comparison env/lib/python3.7/site-packages/cwltool/tests/test_override.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

0:26e78fe6e8c4

import json

from six import StringIO

import pytest

from cwltool.main import main
from cwltool import load_tool
from .util import get_data, needs_docker

override_parameters = [
    ([get_data('tests/override/echo.cwl'),
      get_data('tests/override/echo-job.yml')],
     {"out": "zing hello1\n"}
     ),
    (["--overrides",
      get_data('tests/override/ov.yml'),
      get_data('tests/override/echo.cwl'),
      get_data('tests/override/echo-job.yml')],
     {"out": "zing hello2\n"}
     ),
    ([get_data('tests/override/echo.cwl'),
      get_data('tests/override/echo-job-ov.yml')],
     {"out": "zing hello3\n"}
     ),
    ([get_data('tests/override/echo-job-ov2.yml')],
     {"out": "zing hello4\n"}
     ),
    (["--overrides",
      get_data('tests/override/ov.yml'),
      get_data('tests/override/echo-wf.cwl'),
      get_data('tests/override/echo-job.yml')],
     {"out": "zing hello2\n"}
     ),
    (["--overrides",
      get_data('tests/override/ov2.yml'),
      get_data('tests/override/echo-wf.cwl'),
      get_data('tests/override/echo-job.yml')],
     {"out": "zing hello5\n"}
     ),
    (["--overrides",
      get_data('tests/override/ov3.yml'),
      get_data('tests/override/echo-wf.cwl'),
      get_data('tests/override/echo-job.yml')],
     {"out": "zing hello6\n"}
     ),
    ([get_data('tests/override/env-tool_v1.1.cwl'),
      get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
     {"value": "hello test env"}
     ),
    (["--enable-dev",
      get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],
     {"value": "hello test env"}
     ),
]

@needs_docker
@pytest.mark.parametrize('parameters,result', override_parameters)
def test_overrides(parameters, result):
    sio = StringIO()

    assert main(parameters, stdout=sio) == 0
    assert json.loads(sio.getvalue()) == result


failing_override_parameters = [
    ([get_data('tests/override/env-tool.cwl'),
      get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
     "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
     "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
     "v1.1"
     ),
    ([get_data('tests/override/env-tool_v1.1.0-dev1.cwl'),
      get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
     "Version 'v1.1.0-dev1' is a development or deprecated version.\n"
     " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to "
     "enable support for development and deprecated versions."
     ),
    ([get_data('tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml')],
     "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
     "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
     "v1.1 or greater."
     ),
    ([get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],
     "Version 'v1.1.0-dev1' is a development or deprecated version.\n"
     " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to "
     "enable support for development and deprecated versions."
     ),
]

@needs_docker
@pytest.mark.parametrize('parameters,expected_error', failing_override_parameters)
def test_overrides_fails(parameters, expected_error):
    sio = StringIO()

    assert main(parameters, stderr=sio) == 1
    stderr = sio.getvalue()
    assert expected_error in stderr, stderr