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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
Kaushik Ghose
@kaushik-work
Thanks so much @denis-yuen !
Denis Yuen
@denis-yuen
no problem
Michael R. Crusoe
@mr-c
It should be handling the subworflows and tools, yes.
Kaushik Ghose
@kaushik-work
Thanks @mr-c . Also, I'm unclear as to what string I should be passing to cwltool for the main workflow path
(and how to get that from the information I can get from https://dockstore.org/api/api/ga4gh/v1/tools)
Denis Yuen
@denis-yuen
The commands in the PR seem to still work, for example cwltool --make-template \#workflow/github.com/dockstore-testing/md5sum-checker:develop and then cwltool \#workflow/github.com/dockstore-testing/md5sum-checker:develop test.json after setting up test data
curl https://dockstore.org/api/api/ga4gh/v1/tools | python3 -m json.tool | grep \"id\" gets you some examples of IDs (its a mix of WDL and CWL this way)