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 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_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_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_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_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_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_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_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_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_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_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_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 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)
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_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_scatter_method_correct(self):
scatter_methods = [
'dotproduct', 'nested_crossproduct', 'flat_crossproduct'
]
for method in scatter_methods:
wf = WorkflowGenerator()
wf.load('tests/data/tools')
msgs = wf.add_input(wfmessages='string[]')
echoed = wf.echo(
message=msgs, scatter='message', scatter_method=method)
assert echoed.step_name == 'echo'
assert echoed.output_name == '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_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_generate_step_name(self):
wf = WorkflowGenerator()
wf.load('tests/data/tools')
wfmessage = wf.add_input(wfmessage='string')
name = wf._generate_step_name('echo')
echoed = wf.echo(message=wfmessage)
assert name == 'echo'
assert name == echoed.step_name
name = wf._generate_step_name('echo')
echoed2 = wf.echo(message=wfmessage)
assert name != 'echo'
assert name == echoed2.step_name
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
