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  • May 20 02:07
    dependabot[bot] labeled #417
  • May 20 02:07
    dependabot[bot] opened #417
  • May 20 02:07

    dependabot[bot] on maven

    Bump junit-jupiter from 1.17.1 … (compare)

  • May 20 02:06
    dependabot[bot] labeled #416
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    dependabot[bot] on maven

    Bump postgresql from 1.17.1 to … (compare)

  • May 16 12:03

    mr-c on main

    Update spring boot, liquibase, … Use Java 17 LTS (compare)

  • May 16 12:03
    mr-c closed #413
  • May 16 11:18
    kinow commented #413
  • May 16 11:17
    kinow commented #413
  • May 16 11:10
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  • May 16 11:07

    mr-c on maven

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  • May 16 11:07

    mr-c on main

    Bump jackson-core from 2.13.2 t… (compare)

  • May 16 11:07
    mr-c closed #414
  • May 16 10:54
    kinow commented #415
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    mr-c auto_merge_enabled #414
  • May 16 10:53
    mr-c synchronize #414
  • May 16 10:53

    mr-c on maven

    Bump jackson-core from 2.13.2 t… (compare)

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  • May 16 10:53

    mr-c on main

    Bump spring-data-commons from 2… (compare)

Peter Amstutz
@tetron
@obasekiosa:matrix.org thank you, yes I am back from vacation, I had a great time
Peter Amstutz
@tetron:matrix.org
[m]
obasekiosa: are you joining the meet?
1 reply
Peter Amstutz
@tetron
@obasekiosa:matrix.org I hope everything is all right?
1 reply
obasekiosa
@obasekiosa:matrix.org
[m]
yes
Peter Amstutz
@tetron:matrix.org
[m]
obasekiosa: we have a little bit of a problem the free tier of docker hub only allows 3 members in an organization and we have 5
so I suggest pushing the docker image to your own docker account
and we pull from there
obasekiosa
@obasekiosa:matrix.org
[m]
oh alright
obasekiosa
@obasekiosa:matrix.org
[m]
Hello and good day.
I was able to complete the tasks last week.
but I can't set the secrets (login credentials for docker)
Peter Amstutz
@tetron
@obasekiosa:matrix.org ok, we have a meeting later today, we can talk about it then
Peter Amstutz
@tetron
@obasekiosa:matrix.org I will be joining shortly
just stuck on another meeting
Peter Amstutz
@tetron:matrix.org
[m]
obasekiosa: I am on the meet now
obasekiosa
@obasekiosa:matrix.org
[m]
oh ok
Peter Amstutz
@tetron
@obasekiosa:matrix.org how are you this evening, were you able to get the docker image build to work on your personal github account?
obasekiosa
@obasekiosa:matrix.org
[m]
good day @tetron I faced some issues I am currently debugging.
1 reply
Peter Amstutz
@tetron
do you want to tell me about it?
obasekiosa
@obasekiosa:matrix.org
[m]
yes.
It was logging into docker hub
the pipeline could not see the secret
@tetron:
Also previously to that GitHub could not see the pipeline file for some reason.
So I deleted it and created it directly from GitHub's interface.
Same issue so I just restarted my browser.
obasekiosa
@obasekiosa:matrix.org
[m]

I was able to fix the problem.

Currently trying to use the image locally

then will proceed to add descriptions during the build and the appropriate tag
obasekiosa
@obasekiosa:matrix.org
[m]
Also I did a bit of research and it seems the sh login and pull could be done from github (without actions) by setting up deploy keys.
@tetron:
Peter Amstutz
@tetron
great, sounds like progress and you are learning a lot
obasekiosa
@obasekiosa:matrix.org
[m]
yes I did.
I have two MR's on the repository
Peter Amstutz
@tetron:matrix.org
[m]
obasekiosa: I'm on the meet
Peter Amstutz
@tetron:matrix.org
[m]
obasekiosa: we now finally have https://cwlviewer-dev.arvados.org/ which is auto-deployed from github main
crusoe
@mr-c:matrix.org
[m]
Bruno P. Kinoshita: Can you DM me your email address?
crusoe
@mr-c:matrix.org
[m]
Attention users of the cwlviewer elsewhere than view.commonwl.org: please upgrade as soon as possible; we have just released a security notice: https://github.com/common-workflow-language/cwlviewer/security/advisories/GHSA-7g7j-f5g3-fqp7
Big thanks to Bruno P. Kinoshita for finding and fixing this!
Bruno P. Kinoshita
@kinow:matrix.org
[m]
Thanks crusoe ! And next time will use the GH security advisory & wait to prepare the PR 😬😳
1 reply

Happy to review it!

Are you writing one for cwlviewer, or one-works-for-all for the projects under common-workflow-language org? If the latter that can be added to a template-repo in the organization, so new projects just copy it (including things like license, contributing, security, etc, like a cookiecutter for GH?)

crusoe
@mr-c:matrix.org
[m]
The later, yep
Yep, it would go in https://github.com/common-workflow-language/.github
Also need to write up this huge changelog for cwlviewer since the 2018 release (!!) https://github.com/common-workflow-language/cwlviewer/compare/v1.3.0...v1.4
1 reply
Hmm.. https://github.com/common-workflow-language/cwltool/releases is more my style
Bruno P. Kinoshita
@kinow:matrix.org
[m]
Easier to understand, from a user/dev POV. Harder on you to write it though, so let me know if you need any help. Just doing simple tasks today at $work (dependabot, triaging issues, timesheets, e-mails, intranet, ...)
crusoe
@mr-c:matrix.org
[m]
It is after midnight, so first I will go to bed 😀
crusoe
@mr-c:matrix.org
[m]
Bruno P. Kinoshita your discovery continues to spread improvements https://github.com/broadinstitute/cromwell/pull/6510#issuecomment-932368194
crusoe
@mr-c:matrix.org
[m]
CWL Viewer v1.4 is released; full changelog is at https://github.com/common-workflow-language/cwlviewer/releases/tag/v1.4
Michael Crusoe
@mr-c:matrix.org
[m]

Nice, a CWL viewer permalink was cited recently. Unclear if they used CWL throughout, or meant to cite FASTQC the tool itself

Andrews S. FASTQC a quality control tool for high throughput sequence data. 2015 ; https://w3id.org/cwl/view/git/e0a30aa1ad516dd2ec0e9ce006428964b840daf4/workflows/fastqc.cwl.

Michael Crusoe
@mr-c:matrix.org
[m]

:point_up: Edit: Nice, a CWL viewer permalink was cited recently. Unclear if they used CWL throughout, or meant to cite FASTQC the tool itself

Andrews S. FASTQC a quality control tool for high throughput sequence data. 2015 ; https://w3id.org/cwl/view/git/e0a30aa1ad516dd2ec0e9ce006428964b840daf4/workflows/fastqc.cwl.

From https://doi.org/10.1093/nar/gkab1179

Bruno P. Kinoshita
@kinow:matrix.org
[m]
Cutting a new release of cwlviewer this week 👍️ It includes a fix for spring/thymeleaf templates, but that only affects main branch code (so only our dev instance, or anyone running the bleeding edge version).
Bruno P. Kinoshita
@kinow:matrix.org
[m]

v1.4.3 is out 🎉 https://github.com/common-workflow-language/cwlviewer/releases/tag/v1.4.3

Could someone with karma in docker hub please build & upload the v1.4.3 image? https://github.com/common-workflow-language/cwlviewer#making-a-release-and-publishing-to-github-dockerhub-and-quayio

I did the GitHub part, and also uploaded to Quay.io. Also noticed that for the previous version, v1.4.2, I uploaded the tag with a typo (vv1.4.2). I'm re-building the v1.4.2 tag locally and will replace that tag. The v1.4.2 tag in Docker Hub looks OK!

Cheers

Simon Gene Gottlieb
@simon:gottliebtfreitag.de
[m]
https://github.com/deNBI-cibi/tool_description_lib