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Yaobo Xu
@byb121
Great!
If you could let me know when can be fixed as early as possible, that'll help me a lot. Thanks.
Denis Yuen
@denis-yuen
@byb121 so currently, most staff is working on the next major release which should be roughly end of March, I think I can guarantee that we can work on this as a high priority fix during that process. Do you have a workaround in the meantime? Otherwise, we do have some capacity to work on a hotfix, but I can't guarantee that at this time
Denis Yuen
@denis-yuen
@ypriverol so one quick thing I did, we have some docs on a TRS validator that might be helpful at https://ga4gh.github.io/tool-registry-service-schemas/Validator/ . For example, the validation report for the api you're working on is http://142.1.177.188:8080/trs/validator/debug?url=http://api.biocontainers.pro/api/v2/
One easy fix as an example is probably the header "application/problem+json"
Yasset Perez-Riverol
@ypriverol
cool, didn’t knwo you have a validator
I will check and work in the report
Denis Yuen
@denis-yuen
The source code is at https://github.com/ga4gh/tool-registry-validator/tree/develop . It could probably do with some improvements since we haven't been able to work on it as much as we'd like but hopefully its useful (and feel free to contribute if its validating incorrectly). @garyluu will have more insight than me for that report
Yaobo Xu
@byb121
@denis-yuen it's fine. I think I have a workaround, just need some tests.
Denis Yuen
@denis-yuen
:+1:
Yasset Perez-Riverol
@ypriverol
Thanks I just got the validator in my hands we are now validating everything
thanks a lot
Yasset Perez-Riverol
@ypriverol
Hi everyone @garyluu and @denis-yuen why the url path is forcing to have ga4gh?
it makes more sense for exampel to force another name such as “trs” or not forcing the path?
Gary Luu
@garyluu
It's just following the schema in the TRS repo. Feel free to make a PR to the TRS repo and everyone can review the change.
Gary Luu
@garyluu
If you're running my validator locally, you can remove/modify the basePath in the processed-ga4gh-tool-discovery.yaml while you're inside the docker container and that should bypass it
Yasset Perez-Riverol
@ypriverol
I was running the online version
i will try locally
Gary Luu
@garyluu

I modified my validator temporarily, 3 are passing:

pass: GET (200) /api/v2/metadata duration: 348ms
pass: GET (200) /api/v2/toolClasses duration: 308ms
pass: GET (200) /api/v2/tools?limit=30 duration: 1736ms

the rest are skipped because my validator doesn't proceed further until it can retrieve a tool id, version id, and descriptor type. I'll make an issue for it. It should probably go as far as it can even without the descriptor type

Yasset Perez-Riverol
@ypriverol
nice
I’m attending to the metting on Monday, probably we can discuss some details !!! Thanks a lot
Gary Luu
@garyluu
No problem
kuzotelohe
@kuzotelohe
Hello, is this the right chatroom where I can ask about ga4gh projects on GSoC 2019?
Denis Yuen
@denis-yuen
probably not, but we might be able to point you to the right place. Is there a project you're interested in?
kuzotelohe
@kuzotelohe
Thank you. Yes, I am interested in one of the projects i.e, data-repository-service on GSoC and looking for some guidance. I will be very much thankful if you could help me.
Denis Yuen
@denis-yuen
Do you happen to have a link or a snippet of the description?
nvm, found it. It looks like that particular task is handled by EBI
kuzotelohe
@kuzotelohe
@denis-yuen Thank you so much . Do you have any idea whether they got separate chatroom for the said project?
Michael R. Crusoe
@mr-c
@kuzotelohe not that I know of
Denis Yuen
@denis-yuen
@kuzotelohe ditto
Yaobo Xu
@byb121
Will Dockstore work ok with OpenJDK? Oracle changed their JAVA license significantly, which makes auto installation almost impossible.
Gary Luu
@garyluu
I've been using OpenJDK with Dockstore all along. Seems to work fine.
Yaobo Xu
@byb121
@garyluu Thanks, we just have a quick go. It worked fine as well.
Kaushik Ghose
@kaushik-work
Folks, I'm looking at the API call list (https://dockstore.org/api/static/swagger-ui/index.html#/) and I can't figure out how to retrieve the workflowId. I thought this was the id field retrieved when doing a https://dockstore.org/api/api/ga4gh/v1/tools/ query, but this doesn't seem to work. Thanks!
Denis Yuen
@denis-yuen
Hi, it can be a bit confusing. Basically, we have a proprietary API (including things like authentication, write operations, etc.) and a standardized GA4GH API (anything that starts with /api/ga4gh/(v1/cv2) both being served from the same webservice.
For the former API, ids are just numeric, e.g. https://dockstore.org/api/workflows/published/6915
So for this particular workflow the ID is 6915 in our API, #workflow/github.com/nf-core/vipr in TRS
@kaushik-work browsing, I think we normally use {workflowId} for the former
Kaushik Ghose
@kaushik-work
Ah, thanks! My use case is - I want to retrieve CWL tools/workflows and validate them. I see that cwltool will accept TRS ids, but I also think that cwltool just validates the top level workflow. So best for me would be to download the ZIP and validate each component. How can I go from what I get back in the search results (https://dockstore.org/api/api/ga4gh/v1/tools) to getting the workflowId for each one of them so I can make the https://dockstore.org/api/workflows/{workflowId}/zip/{workflowVersionId} call? Thanks!
(The Dockstore UI does this, but I couldn't trace the code that ends up generating the url that goes into the Download ZIP button)
Denis Yuen
@denis-yuen
Hmmm, I think cwltool does validate imports, did the following experiment using git@github.com:dockstore-testing/dockstore-workflow-md5sum-unified.git
$ cwltool --validate checker_workflow_wrapping_workflow.cwl
INFO /usr/local/bin/cwltool 1.0.20190621234233
INFO Resolved 'checker_workflow_wrapping_workflow.cwl' to 'file:///home/dyuen/dockstore_tools/dockstore-workflow-md5sum-unified/checker_workflow_wrapping_workflow.cwl'
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
checker_workflow_wrapping_workflow.cwl is valid CWL.
$ vim md5sum/md5sum.cwl
(messed up the import)
$ cwltool --validate checker_workflow_wrapping_workflow.cwl
INFO /usr/local/bin/cwltool 1.0.20190621234233
INFO Resolved 'checker_workflow_wrapping_workflow.cwl' to 'file:///home/dyuen/dockstore_tools/dockstore-workflow-md5sum-unified/checker_workflow_wrapping_workflow.cwl'
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
md5sum/md5sum.cwl:14:3: object id `md5sum/md5sum.cwl#input_file` previously defined
ERROR Tool definition failed initialization:
Tool definition file:///home/dyuen/dockstore_tools/dockstore-workflow-md5sum-unified/md5sum/md5sum.cwl failed validation:
md5sum/md5sum.cwl:16:1:   checking field `outputs`
md5sum/md5sum.cwl:17:3:     checking object `md5sum/md5sum.cwl#output_file`
md5sum/md5sum.cwl:19:5:       Field `outputSource` references unknown identifier `md5sum/output_file`, tried file:///home/dyuen/dockstore_tools/dockstore-workflow-md5sum-unified/md5sum/md5sum.cwl#output_file/md5sum/output_file, file:///home/dyuen/dockstore_tools/dockstore-workflow-md5sum-unified/md5sum/md5sum.cwl#md5sum/output_file
Oh, do you mean it validates for local but not for URLs?
For the conversion between the two, we use https://dockstore.org/api/workflows/path/entry/github.com%2Fnf-core%2Fvipr/published so you can convert and plug a TRS id into the proprietary API
Kaushik Ghose
@kaushik-work
@denis-yuen I don't actually know if cwltool downloads all the sub-workflows/tools and validates each one if a TRS query is passed.
Denis Yuen
@denis-yuen
Hmm, I would be surprised if it didn't because it would need the sub-workflows to run it
@kaushik-work might be useful, was the last time I looked at the cwltool code common-workflow-language/cwltool#1093