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Michael R. Crusoe
@mr-c
Probably :-)
Yaobo Xu
@byb121
sure, I'll have a go again on the latest version.
Looks like an issue with dockstore.org itself
Denis Yuen
@denis-yuen
Yaobo Xu
@byb121
latest version of cwl-runner returns the same error.
Michael R. Crusoe
@mr-c
l$ cwltool --validate https://github.com/cancerit/workflow-seq-import/raw/0.4.0/cwls/chksum_seqval_wf_interleaved_fq.cwl
/home/michael/cwltool/env3/bin/cwltool 1.0.20181217162649
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?
https://github.com/cancerit/workflow-seq-import/raw/0.4.0/cwls/chksum_seqval_wf_interleaved_fq.cwl is valid CWL.
Yaobo Xu
@byb121
if_file_name_is_bz2_then_return_null_else_return_in_json_to_output.cwl is indeed in a directory called toolkit
Denis Yuen
@denis-yuen
Yeah, I think it looks like an indexing error. For some reason, it looks like toolkit/if_input_is_bz2_convert_to_gz_else_just_rename.cwl and toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl are being indexed in the toolkit directory. if_file_name_is_bz2_then_return_null_else_return_in_json_to_output.cwl is being indexed in the pwd, possibly because its an import in an import. What I can't explain is why it launches properly using the very first command but I think its still a bug one way or another. I'll create an issue for it
Yaobo Xu
@byb121
Thanks.
When it's fixed, will this registry be fixed automatically?
Denis Yuen
@denis-yuen
Created ga4gh/dockstore#2154 , so chances are if its an indexing error. We'll need to fix the refresh behaviour and then you'll need to hit the refresh button when we do a release
I'm having difficulty explaining why the first launch command works since it uses cwltool under the hood, so there may be something more complicated I'm missing. But that's my first explaination
Yaobo Xu
@byb121
That's why it's interesting :)
Yasset Perez-Riverol
@ypriverol
Hi everyone, Im happy to announce that Biocontainers has implemented already the TRS implementation for tool and tool versions
We are working towards to have all the endpoints
Peter Amstutz
@tetron
@ypriverol oh cool
Yasset Perez-Riverol
@ypriverol
Thanks @denis-yuen for your support
We have done some changes to the API and probably a PR will come next week
Denis Yuen
@denis-yuen
Ah, cool. Just in time for the Monday GA4GH TRS update!
Michael R. Crusoe
@mr-c
@ypriverol Yay!
Yasset Perez-Riverol
@ypriverol
for example, Apart of docker containers must of our consumers use singularity or "Conda containers"
we have extend the classification to container image to provide more details about the tipe of container
like conda package, or singularity or Docker
this will allow us to connect to workflows that use conda for example
make sense?
Peter Amstutz
@tetron
does that mean there are/will be CWL tool wrappers for biocontainers?
Yasset Perez-Riverol
@ypriverol
I hope
Denis Yuen
@denis-yuen
@ypriverol I think that makes sense, we'll see/discuss more in the PR I think
Yasset Perez-Riverol
@ypriverol
Another important issue is the license, we have move the license into the tool object because our users want to know from the very top which type of license is associated with the tool
lot of work going on now in our UI
@denis-yuen can I attend to the Monday meeting, is that remotly I guess
?
Denis Yuen
@denis-yuen
The license should be fine as long as its optional
so 7am pacific is 3pm gmt?
Yasset Perez-Riverol
@ypriverol
thanks
Denis Yuen
@denis-yuen
@mr-c @byb121 FYI, I can verify that yes, the workflow runs for me too which is cool (yay!) but also puzzling. I can also confirm that dockstore workflow download --entry github.com/cancerit/workflow-seq-import/chksum_seqval_wf_interleaved_fq:0.4.0 works to download the correct directory structure which is probably related to why it works that way (and might be a workaround depending on what you're working on). Right now I'm thinking that its not the indexing, but an issue with how we translate the paths for display/TRS, so it may be the case that after we fix it, it might just work. Will update in the ticket when we have more
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: