc(file2count=infile)
with pytest.raises(ValueError):
echoed = wf.echo(message=wced)
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_scattered_step_with_scalar_input(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(message='string')
with pytest.raises(ValueError):
echoed = wf.echo(message=wfmessage, scatter='message',
scatter_method='dotproduct')
def test_load_with_list(self):
wf = WorkflowGenerator()
wf.load(step_list=['tests/data/workflows/echo-wc.cwl',
'tests/data/tools'])
# 'https://raw.githubusercontent.com/WhatWorksWhenForWhom/nlppln/develop/cwl/anonymize.cwl',\
step_keys = wf.steps_library.steps.keys()
step_keys = sorted(step_keys)
assert step_keys == ['echo', 'echo-wc', 'multiple-out-args', 'wc']
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_step_with_scattered_input_no_scatter_method(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
wf.echo(message=msgs, scatter='message')
wf.validate()
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_step_with_compatible_input(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
wf.validate()
def test_step_with_scattered_step_output(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(msgs='string[]')
echoed = wf.echo(message=msgs, scatter='message',
scatter_method='dotproduct')
wced = wf.wc(file2count=echoed, scatter='file2count',
scatter_method='dotproduct')
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_missing_scatter_method_argument(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wf.load('tests/data/misc')
msgs = wf.add_input(wfmessages='string[]')
with pytest.raises(ValueError):
wf.echo3(msg1=msgs, msg2=msgs, scatter=['msg1', 'msg2'])
def test_optional_to_optional_type(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wf_infiles = wf.add_input(in_files='File[]')
wf_outdir = wf.add_input(out_dir='string?')
wf_counselors = wf.add_input(counselors='string[]')
out_files, meta_out = wf.multiple_out_args(
in_files=wf_infiles, out_dir=wf_outdir,
counselors=wf_counselors)
def test_enum_as_workflow_input(self):
wf = WorkflowGenerator()
wf.add_input(input1='enum', symbols=['one', 'two', 'three'])
wf.validate()
obj = wf.to_obj()['inputs']['input1']
assert obj['type']['type'] == 'enum'
assert obj['type']['symbols'] == ['one', 'two', 'three']
def test_label_for_workflow_input(self):
wf = WorkflowGenerator()
wf.add_input(input1='string', label='test label')
wf.validate()
obj = wf.to_obj()['inputs']['input1']
assert obj['type'] == 'string'
assert obj['label'] == 'test label'
def test_validate_with_inline_tools(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
echoed = wf.echo(message=wfmessage)
echoed2 = wf.echo(message=wfmessage)
wf.add_outputs(echoed2=echoed2)
wf.validate(inline=True)
def test_scatter_variable_incorrect(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
with pytest.raises(ValueError):
wf.echo(
message=msgs,
scatter='incorrect',
scatter_method='nested_crossproduct')
def setup_workflowgenerator(tmpdir):
toolsdir = tmpdir.join('tools').strpath
workflows = tmpdir.join('workflows').strpath
filenames = tmpdir.join('file-names').strpath
misc = tmpdir.join('misc').strpath
copytree('tests/data/tools', toolsdir)
copytree('tests/data/workflows', workflows)
copytree('tests/data/file-names', filenames)
copytree('tests/data/misc', misc)
wf = WorkflowGenerator()
return wf
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_required_to_optional(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
# out_dir is optional, attaching to non-optional input
# should work.
wf_infiles = wf.add_input(in_files='File[]')
wf_outdir = wf.add_input(out_dir='string')
wf_counselors = wf.add_input(counselors='string[]')
out_files, meta_out = wf.multiple_out_args(
in_files=wf_infiles, out_dir=wf_outdir,
counselors=wf_counselors)