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

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

0:26e78fe6e8c4

import shutil
import sys
import tempfile
import pytest
from cwltool.secrets import SecretStore
from cwltool.main import main
from .util import (get_data, needs_docker, needs_singularity,
                   windows_needs_docker)
from io import StringIO


@pytest.fixture
def secrets():
    sec_store = SecretStore()
    job = {'foo': 'bar',
           'baz': 'quux'}

    sec_store.store(['foo'], job)
    return sec_store, job

def test_obscuring(secrets):
    storage, obscured = secrets
    assert obscured['foo'] != 'bar'
    assert obscured['baz'] == 'quux'
    assert storage.retrieve(obscured)['foo'] == 'bar'

obscured_factories_expected = [
    ((lambda x: 'hello %s' % x), 'hello bar'),
    ((lambda x: ['echo', 'hello %s' % x]), ['echo', 'hello bar']),
    ((lambda x: {'foo': x}), {'foo': 'bar'}),
]

@pytest.mark.parametrize('factory,expected', obscured_factories_expected)
def test_secrets(factory, expected, secrets):
    storage, obscured = secrets
    pattern = factory(obscured['foo'])
    assert pattern != expected

    assert storage.has_secret(pattern)
    assert storage.retrieve(pattern) == expected

    assert obscured['foo'] != 'bar'
    assert obscured['baz'] == 'quux'

@needs_docker
def test_secret_workflow_log():
    stream = StringIO()
    tmpdir = tempfile.mkdtemp()
    main(["--debug", "--enable-ext", "--outdir", tmpdir,
          get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
         stderr=stream)

    shutil.rmtree(tmpdir)
    assert "Hoopla!" not in stream.getvalue()

@needs_singularity
def test_secret_workflow_log_singularity():
    stream = StringIO()
    tmpdir = tempfile.mkdtemp()
    main(["--debug", "--outdir", tmpdir, "--singularity",
          get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
         stderr=stream)

    shutil.rmtree(tmpdir)
    assert "Hoopla!" not in stream.getvalue()

@needs_docker
def test_secret_workflow_log_override():
    stream = StringIO()
    tmpdir = tempfile.mkdtemp()
    main(["--debug", "--outdir", tmpdir, "--enable-ext", "--overrides",
          get_data("tests/wf/override-no-secrets.yml"),
          get_data("tests/wf/secret_wf.cwl"), "--pw", "Hoopla!"],
         stderr=stream)
    shutil.rmtree(tmpdir)

    assert "Hoopla!" in stream.getvalue()