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Yasset Perez-Riverol
@ypriverol
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:
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.