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Fix endpoint for TRS #15
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Hello @kinow -san, I apologize for the delayed response. This error appears to occur because As stated at https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh/tool-registry-schemas/develop/openapi/openapi.yaml, "Descriptors can often include imports that refer to additional descriptors. This returns additional descriptors for the specified tool in the same or other directories that can be reached as a relative path. This endpoint can be useful for workflow engine implementations like cwltool to programmatically download all the descriptors for a tool and run it. This can optionally include other files described with FileWrappers such as test parameters and containerfiles.", the original TRS definition indeed expects that behavior. However, in yevis, due to the specification that returns TRS responses via GitHub pages, we are unable to implement this behavior. Instead, we're including the download link in the Given yevis's constraints of not wanting to have a REST API server (or any server resource), this is quite a predicament. Any suggestions on how we could navigate this issue would be much appreciated. (@inutano) |
Thanks for the reply @suecharo , no worries about delay 🙆♂️
Hmm, can't think of any suggestion on how to workaround this issue. Maybe we can just document this for users of the endpoint? Thanks! |
Hi @jmfernandez ! 👋 The WfExS file I used was this one from the top comment:
Not sure if the syntax changed. The last time I tried it it was months ago. I think it'd be useful if you can find a way to circumvent or give some feedback to users about the response not matching the expected standard. |
DDBJ workflow registry TRS endpoint returns URLs instead of TRS files. This commit tries circumventing the arosen issues in WfExS code.
I have just pushed a fix to the main branch of WfExS-backend. Hope this helps! |
Thank you @kinow @suecharo and @jmfernandez !! I understand this is the limitation of our strategy to implement a registry with gh pages, a fully static website. I'm closing this, but as @kinow suggested, at least we need to mention this in our documentation. Thanks for your testing and additional contribution @kinow @jmfernandez 🙏 🙏 |
I am experimenting running WfExS (cc @jmfernandez) with Yevis/DDBJ. Here's what I did so far:
nf-core - rnaseq
.python WfExS-backend.py execute -W tests/yevis-test.yaml
It had failed with an error about
toolclass
vs.tool_class
, already fixed by @suecharo (thanks!).But now it is failing with another error:
Thanks! 👍
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