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  • Aug 03 08:43

    mr-c on maven

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  • Jul 16 16:10
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  • Jul 10 16:10
    stain commented #254
Michael R. Crusoe
@mr-c
@only1chunts Thanks for linking to the CWL Viewer! The .cwl is missing from the link, here's the correct one: https://view.commonwl.org/workflows/github.com/vetscience/Assemblosis/blob/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly.cwl
@only1chunts You could put that URL in an iframe? Oh, and you should use the permalink version instead of the view.commonwl.org version: https://w3id.org/cwl/view/git/66660a64824e4c1019680c6c7ea489ea359cd5f6/Run/assembly.cwl
Stian Soiland-Reyes
@stain
Hi, @only1chunts - you can use the SVG directly, I am not sure what interactivity you want, the same zoom-buttons, selection etc. as on the CWL Viewer page?
but if the workflow is not in a git repository it's a bit more tricky because of versioning and relative links. In theory it will work straight on the web (we used to do that) but now we always checkout from git in a way to force people to do the "right thing"
@only1chunts - are you perhaps considering storing the CWL definitions also within GigaDB? We would need them to be directly on the web (no landing pages) and either all-in-one-file (which is not common in CWL community as people like to split out their tools) or with neighbouring CWL files available from the same base URI. If GitHub/GitLab is tricky for you to require, perhaps some in-between solution would be a downloadable .git zip archive which would be easier for us to integrate? Harder for users to upload to you though.
Stian Soiland-Reyes
@stain

@mr-c

stain@heater:~$ crontab -e
*/6 * * * * /home/stain/cwlviewer-dev/update.sh

It's the update of the dev instance from master that is responsible for most of those 100.000 pulls.. I've reduced it down to once an hour.

Michael R. Crusoe
@mr-c
@stain Ah-ha! Good to know :-)
Chris Hunter
@only1chunts
@mr-c thanks for the pointer about using the permalink, i thought i had! but obvious just cut and paste the wrong link. I'll change that now, it will also reduce the length which is why the .cwl was missing, (our database table truncated it). The iFrame is exactly what we want to do, but would like it to point to a place that has been specifically designed to view in a smaller frame (i.e. cut down to remove surround stuff like the the full list of tables below the interactive viewer is not required for a simple iframe view, If I can workout how to append an image I'll show you the view that we would like to see from within a GigaDB dataset , but if you dont feel the need for it then we could iframe the entire page within GigaDB.
I cant see how to add an image so I'll email it to you @mr-c
Chris Hunter
@only1chunts
Hi @stain , sorry I perhaps have not explained my use case very well. We are not (at this point) concerned with how an author /user gets their workflow in CWL viewer, just how we can present it IF they have done so. A static SVG image is an option, but its not great to look at when its a complex workflow where the boxes are tiny, the zoom functions in the viewer are very useful then. Plus, I'm assuming at some point in the future the viewer will have more interactivity added for links to tools and intersecting workflows etc, which would then be lost in the SVG version. Thanks.
Stian Soiland-Reyes
@stain
ah, so you would prefer some kind of 'embed' view that avoids the footer/header really?
I think that could be doable by a small change to the templates
Stian Soiland-Reyes
@stain
https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/templates/workflow.html is the normal workflow page template, note that it has the SVG viewer twice as there is also the modal pop-up. Perhaps adding ?embed=trueto the permalinks would be an option? It already works with ?format=html although that gives the big page now https://w3id.org/cwl/view/git/f55f0011de7db66f873ffb0f700f3fe26b33911e/genomel/cwl/workflows/harmonization/harmonization_bwa_mem.cwl?format=html
Michael R. Crusoe
@mr-c
I think the embed should still have the footer (or a version of it)
Should the steps, inputs & output be included? Or should they be replaced with a link to the "full" view?
Chris Hunter
@only1chunts
Thanks for thinking I might be a developer, but sadly you've just gone way past my knowledge on html (or programming of any sort). If developing a widget viewer is not something anyone else needs/wants and its not on your todo list then thats fine, we'll just have to stick with the URL link for now.
Michael R. Crusoe
@mr-c
@only1chunts You can load the URL into an iframe the same way the other widget works today. Later we'll add an ?embed=true mode that is better formatted
Chris Hunter
@only1chunts
perfect, thanks
Stian Soiland-Reyes
@stain
Would something like cwl|valid also be cool on the CWL Viewer?
Is it too late to make GSOC2019 suggestions for CWL, @mr-c ?
Michael R. Crusoe
@mr-c
@stain nope, but needs to get up asap to attract student talent
Michael R. Crusoe
@mr-c
@stain Also, that badge looks great!
@stain time to reboot?
Error: cwltool version failed to run on this workflow:
! Cwltool ran successfully, but an unexpected error occurred in CWLViewer!
Help us by reporting it on Gitter or a Github issue
Stian Soiland-Reyes
@stain

hmm.. I get the same error as with cwltool --validate really.
Viewer:

Tool definition failed validation:
../data/git/aa420273539ad7bcf384c37614f6f636810042f2/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl:170:16: Workflow step output 'vcf_tbi' does not correspond to
../data/git/aa420273539ad7bcf384c37614f6f636810042f2/Tools/gatk3-HaplotypeCaller-XCORE1-ploidy1.cwl:51:1:   tool output (expected 'vcf', 'log')

Command line:

(base) stain@biggie:~$ cwltool --validate https://raw.githubusercontent.com/ddbj/human-reseq/master/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl
/home/stain/miniconda3/bin/cwltool 1.0.20190228200117
Tool definition failed validation:
https://raw.githubusercontent.com/ddbj/human-reseq/master/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl:170:16: Workflow step output 'vcf_tbi' does not correspond to
https://raw.githubusercontent.com/ddbj/human-reseq/master/Tools/gatk3-HaplotypeCaller-XCORE1-ploidy1.cwl:51:1:   tool output (expected 'vcf', 'log')
btw, that badge is just https://img.shields.io/badge/cwl-valid-B5314C.svg?logo=common-workflow-language but the viewer would need to have an in-between resource that checks it live.
Michael R. Crusoe
@mr-c
@stain both shields.io and badget.net support json endpoints
(shields is thought to have timeout issues; badgen is said to be faster in rendering)
Stian Soiland-Reyes
@stain
I suggested that as well on https://github.com/OBF/GSoC/pull/44/files (feel free to modulate)
Michael R. Crusoe
@mr-c
@stain I think this was the commit making the problem I reported earlier? But now it works! https://github.com/ddbj/human-reseq/blob/9064c301d858a796f8340d1e762e5916fd199da0/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl
Stian Soiland-Reyes
@stain
cwltool --validate https://raw.githubusercontent.com/ddbj/human-reseq/9064c301d858a796f8340d1e762e5916fd199da0/Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl gives similar validation error, but this time about secondaryFiles - so in a way it should not have worked! ;)
Michael R. Crusoe
@mr-c
A CWL v1.0.x to CWL v1.1 standalone converter common-workflow-language/cwl-upgrader#26
Stian Soiland-Reyes
@stain

might it be because of this?

URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
@prefix ns2: <foaf:> .

also the old sbg: 'https://sevenbridges.com'
mr-c @mr-c waves hello
Michael R. Crusoe
@mr-c
University of Manchester is having site-wide network issues today, which may mean the CWL Viewer seems unstable. The server is still up, but it's connectivity may come and go for the next hours. There might be intermittent errors if the server tries to check out from git during network outage.
Michael R. Crusoe
@mr-c
Uh oh, every time I use the viewer, the workflow comes out having 0 steps, 0 inputs, and 0 outputs
SWZ
@swzCuroverse
Hi there - cwlviewer seems to down.
Everytime I have used it in the last few days I get "Error: An internal server error occurred"
Peter Amstutz
@tetron
@stain
SWZ
@swzCuroverse
Also, not sure it if it is possible but maybe we can put some of our upcoming CZI money into helping host it if @stain would like that?
Peter Amstutz
@tetron
+1
SWZ
@swzCuroverse
Don't want to step on any toes or anything...obviously
Michael R. Crusoe
@mr-c
I don't think Stian would mind if someone took over the hosting.
SWZ
@swzCuroverse
:)
SWZ
@swzCuroverse
OK, let's see if we can help then and put it into the plan