Entering edit mode
8.4 years ago
gijsmolenaar
▴
20
Hi!
I'm running the cwl confirmation test suite (OSX) and I want to examine the resulting files.
here an example:
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| λ ./run_test.sh --debug -n88 RUNNER=/Users/gijs/Work/cwltool/.virtualenv/bin/cwltool | |
| --- Running conformance test v1.0 on /Users/gijs/Work/cwltool/.virtualenv/bin/cwltool --- | |
| /Users/gijs/Work/cwltool/.virtualenv/bin/cwltool 1.0.20170213175853 | |
| Test [88/88] Test failed: /Users/gijs/Work/cwltool/.virtualenv/bin/cwltool --tmp-outdir-prefix=/Users/gijs/Work/common-workflow-language/v1.02_w88T --tmpdir-prefix=/Users/gijs/Work/common-workflow-language/v1.02_w88T --outdir=/Users/gijs/Work/common-workflow-language/v1.02_w88T --quiet v1.0/recursive-input-directory.cwl v1.0/recursive-input-directory.json | |
| Test if a writable input directory is recursivly copied and writable | |
| Compare failure expected: { | |
| "output_dir": { | |
| "basename": "work_dir", | |
| "class": "Directory", | |
| "listing": [ | |
| { | |
| "basename": "a", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "work_dir/a", | |
| "size": 0 | |
| }, | |
| { | |
| "basename": "b", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "work_dir/b", | |
| "size": 0 | |
| }, | |
| { | |
| "basename": "c", | |
| "class": "Directory", | |
| "listing": [ | |
| { | |
| "basename": "d", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "work_dir/c/d", | |
| "size": 0 | |
| } | |
| ], | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.0R35DHF/work_dir/c" | |
| }, | |
| { | |
| "basename": "e", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "work_dir/e", | |
| "size": 0 | |
| } | |
| ], | |
| "location": "work_dir" | |
| }, | |
| "test_result": { | |
| "basename": "output.txt", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "output.txt", | |
| "size": 0 | |
| } | |
| } | |
| got: { | |
| "output_dir": { | |
| "basename": "work_dir", | |
| "class": "Directory", | |
| "listing": [ | |
| { | |
| "basename": "a", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/a", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/a", | |
| "size": 0 | |
| }, | |
| { | |
| "basename": "b", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/b", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/b", | |
| "size": 0 | |
| }, | |
| { | |
| "basename": "c", | |
| "class": "Directory", | |
| "listing": [ | |
| { | |
| "basename": "d", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/c/d", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/c/d", | |
| "size": 0 | |
| } | |
| ], | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/c", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/c" | |
| }, | |
| { | |
| "basename": "e", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/e", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir/e", | |
| "size": 0 | |
| } | |
| ], | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/work_dir" | |
| }, | |
| "test_result": { | |
| "basename": "output.txt", | |
| "checksum": "sha1$a507d94dea7e758fbe8a143e608c3b048e37c9d2", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", | |
| "size": 50 | |
| } | |
| } | |
| caused by: failed comparison for key 'test_result': expected: { | |
| "basename": "output.txt", | |
| "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", | |
| "class": "File", | |
| "location": "output.txt", | |
| "size": 0 | |
| } | |
| got: { | |
| "basename": "output.txt", | |
| "checksum": "sha1$a507d94dea7e758fbe8a143e608c3b048e37c9d2", | |
| "class": "File", | |
| "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", | |
| "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", | |
| "size": 50 | |
| } | |
| caused by: field 'checksum' failed comparison: expected: "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709" | |
| got: "sha1$a507d94dea7e758fbe8a143e608c3b048e37c9d2" | |
| 0 tests passed, 1 failures, 0 unsupported features | |
| 1 tool tests failed |
lets say I want to examine the output.txt file:
"test_result": { "basename": "output.txt", "checksum": "sha1$a507d94dea7e758fbe8a143e608c3b048e37c9d2", "class": "File", "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt", "size": 50 }
First of all v1.02_w88T doesn't exists, but v1.02_w88TsyMZ0b does. But the output files are nowhere to be found, only the files prepared by InitialWorkDirRequirement are inside. Que?
Hey Gijs,
Can you run the test manually with
--debug?If you want to examine the intermediate files, check out
--leave-tmpdirand--leave-outputsSo why are there still temp folder is i didn't explicitly supply a
--leave-something?Interesting, when you run the conformance test directly you don't get the
2_w88Tin the paths like before. Looks like there is some OS X specific behaviour to cwltest: https://github.com/common-workflow-language/cwltest/blob/master/cwltest/__init__.py#L167To confirm, are you saying that
/Users/gijs/Work/common-workflow-language/v1.0/output.txtdoesn't get created when you run the test manually?The following might also produces the output you seek: