@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
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.
@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
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.
I think that could be doable by a small change to the templates
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
Should the steps, inputs & output be included? Or should they be replaced with a link to the "full" view?
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.
also be cool on the CWL Viewer?
@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
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.
(shields is thought to have timeout issues; badgen is said to be faster in rendering)
@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
also the old
sbg: 'https://sevenbridges.com'
raised as DataBiosphere/topmed-workflows#97 although there is some other bug as https://view.commonwl.org/workflows/github.com/stain/topmed-workflows/blob/namespaces/aligner/sbg-alignment-cwl/topmed-alignment.cwl# turns out empty - seems to be because id confuses the CWL Viewer :(
https://view.commonwl.org/workflows/github.com/stain/topmed-workflows/blob/no-id/aligner/sbg-alignment-cwl/topmed-alignment.cwl works when I deleted id as well
mr-c @mr-c waves hello
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.
Everytime I have used it in the last few days I get "Error: An internal server error occurred"
