What next? test sdk/cwl -v -m "cwl_conformance" ======= install sdk/cwl Processing ./sdk/cwl Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Requirement already satisfied: arvados-python-client~=3.2.0.dev0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-cwl-runner==3.2.0.dev20250814184714) (3.2.0.dev20250804004422) Requirement already satisfied: crunchstat_summary~=3.2.0.dev0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-cwl-runner==3.2.0.dev20250814184714) (3.2.0.dev20250804004422) Requirement already satisfied: cwltool==3.1.20240508115724 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-cwl-runner==3.2.0.dev20250814184714) (3.1.20240508115724) Requirement already satisfied: schema-salad==8.5.20240503091721 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-cwl-runner==3.2.0.dev20250814184714) (8.5.20240503091721) Requirement already satisfied: ciso8601>=2.0.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-cwl-runner==3.2.0.dev20250814184714) (2.3.2) Requirement already satisfied: setuptools in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (80.9.0) Requirement already satisfied: requests>=2.6.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (2.32.4) Requirement already satisfied: ruamel.yaml<0.19,>=0.16 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (0.18.14) Requirement already satisfied: rdflib<7.1.0,>=4.2.2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (7.0.0) Requirement already satisfied: shellescape<3.9,>=3.4.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.8.1) Requirement already satisfied: prov==1.5.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (1.5.1) Requirement already satisfied: mypy-extensions in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (1.1.0) Requirement already satisfied: psutil>=5.6.6 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (7.0.0) Requirement already satisfied: coloredlogs in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (15.0.1) Requirement already satisfied: pydot>=1.4.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (4.0.1) Requirement already satisfied: argcomplete in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.6.2) Requirement already satisfied: pyparsing!=3.0.2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.2.3) Requirement already satisfied: cwl-utils>=0.32 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (0.35) Requirement already satisfied: spython>=0.3.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (0.3.14) Requirement already satisfied: mistune<3.1,>=3 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from schema-salad==8.5.20240503091721->arvados-cwl-runner==3.2.0.dev20250814184714) (3.0.2) Requirement already satisfied: CacheControl[filecache]<0.15,>=0.11.7 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from schema-salad==8.5.20240503091721->arvados-cwl-runner==3.2.0.dev20250814184714) (0.14.3) Requirement already satisfied: lxml in ./tmp/VENV3DIR/lib/python3.11/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (6.0.0) Requirement already satisfied: networkx in ./tmp/VENV3DIR/lib/python3.11/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.5) Requirement already satisfied: python-dateutil in ./tmp/VENV3DIR/lib/python3.11/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (2.9.0.post0) Requirement already satisfied: six>=1.9.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from prov==1.5.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (1.17.0) Requirement already satisfied: boto3 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (1.40.9) Requirement already satisfied: google-api-python-client>=2.1.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (2.179.0) Requirement already satisfied: google-auth in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (2.40.3) Requirement already satisfied: httplib2>=0.9.2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (0.22.0) Requirement already satisfied: pycurl>=7.19.5.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (7.45.6) Requirement already satisfied: websockets>=11.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (15.0.1) Requirement already satisfied: msgpack<2.0.0,>=0.5.2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from CacheControl[filecache]<0.15,>=0.11.7->schema-salad==8.5.20240503091721->arvados-cwl-runner==3.2.0.dev20250814184714) (1.1.1) Requirement already satisfied: filelock>=3.8.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from CacheControl[filecache]<0.15,>=0.11.7->schema-salad==8.5.20240503091721->arvados-cwl-runner==3.2.0.dev20250814184714) (3.18.0) Requirement already satisfied: cwl-upgrader>=1.2.3 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwl-utils>=0.32->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (1.2.12) Requirement already satisfied: packaging in ./tmp/VENV3DIR/lib/python3.11/site-packages (from cwl-utils>=0.32->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (25.0) Requirement already satisfied: google-auth-httplib2<1.0.0,>=0.2.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (0.2.0) Requirement already satisfied: google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0,>=1.31.5 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (2.25.1) Requirement already satisfied: uritemplate<5,>=3.0.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (4.2.0) Requirement already satisfied: cachetools<6.0,>=2.0.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-auth->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (5.5.2) Requirement already satisfied: pyasn1-modules>=0.2.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-auth->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (0.4.2) Requirement already satisfied: rsa<5,>=3.1.4 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-auth->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (4.9.1) Requirement already satisfied: isodate<0.7.0,>=0.6.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from rdflib<7.1.0,>=4.2.2->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (0.6.1) Requirement already satisfied: charset_normalizer<4,>=2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from requests>=2.6.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.4.3) Requirement already satisfied: idna<4,>=2.5 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from requests>=2.6.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from requests>=2.6.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from requests>=2.6.1->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (2025.8.3) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from ruamel.yaml<0.19,>=0.16->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (0.2.12) Requirement already satisfied: botocore<1.41.0,>=1.40.9 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from boto3->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (1.40.9) Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from boto3->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (1.0.1) Requirement already satisfied: s3transfer<0.14.0,>=0.13.0 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from boto3->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (0.13.1) Requirement already satisfied: humanfriendly>=9.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from coloredlogs->cwltool==3.1.20240508115724->arvados-cwl-runner==3.2.0.dev20250814184714) (10.0) Requirement already satisfied: googleapis-common-protos<2.0.0,>=1.56.2 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0,>=1.31.5->google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (1.70.0) Requirement already satisfied: protobuf!=3.20.0,!=3.20.1,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<7.0.0,>=3.19.5 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0,>=1.31.5->google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (6.31.1) Requirement already satisfied: proto-plus<2.0.0,>=1.22.3 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from google-api-core!=2.0.*,!=2.1.*,!=2.2.*,!=2.3.0,<3.0.0,>=1.31.5->google-api-python-client>=2.1.0->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (1.26.1) Requirement already satisfied: pyasn1<0.7.0,>=0.6.1 in ./tmp/VENV3DIR/lib/python3.11/site-packages (from pyasn1-modules>=0.2.1->google-auth->arvados-python-client~=3.2.0.dev0->arvados-cwl-runner==3.2.0.dev20250814184714) (0.6.1) Building wheels for collected packages: arvados-cwl-runner Building wheel for arvados-cwl-runner (pyproject.toml) ... done Created wheel for arvados-cwl-runner: filename=arvados_cwl_runner-3.2.0.dev20250814184714-py3-none-any.whl size=1926592 sha256=2a593d767352e44ea88b7cbf5ed31c5faf1f61c32f1f8e002207a87551437d9d Stored in directory: /tmp/pip-ephem-wheel-cache-emqwa0l4/wheels/b6/0e/0d/50669789d4e35d3282dc1eaf5c7d3b13db0a27e10f3c8d632e Successfully built arvados-cwl-runner Installing collected packages: arvados-cwl-runner Attempting uninstall: arvados-cwl-runner Found existing installation: arvados-cwl-runner 3.2.0.dev20250814184714 Uninstalling arvados-cwl-runner-3.2.0.dev20250814184714: Successfully uninstalled arvados-cwl-runner-3.2.0.dev20250814184714 Successfully installed arvados-cwl-runner-3.2.0.dev20250814184714 ======= install sdk/cwl -- 4s dispatch pid is 1493518 keep0.pid is 1493682 keep1.pid is 1493701 ======= test sdk/cwl ============================================================================= test session starts ============================================================================= platform linux -- Python 3.11.2, pytest-8.4.1, pluggy-1.6.0 -- /home/tom/arvados/tmp/VENV3DIR/bin/python3 cachedir: .pytest_cache rootdir: /home/tom/arvados/sdk/cwl configfile: pytest.ini testpaths: tests plugins: cwltest-2.6.20250314152537 collected 138 items / 135 deselected / 3 selected tests/test_conformance.py::test_conformance_1_0 FAILED [ 33%] tests/test_conformance.py::test_conformance_1_1 FAILED [ 66%] tests/test_conformance.py::test_conformance_1_2 FAILED [100%] ================================================================================== FAILURES =================================================================================== ____________________________________________________________________________ test_conformance_1_0 _____________________________________________________________________________ acr_script = PosixPath('/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner'), badges_dir = PosixPath('/tmp/pytest-of-tom/pytest-23/test_conformance_1_00/badges') cwl1_0git = PosixPath('/tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0'), jobs_docker_image = 'arvados/jobs:3.2.0.dev20250814184714', skipped_tests_for_config = [] @pytest.mark.cwl_conformance @pytest.mark.integration def test_conformance_1_0(acr_script, badges_dir, cwl1_0git, jobs_docker_image, skipped_tests_for_config): cwltest = run_cwltest( cwl1_0git / 'v1.0/conformance_test_v1.0.yaml', acr_script, badges_dir, test_args=skipped_tests_for_config, ) > assert cwltest.returncode == os.EX_OK E AssertionError: assert 1 == 0 E + where 1 = CompletedProcess(args=['cwltest', '--test', '/tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/conformance_test_v1.0.yaml', '--tool', '/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner', '-j', '3', '--', '--compute-checksum', '--disable-reuse', '--enable-dev', '--verbose'], returncode=1).returncode E + and 0 = os.EX_OK tests/test_conformance.py:123: AssertionError ---------------------------------------------------------------------------- Captured stdout setup ---------------------------------------------------------------------------- zzzzz-4zz18-dds3n0tupwzkxe1 ---------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------- The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. The `label` field is deprecated. Use `id` field instead. Test [1/197] cl_basic_generation: General test of command line generation Test [2/197] nested_prefixes_arrays: Test nested prefixes with arrays Test [3/197] nested_cl_bindings: Test nested command line bindings Test 2 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp29vvjjpc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/binding-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/bwa-mem-job.json Test nested prefixes with arrays Returned non-zero Test [4/197] cl_optional_inputs_missing: Test command line with optional input (missing) Test 1 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpebj8isvy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/bwa-mem-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/bwa-mem-job.json General test of command line generation Returned non-zero Test [5/197] cl_optional_bindings_provided: Test command line with optional input (provided) Test 3 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9n5mry6f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/tmap-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/tmap-job.json Test nested command line bindings Returned non-zero Test [6/197] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Test 4 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp52k4nu28 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command line with optional input (missing) Returned non-zero Test [7/197] stdout_redirect_docker: Test command execution in Docker with stdout redirection Test 5 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprjlqqvi5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-n-job.json Test command line with optional input (provided) Returned non-zero Test [8/197] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection Test 6 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgpkm2iv_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/template-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Returned non-zero Test [9/197] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection Test 7 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqpm2sty5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-tool-docker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command execution in Docker with stdout redirection Returned non-zero Test [10/197] stderr_redirect: Test command line with stderr redirection Test 8 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptu6wm5ne --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-tool-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command execution in Docker with shortcut stdout redirection Returned non-zero Test [11/197] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax Test 9 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb0og_jaf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-tool-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command execution in Docker with mediumcut stdout redirection Returned non-zero Test [12/197] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax Test 11 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpaih126c4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stderr-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test command line with stderr redirection, brief syntax Returned non-zero Test [13/197] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection Test 10 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppmjtfmw6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stderr.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test command line with stderr redirection Returned non-zero Test [14/197] expression_any: Test default usage of Any in expressions. Test 12 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzjpyd7wi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stderr-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test command line with stderr redirection, named brief syntax Returned non-zero Test [15/197] expression_any_null: Test explicitly passing null to Any type inputs with default values. Test 13 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp27svkr0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command execution in Docker with stdin and stdout redirection Returned non-zero Test [16/197] expression_any_string: Testing the string 'null' does not trip up an Any with a default value. Test 15 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfylgmqq7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression1-job.json Test explicitly passing null to Any type inputs with default values. Returned non-zero Test [17/197] expression_any_nodefaultany: Test Any without defaults cannot be unspecified. Test 14 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx114xyi8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default usage of Any in expressions. Returned non-zero Test [18/197] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value. Test 16 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplu0n0a1m --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression2-job.json Testing the string 'null' does not trip up an Any with a default value. Returned non-zero Test [19/197] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value. Test [20/197] any_outputSource_compatibility: Testing Any type compatibility in outputSource Test [21/197] stdinout_redirect: Test command execution in with stdin and stdout redirection Test 19 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpffz00qx5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-expression2-job.json Testing the string 'null' does not trip up an Any without a default value. Returned non-zero Test [22/197] expression_parseint: Test ExpressionTool with Javascript engine Test 20 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0vcuwnwo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/any-type-compat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/any-type-job.json Testing Any type compatibility in outputSource Returned non-zero Test [23/197] expression_outputEval: Test outputEval to transform output Test 21 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfo8y1i25 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test command execution in with stdin and stdout redirection Returned non-zero Test [24/197] wf_wc_parseInt: Test two step workflow with imported tools Test 22 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp17_u9vxr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/parseInt-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/parseInt-job.json Test ExpressionTool with Javascript engine Returned non-zero Test [25/197] wf_wc_expressiontool: Test two step workflow with inline tools Test 23 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppvx2quzf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test outputEval to transform output Returned non-zero Test [26/197] wf_wc_scatter: Test single step workflow with Scatter step Test 24 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxdz12d_a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines1-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test two step workflow with imported tools Returned non-zero Test [27/197] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Test 25 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6ztl5r6y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test two step workflow with inline tools Returned non-zero Test [28/197] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Test 26 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp5g60d1o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines3-job.json Test single step workflow with Scatter step Returned non-zero Test [29/197] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Test 27 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwihs0swz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines4-job.json Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Returned non-zero Test [30/197] wf_wc_nomultiple: Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list Test 28 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpghgblty_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines6-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Returned non-zero Test [31/197] wf_input_default_missing: Test workflow with default value for input parameter (missing) Test 29 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp47rmdzjb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines7-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Returned non-zero Test [32/197] wf_input_default_provided: Test workflow with default value for input parameter (provided) Test 30 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmple5ul9t_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines13-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines6-job.json Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list Returned non-zero Test [33/197] wf_default_tool_default: Test that workflow defaults override tool defaults Test 31 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8xndq3v2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test workflow with default value for input parameter (missing) Returned non-zero Test [34/197] envvar_req: Test EnvVarRequirement Test 32 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppyah2ytc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test workflow with default value for input parameter (provided) Returned non-zero Test [35/197] wf_scatter_single_param: Test workflow scatter with single scatter parameter Test 33 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpujnnwwjq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/echo-wf-default.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that workflow defaults override tool defaults Returned non-zero Test [36/197] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method Test 34 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprqfidgt8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-tool1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-job.json Test EnvVarRequirement Returned non-zero Test [37/197] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method Test 35 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpukjevzq3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-job1.json Test workflow scatter with single scatter parameter Returned non-zero Test [38/197] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method Test 36 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpy9jvo5fz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method Returned non-zero Test [39/197] wf_scatter_emptylist: Test workflow scatter with single empty list parameter Test 37 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyfphty2m --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method Returned non-zero Test [40/197] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Test 38 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv1sn5za_ --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-job2.json Test workflow scatter with two scatter parameters and dotproduct join method Returned non-zero Test [41/197] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Test 39 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpm9ga0e76 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-empty-job1.json Test workflow scatter with single empty list parameter Returned non-zero Test [42/197] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Test 40 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbomozvuf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-empty-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Returned non-zero Test [43/197] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method Test 42 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp969p99r5 --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-empty-job2.json Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Returned non-zero Test [44/197] any_input_param: Test Any type input parameter Test 41 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpeh0h_gu3 --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-empty-job3.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Returned non-zero Test [45/197] nested_workflow: Test nested workflow Test 43 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2e491ica --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-empty-job4.json Test workflow scatter with two empty scatter parameters and dotproduct join method Returned non-zero Test [46/197] requirement_priority: Test requirement priority Test 44 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8co89mw_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/echo-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-job.json Test Any type input parameter Returned non-zero Test [47/197] requirement_override_hints: Test requirements override hints Test 45 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpavsvg7wc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines8-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test nested workflow Returned non-zero Test [48/197] requirement_workflow_steps: Test requirements on workflow steps Test 46 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpy9xwu2sf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-job.json Test requirement priority Returned non-zero Test [49/197] step_input_default_value: Test default value on step input parameter Test 47 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpulwcjkc6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-job.json Test requirements override hints Returned non-zero Test [50/197] step_input_default_value_nosource: Test use default value on step input parameter with empty source Test 48 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjljclq80 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-wf3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/env-job.json Test requirements on workflow steps Returned non-zero Test [51/197] step_input_default_value_nullsource: Test use default value on step input parameter with null source Test 49 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpan1ufarl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines9-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default value on step input parameter Returned non-zero Test [52/197] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source Test 50 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpl6g9_fnz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test use default value on step input parameter with empty source Returned non-zero Test [53/197] wf_simple: Test simple workflow Test 51 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp592p33ks --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/file1-null.json Test use default value on step input parameter with null source Returned non-zero Test [54/197] hints_unknown_ignored: Test unknown hints are ignored. Test 52 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1fudqr9j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test default value on step input parameter overridden by provided source Returned non-zero Test [55/197] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Test 53 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpy_bwfteq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/revsort.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/revsort-job.json Test simple workflow Returned non-zero Test [56/197] rename: Test InitialWorkDirRequirement with expression in filename. Test 54 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7toayxd8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat5-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test unknown hints are ignored. Returned non-zero Test [57/197] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir Test 55 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj5pidrwm --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/search.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/search-job.json Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Returned non-zero Test [58/197] inline_expressions: Test inline expressions Test 56 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmdqhhk_f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/rename.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/rename-job.json Test InitialWorkDirRequirement with expression in filename. Returned non-zero Test [59/197] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter Test 57 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0ihalkoy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/iwdr-entry.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/string-job.json Test if trailing newline is present in file entry in InitialWorkDir Returned non-zero Test [60/197] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter Test 58 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpstu20al0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test inline expressions Returned non-zero Test [61/197] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions Test 59 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg_7erlp9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/schemadef-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/schemadef-job.json Test SchemaDefRequirement definition used in tool parameter Returned non-zero Test [62/197] param_evaluation_expr: Test parameter evaluation, with support for JS expressions Test 60 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6xb1_lcm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/schemadef-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/schemadef-job.json Test SchemaDefRequirement definition used in workflow parameter Returned non-zero Test [63/197] metadata: Test metadata Test 61 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphq1sof69 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/params.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test parameter evaluation, no support for JS expressions Returned non-zero Test [64/197] format_checking: Test simple format checking. Test 62 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmo3x3ovd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/params2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test parameter evaluation, with support for JS expressions Returned non-zero Test [65/197] format_checking_subclass: Test format checking against ontology using subclassOf. Test 63 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2jf2zkfq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/metadata.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test metadata Returned non-zero Test [66/197] format_checking_equivalentclass: Test format checking against ontology using equivalentClass. Test 64 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2238jcjm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest-job.json Test simple format checking. Returned non-zero Test [67/197] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output. Test 65 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsr_31vav --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest2-job.json Test format checking against ontology using subclassOf. Returned non-zero Test [68/197] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null Test 66 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz1125v72 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/formattest2-job.json Test format checking against ontology using equivalentClass. Returned non-zero Test [69/197] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored Test 67 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe5scm1wq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/optional-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test optional output file and optional secondaryFile on output. Returned non-zero Test [70/197] valuefrom_wf_step: Test valueFrom on workflow step. Test 68 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpquniacu0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that valueFrom is ignored when the parameter is null Returned non-zero Test [71/197] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources Test 69 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6z6ycjso --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test that second expression in concatenated valueFrom is not ignored Returned non-zero Test [72/197] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs Test 70 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5w4iblc5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom-wf.json Test valueFrom on workflow step. Returned non-zero Test [73/197] record_output_binding: Test record type output binding. Test 71 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpq7xn9uaa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom-job.json Test valueFrom on workflow step with multiple sources Returned non-zero Test [74/197] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Test 72 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1zos5csr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom-job.json Test valueFrom on workflow step referencing other inputs Returned non-zero Test [75/197] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Test 73 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyao5tgwb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/record-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/record-output-job.json Test record type output binding. Returned non-zero Test [76/197] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression Test 74 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxiac7uv_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/test-cwl-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Returned non-zero Test [77/197] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Test 75 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6jkq6bmh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/test-cwl-out2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Returned non-zero Test [78/197] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Test 76 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk76sz9mj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/glob-expr-list.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/abc.json Test support for returning multiple glob patterns from expression Returned non-zero Test [79/197] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Test 77 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp53impf2j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Returned non-zero Test [80/197] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Test 78 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpn0a4aglr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Returned non-zero Test [81/197] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Test 79 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppyxd6pez --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Returned non-zero Test [82/197] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter Test 81 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8fla4q0d --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Returned non-zero Test [83/197] wf_two_inputfiles_namecollision: Test workflow two input files with same name. Test 80 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7mblt3zm --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Returned non-zero Test [84/197] directory_input_param_ref: Test directory input with parameter reference Test 82 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6p79kjso --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-wf6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job3.json Test valueFrom eval on scattered input parameter Returned non-zero Test [85/197] directory_input_docker: Test directory input in Docker Test 83 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwdm0ojme --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/conflict-wf.cwl#collision' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/conflict-job.json Test workflow two input files with same name. Returned non-zero Test [86/197] directory_output: Test directory output Test 84 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc1yvu4m4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir-job.yml Test directory input with parameter reference Returned non-zero Test [87/197] directory_secondaryfiles: Test directories in secondaryFiles Test 85 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo1hx01l3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir-job.yml Test directory input in Docker Returned non-zero Test [88/197] dynamic_initial_workdir: Test dynamic initial work dir Test 86 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphhb0igfz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir3-job.yml Test directory output Returned non-zero Test [89/197] writable_stagedfiles: Test writable staged files. Test 87 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprtkrhzet --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4-job.yml Test directories in secondaryFiles Returned non-zero Test [90/197] input_file_literal: Test file literal as input Test 88 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppm1asyt1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir-job.yml Test dynamic initial work dir Returned non-zero Test [91/197] initial_workdir_expr: Test expression in InitialWorkDir listing Test 89 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpdcccwg1z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stagefile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stagefile-job.yml Test writable staged files. Returned non-zero Test [92/197] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout Test 90 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt2lfit56 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/file-literal.yml Test file literal as input Returned non-zero Test [93/197] input_dir_inputbinding: Test directory input with inputBinding Test 91 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqsqygbcd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/linkfile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/arguments-job.yml Test expression in InitialWorkDir listing Returned non-zero Test [94/197] cl_gen_arrayofarrays: Test command line generation of array-of-arrays Test 92 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpglln_urp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/nameroot.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test nameroot/nameext expression in arguments, stdout Returned non-zero Test [95/197] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly Test 93 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp29_wxeyn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir-job.yml Test directory input with inputBinding Returned non-zero Test [96/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker Test 94 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyk7atcoh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/nested-array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/nested-array-job.yml Test command line generation of array-of-arrays Returned non-zero Test [97/197] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Test 95 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc0z_0c2h --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/envvar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test $HOME and $TMPDIR are set correctly Returned non-zero Test [98/197] initial_workdir_output: Test output of InitialWorkDir Test 96 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqiky5tzx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/envvar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test $HOME and $TMPDIR are set correctly in Docker Returned non-zero Test [99/197] embedded_subworkflow: Test embedded subworkflow Test 97 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplbbp4hgf --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/js-expr-req-wf.cwl#wf' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Returned non-zero Test [100/197] filesarray_secondaryfiles: Test secondaryFiles on array of files. Test 98 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfarq8b9x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/initialworkdirrequirement-docker-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/initialworkdirrequirement-docker-out-job.json Test output of InitialWorkDir Returned non-zero Test [101/197] exprtool_directory_literal: Test directory literal output created by ExpressionTool Test 99 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpuc53i1x3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines10-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test embedded subworkflow Returned non-zero Test [102/197] exprtool_file_literal: Test file literal output created by ExpressionTool Test 100 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfsekn8jg --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/docker-array-secondaryfiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/docker-array-secondaryfiles-job.json Test secondaryFiles on array of files. Returned non-zero Test [103/197] dockeroutputdir: Test dockerOutputDirectory Test 101 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi5m31wpc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir7.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir7.yml Test directory literal output created by ExpressionTool Returned non-zero Test [104/197] hints_import: Test hints with $import Test 102 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkc4vmqqp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/file-literal-ex.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test file literal output created by ExpressionTool Returned non-zero Test [105/197] default_path_notfound_warning: Test warning instead of error when default path is not found Test 103 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp10m6bx1y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/docker-output-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test dockerOutputDirectory Returned non-zero Test [106/197] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool Test 104 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv565amb7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/imported-hint.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test hints with $import Returned non-zero Test [107/197] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable Test 105 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgzlm4aub --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/default_path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/default_path_job.yml Test warning instead of error when default path is not found Returned non-zero Test [108/197] null_missing_params: Test that missing parameters are null (not undefined) in expression Test 106 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgjj0cgg5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/inline-js.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test InlineJavascriptRequirement with multiple expressions in the same tool Returned non-zero Test [109/197] param_notnull_expr: Test that provided parameter is not null in expression Test 107 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfuyxuzie --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/recursive-input-directory.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/recursive-input-directory.yml Test if a writable input directory is recursively copied and writable Returned non-zero Test [110/197] wf_compound_doc: Test compound workflow document Test 108 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwhehs45i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that missing parameters are null (not undefined) in expression Returned non-zero Test [111/197] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner Test 109 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk7cpvs9o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test that provided parameter is not null in expression Returned non-zero Test [112/197] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir). Test 110 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0eejj7ct --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/revsort-packed.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/revsort-job.json Test compound workflow document Returned non-zero Test [113/197] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Test 111 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe2p89dz7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/basename-fields-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/basename-fields-job.yml Test that nameroot and nameext are generated from basename at execution time by the runner Returned non-zero Test [114/197] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types Test 112 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpirwg7sqv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/initialwork-path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test that file path in $(inputs) for initialworkdir is in $(outdir). Returned non-zero Test [115/197] shelldir_notinterpreted: Test that shell directives are not interpreted. Test 113 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwe7tqfge --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines12-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Returned non-zero Test [116/197] shelldir_quoted: Test that shell directives are quoted. Test 114 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsgpxpf2p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/sum-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/sum-job.json Test step input with multiple sources with multiple types Returned non-zero Test [117/197] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement Test 115 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt5_rq3lu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/shellchar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that shell directives are not interpreted. Returned non-zero Test [118/197] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker Test 116 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcf_nntf1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/shellchar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that shell directives are quoted. Returned non-zero Test [119/197] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs Test 117 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp92vrqdv0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/writable-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test empty writable dir with InitialWorkDirRequirement Returned non-zero Test [120/197] fileliteral_input_docker: Test file literal as input without Docker Test 118 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprjlcs4mr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/writable-dir-docker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test empty writable dir with InitialWorkDirRequirement inside Docker Returned non-zero Test [121/197] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX Test 119 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5udg0my8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-job.yaml Test dynamic resource reqs referencing inputs Returned non-zero Test [122/197] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step Test 120 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc2mdvev5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-nodocker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/file-literal.yml Test file literal as input without Docker Returned non-zero Test [123/197] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null Test 121 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt80y6jo8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/glob_test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that OutputBinding.glob is sorted as specified by POSIX Returned non-zero Test [124/197] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input Test 122 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpui5h6tem --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/iwdr_with_nested_dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test InitialWorkDirRequirement with a nested directory structure from another step Returned non-zero Test [125/197] success_codes: Test successCodes Test 123 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj1ypqoss --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/bool-empty-inputbinding.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/bool-empty-inputbinding-job.json Test that boolean flags do not appear on command line if inputBinding is empty and not null Returned non-zero Test [126/197] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement Test 124 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp10afp04j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/stage-unprovided-file.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that expression engine does not fail to evaluate reference to self with unprovided input Returned non-zero Test [127/197] cl_empty_array_input: Test that empty array input does not add anything to command line Test 125 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzteup1oo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/exit-success.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test successCodes Returned non-zero Test [128/197] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level Test 126 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprawm5rzw --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-workflow.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-job.yaml Test simple workflow with a dynamic resource requirement Returned non-zero Test [129/197] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs Test 127 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxq22mefv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty-array-input.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty-array-job.json Test that empty array input does not add anything to command line Returned non-zero Test [130/197] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory Test 128 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6ekervua --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/steplevel-resreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that ResourceRequirement on a step level redefines requirement on the workflow level Returned non-zero Test [131/197] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Test 129 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsbapb5wu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/valueFrom-constant.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/array-of-strings-job.yml Test valueFrom with constant value overriding provided array inputs Returned non-zero Test [132/197] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. Test 130 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1lccjm_h --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-dir-job.yaml Test dynamic resource reqs referencing the size of Files inside a Directory Returned non-zero Test [133/197] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker without using return code Test 131 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpes8shxj_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/pass-unconnected.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Returned non-zero Test [134/197] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Test [135/197] packed_import_schema: SchemaDefRequirement with $import, and packed Test 133 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvj298tx0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/envvar3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test $HOME and $TMPDIR are set correctly in Docker without using return code Returned non-zero Test [136/197] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document. Test 134 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpocxgpwgh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-inputs-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Returned non-zero Test [137/197] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Test 135 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxuw9mvaw --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/import_schema-def_packed.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/import_schema-def_job.yml SchemaDefRequirement with $import, and packed Returned non-zero Test [138/197] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow Test 136 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsam85h4h --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4-subdir-1-job.yml Test specifying secondaryFiles in subdirectories of the job input document. Returned non-zero Test [139/197] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow Test 137 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7258i0ob --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dir4-subdir-2-job.yml Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Returned non-zero Test [140/197] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow Test 138 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5_kckc1h --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines18-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines3-job.json Test simple scatter over an embedded subworkflow Returned non-zero Test [141/197] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first Test 139 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1ebpl6j2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines14-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines4-job.json Test simple multiple input scatter over an embedded subworkflow Returned non-zero Test [142/197] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after Test 140 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvawr4ojv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines15-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test twice nested subworkflow Returned non-zero Test [143/197] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows. Test 141 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpa3rsk3t1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines16-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test subworkflow of mixed depth with tool first Returned non-zero Test [144/197] workflow_integer_input: Test integer workflow input and outputs Test 142 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpym989z2r --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines17-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test subworkflow of mixed depth with tool after Returned non-zero Test [145/197] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified) Test 143 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpaq16p1yk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/record-output-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/record-output-job.json Test record type inputs to and outputs from workflows. Returned non-zero Test [146/197] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified) Test 144 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfn3qb3jb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int.json Test integer workflow input and outputs Returned non-zero Test [147/197] workflow_integer_input_default_specified: Test default integer workflow inputs (specified) Test 145 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptavp_idq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int.json Test optional integer workflow inputs (specified) Returned non-zero Test [148/197] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified) Test 146 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp27bofd3u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test optional integer workflow inputs (unspecified) Returned non-zero Test [149/197] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified) Test 147 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8vboi_pn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int.json Test default integer workflow inputs (specified) Returned non-zero Test [150/197] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow Test 148 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3ksg_hhh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default integer workflow inputs (unspecified) Returned non-zero Test [151/197] workflow_file_input_default_specified: Test File input with default specified to workflow Test 149 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplhp1q37_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-int-default-tool-and-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default integer tool and workflow inputs (unspecified) Returned non-zero Test [152/197] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified. Test 150 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcgt9tnkr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test File input with default unspecified to workflow Returned non-zero Test [153/197] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified. Test 151 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplxzq2y_4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/default_path_job.yml Test File input with default specified to workflow Returned non-zero Test [154/197] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified. Test 152 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp44jolkll --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-array-one-empty-file.json Test input union type or File or File array to a tool with one file in array specified. Returned non-zero Test [155/197] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified. Test 153 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmor0kqug --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-array-few-files.json Test input union type or File or File array to a tool with a few files in array specified. Returned non-zero Test [156/197] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool Test 154 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpck2yx25_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-one-file.json Test input union type or File or File array to a tool with one file specified. Returned non-zero Test [157/197] clt_any_input_with_string_provided: Test Any parameter with string input to a tool Test 155 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptbfz35v8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-null.json Test input union type or File or File array to a tool with null specified. Returned non-zero Test [158/197] clt_any_input_with_file_provided: Test Any parameter with file input to a tool Test 156 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxgmq48mi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-int.json Test Any parameter with integer input to a tool Returned non-zero Test [159/197] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool Test 157 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjx9bwevn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-string.json Test Any parameter with string input to a tool Returned non-zero Test [160/197] clt_any_input_with_record_provided: Test Any parameter with record input to a tool Test 158 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9p7t6pwv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-file.json Test Any parameter with file input to a tool Returned non-zero Test [161/197] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow Test 159 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp04_wb99x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-array.json Test Any parameter with array input to a tool Returned non-zero Test [162/197] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow Test 160 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk0mljdmm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [163/197] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow Test 161 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9_om9kor --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-int.json Test Any parameter with integer input to a workflow Returned non-zero Test [164/197] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow Test 162 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp36ej9_48 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-string.json Test Any parameter with string input to a workflow Returned non-zero Test [165/197] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool Test 163 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp11pifm64 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-file.json Test Any parameter with file input to a workflow Returned non-zero Test [166/197] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified Test 164 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkjeh2y0s --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-array.json Test Any parameter with array input to a workflow Returned non-zero Test [167/197] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file Test 165 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0t0z3ndd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [168/197] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string). Test 166 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpiyks3b2i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test union type input to workflow with default unspecified Returned non-zero Test [169/197] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename. Test 167 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6s64axke --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/io-any-file.json Test union type input to workflow with default specified as file Returned non-zero Test [170/197] expression_tool_int_array_output: Test output arrays in a tool (with ints). Test 168 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc4_i2e_4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test valueFrom on workflow step from literal (string). Returned non-zero Test [171/197] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints). Test 169 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbi01tgh1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/step-valuefrom5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test valueFrom on workflow step using basename. Returned non-zero Test [172/197] workflow_file_array_output: Test output arrays in a workflow (with Files). Test 170 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2gqj2r60 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-int.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-int-job.json Test output arrays in a tool (with ints). Returned non-zero Test [173/197] docker_entrypoint: Test Docker ENTRYPOINT usage Test 171 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8cyour1i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-int-job.json Test output arrays in a workflow (with ints). Returned non-zero Test [174/197] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file Test 172 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpstmmc6bo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-file-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/output-arrays-file-job.json Test output arrays in a workflow (with Files). Returned non-zero Test [175/197] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files Test 173 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4gqtjzt8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/docker-run-cmd.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test Docker ENTRYPOINT usage Returned non-zero Test [176/197] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail. Test 174 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9nm_b11o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-array-one-empty-file.json Test use of size in expressions for an empty file Returned non-zero Test [177/197] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail. Test 175 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmkr0cp55 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/job-input-array-few-files.json Test use of size in expressions for a few files Returned non-zero Test [178/197] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool Test [179/197] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool Test [180/197] nested_workflow_noexp: Test nested workflow, without ExpressionTool Test 178 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgwwcxuet --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines9-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default value on step input parameter, no ExpressionTool Returned non-zero Test [181/197] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool Test 179 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7xjz8ojb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test default value on step input parameter overridden by provided source, no ExpressionTool Returned non-zero Test [182/197] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Test 180 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw824ryy_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines8-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/wc-job.json Test nested workflow, without ExpressionTool Returned non-zero Test [183/197] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Test 181 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5owf_fih --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/sum-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/sum-job.json Test step input with multiple sources with multiple types, without ExpressionTool Returned non-zero Test [184/197] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Test 182 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz5zt_npi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-workflow-tooldefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Returned non-zero Test [185/197] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step Test 183 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgafq6h3y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-workflow-stepdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Returned non-zero Test [186/197] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Test 184 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjmb8338o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/dynresreq-workflow-inputdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Returned non-zero Test [187/197] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step Test 185 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8jndyctv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-extra-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step Returned non-zero Test [188/197] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Test 186 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzq2jza05 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Returned non-zero Test [189/197] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal Test 187 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvyqku1a3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-null-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default value on step input parameter overridden by provided source. With null producing first step Returned non-zero Test [190/197] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal Test 188 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1w3yz0ef --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/count-lines11-null-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/empty.json Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Returned non-zero Test [191/197] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal Test 189 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpien7ueyf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-from-dir-job.yaml Pipe to stdin from user provided local File via a Directory literal Returned non-zero Test [192/197] no_inputs_commandlinetool: Test CommandLineTool without inputs Test 190 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr4lfdtl8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-from-dir-with-literal-file.yaml Pipe to stdin from literal File via a Directory literal Returned non-zero Test [193/197] no_outputs_commandlinetool: Test CommandLineTool without outputs Test 191 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpde8v0meu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat3-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-from-dir-with-literal-file.yaml Test non-stdin reference to literal File via a Directory literal Returned non-zero Test [194/197] no_inputs_workflow: Test Workflow without inputs Test 192 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7upmv1xo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/no-inputs-tool.cwl Test CommandLineTool without inputs Returned non-zero Test [195/197] no_outputs_workflow: Test Workflow without outputs Test 193 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0v3y_j7y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/no-outputs-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test CommandLineTool without outputs Returned non-zero Test [196/197] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record Test 194 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb53tw5wm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/no-inputs-wf.cwl Test Workflow without inputs Returned non-zero Test [197/197] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement Test 195 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpdx_d7uue --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/no-outputs-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/cat-job.json Test Workflow without outputs Returned non-zero Test 196 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz7itpizw --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/anon_enum_inside_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/anon_enum_inside_array.yml Test an anonymous enum inside an array inside a record Returned non-zero Test 197 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5du0_uv_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/anon_enum_inside_array_inside_schemadef.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.0_tags_v1.0.2_0/v1.0/v1.0/anon_enum_inside_array_inside_schemadef.yml Test an anonymous enum inside an array inside a record, SchemaDefRequirement Returned non-zero 5 tests passed, 192 failures, 0 unsupported features ____________________________________________________________________________ test_conformance_1_1 _____________________________________________________________________________ acr_script = PosixPath('/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner'), badges_dir = PosixPath('/tmp/pytest-of-tom/pytest-23/test_conformance_1_10/badges') cwl1_1git = PosixPath('/tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0'), jobs_docker_image = 'arvados/jobs:3.2.0.dev20250814184714' skipped_tests_for_config = [] @pytest.mark.cwl_conformance @pytest.mark.integration def test_conformance_1_1(acr_script, badges_dir, cwl1_1git, jobs_docker_image, skipped_tests_for_config): cwltest = run_cwltest( cwl1_1git / 'conformance_tests.yaml', acr_script, badges_dir, test_args=skipped_tests_for_config + ['-N', '199'], ) > assert cwltest.returncode == os.EX_OK E AssertionError: assert 1 == 0 E + where 1 = CompletedProcess(args=['cwltest', '--test', '/tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/conformance_tests.yaml', '--tool', '/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner', '-j', '3', '-N', '199', '--', '--compute-checksum', '--disable-reuse', '--enable-dev', '--verbose'], returncode=1).returncode E + and 0 = os.EX_OK tests/test_conformance.py:135: AssertionError ---------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------- Test [1/253] cl_basic_generation: General test of command line generation Test [2/253] nested_prefixes_arrays: Test nested prefixes with arrays Test [3/253] nested_cl_bindings: Test nested command line bindings Test 3 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyqahsrcr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/tmap-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/tmap-job.json Test nested command line bindings Returned non-zero Test [4/253] cl_optional_inputs_missing: Test command line with optional input (missing) Test 1 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj52essv9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/bwa-mem-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/bwa-mem-job.json General test of command line generation Returned non-zero Test [5/253] cl_optional_bindings_provided: Test command line with optional input (provided) Test 2 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplqo5edps --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/binding-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/bwa-mem-job.json Test nested prefixes with arrays Returned non-zero Test [6/253] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Test 4 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprz5fo3i7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command line with optional input (missing) Returned non-zero Test [7/253] stdout_redirect_docker: Test command execution in Docker with stdout redirection Test 6 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7ll4pc2r --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/template-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Returned non-zero Test [8/253] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection Test 5 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp47ok98g_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-n-job.json Test command line with optional input (provided) Returned non-zero Test [9/253] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection Test 7 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp2teblmz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command execution in Docker with stdout redirection Returned non-zero Test [10/253] stderr_redirect: Test command line with stderr redirection Test 9 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprq68_y_2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-tool-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command execution in Docker with mediumcut stdout redirection Returned non-zero Test [11/253] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax Test 8 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptdxh8n0o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-tool-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command execution in Docker with shortcut stdout redirection Returned non-zero Test [12/253] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax Test 10 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpboin6nyi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stderr.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test command line with stderr redirection Returned non-zero Test [13/253] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection Test 12 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd9soyem1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stderr-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test command line with stderr redirection, named brief syntax Returned non-zero Test [14/253] expression_any: Test default usage of Any in expressions. Test 11 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpznwuy834 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stderr-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test command line with stderr redirection, brief syntax Returned non-zero Test [15/253] expression_any_null: Test explicitly passing null to Any type inputs with default values. Test 13 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpenr9dwny --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command execution in Docker with stdin and stdout redirection Returned non-zero Test [16/253] expression_any_string: Testing the string 'null' does not trip up an Any with a default value. Test 14 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpuzheg8q8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default usage of Any in expressions. Returned non-zero Test [17/253] expression_any_nodefaultany: Test Any without defaults cannot be unspecified. Test 15 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwztt1ayf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression1-job.json Test explicitly passing null to Any type inputs with default values. Returned non-zero Test [18/253] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value. Test 16 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpev1mpioz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression2-job.json Testing the string 'null' does not trip up an Any with a default value. Returned non-zero Test [19/253] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value. Test [20/253] any_outputSource_compatibility: Testing Any type compatibility in outputSource Test [21/253] stdinout_redirect: Test command execution in with stdin and stdout redirection Test 19 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc36g39wy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-expression2-job.json Testing the string 'null' does not trip up an Any without a default value. Returned non-zero Test [22/253] expression_parseint: Test ExpressionTool with Javascript engine Test 20 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzwnom0sk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/any-type-compat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/any-type-job.json Testing Any type compatibility in outputSource Returned non-zero Test [23/253] expression_outputEval: Test outputEval to transform output Test 21 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqxplb4n5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test command execution in with stdin and stdout redirection Returned non-zero Test [24/253] wf_wc_parseInt: Test two step workflow with imported tools Test 22 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp74gynr8v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/parseInt-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/parseInt-job.json Test ExpressionTool with Javascript engine Returned non-zero Test [25/253] wf_wc_expressiontool: Test two step workflow with inline tools Test 24 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpygx9vup3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines1-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test two step workflow with imported tools Returned non-zero Test [26/253] wf_wc_scatter: Test single step workflow with Scatter step Test 23 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgg7k3lhu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test outputEval to transform output Returned non-zero Test [27/253] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Test 25 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx4v1ybl7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test two step workflow with inline tools Returned non-zero Test [28/253] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Test 26 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0k61ym0u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines3-job.json Test single step workflow with Scatter step Returned non-zero Test [29/253] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Test 27 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8u5a8k_t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines4-job.json Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Returned non-zero Test [30/253] wf_wc_nomultiple: Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list Test 28 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp_w74yvr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines6-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Returned non-zero Test [31/253] wf_input_default_missing: Test workflow with default value for input parameter (missing) Test 29 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpniig47m9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines7-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Returned non-zero Test [32/253] wf_input_default_provided: Test workflow with default value for input parameter (provided) Test 30 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1lc0lg_b --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines13-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines6-job.json Test that no MultipleInputFeatureRequirement is necessary when workflow step source is a single-item list Returned non-zero Test [33/253] wf_default_tool_default: Test that workflow defaults override tool defaults Test 31 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpts2t6yr6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test workflow with default value for input parameter (missing) Returned non-zero Test [34/253] envvar_req: Test EnvVarRequirement Test 32 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpax0a0x48 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test workflow with default value for input parameter (provided) Returned non-zero Test [35/253] wf_scatter_single_param: Test workflow scatter with single scatter parameter Test 33 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2h6sqvwf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-wf-default.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that workflow defaults override tool defaults Returned non-zero Test [36/253] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method Test 34 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkkpe473g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-tool1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test EnvVarRequirement Returned non-zero Test [37/253] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method Test 35 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpogj37tpp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-job1.json Test workflow scatter with single scatter parameter Returned non-zero Test [38/253] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method Test 36 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfy20qe1x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method Returned non-zero Test [39/253] wf_scatter_emptylist: Test workflow scatter with single empty list parameter Test 37 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8qjluwnn --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method Returned non-zero Test [40/253] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Test 38 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5wzc8zcp --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and dotproduct join method Returned non-zero Test [41/253] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Test 39 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr3b7h74w --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-empty-job1.json Test workflow scatter with single empty list parameter Returned non-zero Test [42/253] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Test 40 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgvz2xocs --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-empty-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Returned non-zero Test [43/253] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method Test 41 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8uevf47m --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-empty-job3.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Returned non-zero Test [44/253] any_input_param: Test Any type input parameter Test 42 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx78mh_mq --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-empty-job2.json Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Returned non-zero Test [45/253] nested_workflow: Test nested workflow Test 43 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphzmsiplg --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-empty-job4.json Test workflow scatter with two empty scatter parameters and dotproduct join method Returned non-zero Test [46/253] requirement_priority: Test requirement priority Test 44 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp77km8g3k --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test Any type input parameter Returned non-zero Test [47/253] requirement_override_hints: Test requirements override hints Test 45 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx26a4h61 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines8-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test nested workflow Returned non-zero Test [48/253] requirement_workflow_steps: Test requirements on workflow steps Test 46 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbz4iuxqf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test requirement priority Returned non-zero Test [49/253] step_input_default_value: Test default value on step input parameter Test 47 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe83nj8j0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test requirements override hints Returned non-zero Test [50/253] step_input_default_value_nosource: Test use default value on step input parameter with empty source Test 48 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfli9rcxz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-wf3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test requirements on workflow steps Returned non-zero Test [51/253] step_input_default_value_nullsource: Test use default value on step input parameter with null source Test 49 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2gje2ufa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines9-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default value on step input parameter Returned non-zero Test [52/253] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source Test 50 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph4ho294g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test use default value on step input parameter with empty source Returned non-zero Test [53/253] wf_simple: Test simple workflow Test 51 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnb5vis00 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/file1-null.json Test use default value on step input parameter with null source Returned non-zero Test [54/253] hints_unknown_ignored: Test unknown hints are ignored. Test 52 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgu_868o3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test default value on step input parameter overridden by provided source Returned non-zero Test [55/253] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Test 53 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprpsydrab --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/revsort.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/revsort-job.json Test simple workflow Returned non-zero Test [56/253] rename: Test InitialWorkDirRequirement with expression in filename. Test 54 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp266t8brf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat5-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test unknown hints are ignored. Returned non-zero Test [57/253] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir Test 55 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp11nsy2dp --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/search.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/search-job.json Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Returned non-zero Test [58/253] inline_expressions: Test inline expressions Test 57 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw477_n__ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/iwdr-entry.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/string-job.json Test if trailing newline is present in file entry in InitialWorkDir Returned non-zero Test [59/253] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter Test 56 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpiagdm7ad --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/rename.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/rename-job.json Test InitialWorkDirRequirement with expression in filename. Returned non-zero Test [60/253] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter Test 58 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpftenbh14 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test inline expressions Returned non-zero Test [61/253] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions Test 60 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4e9i_usa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/schemadef-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/schemadef-job.json Test SchemaDefRequirement definition used in workflow parameter Returned non-zero Test [62/253] param_evaluation_expr: Test parameter evaluation, with support for JS expressions Test 59 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1j90_3n1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/schemadef-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/schemadef-job.json Test SchemaDefRequirement definition used in tool parameter Returned non-zero Test [63/253] metadata: Test metadata Test 61 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi_z0idoq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/params.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test parameter evaluation, no support for JS expressions Returned non-zero Test [64/253] format_checking: Test simple format checking. Test 63 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpew0qozem --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/metadata.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test 62 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6w5wg34p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/params2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test metadata Test parameter evaluation, with support for JS expressions Returned non-zero Test [65/253] format_checking_subclass: Test format checking against ontology using subclassOf. Returned non-zero Test [66/253] format_checking_equivalentclass: Test format checking against ontology using equivalentClass. Test 64 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2z1y3a6v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest-job.json Test simple format checking. Returned non-zero Test [67/253] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output. Test 66 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_8917t78 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest2-job.json Test format checking against ontology using equivalentClass. Returned non-zero Test [68/253] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null Test 65 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppi06gc1n --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/formattest2-job.json Test format checking against ontology using subclassOf. Returned non-zero Test [69/253] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored Test 67 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcytl84ph --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/optional-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test optional output file and optional secondaryFile on output. Returned non-zero Test [70/253] valuefrom_wf_step: Test valueFrom on workflow step. Test 69 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6o6lqsxv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test that second expression in concatenated valueFrom is not ignored Returned non-zero Test [71/253] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources Test 68 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpu_amohfy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that valueFrom is ignored when the parameter is null Returned non-zero Test [72/253] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs Test 70 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp30c6urgf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom-wf.json Test valueFrom on workflow step. Returned non-zero Test [73/253] record_output_binding: Test record type output binding. Test 72 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg8gyfnwl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom-job.json Test valueFrom on workflow step referencing other inputs Returned non-zero Test [74/253] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Test 71 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3sbzed74 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom-job.json Test valueFrom on workflow step with multiple sources Returned non-zero Test [75/253] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Test 73 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplt0yej26 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-output-job.json Test record type output binding. Returned non-zero Test [76/253] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression Test 74 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt56clbz7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/test-cwl-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Returned non-zero Test [77/253] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Test 75 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppukg2412 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/test-cwl-out2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Returned non-zero Test [78/253] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Test 76 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_pifxlux --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/glob-expr-list.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/abc.json Test support for returning multiple glob patterns from expression Returned non-zero Test [79/253] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Test 77 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzt57nr6x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Returned non-zero Test [80/253] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Test 78 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpncda7d4t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Returned non-zero Test [81/253] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Test 79 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpglzjvj54 --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Returned non-zero Test [82/253] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter Test 80 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0iuwgz0b --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Returned non-zero Test [83/253] wf_two_inputfiles_namecollision: Test workflow two input files with same name. Test 81 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxqoy3rhk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Returned non-zero Test [84/253] directory_input_param_ref: Test directory input with parameter reference Test 82 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb_ijsljc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-wf6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job3.json Test valueFrom eval on scattered input parameter Returned non-zero Test [85/253] directory_input_docker: Test directory input in Docker Test 83 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp67d6u300 --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/conflict-wf.cwl#collision' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/conflict-job.json Test workflow two input files with same name. Returned non-zero Test [86/253] directory_output: Test directory output Test 84 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnt64lt6x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir-job.yml Test directory input with parameter reference Returned non-zero Test [87/253] directory_secondaryfiles: Test directories in secondaryFiles Test 85 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsvszkne4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir-job.yml Test directory input in Docker Returned non-zero Test [88/253] dynamic_initial_workdir: Test dynamic initial work dir Test 86 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2u6q730l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir3-job.yml Test directory output Returned non-zero Test [89/253] writable_stagedfiles: Test writable staged files. Test 87 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp54eigzn2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4-job.yml Test directories in secondaryFiles Returned non-zero Test [90/253] input_file_literal: Test file literal as input Test 88 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpskj11b1p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir-job.yml Test dynamic initial work dir Returned non-zero Test [91/253] initial_workdir_expr: Test expression in InitialWorkDir listing Test 89 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_8t3qq7p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stagefile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stagefile-job.yml Test writable staged files. Returned non-zero Test [92/253] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout Test 90 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpev9m_cw4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/file-literal.yml Test file literal as input Returned non-zero Test [93/253] input_dir_inputbinding: Test directory input with inputBinding Test 91 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpya_t2i16 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/linkfile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/arguments-job.yml Test expression in InitialWorkDir listing Returned non-zero Test [94/253] cl_gen_arrayofarrays: Test command line generation of array-of-arrays Test 92 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9asvfpt8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/nameroot.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test nameroot/nameext expression in arguments, stdout Returned non-zero Test [95/253] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly Test 93 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpigrlbeba --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir-job.yml Test directory input with inputBinding Returned non-zero Test [96/253] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker Test 94 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9w_1kfa9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/nested-array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/nested-array-job.yml Test command line generation of array-of-arrays Returned non-zero Test [97/253] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Test 95 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvjxvtg85 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/envvar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test $HOME and $TMPDIR are set correctly Returned non-zero Test [98/253] initial_workdir_output: Test output of InitialWorkDir Test 96 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp654icy5n --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/envvar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test $HOME and $TMPDIR are set correctly in Docker Returned non-zero Test [99/253] embedded_subworkflow: Test embedded subworkflow Test 97 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfesxg0sv --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/js-expr-req-wf.cwl#wf' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Returned non-zero Test [100/253] filesarray_secondaryfiles: Test required, optional and null secondaryFiles on array of files. Test 98 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp515phh_k --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdirrequirement-docker-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdirrequirement-docker-out-job.json Test output of InitialWorkDir Returned non-zero Test [101/253] filesarray_secondaryfiles2: Test required, optional and null secondaryFiles on array of files. Test 99 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqnhhk4am --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines10-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test embedded subworkflow Returned non-zero Test [102/253] exprtool_directory_literal: Test directory literal output created by ExpressionTool Test 100 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpppikkt0t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/docker-array-secondaryfiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/docker-array-secondaryfiles-job.json Test required, optional and null secondaryFiles on array of files. Returned non-zero Test [103/253] exprtool_file_literal: Test file literal output created by ExpressionTool Test [104/253] dockeroutputdir: Test dockerOutputDirectory Test 102 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9vwmumv5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir7.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir7.yml Test directory literal output created by ExpressionTool Returned non-zero Test [105/253] hints_import: Test hints with $import Test 103 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqfn2tv04 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/file-literal-ex.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test file literal output created by ExpressionTool Returned non-zero Test [106/253] default_path_notfound_warning: Test warning instead of error when default path is not found Test 104 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx3vi2io_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/docker-output-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test dockerOutputDirectory Returned non-zero Test [107/253] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool Test 105 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr6_r9ao9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/imported-hint.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test hints with $import Returned non-zero Test [108/253] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable Test 106 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcw7e015i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/default_path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/default_path_job.yml Test warning instead of error when default path is not found Returned non-zero Test [109/253] null_missing_params: Test that missing parameters are null (not undefined) in expression Test 107 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp07nkdeqi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/inline-js.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test InlineJavascriptRequirement with multiple expressions in the same tool Returned non-zero Test [110/253] param_notnull_expr: Test that provided parameter is not null in expression Test 108 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmbu9wlzu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/recursive-input-directory.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/recursive-input-directory.yml Test if a writable input directory is recursively copied and writable Returned non-zero Test [111/253] wf_compound_doc: Test compound workflow document Test 109 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_f8zmr2l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that missing parameters are null (not undefined) in expression Returned non-zero Test [112/253] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner Test 110 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnptqwm4d --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test that provided parameter is not null in expression Returned non-zero Test [113/253] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir). Test 111 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpztcppksp --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/revsort-packed.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/revsort-job.json Test compound workflow document Returned non-zero Test [114/253] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Test 112 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvou0f22v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/basename-fields-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/basename-fields-job.yml Test that nameroot and nameext are generated from basename at execution time by the runner Returned non-zero Test [115/253] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types Test 113 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyq4x2g28 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialwork-path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test that file path in $(inputs) for initialworkdir is in $(outdir). Returned non-zero Test [116/253] shelldir_notinterpreted: Test that shell directives are not interpreted. Test 114 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph7j800jz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines12-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Returned non-zero Test [117/253] shelldir_quoted: Test that shell directives are quoted. Test 115 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmj6t9dbn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/sum-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/sum-job.json Test step input with multiple sources with multiple types Returned non-zero Test [118/253] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement Test 116 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7b0whhv1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/shellchar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that shell directives are not interpreted. Returned non-zero Test [119/253] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker Test 117 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1x7zlask --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/shellchar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that shell directives are quoted. Returned non-zero Test [120/253] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs Test 118 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfnzea4qn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/writable-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test empty writable dir with InitialWorkDirRequirement Returned non-zero Test [121/253] fileliteral_input_docker: Test file literal as input without Docker Test 119 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpn8vf5me4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/writable-dir-docker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test empty writable dir with InitialWorkDirRequirement inside Docker Returned non-zero Test [122/253] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX Test 120 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx8gy9ib3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-job.yaml Test dynamic resource reqs referencing inputs Returned non-zero Test [123/253] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step Test 121 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpdk68s210 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-nodocker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/file-literal.yml Test file literal as input without Docker Returned non-zero Test [124/253] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null Test 122 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3egfj1at --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/glob_test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that OutputBinding.glob is sorted as specified by POSIX Returned non-zero Test [125/253] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input Test 123 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk57d3di4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/iwdr_with_nested_dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test InitialWorkDirRequirement with a nested directory structure from another step Returned non-zero Test [126/253] success_codes: Test successCodes Test 124 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8qcsot7y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/bool-empty-inputbinding.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/bool-empty-inputbinding-job.json Test that boolean flags do not appear on command line if inputBinding is empty and not null Returned non-zero Test [127/253] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement Test 125 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfsybav6m --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage-unprovided-file.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that expression engine does not fail to evaluate reference to self with unprovided input Returned non-zero Test [128/253] cl_empty_array_input: Test that empty array input does not add anything to command line Test 126 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4iopver4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/exit-success.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test successCodes Returned non-zero Test [129/253] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level Test 127 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp7u59u0o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-workflow.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-job.yaml Test simple workflow with a dynamic resource requirement Returned non-zero Test [130/253] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs Test 128 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2r3ijzhd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty-array-input.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty-array-job.json Test that empty array input does not add anything to command line Returned non-zero Test [131/253] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory Test 129 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8ubtw5za --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/steplevel-resreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that ResourceRequirement on a step level redefines requirement on the workflow level Returned non-zero Test [132/253] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Test 130 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6_w_m3d0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/valueFrom-constant.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/array-of-strings-job.yml Test valueFrom with constant value overriding provided array inputs Returned non-zero Test [133/253] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. Test 131 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7gsa7n2w --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-dir-job.yaml Test dynamic resource reqs referencing the size of Files inside a Directory Returned non-zero Test [134/253] env_home_tmpdir_docker_no_return_code: Test $HOME and $TMPDIR are set correctly in Docker without using return code Test 132 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgde82r_6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/pass-unconnected.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Returned non-zero Test [135/253] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Test [136/253] packed_import_schema: SchemaDefRequirement with $import, and packed Test 134 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp42s_be82 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/envvar3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test $HOME and $TMPDIR are set correctly in Docker without using return code Returned non-zero Test [137/253] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document. Test 135 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvo5i5ptm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-inputs-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Returned non-zero Test [138/253] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Test 136 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppeuugbfn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/import_schema-def_packed.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/import_schema-def_job.yml SchemaDefRequirement with $import, and packed Returned non-zero Test [139/253] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow Test 137 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjj_489fg --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4-subdir-1-job.yml Test specifying secondaryFiles in subdirectories of the job input document. Returned non-zero Test [140/253] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow Test 138 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprzsty61a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dir4-subdir-2-job.yml Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Returned non-zero Test [141/253] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow Test 139 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi_ar7vwd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines18-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines3-job.json Test simple scatter over an embedded subworkflow Returned non-zero Test [142/253] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first Test 140 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjnvr4bxx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines14-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines4-job.json Test simple multiple input scatter over an embedded subworkflow Returned non-zero Test [143/253] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after Test 141 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplvsaif_t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines15-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test twice nested subworkflow Returned non-zero Test [144/253] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows. Test 142 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxq9q_dn0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines16-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test subworkflow of mixed depth with tool first Returned non-zero Test [145/253] workflow_integer_input: Test integer workflow input and outputs Test 143 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8uqdmy1b --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines17-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test subworkflow of mixed depth with tool after Returned non-zero Test [146/253] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified) Test 144 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmv97ckow --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-output-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-output-job.json Test record type inputs to and outputs from workflows. Returned non-zero Test [147/253] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified) Test 145 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1sxb_t_d --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int.json Test integer workflow input and outputs Returned non-zero Test [148/253] workflow_integer_input_default_specified: Test default integer workflow inputs (specified) Test 146 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2a78hd7w --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int.json Test optional integer workflow inputs (specified) Returned non-zero Test [149/253] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified) Test 147 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3uxzv4ki --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test optional integer workflow inputs (unspecified) Returned non-zero Test [150/253] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified) Test 148 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbomk1fa8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int.json Test default integer workflow inputs (specified) Returned non-zero Test [151/253] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow Test 149 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnb1sjj4z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default integer workflow inputs (unspecified) Returned non-zero Test [152/253] workflow_file_input_default_specified: Test File input with default specified to workflow Test 150 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe28m8844 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-int-default-tool-and-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default integer tool and workflow inputs (unspecified) Returned non-zero Test [153/253] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified. Test 151 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi6iyzxgx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test File input with default unspecified to workflow Returned non-zero Test [154/253] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified. Test 152 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj8kfu66f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/default_path_job.yml Test File input with default specified to workflow Returned non-zero Test [155/253] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified. Test 153 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv52atxhm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-array-one-empty-file.json Test input union type or File or File array to a tool with one file in array specified. Returned non-zero Test [156/253] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified. Test 154 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw9z7ndwa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-array-few-files.json Test input union type or File or File array to a tool with a few files in array specified. Returned non-zero Test [157/253] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool Test 155 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcoynvuwd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-one-file.json Test input union type or File or File array to a tool with one file specified. Returned non-zero Test [158/253] clt_any_input_with_string_provided: Test Any parameter with string input to a tool Test 156 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpol8g2r8g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-null.json Test input union type or File or File array to a tool with null specified. Returned non-zero Test [159/253] clt_any_input_with_file_provided: Test Any parameter with file input to a tool Test 157 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi3hbyyez --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-int.json Test Any parameter with integer input to a tool Returned non-zero Test [160/253] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool Test 158 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo39f8y6z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-string.json Test Any parameter with string input to a tool Returned non-zero Test [161/253] clt_any_input_with_record_provided: Test Any parameter with record input to a tool Test 159 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpabg36djx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-file.json Test Any parameter with file input to a tool Returned non-zero Test [162/253] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow Test 160 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj46v_3ug --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-array.json Test Any parameter with array input to a tool Returned non-zero Test [163/253] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow Test 161 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1wiit66u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [164/253] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow Test 162 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7e9494aa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-int.json Test Any parameter with integer input to a workflow Returned non-zero Test [165/253] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow Test 163 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpa4fxw1q9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-string.json Test Any parameter with string input to a workflow Returned non-zero Test [166/253] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool Test 164 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpks7j01zu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-file.json Test Any parameter with file input to a workflow Returned non-zero Test [167/253] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified Test 165 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_9305xy5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-array.json Test Any parameter with array input to a workflow Returned non-zero Test [168/253] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file Test 166 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpana70pxw --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [169/253] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string). Test 167 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0g51gw_c --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test union type input to workflow with default unspecified Returned non-zero Test [170/253] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename. Test 168 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbnif4ssl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/io-any-file.json Test union type input to workflow with default specified as file Returned non-zero Test [171/253] expression_tool_int_array_output: Test output arrays in a tool (with ints). Test 169 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmps4rwxtgv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test valueFrom on workflow step from literal (string). Returned non-zero Test [172/253] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints). Test 171 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpm_uy1m9o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-int.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-int-job.json Test output arrays in a tool (with ints). Returned non-zero Test [173/253] workflow_file_array_output: Test output arrays in a workflow (with Files). Test 170 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0iwxmswq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/step-valuefrom5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test valueFrom on workflow step using basename. Returned non-zero Test [174/253] docker_entrypoint: Test Docker ENTRYPOINT usage Test 172 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxfyakp0g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-int-job.json Test output arrays in a workflow (with ints). Returned non-zero Test [175/253] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file Test 174 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2yiv8x9r --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/docker-run-cmd.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test Docker ENTRYPOINT usage Returned non-zero Test [176/253] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files Test 173 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpct1p3vxk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-file-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/output-arrays-file-job.json Test output arrays in a workflow (with Files). Returned non-zero Test [177/253] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail. Test 175 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpakb9y333 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-array-one-empty-file.json Test use of size in expressions for an empty file Returned non-zero Test [178/253] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail. Test 176 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpa_irgt4w --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/job-input-array-few-files.json Test use of size in expressions for a few files Returned non-zero Test [179/253] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool Test [180/253] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool Test [181/253] nested_workflow_noexp: Test nested workflow, without ExpressionTool Test 179 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp23camp3x --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines9-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default value on step input parameter, no ExpressionTool Returned non-zero Test [182/253] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool Test 180 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9vpws57z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test default value on step input parameter overridden by provided source, no ExpressionTool Returned non-zero Test [183/253] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Test 181 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4j20j20q --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines8-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wc-job.json Test nested workflow, without ExpressionTool Returned non-zero Test [184/253] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Test 182 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpre4olyor --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/sum-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/sum-job.json Test step input with multiple sources with multiple types, without ExpressionTool Returned non-zero Test [185/253] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Test 183 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr6al65p8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-workflow-tooldefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Returned non-zero Test [186/253] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step Test 184 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfkiq8wol --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-workflow-stepdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Returned non-zero Test [187/253] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Test 186 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgwlj_yft --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-extra-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step Returned non-zero Test [188/253] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step Test 185 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpoq5ploc4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/dynresreq-workflow-inputdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Returned non-zero Test [189/253] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Test 187 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvqimfux7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-extra-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Returned non-zero Test [190/253] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal Test 188 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz1trji7l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-null-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default value on step input parameter overridden by provided source. With null producing first step Returned non-zero Test [191/253] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal Test 189 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk6vb7a98 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/count-lines11-null-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Returned non-zero Test [192/253] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal Test 190 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp44zv5zoq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-from-dir-job.yaml Pipe to stdin from user provided local File via a Directory literal Returned non-zero Test [193/253] no_inputs_commandlinetool: Test CommandLineTool without inputs Test 191 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp045mh617 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-from-dir-with-literal-file.yaml Pipe to stdin from literal File via a Directory literal Returned non-zero Test [194/253] no_outputs_commandlinetool: Test CommandLineTool without outputs Test 192 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmybqxjrq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat3-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-from-dir-with-literal-file.yaml Test non-stdin reference to literal File via a Directory literal Returned non-zero Test [195/253] no_inputs_workflow: Test Workflow without inputs Test 193 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmctv6va1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/no-inputs-tool.cwl Test CommandLineTool without inputs Returned non-zero Test [196/253] no_outputs_workflow: Test Workflow without outputs Test 194 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsw99mg4f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/no-outputs-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test CommandLineTool without outputs Returned non-zero Test [197/253] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record Test 195 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpck4t4lp1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/no-inputs-wf.cwl Test Workflow without inputs Returned non-zero Test [198/253] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement Test 196 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd6vzz_68 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/no-outputs-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/cat-job.json Test Workflow without outputs Returned non-zero Test [200/253] secondary_files_in_unnamed_records: Test secondaryFiles on anonymous record fields Test 197 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9d4b0laj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/anon_enum_inside_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/anon_enum_inside_array.yml Test an anonymous enum inside an array inside a record Returned non-zero Test [201/253] secondary_files_in_named_records: Test secondaryFiles on SchemaDefRequirement record fields Test 198 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1gk5d0fj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/anon_enum_inside_array_inside_schemadef.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/anon_enum_inside_array_inside_schemadef.yml Test an anonymous enum inside an array inside a record, SchemaDefRequirement Returned non-zero Test [202/253] secondary_files_in_output_records: Test secondaryFiles on output record fields Test 200 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplz05a6jy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-in-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-secondaryFiles-job.yml Test secondaryFiles on anonymous record fields Returned non-zero Test [203/253] secondary_files_workflow_propagation: Test secondaryFiles propagation through workflow Test 201 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3xoxtjvl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-sd-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-secondaryFiles-job.yml Test secondaryFiles on SchemaDefRequirement record fields Returned non-zero Test [204/253] secondary_files_missing: Test checking when secondaryFiles are missing Test 202 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9vmnt4dd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-out-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test secondaryFiles on output record fields Returned non-zero Test [205/253] input_records_file_entry_with_format: Test format on anonymous record fields Test 203 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx___k4rk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-in-secondaryFiles-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-secondaryFiles-job.yml Test secondaryFiles propagation through workflow Returned non-zero Test [206/253] input_records_file_entry_with_format_and_bad_regular_input_file_format: Test file format checking on parameter Test [207/253] input_records_file_entry_with_format_and_bad_entry_file_format: Test file format checking on record field Test 205 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpm76zq6wm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-in-format.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-format-job.yml Test format on anonymous record fields Returned non-zero Test [208/253] input_records_file_entry_with_format_and_bad_entry_array_file_format: Test file format checking on array item Test [209/253] record_output_file_entry_format: Test format on output record fields Test [210/253] workflow_input_inputBinding_loadContents: Test WorkflowInputParameter.inputBinding.loadContents Test [211/253] workflow_input_loadContents_without_inputBinding: Test WorkflowInputParameter.loadContents Test 209 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvf7i5gd4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-out-format.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/record-secondaryFiles-job.yml Test format on output record fields Returned non-zero Test [212/253] expression_tool_input_loadContents: Test loadContents on InputParameter.loadContents (expression) Test 210 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg1j1t4td --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents-job.yml Test WorkflowInputParameter.inputBinding.loadContents Returned non-zero Test [213/253] workflow_step_in_loadContents: Test WorkflowStepInput.loadContents Test 211 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphk_rv25b --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents-job.yml Test WorkflowInputParameter.loadContents Returned non-zero Test [214/253] timelimit_basic: Test that job fails when exceeding time limit Test 212 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpq9urp0j2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents-job.yml Test loadContents on InputParameter.loadContents (expression) Returned non-zero Test [215/253] timelimit_invalid: Test invalid time limit value Test 213 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7to4xlg4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/wf-loadContents-job.yml Test WorkflowStepInput.loadContents Returned non-zero Test [216/253] timelimit_zero_unlimited: Test zero timelimit means no limit Test [217/253] timelimit_from_expression: Test expression in time limit Test [218/253] timelimit_expressiontool: Test timelimit in expressiontool is ignored Test 216 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpeup2hat1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/timelimit3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test zero timelimit means no limit Returned non-zero Test [219/253] timelimit_basic_wf: Test that tool in workflow fails when exceeding time limit Test [220/253] timelimit_invalid_wf: Test that workflow level time limit is not applied to workflow execution time Test 218 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt7jjm2lc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/timelimit5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test timelimit in expressiontool is ignored Returned non-zero Test [221/253] timelimit_zero_unlimited_wf: Test zero timelimit means no limit in workflow Test [222/253] timelimit_from_expression_wf: Test expression in time limit in workflow Test 220 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6i_iup5a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/timelimit2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that workflow level time limit is not applied to workflow execution time Returned non-zero Test [223/253] networkaccess: Test networkaccess enabled Test 221 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_amb_qn9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/timelimit3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test zero timelimit means no limit in workflow Returned non-zero Test [224/253] networkaccess_disabled: Test networkaccess is disabled by default Test [225/253] stage_null_array: Test null and array input in InitialWorkDirRequirement Test 223 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpddmpp1dm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/networkaccess.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test networkaccess enabled Returned non-zero Test [226/253] stage_array_dirs: Test array of directories InitialWorkDirRequirement Test [227/253] cwl_requirements_addition: Test requirements in input document via EnvVarRequirement Test 225 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe_dggw_f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage-array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage-array-job.json Test null and array input in InitialWorkDirRequirement Returned non-zero Test [228/253] cwl_requirements_override_expression: Test conflicting requirements in input document via EnvVarRequirement and expression Test 226 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpej6e5x4j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage-array-dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage-array-dirs-job.yml Test array of directories InitialWorkDirRequirement Returned non-zero Test [229/253] cwl_requirements_override_static: Test conflicting requirements in input document via EnvVarRequirement Test 227 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8k8ukf4a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-tool3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job3.yaml Test requirements in input document via EnvVarRequirement Returned non-zero Test [230/253] initial_work_dir_output: Test output of InitialWorkDir Test 228 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9t3f6lwt --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-tool4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job3.yaml Test conflicting requirements in input document via EnvVarRequirement and expression Returned non-zero Test [231/253] glob_full_path: Test if full paths are allowed in glob Test 229 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph5yskbcd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-tool3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job4.yaml Test conflicting requirements in input document via EnvVarRequirement Returned non-zero Test [232/253] fail_glob_outside_output_dir: Test fail trying to glob outside output directory Test 230 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw9w45h7v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdir-glob-fullpath.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdirrequirement-docker-out-job.json Test output of InitialWorkDir Returned non-zero Test [233/253] symlink_to_file_out_of_workdir_illegal: symlink to file outside of working directory should NOT be retrieved Test 231 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpay10me9f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdir-glob-fullpath.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/initialworkdirrequirement-docker-out-job.json Test if full paths are allowed in glob Returned non-zero Test [234/253] symlink-to-file-in-workdir-legal: symlink to file inside of working directory should be retrieved Test [235/253] inplace_update_on_file_content: inplace update has side effect on file content Test [236/253] inplace_update_on_dir_content: inplace update has side effect on directory content Test 234 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0qgi1trb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/symlink-legal.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json symlink to file inside of working directory should be retrieved Returned non-zero Test [237/253] outputbinding_glob_directory: Test that OutputBinding.glob accepts Directories Test 235 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6a2hj9uh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/inp_update_wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json inplace update has side effect on file content Returned non-zero Test [238/253] stage_file_array_to_dir: Test that array of input files can be staged to directory with entryname Test 236 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkgt8rfq7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/inpdir_update_wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json inplace update has side effect on directory content Returned non-zero Test [239/253] stage_file_array_to_dir_basename: Test that array of input files can be staged to directory with basename Test 237 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpymyxhytj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/glob_directory.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that OutputBinding.glob accepts Directories Returned non-zero Test [240/253] stage_file_array_to_dir_basename_entryname: Test that if array of input files are staged to directory with basename and entryname, entryname overrides Test 238 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzwvt3fs2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array.job.json Test that array of input files can be staged to directory with entryname Returned non-zero Test [241/253] tmpdir_is_not_outdir: Test that runtime.tmpdir is not runtime.outdir Test 239 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpa1a_aj99 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array_basename.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array.job.json Test that array of input files can be staged to directory with basename Returned non-zero Test [242/253] listing_default_none: Test that default behavior is 'no_listing' if not specified Test 240 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxs5kp0a9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array_basename_and_entryname.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/stage_file_array.job.json Test that if array of input files are staged to directory with basename and entryname, entryname overrides Returned non-zero Test [243/253] listing_requirement_none: Test that 'listing' is not present when LoadListingRequirement is 'no_listing' Test 241 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp99q1v817 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/runtime-paths-distinct.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that runtime.tmpdir is not runtime.outdir Returned non-zero Test [244/253] listing_loadListing_none: Test that 'listing' is not present when loadListing on input parameter is 'no_listing' Test 242 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj6g7yd5r --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_none1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that default behavior is 'no_listing' if not specified Returned non-zero Test [245/253] listing_requirement_shallow: Test that 'listing' is present in top directory object but not subdirectory object when LoadListingRequirement is 'shallow_listing' Test 243 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpuanc23pj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_none2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is not present when LoadListingRequirement is 'no_listing' Returned non-zero Test [246/253] listing_loadListing_shallow: Test that 'listing' is present in top directory object but not subdirectory object when loadListing on input parameter loadListing is 'shallow_listing' Test 244 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpusmq94vb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_none3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is not present when loadListing on input parameter is 'no_listing' Returned non-zero Test [247/253] listing_requirement_deep: Test that 'listing' is present in top directory object and in subdirectory objects when LoadListingRequirement is 'deep_listing' Test 245 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz1oiz59a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_shallow1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is present in top directory object but not subdirectory object when LoadListingRequirement is 'shallow_listing' Returned non-zero Test [248/253] listing_loadListing_deep: Test that 'listing' is present in top directory object and in subdirectory objects when input parameter loadListing is 'deep_listing' Test 246 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplary9zf6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_shallow2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is present in top directory object but not subdirectory object when loadListing on input parameter loadListing is 'shallow_listing' Returned non-zero Test [249/253] inputBinding_position_expr: Test for expression in the InputBinding.position field; also test using emoji in CWL document and tool output Test 247 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8tkdylad --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_deep1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is present in top directory object and in subdirectory objects when LoadListingRequirement is 'deep_listing' Returned non-zero Test [250/253] outputEval_exitCode: Can access exit code in outputEval Test 248 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmy1zggpa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing_deep2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/listing-job.yml Test that 'listing' is present in top directory object and in subdirectory objects when input parameter loadListing is 'deep_listing' Returned non-zero Test [251/253] any_input_param_graph_no_default: Test use of $graph without specifying which process to run Test 249 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkzj8452m --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-position-expr.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-position-expr-job.yml Test for expression in the InputBinding.position field; also test using emoji in CWL document and tool output Returned non-zero Test [252/253] any_input_param_graph_no_default_hashmain: Test use of $graph without specifying which process to run, hash-prefixed "main" Test 250 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgy552n70 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/exitcode.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Can access exit code in outputEval Returned non-zero Test [253/253] optional_numerical_output_returns_0_not_null: Test that optional number output is returned as 0, not null Test 251 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpoesphzl1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-tool-packed.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test use of $graph without specifying which process to run Returned non-zero Test 252 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpivnpat2r --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/echo-tool-packed2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/env-job.json Test use of $graph without specifying which process to run, hash-prefixed "main" Returned non-zero Test 253 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplkentxir --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/optional-numerical-output-0.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.1_3e90671b25f7840ef2926ad2bacbf447772dda94_0/tests/empty.json Test that optional number output is returned as 0, not null Returned non-zero 18 tests passed, 234 failures, 0 unsupported features ____________________________________________________________________________ test_conformance_1_2 _____________________________________________________________________________ acr_script = PosixPath('/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner'), badges_dir = PosixPath('/tmp/pytest-of-tom/pytest-23/test_conformance_1_20/badges') cwl1_2git = PosixPath('/tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0'), jobs_docker_image = 'arvados/jobs:3.2.0.dev20250814184714', skipped_tests_for_config = [] @pytest.mark.cwl_conformance @pytest.mark.integration def test_conformance_1_2(acr_script, badges_dir, cwl1_2git, jobs_docker_image, skipped_tests_for_config): cwltest = run_cwltest( cwl1_2git / 'conformance_tests.yaml', acr_script, badges_dir, test_args=skipped_tests_for_config, ) > assert cwltest.returncode == os.EX_OK E AssertionError: assert 1 == 0 E + where 1 = CompletedProcess(args=['cwltest', '--test', '/tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/conformance_tests.yaml', '--tool', '/tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner', '-j', '3', '--', '--compute-checksum', '--disable-reuse', '--enable-dev', '--verbose'], returncode=1).returncode E + and 0 = os.EX_OK tests/test_conformance.py:147: AssertionError ---------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------- Test [1/378] cl_basic_generation: General test of command line generation Test [2/378] nested_prefixes_arrays: Test nested prefixes with arrays Test [3/378] nested_cl_bindings: Test nested command line bindings Test 3 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_s1psu_7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/tmap-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/tmap-job.json Test nested command line bindings Returned non-zero Test [4/378] cl_optional_inputs_missing: Test command line with optional input (missing) Test 1 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppazhktep --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/bwa-mem-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/bwa-mem-job.json General test of command line generation Returned non-zero Test [5/378] cl_optional_bindings_provided: Test command line with optional input (provided) Test 2 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprfua5rlu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/binding-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/bwa-mem-job.json Test nested prefixes with arrays Returned non-zero Test [6/378] initworkdir_expreng_requirements: Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Test 5 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp38va8xxk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-n-job.json Test command line with optional input (provided) Returned non-zero Test [7/378] stdout_redirect_docker: Test command execution in Docker with stdout redirection Test 6 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe70wagod --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/template-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test InitialWorkDirRequirement ExpressionEngineRequirement.engineConfig feature Returned non-zero Test [8/378] stdout_redirect_shortcut_docker: Test command execution in Docker with shortcut stdout redirection Test 4 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2cny64f3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat1-testcli.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command line with optional input (missing) Returned non-zero Test [9/378] stdout_redirect_mediumcut_docker: Test command execution in Docker with mediumcut stdout redirection Test 9 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpentbr5p0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-tool-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command execution in Docker with mediumcut stdout redirection Returned non-zero Test [10/378] stderr_redirect: Test command line with stderr redirection Test 7 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmples_vb06 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command execution in Docker with stdout redirection Returned non-zero Test [11/378] stderr_redirect_shortcut: Test command line with stderr redirection, brief syntax Test 8 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp02767kdd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-tool-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command execution in Docker with shortcut stdout redirection Returned non-zero Test [12/378] stderr_redirect_mediumcut: Test command line with stderr redirection, named brief syntax Test 11 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprgyztb1k --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stderr-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test command line with stderr redirection, brief syntax Returned non-zero Test [13/378] stdinout_redirect_docker: Test command execution in Docker with stdin and stdout redirection Test 10 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9txg6431 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stderr.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test command line with stderr redirection Returned non-zero Test [14/378] expression_any: Test default usage of Any in expressions. Test 12 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpy8aj4jqm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stderr-mediumcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test command line with stderr redirection, named brief syntax Returned non-zero Test [15/378] expression_any_null: Test explicitly passing null to Any type inputs with default values. Test 13 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_0bex1rf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command execution in Docker with stdin and stdout redirection Returned non-zero Test [16/378] expression_any_string: Testing the string 'null' does not trip up an Any with a default value. Test 14 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjaulbp4l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default usage of Any in expressions. Returned non-zero Test [17/378] expression_any_nodefaultany: Test Any without defaults cannot be unspecified. Test 15 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprqkpl_04 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression1-job.json Test explicitly passing null to Any type inputs with default values. Returned non-zero Test [18/378] expression_any_null_nodefaultany: Test explicitly passing null to Any type without a default value. Test 16 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp90d66sw_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression1-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression2-job.json Testing the string 'null' does not trip up an Any with a default value. Returned non-zero Test [19/378] expression_any_nullstring_nodefaultany: Testing the string 'null' does not trip up an Any without a default value. Test [20/378] any_outputSource_compatibility: Testing Any type compatibility in outputSource Test [21/378] stdinout_redirect: Test command execution in with stdin and stdout redirection Test 19 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpu8fn3d53 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-expression2-job.json Testing the string 'null' does not trip up an Any without a default value. Returned non-zero Test [22/378] expression_parseint: Test ExpressionTool with Javascript engine Test 20 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx8likptk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/any-type-compat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/any-type-job.json Testing Any type compatibility in outputSource Returned non-zero Test [23/378] expression_outputEval: Test outputEval to transform output Test 21 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwhbb_1ed --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test command execution in with stdin and stdout redirection Returned non-zero Test [24/378] wf_wc_parseInt: Test two step workflow with imported tools Test 22 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptix5kebn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/parseInt-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/parseInt-job.json Test ExpressionTool with Javascript engine Returned non-zero Test [25/378] wf_wc_expressiontool: Test two step workflow with inline tools Test 24 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1l8e98wr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines1-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test two step workflow with imported tools Returned non-zero Test [26/378] wf_wc_scatter: Test single step workflow with Scatter step Test 23 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp70im5h7i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc2-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test outputEval to transform output Returned non-zero Test [27/378] wf_wc_scatter_multiple_merge: Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Test 25 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwz20xb6s --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test two step workflow with inline tools Returned non-zero Test [28/378] wf_wc_scatter_multiple_nested: Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Test 26 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgju_396_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines3-job.json Test single step workflow with Scatter step Returned non-zero Test [29/378] wf_wc_scatter_multiple_flattened: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Test 27 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpljtu7fbr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines4-job.json Test single step workflow with Scatter step and two data links connected to same input, default merge behavior Returned non-zero Test [30/378] wf_wc_nomultiple: Test when step source is a single-item list and there is no linkMerge, then it not wrapped in a list, and that MultipleInputFeatureRequirement is not required. Test 28 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz9iudzqh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines6-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, nested merge behavior Returned non-zero Test [31/378] wf_wc_nomultiple_merge_nested: Test when step source is a single-item list and linkMerge is listed, then it is wrapped in a list. Test 29 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0nokiz9j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines7-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior Returned non-zero Test [32/378] wf_input_default_missing: Test workflow with default value for input parameter (missing) Test 30 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpft9ruxht --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines13-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines4-job.json Test when step source is a single-item list and there is no linkMerge, then it not wrapped in a list, and that MultipleInputFeatureRequirement is not required. Returned non-zero Test [33/378] wf_input_default_provided: Test workflow with default value for input parameter (provided) Test 31 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz5skp862 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines19-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines4-job.json Test when step source is a single-item list and linkMerge is listed, then it is wrapped in a list. Returned non-zero Test [34/378] wf_default_tool_default: Test that workflow defaults override tool defaults Test 32 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkaurw1fq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test workflow with default value for input parameter (missing) Returned non-zero Test [35/378] envvar_req: Test EnvVarRequirement Test 33 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptuvzpwta --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test workflow with default value for input parameter (provided) Returned non-zero Test [36/378] wf_scatter_single_param: Test workflow scatter with single scatter parameter Test 34 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2bsc8an1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-wf-default.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that workflow defaults override tool defaults Returned non-zero Test [37/378] wf_scatter_two_nested_crossproduct: Test workflow scatter with two scatter parameters and nested_crossproduct join method Test 35 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprz79xy7g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-tool1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test EnvVarRequirement Returned non-zero Test [38/378] wf_scatter_two_flat_crossproduct: Test workflow scatter with two scatter parameters and flat_crossproduct join method Test 36 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo96_9s_9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-job1.json Test workflow scatter with single scatter parameter Returned non-zero Test [39/378] wf_scatter_two_dotproduct: Test workflow scatter with two scatter parameters and dotproduct join method Test 37 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo25c7akd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method Returned non-zero Test [40/378] wf_scatter_emptylist: Test workflow scatter with single empty list parameter Test 38 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp377t5bxo --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method Returned non-zero Test [41/378] wf_scatter_nested_crossproduct_secondempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Test 39 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7_qb2ity --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-job2.json Test workflow scatter with two scatter parameters and dotproduct join method Returned non-zero Test [42/378] wf_scatter_nested_crossproduct_firstempty: Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Test 40 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd__x7mkj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-empty-job1.json Test workflow scatter with single empty list parameter Returned non-zero Test [43/378] wf_scatter_flat_crossproduct_oneempty: Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Test 41 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnfv2u3ml --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-empty-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with second list empty Returned non-zero Test [44/378] wf_scatter_dotproduct_twoempty: Test workflow scatter with two empty scatter parameters and dotproduct join method Test 42 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo2nhx4hk --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-empty-job3.json Test workflow scatter with two scatter parameters and nested_crossproduct join method with first list empty Returned non-zero Test [45/378] any_input_param: Test Any type input parameter Test 43 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnqqhjmwl --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-empty-job2.json Test workflow scatter with two scatter parameters, one of which is empty and flat_crossproduct join method Returned non-zero Test [46/378] nested_workflow: Test nested workflow Test 44 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmps2q3k4do --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-empty-job4.json Test workflow scatter with two empty scatter parameters and dotproduct join method Returned non-zero Test [47/378] requirement_priority: Test requirement priority Test 45 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkzbxf5r_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test Any type input parameter Returned non-zero Test [48/378] requirement_override_hints: Test requirements override hints Test 46 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpthuigax5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines8-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test nested workflow Returned non-zero Test [49/378] requirement_workflow_steps: Test requirements on workflow steps Test 47 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpl0tf93yf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test requirement priority Returned non-zero Test [50/378] step_input_default_value: Test default value on step input parameter Test 48 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpepsb3c2f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test requirements override hints Returned non-zero Test [51/378] step_input_default_value_nosource: Test use default value on step input parameter with empty source Test 49 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsf7av090 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-wf3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test requirements on workflow steps Returned non-zero Test [52/378] step_input_default_value_nullsource: Test use default value on step input parameter with null source Test 50 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgpk9h7b9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines9-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default value on step input parameter Returned non-zero Test [53/378] step_input_default_value_overriden: Test default value on step input parameter overridden by provided source Test 51 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxrt3q0i2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test use default value on step input parameter with empty source Returned non-zero Test [54/378] wf_simple: Test simple workflow Test 52 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgnd9bluc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/file1-null.json Test use default value on step input parameter with null source Returned non-zero Test [55/378] hints_unknown_ignored: Test unknown hints are ignored. Test 53 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1qh0ll5b --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test default value on step input parameter overridden by provided source Returned non-zero Test [56/378] initial_workdir_secondary_files_expr: Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Test 54 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3dc3xvvz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/revsort.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/revsort-job.json Test simple workflow Returned non-zero Test [57/378] rename: Test InitialWorkDirRequirement with expression in filename. Test 55 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd040_xfe --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat5-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test unknown hints are ignored. Returned non-zero Test [58/378] initial_workdir_trailingnl: Test if trailing newline is present in file entry in InitialWorkDir Test 56 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc13em9pt --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/search.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/search-job.json Test InitialWorkDirRequirement linking input files and capturing secondaryFiles on input and output. Also tests the use of a variety of parameter references and expressions in the secondaryFiles field. Returned non-zero Test [59/378] inline_expressions: Test inline expressions Test 57 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpj579h21f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/rename.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/rename-job.json Test InitialWorkDirRequirement with expression in filename. Returned non-zero Test [60/378] schemadef_req_tool_param: Test SchemaDefRequirement definition used in tool parameter Test 58 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0z992a35 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwdr-entry.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/string-job.json Test if trailing newline is present in file entry in InitialWorkDir Returned non-zero Test [61/378] schemadef_req_wf_param: Test SchemaDefRequirement definition used in workflow parameter Test 59 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwyt8omi4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc4-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test inline expressions Returned non-zero Test [62/378] param_evaluation_noexpr: Test parameter evaluation, no support for JS expressions Test 60 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpozoc0dt8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef-job.json Test SchemaDefRequirement definition used in tool parameter Returned non-zero Test [63/378] param_evaluation_expr: Test parameter evaluation, with support for JS expressions Test 61 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb93reg88 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef-job.json Test SchemaDefRequirement definition used in workflow parameter Returned non-zero Test [64/378] metadata: Test metadata Test 62 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8l7urfkb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/params.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test parameter evaluation, no support for JS expressions Returned non-zero Test [65/378] format_checking: Test simple format checking. Test 63 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvllhfpep --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/params2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test parameter evaluation, with support for JS expressions Returned non-zero Test [66/378] format_checking_subclass: Test format checking against ontology using subclassOf. Test 64 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwj3xiyei --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/metadata.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test metadata Returned non-zero Test [67/378] format_checking_equivalentclass: Test format checking against ontology using equivalentClass. Test 65 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmhvvw6qa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest-job.json Test simple format checking. Returned non-zero Test [68/378] output_secondaryfile_optional: Test optional output file and optional secondaryFile on output. Test 66 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmps54z492b --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest2-job.json Test format checking against ontology using subclassOf. Returned non-zero Test [69/378] valuefrom_ignored_null: Test that valueFrom is ignored when the parameter is null Test 67 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprnmz33ab --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/formattest2-job.json Test format checking against ontology using equivalentClass. Returned non-zero Test [70/378] valuefrom_secondexpr_ignored: Test that second expression in concatenated valueFrom is not ignored Test 68 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplwlqf9g3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/optional-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test optional output file and optional secondaryFile on output. Returned non-zero Test [71/378] valuefrom_wf_step: Test valueFrom on workflow step. Test 69 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2qyrjq84 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that valueFrom is ignored when the parameter is null Returned non-zero Test [72/378] valuefrom_wf_step_multiple: Test valueFrom on workflow step with multiple sources Test 70 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmtvvzlfe --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/vf-concat.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test that second expression in concatenated valueFrom is not ignored Returned non-zero Test [73/378] valuefrom_wf_step_other: Test valueFrom on workflow step referencing other inputs Test 71 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi6rwf7k9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom-wf.json Test valueFrom on workflow step. Returned non-zero Test [74/378] record_output_binding: Test record type output binding. Test 72 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmsk7ub8c --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom-job.json Test valueFrom on workflow step with multiple sources Returned non-zero Test [75/378] docker_json_output_path: Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Test 73 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw_3th1e1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom-job.json Test valueFrom on workflow step referencing other inputs Returned non-zero Test [76/378] docker_json_output_location: Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Test 74 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmtrf6vqr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-output-job.json Test record type output binding. Returned non-zero Test [77/378] json_output_path_relative: Test support for reading cwl.output.json where 'path' is relative path in output dir. Test 75 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptwyifgi8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/test-cwl-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'path' is provided. Returned non-zero Test [78/378] json_output_location_relative: Test support for reading cwl.output.json where 'location' is relative reference to output dir. Test 76 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfb2x_gdl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/test-cwl-out2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test support for reading cwl.output.json when running in a Docker container and just 'location' is provided. Returned non-zero Test [79/378] multiple_glob_expr_list: Test support for returning multiple glob patterns from expression Test 77 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9g7poym_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/test-cwl-out3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test support for reading cwl.output.json where 'path' is relative path in output dir. Returned non-zero Test [80/378] wf_scatter_oneparam_valuefrom: Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Test 78 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsurbu7ky --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/test-cwl-out4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test support for reading cwl.output.json where 'location' is relative reference to output dir. Returned non-zero Test [81/378] wf_scatter_twoparam_nested_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Test 79 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg0uj_dry --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/glob-expr-list.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/abc.json Test support for returning multiple glob patterns from expression Returned non-zero Test [82/378] wf_scatter_twoparam_flat_crossproduct_valuefrom: Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Test 81 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4454v7tg --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and nested_crossproduct join method and valueFrom on step input Returned non-zero Test [83/378] wf_scatter_twoparam_dotproduct_valuefrom: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Test 80 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw5_h8nr6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (first and current el) Returned non-zero Test [84/378] wf_scatter_oneparam_valuefrom_twice_current_el: Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Test 82 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpq5llpk_w --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf3.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and flat_crossproduct join method and valueFrom on step input Returned non-zero Test [85/378] wf_scatter_oneparam_valueFrom: Test valueFrom eval on scattered input parameter Test 83 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9bb0084v --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf4.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job2.json Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input Returned non-zero Test [86/378] wf_two_inputfiles_namecollision: Test workflow two input files with same name. Test 84 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp43epe37v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom on step input (current el twice) Returned non-zero Test [87/378] directory_input_param_ref: Test directory input with parameter reference Test 85 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptyoui0y5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-wf6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job3.json Test valueFrom eval on scattered input parameter Returned non-zero Test [88/378] directory_input_docker: Test directory input in Docker Test 86 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6fq_hrjw --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conflict-wf.cwl#collision' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conflict-job.json Test workflow two input files with same name. Returned non-zero Test [89/378] directory_output: Test directory output Test 87 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmea1te_3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir-job.yml Test directory input with parameter reference Returned non-zero Test [90/378] directory_secondaryfiles: Test directories in secondaryFiles Test 88 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk0tvcpm9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir-job.yml Test directory input in Docker Returned non-zero Test [91/378] dynamic_initial_workdir: Test dynamic initial work dir Test 89 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxhmak4v8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir3-job.yml Test directory output Returned non-zero Test [92/378] writable_stagedfiles: Test writable staged files. Test 90 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6yoczq97 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4-job.yml Test directories in secondaryFiles Returned non-zero Test [93/378] input_file_literal: Test file literal as input Test 91 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpww2cokzk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir-job.yml Test dynamic initial work dir Returned non-zero Test [94/378] initial_workdir_expr: Test expression in InitialWorkDir listing Test 92 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9u0bu_wk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stagefile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stagefile-job.yml Test writable staged files. Returned non-zero Test [95/378] nameroot_nameext_stdout_expr: Test nameroot/nameext expression in arguments, stdout Test 93 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3bv46xyv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/file-literal.yml Test file literal as input Returned non-zero Test [96/378] input_dir_inputbinding: Test directory input with inputBinding Test 94 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpp2v7xmrg --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/linkfile.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/arguments-job.yml Test expression in InitialWorkDir listing Returned non-zero Test [97/378] cl_gen_arrayofarrays: Test command line generation of array-of-arrays Test 95 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqzgfmktf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/nameroot.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test nameroot/nameext expression in arguments, stdout Returned non-zero Test [98/378] env_home_tmpdir: Test $HOME and $TMPDIR are set correctly Test 96 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3ycmip72 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir6.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir-job.yml Test directory input with inputBinding Returned non-zero Test [99/378] env_home_tmpdir_docker: Test $HOME and $TMPDIR are set correctly in Docker Test 97 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjgwbpucd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/nested-array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/nested-array-job.yml Test command line generation of array-of-arrays Returned non-zero Test [100/378] expressionlib_tool_wf_override: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Test 98 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpne8njded --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/envvar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test $HOME and $TMPDIR are set correctly Returned non-zero Test [101/378] initial_workdir_output: Test output of InitialWorkDir Test 99 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwwgssa3f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/envvar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test $HOME and $TMPDIR are set correctly in Docker Returned non-zero Test [102/378] embedded_subworkflow: Test embedded subworkflow Test 100 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2_del20p --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/js-expr-req-wf.cwl#wf' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that expressionLib requirement of individual tool step overrides expressionLib of workflow. Returned non-zero Test [103/378] filesarray_secondaryfiles: Test required, optional and null secondaryFiles on array of files. Test 101 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2jmjb_u3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/initialworkdirrequirement-docker-out.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/initialworkdirrequirement-docker-out-job.json Test output of InitialWorkDir Returned non-zero Test [104/378] filesarray_secondaryfiles2: Test required, optional and null secondaryFiles on array of files. Test 102 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1_0nkblc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines10-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test embedded subworkflow Returned non-zero Test [105/378] exprtool_directory_literal: Test directory literal output created by ExpressionTool Test 103 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsq7m1nfu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/docker-array-secondaryfiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/docker-array-secondaryfiles-job.json Test required, optional and null secondaryFiles on array of files. Returned non-zero Test [106/378] exprtool_file_literal: Test file literal output created by ExpressionTool Test [107/378] dockeroutputdir: Test dockerOutputDirectory Test 105 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzw479wr9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir7.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir7.yml Test directory literal output created by ExpressionTool Returned non-zero Test [108/378] hints_import: Test hints with $import Test 106 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw5oys085 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/file-literal-ex.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test file literal output created by ExpressionTool Returned non-zero Test [109/378] default_path_notfound_warning: Test warning instead of error when default path is not found Test 107 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv96u_lze --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/docker-output-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test dockerOutputDirectory Returned non-zero Test [110/378] inlinejs_req_expressions: Test InlineJavascriptRequirement with multiple expressions in the same tool Test 108 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsrkldafn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/imported-hint.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test hints with $import Returned non-zero Test [111/378] input_dir_recurs_copy_writable: Test if a writable input directory is recursively copied and writable Test 109 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpipkc8khq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/default_path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/default_path_job.yml Test warning instead of error when default path is not found Returned non-zero Test [112/378] null_missing_params: Test that missing parameters are null (not undefined) in expression Test 110 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8042z3nj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/inline-js.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test InlineJavascriptRequirement with multiple expressions in the same tool Returned non-zero Test [113/378] param_notnull_expr: Test that provided parameter is not null in expression Test 111 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpf_rq6jfu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/recursive-input-directory.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/recursive-input-directory.yml Test if a writable input directory is recursively copied and writable Returned non-zero Test [114/378] wf_compound_doc: Test compound workflow document Test 112 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3ly_w6lp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that missing parameters are null (not undefined) in expression Returned non-zero Test [115/378] nameroot_nameext_generated: Test that nameroot and nameext are generated from basename at execution time by the runner Test 113 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjuiktvyt --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/null-defined.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test that provided parameter is not null in expression Returned non-zero Test [116/378] initialworkpath_output: Test that file path in $(inputs) for initialworkdir is in $(outdir). Test 114 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpl85cpkan --quiet 'file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/revsort-packed.cwl#main' file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/revsort-job.json Test compound workflow document Returned non-zero Test [117/378] wf_scatter_twopar_oneinput_flattenedmerge: Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Test 115 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpga3cpjez --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/basename-fields-test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/basename-fields-job.yml Test that nameroot and nameext are generated from basename at execution time by the runner Returned non-zero Test [118/378] wf_multiplesources_multipletypes: Test step input with multiple sources with multiple types Test 116 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprecj0vd4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/initialwork-path.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test that file path in $(inputs) for initialworkdir is in $(outdir). Returned non-zero Test [119/378] shelldir_notinterpreted: Test that shell directives are not interpreted. Test 117 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsnjskaql --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines12-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines6-job.json Test single step workflow with Scatter step and two data links connected to same input, flattened merge behavior. Workflow inputs are set as list Returned non-zero Test [120/378] shelldir_quoted: Test that shell directives are quoted. Test 118 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg08_tlz2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/sum-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/sum-job.json Test step input with multiple sources with multiple types Returned non-zero Test [121/378] initial_workdir_empty_writable: Test empty writable dir with InitialWorkDirRequirement Test 119 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc0t3ccdi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/shellchar.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that shell directives are not interpreted. Returned non-zero Test [122/378] initial_workdir_empty_writable_docker: Test empty writable dir with InitialWorkDirRequirement inside Docker Test 120 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpynvi6rki --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/shellchar2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that shell directives are quoted. Returned non-zero Test [123/378] dynamic_resreq_inputs: Test dynamic resource reqs referencing inputs Test 121 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqlg2esw_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/writable-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test empty writable dir with InitialWorkDirRequirement Returned non-zero Test [124/378] fileliteral_input_docker: Test file literal as input without Docker Test 122 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpemt5kjo1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/writable-dir-docker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test empty writable dir with InitialWorkDirRequirement inside Docker Returned non-zero Test [125/378] outputbinding_glob_sorted: Test that OutputBinding.glob is sorted as specified by POSIX Test 123 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvgi8tu5a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-job.yaml Test dynamic resource reqs referencing inputs Returned non-zero Test [126/378] initialworkdir_nesteddir: Test InitialWorkDirRequirement with a nested directory structure from another step Test 124 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpy6qoe68a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-nodocker.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/file-literal.yml Test file literal as input without Docker Returned non-zero Test [127/378] booleanflags_cl_noinputbinding: Test that boolean flags do not appear on command line if inputBinding is empty and not null Test 125 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpavom3lgh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/glob_test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that OutputBinding.glob is sorted as specified by POSIX Returned non-zero Test [128/378] expr_reference_self_noinput: Test that expression engine does not fail to evaluate reference to self with unprovided input Test 126 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8wa1r4j0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwdr_with_nested_dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test InitialWorkDirRequirement with a nested directory structure from another step Returned non-zero Test [129/378] success_codes: Test successCodes Test 127 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph71js2zl --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/bool-empty-inputbinding.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/bool-empty-inputbinding-job.json Test that boolean flags do not appear on command line if inputBinding is empty and not null Returned non-zero Test [130/378] dynamic_resreq_wf: Test simple workflow with a dynamic resource requirement Test 128 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4j7ietb4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage-unprovided-file.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that expression engine does not fail to evaluate reference to self with unprovided input Returned non-zero Test [131/378] cl_empty_array_input: Test that empty array input does not add anything to command line Test 129 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk1q0qdrh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/exit-success.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test successCodes Returned non-zero Test [132/378] resreq_step_overrides_wf: Test that ResourceRequirement on a step level redefines requirement on the workflow level Test 130 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpspw7o1uq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-workflow.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-job.yaml Test simple workflow with a dynamic resource requirement Returned non-zero Test [133/378] valuefrom_constant_overrides_inputs: Test valueFrom with constant value overriding provided array inputs Test 131 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpml8hqm1g --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty-array-input.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty-array-job.json Test that empty array input does not add anything to command line Returned non-zero Test [134/378] dynamic_resreq_filesizes: Test dynamic resource reqs referencing the size of Files inside a Directory Test 132 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx4a3ul2f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/steplevel-resreq.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that ResourceRequirement on a step level redefines requirement on the workflow level Returned non-zero Test [135/378] wf_step_connect_undeclared_param: Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Test 133 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbkm4w8vj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/valueFrom-constant.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/array-of-strings-job.yml Test valueFrom with constant value overriding provided array inputs Returned non-zero Test [136/378] wf_step_access_undeclared_param: Test that parameters that don't appear in the `run` process inputs are not present in the input object used to run the tool. Test 134 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpstdw_q16 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-dir-job.yaml Test dynamic resource reqs referencing the size of Files inside a Directory Returned non-zero Test [137/378] env_home_tmpdir_docker_no_return_code: Test $HOME and $TMPDIR are set correctly in Docker without using return code Test 135 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzmtwgh8u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/pass-unconnected.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that it is not an error to connect a parameter to a workflow step, even if the parameter doesn't appear in the `run` process inputs. Returned non-zero Test [138/378] wf_scatter_oneparam_valuefrom_inputs: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Test [139/378] packed_import_schema: SchemaDefRequirement with $import, and packed Test 137 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpzht8_546 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/envvar3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test $HOME and $TMPDIR are set correctly in Docker without using return code Returned non-zero Test [140/378] job_input_secondary_subdirs: Test specifying secondaryFiles in subdirectories of the job input document. Test 138 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9j6bikzp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-inputs-wf1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter-valuefrom-job1.json Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el) Returned non-zero Test [141/378] job_input_subdir_primary_and_secondary_subdirs: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Test 139 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1te151rq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/import_schema-def_packed.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/import_schema-def_job.yml SchemaDefRequirement with $import, and packed Returned non-zero Test [142/378] scatter_embedded_subworkflow: Test simple scatter over an embedded subworkflow Test 140 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbify5lck --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4-subdir-1-job.yml Test specifying secondaryFiles in subdirectories of the job input document. Returned non-zero Test [143/378] scatter_multi_input_embedded_subworkflow: Test simple multiple input scatter over an embedded subworkflow Test 141 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp71c533qv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir4-subdir-2-job.yml Test specifying secondaryFiles in same subdirectory of the job input as the primary input file. Returned non-zero Test [144/378] workflow_embedded_subworkflow_embedded_subsubworkflow: Test twice nested subworkflow Test 142 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsryl79eo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines18-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines3-job.json Test simple scatter over an embedded subworkflow Returned non-zero Test [145/378] workflow_embedded_subworkflow_with_tool_and_subsubworkflow: Test subworkflow of mixed depth with tool first Test 143 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmkgcprnx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines14-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines4-job.json Test simple multiple input scatter over an embedded subworkflow Returned non-zero Test [146/378] workflow_embedded_subworkflow_with_subsubworkflow_and_tool: Test subworkflow of mixed depth with tool after Test 144 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprp42fcpu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines15-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test twice nested subworkflow Returned non-zero Test [147/378] workflow_records_inputs_and_outputs: Test record type inputs to and outputs from workflows. Test 145 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7q2cwfk5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines16-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test subworkflow of mixed depth with tool first Returned non-zero Test [148/378] workflow_integer_input: Test integer workflow input and outputs Test 146 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgo8wc2fy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines17-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test subworkflow of mixed depth with tool after Returned non-zero Test [149/378] workflow_integer_input_optional_specified: Test optional integer workflow inputs (specified) Test 147 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_scstls9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-output-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-output-job.json Test record type inputs to and outputs from workflows. Returned non-zero Test [150/378] workflow_integer_input_optional_unspecified: Test optional integer workflow inputs (unspecified) Test 148 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpllz052re --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int.json Test integer workflow input and outputs Returned non-zero Test [151/378] workflow_integer_input_default_specified: Test default integer workflow inputs (specified) Test 149 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0wvzk3eu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int.json Test optional integer workflow inputs (specified) Returned non-zero Test [152/378] workflow_integer_input_default_unspecified: Test default integer workflow inputs (unspecified) Test 150 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7nzoet8o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-optional-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test optional integer workflow inputs (unspecified) Returned non-zero Test [153/378] workflow_integer_input_default_and_tool_integer_input_default: Test default integer tool and workflow inputs (unspecified) Test 151 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpovfbaq05 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int.json Test default integer workflow inputs (specified) Returned non-zero Test [154/378] workflow_file_input_default_unspecified: Test File input with default unspecified to workflow Test 152 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0zdy4ln9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default integer workflow inputs (unspecified) Returned non-zero Test [155/378] workflow_file_input_default_specified: Test File input with default specified to workflow Test 153 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1xqklqq8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-int-default-tool-and-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default integer tool and workflow inputs (unspecified) Returned non-zero Test [156/378] clt_optional_union_input_file_or_files_with_array_of_one_file_provided: Test input union type or File or File array to a tool with one file in array specified. Test 154 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp2w0dqgj5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test File input with default unspecified to workflow Returned non-zero Test [157/378] clt_optional_union_input_file_or_files_with_many_files_provided: Test input union type or File or File array to a tool with a few files in array specified. Test 155 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp717ccpxo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/default_path_job.yml Test File input with default specified to workflow Returned non-zero Test [158/378] clt_optional_union_input_file_or_files_with_single_file_provided: Test input union type or File or File array to a tool with one file specified. Test 156 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplve53qyq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-array-one-empty-file.json Test input union type or File or File array to a tool with one file in array specified. Returned non-zero Test [159/378] clt_optional_union_input_file_or_files_with_nothing_provided: Test input union type or File or File array to a tool with null specified. Test 157 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpin0u22vt --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-array-few-files.json Test input union type or File or File array to a tool with a few files in array specified. Returned non-zero Test [160/378] clt_any_input_with_integer_provided: Test Any parameter with integer input to a tool Test 158 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph7bx9xk4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-one-file.json Test input union type or File or File array to a tool with one file specified. Returned non-zero Test [161/378] clt_any_input_with_string_provided: Test Any parameter with string input to a tool Test 159 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1vvednz9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-file-or-files.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-null.json Test input union type or File or File array to a tool with null specified. Returned non-zero Test [162/378] clt_any_input_with_file_provided: Test Any parameter with file input to a tool Test 160 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp39z2sriy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-int.json Test Any parameter with integer input to a tool Returned non-zero Test [163/378] clt_any_input_with_mixed_array_provided: Test Any parameter with array input to a tool Test 161 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5ze95dp5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-string.json Test Any parameter with string input to a tool Returned non-zero Test [164/378] clt_any_input_with_record_provided: Test Any parameter with record input to a tool Test 162 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpk79veaoo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-file.json Test Any parameter with file input to a tool Returned non-zero Test [165/378] workflow_any_input_with_integer_provided: Test Any parameter with integer input to a workflow Test 163 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8d3xqlli --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-array.json Test Any parameter with array input to a tool Returned non-zero Test [166/378] workflow_any_input_with_string_provided: Test Any parameter with string input to a workflow Test 164 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4vtv_zzn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [167/378] workflow_any_input_with_file_provided: Test Any parameter with file input to a workflow Test 165 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfptg7rfs --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-int.json Test Any parameter with integer input to a workflow Returned non-zero Test [168/378] workflow_any_input_with_mixed_array_provided: Test Any parameter with array input to a workflow Test 166 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr81gwqbx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-string.json Test Any parameter with string input to a workflow Returned non-zero Test [169/378] workflow_any_input_with_record_provided: Test Any parameter with record input to a tool Test 167 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd89ed0wc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-file.json Test Any parameter with file input to a workflow Returned non-zero Test [170/378] workflow_union_default_input_unspecified: Test union type input to workflow with default unspecified Test 168 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4_jici1l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-array.json Test Any parameter with array input to a workflow Returned non-zero Test [171/378] workflow_union_default_input_with_file_provided: Test union type input to workflow with default specified as file Test 169 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkt3v3sc2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-wf-1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-record.json Test Any parameter with record input to a tool Returned non-zero Test [172/378] workflowstep_valuefrom_string: Test valueFrom on workflow step from literal (string). Test 170 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpju82rinw --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test union type input to workflow with default unspecified Returned non-zero Test [173/378] workflowstep_valuefrom_file_basename: Test valueFrom on workflow step using basename. Test 171 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwqo80djh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-union-input-default-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/io-any-file.json Test union type input to workflow with default specified as file Returned non-zero Test [174/378] expression_tool_int_array_output: Test output arrays in a tool (with ints). Test 172 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_wcctnaq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom4-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test valueFrom on workflow step from literal (string). Returned non-zero Test [175/378] workflowstep_int_array_input_output: Test output arrays in a workflow (with ints). Test 173 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkir01xj9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/step-valuefrom5-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test valueFrom on workflow step using basename. Returned non-zero Test [176/378] workflow_file_array_output: Test output arrays in a workflow (with Files). Test 174 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb9jh9z63 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-int.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-int-job.json Test output arrays in a tool (with ints). Returned non-zero Test [177/378] docker_entrypoint: Test Docker ENTRYPOINT usage Test 175 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw8ask7_z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-int-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-int-job.json Test output arrays in a workflow (with ints). Returned non-zero Test [178/378] clt_file_size_property_with_empty_file: Test use of size in expressions for an empty file Test 176 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfwgpgja0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-file-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output-arrays-file-job.json Test output arrays in a workflow (with Files). Returned non-zero Test [179/378] clt_file_size_property_with_multi_file: Test use of size in expressions for a few files Test 177 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6jc105zy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/docker-run-cmd.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test Docker ENTRYPOINT usage Returned non-zero Test [180/378] any_without_defaults_unspecified_fails: Test Any without defaults, unspecified, should fail. Test 178 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgcn_fhyd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-array-one-empty-file.json Test use of size in expressions for an empty file Returned non-zero Test [181/378] any_without_defaults_specified_fails: Test Any without defaults, specified, should fail. Test 179 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyn1n1xxe --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/size-expression-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/job-input-array-few-files.json Test use of size in expressions for a few files Returned non-zero Test [182/378] step_input_default_value_noexp: Test default value on step input parameter, no ExpressionTool Test [183/378] step_input_default_value_overriden_noexp: Test default value on step input parameter overridden by provided source, no ExpressionTool Test [184/378] nested_workflow_noexp: Test nested workflow, without ExpressionTool Test 182 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpc1s8q0d7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines9-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default value on step input parameter, no ExpressionTool Returned non-zero Test [185/378] wf_multiplesources_multipletypes_noexp: Test step input with multiple sources with multiple types, without ExpressionTool Test 183 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpif7ge2ci --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test default value on step input parameter overridden by provided source, no ExpressionTool Returned non-zero Test [186/378] dynamic_resreq_wf_optional_file_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Test 184 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp32zfwm1e --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines8-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test nested workflow, without ExpressionTool Returned non-zero Test [187/378] dynamic_resreq_wf_optional_file_step_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Test 185 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1ri0xy3y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/sum-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/sum-job.json Test step input with multiple sources with multiple types, without ExpressionTool Returned non-zero Test [188/378] dynamic_resreq_wf_optional_file_wf_default: Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Test 186 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqrwc96mc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-workflow-tooldefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The CommandLineTool input has a default value (a local file) and the workflow nor the workflow step does not provide any value for this input. Returned non-zero Test [189/378] step_input_default_value_overriden_2nd_step: Test default value on step input parameter overridden by provided source. With passthrough first step Test 187 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprxub7xnc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-workflow-stepdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow step provides a default value (a local file) for this input and the workflow itself does not provide any value for this input. Returned non-zero Test [190/378] step_input_default_value_overriden_2nd_step_noexp: Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Test 188 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp29ewoeew --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dynresreq-workflow-inputdefault.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Within a workflow, test accessing the size attribute of an optional input File as part of a CommandLineTool's ResourceRequirement calculation. The workflow itelf provides a default value (a local file) for this input. Returned non-zero Test [191/378] step_input_default_value_overriden_2nd_step_null: Test default value on step input parameter overridden by provided source. With null producing first step Test 189 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt9brzvl9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-extra-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step Returned non-zero Test [192/378] step_input_default_value_overriden_2nd_step_null_noexp: Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Test 190 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpplziifq5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-extra-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test default value on step input parameter overridden by provided source. With passthrough first step and no ExpressionTool Returned non-zero Test [193/378] stdin_from_directory_literal_with_local_file: Pipe to stdin from user provided local File via a Directory literal Test 191 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvajvxenu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-null-step-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default value on step input parameter overridden by provided source. With null producing first step Returned non-zero Test [194/378] stdin_from_directory_literal_with_literal_file: Pipe to stdin from literal File via a Directory literal Test 192 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwh6tsryt --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/count-lines11-null-step-wf-noET.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test default value on step input parameter overridden by provided source. With null producing first step and no ExpressionTool Returned non-zero Test [195/378] directory_literal_with_literal_file_nostdin: Test non-stdin reference to literal File via a Directory literal Test 193 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphzl6q1kc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir-job.yaml Pipe to stdin from user provided local File via a Directory literal Returned non-zero Test [196/378] no_inputs_commandlinetool: Test CommandLineTool without inputs Test 194 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphpku9_ql --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir-with-literal-file.yaml Pipe to stdin from literal File via a Directory literal Returned non-zero Test [197/378] no_outputs_commandlinetool: Test CommandLineTool without outputs Test 195 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpirw02k4d --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat3-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir-with-literal-file.yaml Test non-stdin reference to literal File via a Directory literal Returned non-zero Test [198/378] no_inputs_workflow: Test Workflow without inputs Test 196 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvm6p7un2 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/no-inputs-tool.cwl Test CommandLineTool without inputs Returned non-zero Test [199/378] no_outputs_workflow: Test Workflow without outputs Test 197 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_i193rwi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/no-outputs-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test CommandLineTool without outputs Returned non-zero Test [200/378] anonymous_enum_in_array: Test an anonymous enum inside an array inside a record Test 198 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpaxh32qxf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/no-inputs-wf.cwl Test Workflow without inputs Returned non-zero Test [201/378] schema-def_anonymous_enum_in_array: Test an anonymous enum inside an array inside a record, SchemaDefRequirement Test 199 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptlzd9_gi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/no-outputs-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-job.json Test Workflow without outputs Returned non-zero Test [202/378] stdin_shorcut: Test command execution in with stdin and stdout redirection using stdin shortcut Test 200 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6h6boiyx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/anon_enum_inside_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/anon_enum_inside_array.yml Test an anonymous enum inside an array inside a record Returned non-zero Test [203/378] secondary_files_in_unnamed_records: Test secondaryFiles on anonymous record fields Test 201 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphdyitri5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/anon_enum_inside_array_inside_schemadef.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/anon_enum_inside_array_inside_schemadef.yml Test an anonymous enum inside an array inside a record, SchemaDefRequirement Returned non-zero Test [204/378] secondary_files_in_named_records: Test secondaryFiles on SchemaDefRequirement record fields Test 202 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpesr3d_06 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-tool-shortcut.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wc-job.json Test command execution in with stdin and stdout redirection using stdin shortcut Returned non-zero Test [205/378] secondary_files_in_output_records: Test secondaryFiles on output record fields Test 203 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0fdnixnp --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-in-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-secondaryFiles-job.yml Test secondaryFiles on anonymous record fields Returned non-zero Test [206/378] secondary_files_workflow_propagation: Test secondaryFiles propagation through workflow Test 204 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgl7zm96o --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-sd-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-secondaryFiles-job.yml Test secondaryFiles on SchemaDefRequirement record fields Returned non-zero Test [207/378] secondary_files_missing: Test checking when secondaryFiles are missing Test 205 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp45sqq06p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-out-secondaryFiles.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test secondaryFiles on output record fields Returned non-zero Test [208/378] input_records_file_entry_with_format: Test format on anonymous record fields Test 206 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv4xxzl4j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-in-secondaryFiles-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-secondaryFiles-job.yml Test secondaryFiles propagation through workflow Returned non-zero Test [209/378] input_records_file_entry_with_format_and_bad_regular_input_file_format: Test file format checking on parameter Test [210/378] input_records_file_entry_with_format_and_bad_entry_file_format: Test file format checking on record field Test 208 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkz6s6nid --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-in-format.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-format-job.yml Test format on anonymous record fields Returned non-zero Test [211/378] input_records_file_entry_with_format_and_bad_entry_array_file_format: Test file format checking on array item Test [212/378] record_output_file_entry_format: Test format on output record fields Test [213/378] workflow_input_inputBinding_loadContents: Test WorkflowInputParameter.inputBinding.loadContents Test [214/378] workflow_input_loadContents_without_inputBinding: Test WorkflowInputParameter.loadContents Test 212 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpuwnlbegq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-out-format.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-secondaryFiles-job.yml Test format on output record fields Returned non-zero Test [215/378] expression_tool_input_loadContents: Test loadContents on InputParameter.loadContents (expression) Test 213 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpoa1snwtq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents-job.yml Test WorkflowInputParameter.inputBinding.loadContents Returned non-zero Test [216/378] workflow_step_in_loadContents: Test WorkflowStepInput.loadContents Test 214 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkh89nhy9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents-job.yml Test WorkflowInputParameter.loadContents Returned non-zero Test [217/378] timelimit_basic: Test that job fails when exceeding time limit Test 215 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp__n3jwht --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents-job.yml Test loadContents on InputParameter.loadContents (expression) Returned non-zero Test [218/378] timelimit_invalid: Test invalid time limit value Test 216 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3b6hs6jr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/wf-loadContents-job.yml Test WorkflowStepInput.loadContents Returned non-zero Test [219/378] timelimit_zero_unlimited: Test zero timelimit means no limit Test [220/378] timelimit_from_expression: Test expression in time limit Test [221/378] timelimit_expressiontool: Test timelimit in expressiontool is ignored Test 219 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmkcds9h9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/timelimit3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test zero timelimit means no limit Returned non-zero Test [222/378] timelimit_basic_wf: Test that tool in workflow fails when exceeding time limit Test [223/378] timelimit_invalid_wf: Test that workflow level time limit is not applied to workflow execution time Test 221 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph_zo462c --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/timelimit5.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test timelimit in expressiontool is ignored Returned non-zero Test [224/378] timelimit_zero_unlimited_wf: Test zero timelimit means no limit in workflow Test [225/378] timelimit_from_expression_wf: Test expression in time limit in workflow Test 223 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpaoa4fl1p --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/timelimit2-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that workflow level time limit is not applied to workflow execution time Returned non-zero Test [226/378] networkaccess: Test networkaccess enabled Test 224 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp58ytk8wn --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/timelimit3-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test zero timelimit means no limit in workflow Returned non-zero Test [227/378] networkaccess_disabled: Test networkaccess is disabled by default Test [228/378] initial_work_dir_for_null_and_arrays: Test null and array input in InitialWorkDirRequirement Test 226 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_a2cfkzd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/networkaccess.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test networkaccess enabled Returned non-zero Test [229/378] initial_work_dir_for_array_dirs: Test array of directories InitialWorkDirRequirement Test [230/378] cwl_requirements_addition: Test requirements in input document via EnvVarRequirement Test 228 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpm8ech559 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage-array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage-array-job.json Test null and array input in InitialWorkDirRequirement Returned non-zero Test [231/378] cwl_requirements_override_expression: Test conflicting requirements in input document via EnvVarRequirement and expression Test 229 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpaql2kvc4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage-array-dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage-array-dirs-job.yml Test array of directories InitialWorkDirRequirement Returned non-zero Test [232/378] cwl_requirements_override_static: Test conflicting requirements in input document via EnvVarRequirement Test 230 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptvjfdj4t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-tool3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job3.yaml Test requirements in input document via EnvVarRequirement Returned non-zero Test [233/378] initial_workdir_output_glob: Test full path glob output of InitialWorkDir Test 231 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8k4_l3bq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-tool4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job3.yaml Test conflicting requirements in input document via EnvVarRequirement and expression Returned non-zero Test [234/378] glob_outside_outputs_fails: Test fail trying to glob outside output directory Test 232 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7gq4wkov --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-tool3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job4.yaml Test conflicting requirements in input document via EnvVarRequirement Returned non-zero Test [235/378] illegal_symlink: symlink to file outside of working directory should NOT be retrieved Test 233 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpiwm65lzf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/initialworkdir-glob-fullpath.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/initialworkdirrequirement-docker-out-job.json Test full path glob output of InitialWorkDir Returned non-zero Test [236/378] legal_symlink: symlink to file inside of working directory should be retrieved Test [237/378] modify_file_content: inplace update has side effect on file content Test [238/378] modify_directory_content: inplace update has side effect on directory content Test 236 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_yhghq4k --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/symlink-legal.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json symlink to file inside of working directory should be retrieved Returned non-zero Test [239/378] outputbinding_glob_directory: Test that OutputBinding.glob accepts Directories Test 237 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplxa3nzwi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/inp_update_wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json inplace update has side effect on file content Returned non-zero Test [240/378] stage_file_array: Test that array of input files can be staged to directory with entryname Test 238 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3nxizxn5 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/inpdir_update_wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json inplace update has side effect on directory content Returned non-zero Test [241/378] stage_file_array_basename: Test that array of input files can be staged to directory with basename Test 239 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_6zz3y3e --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/glob_directory.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that OutputBinding.glob accepts Directories Returned non-zero Test [242/378] stage_file_array_entryname_overrides: Test that if array of input files are staged to directory with basename and entryname, entryname overrides Test 240 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpl86oub0q --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array.job.json Test that array of input files can be staged to directory with entryname Returned non-zero Test [243/378] tmpdir_is_not_outdir: Test that runtime.tmpdir is not runtime.outdir Test 241 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphd_u3hiz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array_basename.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array.job.json Test that array of input files can be staged to directory with basename Returned non-zero Test [244/378] listing_default_none: Test that default behavior is 'no_listing' if not specified Test 242 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvv_o2n57 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array_basename_and_entryname.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stage_file_array.job.json Test that if array of input files are staged to directory with basename and entryname, entryname overrides Returned non-zero Test [245/378] listing_requirement_none: Test that 'listing' is not present when LoadListingRequirement is 'no_listing' Test 243 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpyja7m40t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/runtime-paths-distinct.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that runtime.tmpdir is not runtime.outdir Returned non-zero Test [246/378] listing_loadListing_none: Test that 'listing' is not present when loadListing on input parameter is 'no_listing' Test 244 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt0gxgbvh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_none1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that default behavior is 'no_listing' if not specified Returned non-zero Test [247/378] listing_requirement_shallow: Test that 'listing' is present in top directory object but not subdirectory object when LoadListingRequirement is 'shallow_listing' Test 245 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwc1bbyv8 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_none2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is not present when LoadListingRequirement is 'no_listing' Returned non-zero Test [248/378] listing_loadListing_shallow: Test that 'listing' is present in top directory object but not subdirectory object when loadListing on input parameter loadListing is 'shallow_listing' Test 246 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9u53nqrc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_none3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is not present when loadListing on input parameter is 'no_listing' Returned non-zero Test [249/378] listing_outputBinding_loadListing: Test that loadListing works when used on outputBinding. Test 247 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqf5wom75 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_shallow1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is present in top directory object but not subdirectory object when LoadListingRequirement is 'shallow_listing' Returned non-zero Test [250/378] listing_requirement_deep: Test that 'listing' is present in top directory object and in subdirectory objects when LoadListingRequirement is 'deep_listing' Test 248 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphvvo_ob4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_shallow2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is present in top directory object but not subdirectory object when loadListing on input parameter loadListing is 'shallow_listing' Returned non-zero Test [251/378] listing_loadListing_deep: Test that 'listing' is present in top directory object and in subdirectory objects when input parameter loadListing is 'deep_listing' Test 249 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpiar0_cq9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_shallow3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that loadListing works when used on outputBinding. Returned non-zero Test [252/378] inputBinding_position_expr: Test for expression in the InputBinding.position field; also test using emoji in CWL document and tool output Test 250 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpsk8pfjwx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_deep1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is present in top directory object and in subdirectory objects when LoadListingRequirement is 'deep_listing' Returned non-zero Test [253/378] outputEval_exitCode: Can access exit code in outputEval Test 251 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfnvjrf8i --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing_deep2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/listing-job.yml Test that 'listing' is present in top directory object and in subdirectory objects when input parameter loadListing is 'deep_listing' Returned non-zero Test [254/378] any_input_param_graph_no_default: Test use of $graph without specifying which process to run Test 252 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe0zfkbks --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-position-expr.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-position-expr-job.yml Test for expression in the InputBinding.position field; also test using emoji in CWL document and tool output Returned non-zero Test [255/378] any_input_param_graph_no_default_hashmain: Test use of $graph without specifying which process to run, hash-prefixed "main" Test 253 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpez33xl4f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/exitcode.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Can access exit code in outputEval Returned non-zero Test [256/378] optional_numerical_output_returns_0_not_null: Test that optional number output is returned as 0, not null Test 254 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4lyqx2n7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-tool-packed.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test use of $graph without specifying which process to run Returned non-zero Test [257/378] cores_float: Test float value for coresMin(Max) is rounded up in runtime.cores Test 255 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0u0t56rf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/echo-tool-packed2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/env-job.json Test use of $graph without specifying which process to run, hash-prefixed "main" Returned non-zero Test [258/378] storage_float: Test float value for ram/tmpdir/outdir Min(Max) is rounded up Test 256 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5hq6l0kb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/optional-numerical-output-0.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test that optional number output is returned as 0, not null Returned non-zero Test [259/378] cat_synthetic_file: Test the generation of a synthetic file with inline contents. Test 257 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpn7rmif4e --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cores_float.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test float value for coresMin(Max) is rounded up in runtime.cores Returned non-zero Test [260/378] continuation: Line continuations in bash scripts should behave correctly Test 258 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmps67sws06 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/storage_float.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Test float value for ram/tmpdir/outdir Min(Max) is rounded up Returned non-zero Test [261/378] continuation_expression: Line continuations in bash scripts should always behave correctly Test 259 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpwocsrhcb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/synth-file.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/synth-file-job.yml Test the generation of a synthetic file with inline contents. Returned non-zero Test [262/378] quoting_multiple_backslashes: Test quoting multiple backslashes Test 260 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp6ohvkwmy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/string-interpolation/bash-line-continuation.cwl Line continuations in bash scripts should behave correctly Returned non-zero Test [263/378] escaping_expression_no_extra_quotes: Strings returned from JS expressions should not have extra quotes around them Test 261 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgpvgjys7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/string-interpolation/bash-line-continuation-with-expression.cwl Line continuations in bash scripts should always behave correctly Returned non-zero Test [264/378] direct_optional_null_result: Simplest conditional pattern (False) Test 262 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9a1pzurc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/string-interpolation/bash-dollar-quote.cwl Test quoting multiple backslashes Returned non-zero Test [265/378] direct_optional_nonnull_result: Simplest conditional pattern (True) Test 263 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppa5qepmx --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/string-interpolation/js-quote.cwl Strings returned from JS expressions should not have extra quotes around them Returned non-zero Test [266/378] direct_required: Conditional using intermediate WorkflowStep.in input Test 264 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpewsrjprb --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-001.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml Simplest conditional pattern (False) Returned non-zero Test [267/378] pass_through_required_false_when: Pass through pattern with pickValue: first_non_null; 'when' is false Test 265 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9hnjafee --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-001.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.3.job.yaml Simplest conditional pattern (True) Returned non-zero Test [268/378] pass_through_required_true_when: pass through pattern with pickvalue: first_non_null; 'when' is true Test 266 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjh0ar8t7 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-002.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml Conditional using intermediate WorkflowStep.in input Returned non-zero Test [269/378] first_non_null_first_non_null: pickValue: first_non_null first item is non null Test 267 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpb69ttu58 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml Pass through pattern with pickValue: first_non_null; 'when' is false Returned non-zero Test [270/378] first_non_null_all_null: pickValue: first_non_null needs at least one non null Test 268 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpv4wk7v66 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.3.job.yaml pass through pattern with pickvalue: first_non_null; 'when' is true Returned non-zero Test [271/378] first_non_null_second_non_null: pickValue: first_non_null second item is non null Test 269 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpjt5lsgtf --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.0.job.yaml pickValue: first_non_null first item is non null Returned non-zero Test [272/378] pass_through_required_the_only_non_null: pickvalue: the_only_non_null will pass, only for false condition Test [273/378] pass_through_required_fail: pickValue: the_only_non_null will fail due to multiple non nulls Test 271 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcqosiw5v --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.3.job.yaml pickValue: first_non_null second item is non null Returned non-zero Test [274/378] all_non_null_multi_with_non_array_output: pickValue: all_non_null will fail validation Test 272 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpdkrywl2f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-004.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml pickvalue: the_only_non_null will pass, only for false condition Returned non-zero Test [275/378] the_only_non_null_single_true: pickValue: the_only_non_null will pass for only one active node Test [276/378] the_only_non_null_multi_true: pickValue: the_only_non_null will fail with two active nodes Test [277/378] all_non_null_all_null: pickValue: all_non_null will produce a list, even if empty Test 275 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpeozir01l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-006.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml pickValue: the_only_non_null will pass for only one active node Returned non-zero Test [278/378] all_non_null_one_non_null: pickValue: all_non_null will produce a list; even if single item list Test [279/378] all_non_null_multi_non_null: pickValue: all_non_null will produce a list Test 277 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5jluy1oe --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.0.job.yaml pickValue: all_non_null will produce a list, even if empty Returned non-zero Test [280/378] condifional_scatter_on_nonscattered_false: Simple scatter: conditional on a non scattered variable (False) Test 278 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5gl8n5b1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml pickValue: all_non_null will produce a list; even if single item list Returned non-zero Test [281/378] condifional_scatter_on_nonscattered_true: Simple scatter: conditional on a non scattered variable (True) Test 279 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4x15102s --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.3.job.yaml pickValue: all_non_null will produce a list Returned non-zero Test [282/378] scatter_on_scattered_conditional: Simple scatter: Add conditional variable to scatter Test 280 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp74t_8_qc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-009.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond15.job.yaml Simple scatter: conditional on a non scattered variable (False) Returned non-zero Test [283/378] conditionals_nested_cross_scatter: nested cross product scatter with condition on one dimension Test 281 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp7tgsa9f1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-009.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond16.job.yaml Simple scatter: conditional on a non scattered variable (True) Returned non-zero Test [284/378] conditionals_non_boolean_fail: Non-boolean values from "when" should fail Test 282 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpo4dgrho3 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-010.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.6.list.job.yaml Simple scatter: Add conditional variable to scatter Returned non-zero Test [285/378] conditionals_multi_scatter: Scatter two steps, flatten result + pickValue Test 283 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfu0by782 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-011.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond18.job.yaml nested cross product scatter with condition on one dimension Returned non-zero Test [286/378] direct_optional_null_result_nojs: simplest conditional pattern (true), no javascript Test [287/378] direct_optional_nonnull_result_nojs: simplest conditional pattern (false), no javascript Test 285 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpiy579b5c --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-013.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond20.job.yaml Scatter two steps, flatten result + pickValue Returned non-zero Test [288/378] direct_required_nojs: Conditional using intermediate WorkflowStep.in input; no javascript Test 286 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpl7ierlgk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-001_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-true.yml simplest conditional pattern (true), no javascript Returned non-zero Test [289/378] pass_through_required_false_when_nojs: Pass through pattern with pickValue: first_non_null; 'when' is false'; no javascript Test 287 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpck2sj48c --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-001_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-false.yml simplest conditional pattern (false), no javascript Returned non-zero Test [290/378] pass_through_required_true_when_nojs: pass through pattern with pickvalue: first_non_null; 'when' is true'; no javascript Test 288 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqxbhsjsa --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-002_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/val.1.job.yaml Conditional using intermediate WorkflowStep.in input; no javascript Returned non-zero Test [291/378] first_non_null_first_non_null_nojs: pickValue: first_non_null first item is non null; no javascript Test 289 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpz9tpbzuy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-false.yml Pass through pattern with pickValue: first_non_null; 'when' is false'; no javascript Returned non-zero Test [292/378] first_non_null_all_null_nojs: pickValue: first_non_null needs at least one non null; no javascript Test 290 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmppauhmg4_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-true.yml pass through pattern with pickvalue: first_non_null; 'when' is true'; no javascript Returned non-zero Test [293/378] first_non_null_second_non_null_nojs: pickValue: first_non_null second item is non null; no javascript Test 291 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxfbuqjdo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.1_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/first-true.yml pickValue: first_non_null first item is non null; no javascript Returned non-zero Test [294/378] pass_through_required_the_only_non_null_nojs: pickvalue: the_only_non_null will pass, only for false condition; no javascript Test [295/378] pass_through_required_fail_nojs: pickValue: the_only_non_null will fail due to multiple non nulls; no javascript Test 293 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpclyz8ad0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-003.1_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/second-true.yml pickValue: first_non_null second item is non null; no javascript Returned non-zero Test [296/378] all_non_null_multi_with_non_array_output_nojs: pickValue: all_non_null will fail validation; no javascript Test 294 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbdgg7rho --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-004_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-false.yml pickvalue: the_only_non_null will pass, only for false condition; no javascript Returned non-zero Test [297/378] the_only_non_null_single_true_nojs: pickValue: the_only_non_null will pass for only one active node; no javascript Test [298/378] the_only_non_null_multi_true_nojs: pickValue: the_only_non_null will fail with two active nodes; no javascript Test [299/378] all_non_null_all_null_nojs: pickValue: all_non_null will produce a list, even if empty; no javascript Test 297 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp93iq1trh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-006_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/second-true.yml pickValue: the_only_non_null will pass for only one active node; no javascript Returned non-zero Test [300/378] all_non_null_one_non_null_nojs: pickValue: all_non_null will produce a list; even if single item list; no javascript Test [301/378] all_non_null_multi_non_null_nojs: pickValue: all_non_null will produce a list; no javascript Test 299 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplf600dik --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/both-false.yml pickValue: all_non_null will produce a list, even if empty; no javascript Returned non-zero Test [302/378] condifional_scatter_on_nonscattered_false_nojs: Simple scatter: conditional on a non scattered variable (False); no javascript Test 300 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpf72fbidi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/second-true.yml pickValue: all_non_null will produce a list; even if single item list; no javascript Returned non-zero Test [303/378] condifional_scatter_on_nonscattered_true_nojs: Simple scatter: conditional on a non scattered variable (True); no javascript Test 301 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqygc87d1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-007_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/both-true.yml pickValue: all_non_null will produce a list; no javascript Returned non-zero Test [304/378] scatter_on_scattered_conditional_nojs: Simple scatter: Add conditional variable to scatter; no javascript Test 302 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnoe9p7sz --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-009_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-false.yml Simple scatter: conditional on a non scattered variable (False); no javascript Returned non-zero Test [305/378] conditionals_nested_cross_scatter_nojs: nested cross product scatter with condition on one dimension; no javascript Test 303 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxyqps6le --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-009_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/test-true.yml Simple scatter: conditional on a non scattered variable (True); no javascript Returned non-zero Test [306/378] conditionals_non_boolean_fail_nojs: Non-boolean values from "when" should fail; no javascript Test 304 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnfwbyl5m --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-010_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Simple scatter: Add conditional variable to scatter; no javascript Returned non-zero Test [307/378] conditionals_multi_scatter_nojs: Scatter two steps, flatten result + pickValue; no javascript Test 305 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx7v6ar_a --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-011_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json nested cross product scatter with condition on one dimension; no javascript Returned non-zero Test [308/378] cond-with-defaults-1: Default inputs, choose step to run based on what was provided, first case Test [309/378] cond-with-defaults-2: Default inputs, choose step to run based on what was provided, second case Test 308 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpivjy1zto --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-with-defaults.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-job.yaml Default inputs, choose step to run based on what was provided, first case Returned non-zero Test [310/378] command_input_file_expression: Confirm CommandInputParameter expression can receive a File object Test 307 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpt4zb3dnj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-wf-013_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Scatter two steps, flatten result + pickValue; no javascript Returned non-zero Test [311/378] command_output_file_expression: Confirm CommandOutputParameter expression can receive a File object Test 309 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqkymk3f9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-with-defaults.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/conditionals/cond-job2.yaml Default inputs, choose step to run based on what was provided, second case Returned non-zero Test [312/378] mixed_version_v10_wf: test v1.0 workflow document that runs other versions Test 310 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmf_wbw77 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/secondaryfiles/rename-inputs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/secondaryfiles/rename-inputs.yml Confirm CommandInputParameter expression can receive a File object Returned non-zero Test [313/378] mixed_version_v11_wf: test v1.1 workflow document that runs other versions Test 311 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp926pqopk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/secondaryfiles/rename-outputs.cwl Confirm CommandOutputParameter expression can receive a File object Returned non-zero Test [314/378] mixed_version_v12_wf: test v1.2 workflow document that runs other versions Test 312 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5mj7lyj4 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/mixed-versions/wf-v10.cwl test v1.0 workflow document that runs other versions Returned non-zero Test [315/378] invalid_syntax_v10_uses_v12_tool: test tool with v1.2 syntax marked as v1.0 (should fail) Test 314 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpdifbfjj1 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/mixed-versions/wf-v12.cwl test v1.2 workflow document that runs other versions Returned non-zero Test [316/378] invalid_syntax_v11_uses_v12_tool: test tool with v1.2 syntax marked as v1.1 (should fail) Test 313 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmph6k6wr2u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/mixed-versions/wf-v11.cwl test v1.1 workflow document that runs other versions Returned non-zero Test [317/378] invalid_syntax_v10_uses_v12_workflow: test wf with v1.2 syntax marked as v1.0 (should fail) Test [318/378] invalid_syntax_v11_uses_v12_workflow: test wf with v1.2 syntax marked as v1.1 (should fail) Test [319/378] invalid_syntax_mixed_v12_workflow: test 1.2 wf that includes tools that are marked as v1.0 and v1.1 that contain v1.2 features (should fail) Test [320/378] cwloutput_nolimit: Test that loading from cwl.output.json isn't limited to 64k Test [321/378] loadcontents_limit: Test that loadContents on a file larger than 64k fails Test 320 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpht72lggw --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/cwloutput-nolimit.cwl Test that loading from cwl.output.json isn't limited to 64k Returned non-zero Test [322/378] iwd-nolimit: Test that InitialWorkDir contents can be bigger than 64k Test [323/378] iwd-jsondump1: Test dump object to JSON in InitialWorkDir file contents, no trailing newline Test [324/378] iwd-jsondump1-nl: Test dump object to JSON in InitialWorkDir file contents, with trailing newline Test 323 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpncmtqfk0 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump1.cwl Test dump object to JSON in InitialWorkDir file contents, no trailing newline Returned non-zero Test [325/378] iwd-jsondump2: Test array to JSON in InitialWorkDir file contents, no trailing newline Test 322 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp8r5xyqdr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-nolimit.cwl Test that InitialWorkDir contents can be bigger than 64k Returned non-zero Test [326/378] iwd-jsondump2-nl: Test array to JSON in InitialWorkDir file contents, with trailing newline Test 324 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcdmpetzi --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump1-nl.cwl Test dump object to JSON in InitialWorkDir file contents, with trailing newline Returned non-zero Test [327/378] iwd-jsondump3: Test number to JSON in InitialWorkDir file contents, no trailing newline Test 326 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr5emoc9t --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump2-nl.cwl Test array to JSON in InitialWorkDir file contents, with trailing newline Returned non-zero Test [328/378] iwd-jsondump3-nl: Test number to JSON in InitialWorkDir file contents, with trailing newline Test 325 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfs2q_vco --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump2.cwl Test array to JSON in InitialWorkDir file contents, no trailing newline Returned non-zero Test [329/378] iwd-passthrough1: Test InitialWorkDir file passthrough Test 327 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4i6w29ak --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump3.cwl Test number to JSON in InitialWorkDir file contents, no trailing newline Returned non-zero Test [330/378] iwd-passthrough2: Test InitialWorkDir file object is serialized to json Test 329 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqs957mch --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-passthrough1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test InitialWorkDir file passthrough Returned non-zero Test [331/378] iwd-passthrough3: Test InitialWorkDir file object is passed through Test 328 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmhbulmwj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-jsondump3-nl.cwl Test number to JSON in InitialWorkDir file contents, with trailing newline Returned non-zero Test [332/378] iwd-passthrough4: Test InitialWorkDir file object is passed through Test 330 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp59vxqdwu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-passthrough2.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test InitialWorkDir file object is serialized to json Returned non-zero Test [333/378] iwd-fileobjs1: Test File and Directory object in listing Test 331 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcbbses51 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-passthrough3.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test InitialWorkDir file object is passed through Returned non-zero Test [334/378] iwd-fileobjs2: Test File and Directory object in listing Test 332 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpbvsfekhy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-passthrough4.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test InitialWorkDir file object is passed through Returned non-zero Test [335/378] iwd-container-entryname1: Test input mount locations when container required Test 333 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpclsac0j6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-fileobjs1.cwl Test File and Directory object in listing Returned non-zero Test [336/378] iwd-container-entryname2: Test input mount locations when no container (should fail) Test 335 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp49vspsy9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-container-entryname1.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test input mount locations when container required Returned non-zero Test [337/378] iwd-container-entryname3: Test input mount locations when container is a hint (should fail) Test 334 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpg3he1evd --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-fileobjs2.cwl Test File and Directory object in listing Returned non-zero Test [338/378] iwd-container-entryname4: Must fail if entryname starts with ../ Test [339/378] iwdr_dir_literal_real_file: Test directory literal containing a real file Test [340/378] iwd-subdir: Test emitting a subdirectory from initial workdir Test [341/378] simple_simple_scatter: Two level nested scatter Test 339 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpnetqzsyq --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwdr_dir_literal_real_file.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/loadContents/input.yml Test directory literal containing a real file Returned non-zero Test [342/378] dotproduct_simple_scatter: Two level nested scatter: external dotproduct and internal simple Test 341 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpkx5vqyyh --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/simple-simple-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter-job.yml Two level nested scatter Returned non-zero Test [343/378] simple_dotproduct_scatter: Two level nested scatter: external simple and internal dotproduct Test 340 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0udquo1u --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-subdir-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/iwd/iwd-subdir-job.yml Test emitting a subdirectory from initial workdir Returned non-zero Test [344/378] dotproduct_dotproduct_scatter: Two level nested scatter: external dotproduct and internal dotproduct Test 342 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpfm6mnzce --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/dotproduct-simple-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter2-job.yml Two level nested scatter: external dotproduct and internal simple Returned non-zero Test [345/378] flat_crossproduct_simple_scatter: Two level nested scatter: external flat_crossproduct and internal simple Test 343 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpe6_rdll_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/simple-dotproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter3-job.yml Two level nested scatter: external simple and internal dotproduct Returned non-zero Test [346/378] simple_flat_crossproduct_scatter: Two level nested scatter: external simple and internal flat_crossproduct Test 345 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpd216zkxr --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/flat-crossproduct-simple-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter2-job.yml Two level nested scatter: external flat_crossproduct and internal simple Returned non-zero Test [347/378] flat_crossproduct_flat_crossproduct_scatter: Two level nested scatter: external flat_crossproduct and internal flat_crossproduct Test 344 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpw9pwjcd_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/dotproduct-dotproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter4-job.yml Two level nested scatter: external dotproduct and internal dotproduct Returned non-zero Test [348/378] nested_crossproduct_simple_scatter: Two level nested scatter: external nested_crossproduct and internal simple Test 346 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpunt4h_wk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/simple-flat-crossproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter3-job.yml Two level nested scatter: external simple and internal flat_crossproduct Returned non-zero Test [349/378] simple_nested_crossproduct_scatter: Two level nested scatter: external simple and internal nested_crossproduct Test 348 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_jhbkf5f --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/nested-crossproduct-simple-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter2-job.yml Two level nested scatter: external nested_crossproduct and internal simple Returned non-zero Test [350/378] nested_crossproduct_nested_crossproduct_scatter: Two level nested scatter: external nested_crossproduct and internal nested_crossproduct Test 347 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpqmr5b47_ --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/flat-crossproduct-flat-crossproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter4-job.yml Two level nested scatter: external flat_crossproduct and internal flat_crossproduct Returned non-zero Test [351/378] params_broken_null: Test parameter reference that refers to null.something Test 349 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpca6so15j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/simple-nested-crossproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter3-job.yml Two level nested scatter: external simple and internal nested_crossproduct Returned non-zero Test [352/378] length_for_non_array: Test parameter reference that refers to length of non-array input Test 350 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprzg98s8y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/nested-crossproduct-nested-crossproduct-scatter.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/scatter/scatter4-job.yml Two level nested scatter: external nested_crossproduct and internal nested_crossproduct Returned non-zero Test [353/378] user_defined_length_in_parameter_reference: Test 'length' in parameter reference where it does not refer to length of an array input Test [354/378] directory_literal_with_literal_file_in_subdir_nostdin: Test non-stdin reference to literal File via a nested Directory literal Test [355/378] colon_in_paths: Confirm that colons are tolerated in input paths, string values, stdout shortcut, and output file & directory names Test 353 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpcxwmmkmo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/params_input_length_non_array.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/length_non_array_input.yml Test 'length' in parameter reference where it does not refer to length of an array input Returned non-zero Test [356/378] colon_in_output_path: Confirm that colons are tolerated in output directory names Test 354 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpvw_4aqwu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat4-from-dir.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-from-dir-with-literal-file-in-subdir.yaml Test non-stdin reference to literal File via a nested Directory literal Returned non-zero Test [357/378] record_with_default: Confirm that records with defaults are accepted Test 355 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi_ematxj --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/colon:test.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/colon:test:job.yaml Confirm that colons are tolerated in input paths, string values, stdout shortcut, and output file & directory names Returned non-zero Test [358/378] record_outputeval: Use of outputEval on a record itself, not the fields of the record Test 356 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpxw2ecucu --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/colon_test_output.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/colon_test_output_job.yaml Confirm that colons are tolerated in output directory names Returned non-zero Test [359/378] record_outputeval_nojs: Use of outputEval on a record itself, not the fields of the record (without javascript) Test 357 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmplu4l6pws --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/paramref_arguments_roundtrip.cwl Confirm that records with defaults are accepted Returned non-zero Test [360/378] staging-basename: Use of expression tool to change basename of file, then correctly staging the file using the new name. Test 358 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp5fg206dy --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record_outputeval.cwl Use of outputEval on a record itself, not the fields of the record Returned non-zero Test [361/378] runtime-outdir: Use of $(runtime.outdir) for outputBinding glob. Test 359 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp1prk1j4l --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record_outputeval_nojs.cwl Use of outputEval on a record itself, not the fields of the record (without javascript) Returned non-zero Test [362/378] record_order_with_input_bindings: Test sorting arguments at each level (inputBinding for all levels) Test 360 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp4_kze7bc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/staging-basename/wf_ren.cwl Use of expression tool to change basename of file, then correctly staging the file using the new name. Returned non-zero Test [363/378] output_reference_workflow_input: Direct use of Workflow level input fields in the outputs. Test 361 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpi7z2ht6y --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/runtime-outdir.cwl Use of $(runtime.outdir) for outputBinding glob. Returned non-zero Test [364/378] stdout_chained_commands: Test that chaining two echo calls causes the workflow tool to emit the output to stdout. This is to confirm that the workflow tool will **not** create an expression such as `echo a && echo b > out.txt`, but instead will produce the correct `echo a && echo b`, and capture the output correctly. Test 362 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpgtlsi_jk --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-order.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/record-order-job.json Test sorting arguments at each level (inputBinding for all levels) Returned non-zero Test [365/378] multiple-input-feature-requirement: MultipleInputFeatureRequirement on workflow outputs. Test 363 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpr2e8w_1j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/output_reference_workflow_input.cwl Direct use of Workflow level input fields in the outputs. Returned non-zero Test [366/378] js-input-record: A test case for JS with an input record. Test 364 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmphstjhfvs --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/stdout_chained_commands.cwl Test that chaining two echo calls causes the workflow tool to emit the output to stdout. This is to confirm that the workflow tool will **not** create an expression such as `echo a && echo b > out.txt`, but instead will produce the correct `echo a && echo b`, and capture the output correctly. Returned non-zero Test [367/378] schemadef_types_with_import: Test SchemaDefRequirement with a workflow, with the `$import` under types. It is similar to schemadef-wf, but the `$import` is different. Test 365 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp9lwjwvwc --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/multiple_input_feature_requirement.cwl MultipleInputFeatureRequirement on workflow outputs. Returned non-zero Test [368/378] filename_with_hash_mark: Test for correct handling of URL-quoting in filename to refer to filename containing a hash mark Test 366 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpx0xxdrlv --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/js-input-record.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/js-input-record.json A test case for JS with an input record. Returned non-zero Test [369/378] capture_files: Test that a type error is raised if directories are returned by glob evaluation when type is File Test 367 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpf0mjyfte --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef_types_with_import-wf.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/schemadef_types_with_import-job.json Test SchemaDefRequirement with a workflow, with the `$import` under types. It is similar to schemadef-wf, but the `$import` is different. Returned non-zero Test [370/378] capture_dirs: Test that a type error is raised if files are returned by glob evaluation when type is Directory Test 368 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpurmmrm2d --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/cat-tool.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/octo.yml Test for correct handling of URL-quoting in filename to refer to filename containing a hash mark Returned non-zero Test [371/378] capture_files_and_dirs: Test that both files and directories are captured by glob evaluation when type is [Directory, File] Test [372/378] very_big_and_very_floats: Confirm that very big and very small numbers are represented using decimals, not scientific notation Test [373/378] very_big_and_very_floats_nojs: Confirm that very big and very small numbers are represented using decimals, not scientific notation Test 371 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmpmp5k7iuo --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/capture-files-and-dirs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/dir-job.yml Test that both files and directories are captured by glob evaluation when type is [Directory, File] Returned non-zero Test [374/378] default_with_falsey_value: Confirms that "false"-like (but not 'null') values override any default Test 372 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp32e60_mm --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/floats_small_and_large.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Confirm that very big and very small numbers are represented using decimals, not scientific notation Returned non-zero Test [375/378] nested_types: demonstrate usage of nested types Test 373 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3t6204ik --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/floats_small_and_large_nojs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Confirm that very big and very small numbers are represented using decimals, not scientific notation Returned non-zero Test [376/378] paramref_arguments_runtime: confirm that $runtime is available to parameter references in arguments Test 374 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmprb7vx_0j --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/default_with_falsey_value.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json Confirms that "false"-like (but not 'null') values override any default Returned non-zero Test [377/378] paramref_arguments_self: confirm that $self is available and set to null in arguments Test 375 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp_ykaxu52 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/nested_types.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/nested_types.yaml demonstrate usage of nested types Returned non-zero Test [378/378] paramref_arguments_inputs: confirm that $inputs is available to parameter references in arguments Test 376 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmptgiru_7z --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/paramref_arguments_runtime.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json confirm that $runtime is available to parameter references in arguments Returned non-zero Test 377 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp0g2vzcw9 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/paramref_arguments_self.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json confirm that $self is available and set to null in arguments Returned non-zero Test 378 failed: /tmp/pytest-of-tom/pytest-23/bin.0/test-arvados-cwl-runner --compute-checksum --disable-reuse --enable-dev --verbose --outdir=/tmp/tmp3g57ijm6 --quiet file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/paramref_arguments_inputs.cwl file:///tmp/pytest-of-tom/pytest-23/cwl-v1.2_tags_v1.2.1_0/tests/empty.json confirm that $inputs is available to parameter references in arguments Returned non-zero 41 tests passed, 337 failures, 0 unsupported features =========================================================================== short test summary info =========================================================================== FAILED tests/test_conformance.py::test_conformance_1_0 - AssertionError: assert 1 == 0 FAILED tests/test_conformance.py::test_conformance_1_1 - AssertionError: assert 1 == 0 FAILED tests/test_conformance.py::test_conformance_1_2 - AssertionError: assert 1 == 0 ================================================================ 3 failed, 135 deselected in 125.02s (0:02:05) ================================================================ ======= sdk/cwl tests -- FAILED ======= test sdk/cwl -- 126s Sent SIGTERM to 1493682 (/home/tom/arvados/tmp/keep0.pid) Sent SIGTERM to 1493701 (/home/tom/arvados/tmp/keep1.pid) Sent SIGTERM to 1493518 (/home/tom/arvados/tmp/dispatch.pid) Pass: sdk/cwl install (4s) Failures (1): Fail: sdk/cwl tests (126s)