def test_output_directory_with_output_option(runner, client, run):
"""Test directory cleanup with the output option."""
base_sh = ['sh', '-c', 'mkdir -p "$0"; touch "$0/$1"']
assert 0 == run(args=['run'] + base_sh + ['output', 'foo'])
assert (client.path / 'output' / 'foo').exists()
# The output directory is wronly detected.
assert 1 == run(args=['run'] + base_sh + ['output', 'foo'])
assert 0 == run(args=['run', '--no-output'] + base_sh + ['output', 'foo'])
# There should be two command line tools.
tools = list(client.workflow_path.glob('*_sh.cwl'))
assert 2 == len(tools)
cwls = []
for tool_path in tools:
with tool_path.open('r') as f:
cwls.append(CWLClass.from_cwl(yaml.safe_load(f)))
assert cwls[0].inputs != cwls[1].inputs
assert cwls[0].outputs != cwls[1].outputs
# The output directory is cleaned.
assert 0 == run(args=['run', '--output', 'output'] + base_sh +
['output', 'bar'])
assert not (client.path / 'output' / 'foo').exists()
assert (client.path / 'output' / 'bar').exists()
def test_modified_tool(runner, project, capsys):
"""Test detection of modified tool."""
from renku.api import LocalClient
client = LocalClient(project)
repo = client.git
greeting = client.path / 'greeting.txt'
with capsys.disabled():
with greeting.open('wb') as stdout:
try:
old_stdout = sys.stdout
sys.stdout = stdout
try:
cli.cli.main(args=('run', 'echo', 'hello'), )
except SystemExit as e:
assert e.code in {None, 0}
finally:
sys.stdout = old_stdout
cmd = ['status']
result = runner.invoke(cli.cli, cmd)
assert result.exit_code == 0
# There should be only one command line tool.
tools = list(client.workflow_path.glob('*_echo.cwl'))
assert 1 == len(tools)
tool_path = tools[0]
with tool_path.open('r') as f:
command_line_tool = CWLClass.from_cwl(yaml.load(f))
# Simulate a manual edit.
command_line_tool.inputs[0].default = 'ahoj'
command_line_tool.stdout = 'pozdrav.txt'
with tool_path.open('w') as f:
yaml.dump(ascwl(
command_line_tool,
filter=lambda _, x: x is not None,
basedir=client.workflow_path,
),
stream=f,
default_flow_style=False)
repo.git.add('--all')
repo.index.commit('Modified tool', skip_hooks=True)
assert 0 == _run_update(runner, capsys)
output = client.path / 'pozdrav.txt'
assert output.exists()
with output.open('r') as f:
assert 'ahoj\n' == f.read()
cmd = ['status']
result = runner.invoke(cli.cli, cmd)
assert 0 == result.exit_code
def renku_cli(*args):
before_cwl_files = set(client.workflow_path.glob('*.cwl'))
exit_code = run(args)
after_cwl_files = set(client.workflow_path.glob('*.cwl'))
new_files = after_cwl_files - before_cwl_files
assert len(new_files) <= 1
if new_files:
cwl_filepath = new_files.pop()
with cwl_filepath.open('r') as f:
content = CWLClass.from_cwl(yaml.safe_load(f))
else:
content = None
return exit_code, content
def test_with_an_output_option(runner, client, run):
"""Test detection of an output file with an output option."""
assert 0 == run(args=('run', 'touch', 'hello.txt'))
assert 0 == run(args=('run', '--output', 'hello.txt', 'touch',
'hello.txt'))
# There should be two command line tool.
tools = list(client.workflow_path.glob('*_touch.cwl'))
assert 2 == len(tools)
cwls = []
for tool_path in tools:
with tool_path.open('r') as f:
cwls.append(CWLClass.from_cwl(yaml.safe_load(f)))
assert cwls[0].inputs == cwls[1].inputs
assert cwls[0].outputs == cwls[1].outputs
def test_output_directory_without_separate_outputs(runner, client, run):
"""Output files in directory are not listed as separate outputs.
See https://github.com/SwissDataScienceCenter/renku-python/issues/387
"""
base_sh = ['sh', '-c', 'mkdir -p "$0"; touch "$0/$1"']
assert 0 == run(args=['run'] + base_sh + ['output', 'foo'])
assert (client.path / 'output' / 'foo').exists()
# There should be only one command line tool.
tools = list(client.workflow_path.glob('*_sh.cwl'))
assert 1 == len(tools)
with tools[0].open('r') as f:
cwl = CWLClass.from_cwl(yaml.safe_load(f))
assert 1 == len(cwl.outputs)
assert 'Directory' == cwl.outputs[0].type
def read_cwl_file(cwl_filepath):
with cwl_filepath.open('r') as f:
return CWLClass.from_cwl(yaml.safe_load(f))
def test_load_inputs_defined_as_type():
"""Test loading of CWL definition with specific input parameters."""
assert CWLClass.from_cwl(yaml.load(LINK_CWL))