From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=systemreboot.net; s=default; t=1742322115; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references; bh=zXWBw+W6Z7UGkPvKaff8NPNVVb+V3x9gxEYaIxJDbYo=; b=OEozYzLKroVvVz3mbqnKiSZeXjSpYEPCGFlDS8jC+EYJoC0xPhhjcOHgVbTeO6ChkxD3Pq YRnNoe2gH3APesIeyI3dbfNhMjRxnm6k94YORiFE/Qcs6ukKwGY6g4eOIbsSnwSgtZKnBY jT7x8FFODWMgtUGNb1hJBaON9vL/JjKIlGLYMSvkXaIVUlQkjwNWH3rWlc874OeXilJE5j ectWc7caUsaqzHa8B2rIoSw/p+owwedrstpc4jthaHcJaJylB8O69ywpUHWxdHYNDSoZGq BzH5U+t3y30F8SCrTFDwsyzcpqf2jwzcNflJPNCpA95HIbw3st/Ptk2QX5eGXw== Received: from localhost ( [192.168.2.1]) by mugam.systemreboot.net (OpenSMTPD) with ESMTPSA id d3653078 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Tue, 18 Mar 2025 18:21:54 +0000 (UTC) From: Arun Isaac To: Nicolas Graves , ravanan@systemreboot.net Subject: Re: Some ravanan feedback In-Reply-To: <874izxug6f.fsf@ngraves.fr> References: <871pv4kz0h.fsf@ngraves.fr> <87cyenph7i.fsf@systemreboot.net> <874izxug6f.fsf@ngraves.fr> Date: Tue, 18 Mar 2025 18:21:48 +0000 Message-ID: <87bjtyjj2b.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable List-Id: Hi Nicolas, > https://github.com/nfdi4plants/cwl-examples > > and the following changes :=20 > > modified run-python-script/test.cwl I have fixed the issue with running this workflow. It was a bug in canonicalizing File type inputs. https://git.systemreboot.net/ravanan/commit/?id=3D9be0612b4b486f7d96ddd71c1= 56be9284eff30b2 I have also added tests to catch this. https://git.systemreboot.net/ravanan/commit/?id=3Daf43d1fa1bafd8f9e641da16e= ca45e0795af7935 > @@ -3,8 +3,9 @@ > cwlVersion: v1.2 > class: CommandLineTool > hints: > - DockerRequirement: > - dockerPull: python:latest > + SoftwareRequirement: > + packages: > + python > baseCommand: python The baseCommand needs to be changed to python3. If not, you can also use the python-wrapper package. With these changes, I run ravanan like so: ravanan --store=3Dstore /tmp/cwl-examples/run-python-script/test.cwl /tmp/cwl-examples/run-python-script/testRun.yml and I get the following. It works. --8<---------------cut here---------------start------------->8--- WARNING: (guix ui): imported module (guix diagnostics) overrides core bindi= ng `info' WARNING: (ravanan command-line-tool): imported module (rnrs conditions) ove= rrides core binding `&error' /tmp/cwl-examples/run-python-script/test.py previously interned into store = as /home/arun/Projects/ravanan/store/files/fc29e96825193827a8ab943f9201b8a9= 35be4780-test.py building path(s) `/gnu/store/9mqspgkknz3q55x7b12pg830anml975h-ca-certificat= e-bundle' building path(s) `/gnu/store/8agn2i7ykqhbx4jkkiwnfxaknlkx4bsg-emacs-subdirs' building path(s) `/gnu/store/h4k77l6xhrbwqwgin0bc5ljj5bxy19nz-fonts-dir' building path(s) `/gnu/store/cvz9046gm0i2nqpr5nphsr7jg4hbw3ai-info-dir' building path(s) `/gnu/store/xckk1ns8xy49m6m09cn4fx4k4hncrwwf-profile' building path(s) `/gnu/store/4vrfghzrjd4kkkzr32yrjmq0jkvf2pfj-test' Running /gnu/store/4vrfghzrjd4kkkzr32yrjmq0jkvf2pfj-test /gnu/store/4vrfghzrjd4kkkzr32yrjmq0jkvf2pfj-test completed; logs at /home/a= run/Projects/ravanan/store/logs/4vrfghzrjd4kkkzr32yrjmq0jkvf2pfj-test.stdou= t and /home/arun/Projects/ravanan/store/logs/4vrfghzrjd4kkkzr32yrjmq0jkvf2p= fj-test.stderr { "example_out": { "class": "File", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", "size": 110, "checksum": "sha1$7c41bfd87ed9d66d64c44f433f7a7c40bec5d52f", "location": "file:///home/arun/Projects/ravanan/store/files/4vrfghzrjd4= kkkzr32yrjmq0jkvf2pfj-test/output.txt", "path": "/home/arun/Projects/ravanan/store/files/4vrfghzrjd4kkkzr32yrjm= q0jkvf2pfj-test/output.txt" } } --8<---------------cut here---------------end--------------->8--- > I happen to have such a backtrace : > > Backtrace: > In ice-9/eval.scm: > 619:8 19 (_ #(#(#(#(#(#(#(#(#(#(#(=E2=80=A6) =E2=80=A6) =E2=80=A6) = =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6= ) =E2=80=A6)) > 293:34 18 (_ #(#(#(#(#(#(#(#(#(#(#(=E2=80=A6) =E2=80=A6) =E2=80=A6) = =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6) =E2=80=A6= ) =E2=80=A6)) > In ice-9/boot-9.scm: > 724:2 17 (call-with-prompt ("prompt") # =E2=80=A6) > 1752:10 16 (with-exception-handler _ _ #:unwind? _ # _) > 152:2 15 (with-fluid* _ _ _) > In ice-9/exceptions.scm: > 406:15 14 (run-workflow _ _ _ _ _ _ _ _ #:guix-daemon-socket _) > In ice-9/boot-9.scm: > 1752:10 13 (with-exception-handler _ _ #:unwind? _ # _) > In ravanan/workflow.scm: > 592:26 12 (_) > 293:29 11 (schedule _ _ _) > In ravanan/command-line-tool.scm: > 361:10 10 (run-command-line-tool "test" #f #f (("baseCom=E2=80=A6" . #= ) =E2=80=A6) =E2=80=A6) > 828:13 9 (build-command-line-tool-script "test" _ #f _ ((# =E2=80=A6)= =E2=80=A6) =E2=80=A6) > 831:21 8 (_ _) > In ravanan/work/vectors.scm: > 62:3 7 (vector-map->list _ _ . _) > In srfi/srfi-43.scm: > 376:5 6 (vector-fold # =E2=80=A6) > In ice-9/boot-9.scm: > 1685:16 5 (raise-exception _ #:continuable? _) > 1683:16 4 (raise-exception _ #:continuable? _) > In ice-9/eval.scm: > 293:34 3 (_ #(#(# ("p=E2=80=A6")= ) #)) > 182:19 2 (proc #(#(# (#)) #)) > 142:16 1 (compile-top-call # =E2= =80=A6) > In unknown file: > 0 (%resolve-variable (7 . manifest-file-error?) > #) Sorry the backtraces are terrible. I haven't yet invested much effort in fixing them. These are early days for ravanan, I'm afraid. > I don't know if there's a database to test against, here they have the > notion of "self-reported compliance" but it seems unclear / case-by-case > to see where those compliance tests are implemented and if you can use > them as a base to test against. The CWL conformance test suite is at https://github.com/common-workflow-language/cwl-v1.2/tree/main/tests Information on how to run them is at https://github.com/common-workflow-language/cwl-v1.2/blob/main/CONFORMANCE_= TESTS.md I have run the test suite on my local machine. I need to wire this up into the CI. I plan to do that in the coming weeks. Regards, Arun