Closed mr-c closed 3 years ago
___________________ test_disable_dir_overwrite_without_ext ____________________ @needs_docker def test_disable_dir_overwrite_without_ext(): try: tmp = tempfile.mkdtemp() out = tempfile.mkdtemp() > assert main(["--outdir", out, get_data('tests/wf/updatedir.cwl'), "-r", tmp]) == 0 E AssertionError: assert 1 == 0 E + where 1 = main(['--outdir', 'C:\\Users\\Dan\\AppData\\Local\\Temp\\tmpseg_j6s_', 'C:\\jenkins\\workspace\\cwltool_jenkinsfile_upgrade...RZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\\tests\\wf\\updatedir.cwl', '-r', 'C:\\Users\\Dan\\AppData\\Local\\Temp\\tmprb2dgfof']) tests\test_ext.py:104: AssertionError ---------------------------- Captured stdout call ----------------------------- {} ---------------------------- Captured stderr call ----------------------------- 1.0.20181025123047 Resolved 'C:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl' to 'file:///C:/jenkins/workspace/cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ/tests/wf/updatedir.cwl' Parsed job order from command line: { "id": "C:\\jenkins\\workspace\\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\\tests\\wf\\updatedir.cwl", "r": { "class": "Directory", "location": "file:///C:/Users/Dan/AppData/Local/Temp/tmprb2dgfof" } } We are on Microsoft Windows and not all components of this CWL description have a container specified. This means that these steps will be executed in the default container, which is frolvlad/alpine-bash. Note, this could affect portability if this CWL description relies on non-POSIX features or commands in this container. For best results add the following to your CWL description's hints section: hints: DockerRequirement: dockerPull: frolvlad/alpine-bash [job updatedir.cwl] initializing from file:///C:/jenkins/workspace/cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ/tests/wf/updatedir.cwl [job updatedir.cwl] { "r": { "class": "Directory", "location": "file:///C:/Users/Dan/AppData/Local/Temp/tmprb2dgfof", "basename": "tmprb2dgfof" } } [job updatedir.cwl] path mappings is { "file:///C:/Users/Dan/AppData/Local/Temp/tmprb2dgfof": [ "C:\\Users\\Dan\\AppData\\Local\\Temp\\tmprb2dgfof", "/lhGTcZ\\inp", "WritableDirectory", false ] } [job updatedir.cwl] command line bindings is [ { "position": [ 0, 0 ], "datum": "touch" }, { "position": [ 0, 1 ], "datum": "inp/blurb" } ] [job updatedir.cwl] initial work dir { "file:///C:/Users/Dan/AppData/Local/Temp/tmprb2dgfof": [ "C:\\Users\\Dan\\AppData\\Local\\Temp\\tmprb2dgfof", "/lhGTcZ/inp", "WritableDirectory", true ] } [job updatedir.cwl] C:\Users\Dan\AppData\Local\Temp\tmps8uvc9ra$ docker \ run \ -i \ --volume=/c/Users/Dan/AppData/Local/Temp/tmps8uvc9ra:/lhGTcZ:rw \ --volume=/c/Users/Dan/AppData/Local/Temp/tmpqpocc8ko:/tmp:rw \ --workdir=/lhGTcZ \ --read-only=true \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/lhGTcZ \ --cidfile=c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\20181025153604-567287.cid \ frolvlad/alpine-bash \ touch \ inp/blurb [job updatedir.cwl] Job error: Error collecting output for parameter 'out': C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: Traceback (most recent call last): C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\command_line_tool.py", line 604, in collect_output_ports C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: compute_checksum=compute_checksum) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\command_line_tool.py", line 767, in collect_output C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: adjustFileObjs(r, revmap) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\pathmapper.py", line 47, in adjustFileObjs C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: visit_class(rec, ("File",), op) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\utils.py", line 210, in visit_class C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: visit_class(rec[d], cls, op) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\utils.py", line 213, in visit_class C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: visit_class(d, cls, op) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\utils.py", line 208, in visit_class C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: op(rec) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: File "c:\jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\cwltool\command_line_tool.py", line 168, in revmap_file C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: u"file pass through." % (path, builder.outdir)) C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: C:jenkins\workspace\cwltool_jenkinsfile_upgrade-6OTLDHGBVKNOZ56QTWPIRZFBNKMBA4BIOLKLXZ2QMX535JO2PHLQ\tests\wf\updatedir.cwl:13:3: cwltool.errors.WorkflowException: Output file path C:/Users/Dan/AppData/Local/Temp/tmps8uvc9ra/inp/blurb must be within designated output directory (/lhGTcZ) or an input file pass through. [job updatedir.cwl] completed permanentFail [job updatedir.cwl] {} [job updatedir.cwl] Removing input staging directory C:\Users\Dan\AppData\Local\Temp\tmp3fb0tt9l [job updatedir.cwl] Removing temporary directory C:\Users\Dan\AppData\Local\Temp\tmpqpocc8ko Final process status is permanentFail
From https://ci.commonwl.org/blue/organizations/jenkins/cwltool/detail/jenkinsfile_upgrade/1/pipeline
We no longer support running in MS Windows, but we do support running in the Windows Subsystem for Linux 2: https://github.com/common-workflow-language/cwltool#ms-windows-users
From https://ci.commonwl.org/blue/organizations/jenkins/cwltool/detail/jenkinsfile_upgrade/1/pipeline