https://dockstore.org/api/api/ga4gh/v2/tools/%2523workflow%252Fgithub.com%252Fcancerit%252Fworkflow-seq-import%252Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/PLAIN_CWL/descriptor/if_file_name_is_bz2_then_return_null_else_return_in_json_to_output.cwl
is listed but the CWL (output) seems to refer to a toolkit directory
is listed but the CWL (output) seems to refer to a toolkit directory
Skipping dockstore.org, everything seems to validate okay: https://view.commonwl.org/workflows/github.com/cancerit/workflow-seq-import/blob/0.4.0/cwls/chksum_seqval_wf_interleaved_fq.cwl
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.
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
When it's fixed, will this registry be fixed automatically?
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
We are working towards to have all the endpoints
We have done some changes to the API and probably a PR will come next week
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?
lot of work going on now in our UI
@denis-yuen can I attend to the Monday meeting, is that remotly I guess
?
https://github.com/ga4gh/wiki/wiki#weekly-work-stream-meeting has the schedule
so 7am pacific is 3pm gmt?
@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
If you could let me know when can be fixed as early as possible, that'll help me a lot. Thanks.
@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
@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"
One easy fix as an example is probably the header "application/problem+json"
I will check and work in the report
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
@ypriverol The validator is expecting this basePath https://github.com/ga4gh/tool-registry-service-schemas/blob/develop/src/main/resources/swagger/ga4gh-tool-discovery.yaml#L21
thanks a lot
it makes more sense for exampel to force another name such as “trs” or not forcing the path?