Search the registry does not seem to work

[abotzki]

Hi, I recently showed the biocontainers registry to participants in our container and workflow courses. Unfortunately, the search does not seem to work properly.

Do you have any suggestion how to get the information about the location of singularity images? Thanks!

[osallou]

Hi, Thanks for report.

Do you have an example of a failing container?

For info, singularity can run docker containers.

[neoformit]

I can confirm this on Ubuntu 20.04 LTS / Google Chrome. I've tried searching "fastqc" on https://biocontainers.pro/registry and I get a blank loading screen (~60 sec), followed by a console error, server error alert and "No matched data". I then reload the page and it sometimes works (50/50). I have reported an issue for this before so it's not the first time this has come up! Seems like an API error.

Loading... (60 sec):

Result UI:

Console errors:

[osallou]

strange, web ui has been rewritten to remove search on page load, so should get immediate first web page.

A 60s waiting shoumd not occur (and works for me).

Could you try to clear your browser cacje or force reload of the page?

[neoformit]

I just did a hard-refresh and got the same error again. Might be worth seeing if there's a clue in the backend logs? Or maybe the issue is in the CORS error:

Access to XMLHttpRequest at 'https://api.biocontainers.pro/ga4gh/trs/v2/tools?all_fields_search=fastqc&sort_order=asc&sort_field=default&offset=0&limit=30' from origin 'https://biocontainers.pro' has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource.

Happy to help you replicate the issue as we'd like to recommend this resource to our clients.

[osallou]

@chakrabandla @ypriverol can you have a look?

Cors errors do not occur randomly, strange message here.

and it works fine for me, direct access to landing page and fastq search with quick answer

[neoformit]

Still having trouble with this site - and it seems that when I access a container page it's also blank. There should be images available for deseq2, right?

The CORS error is also still present on registry search:

Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at https://api.biocontainers.pro/ga4gh/trs/v2/tools?all_fields_search=fastqc&sort_order=asc&sort_field=default&offset=0&limit=30. (Reason: CORS header ‘Access-Control-Allow-Origin’ missing). Status code: 503.

Same issue on Chrome or Firefox (Ubuntu 20.04) and Chrome (Windows) so doesn't seem like an isolated issue. But still seems to randomly succeed sometimes.

[osallou]

@ypriverol kube cluster is still really really slow to answer.... and api related pods too frequently fail to answer, needing pod restarts

I think requests/db are not optimized related to size of db , mongo often fail to answer

[ypriverol]

We are looking into the issues now.

[osallou]

furthermore, api pods seem to connect to mongo at startup only. on mongo failure, even if restart, pod do not reconnect to mongo, api pods need restart too

tried to restart mongo and api pods, pods seem to fail to connect to mongo, some pods answer, some not (placement issue?)

[osallou]

seems there are inter node (kube) communications issues, some pods are not reachable don't know why though responding if directly on node

[osallou]

I stopped extra masters , failing to communicate (direct calls on node are ok but not reachable from other network points). Now system is "ok" but need anyway to restart masters and find network issue

[osallou]

I restarted masters preventing pod scheduling on those, issue is gone for the moment (though pod timeout/access to mongo should still be fixed for better handling)

[lescai]

this is a recurring issue, I'm surprised it's not being reported more frequently. I've been stumbling upon this problem from time to time, but regularly over the past year. right now, not working again.

[neoformit]

Also not working for me right now.

[groverj3]

Adding my voice to the choir. I can search through quay.io, but that's not ideal.

[ypriverol]

Hi all, thanks for reporting, this. Quay.io and dockerhub have recently changed their API which makes difficult the indexing process, we are working to recover the API backend. I will keep you all posted.

[mari-ga]

Same here, I could find the docker containers through quay.io, but I can't find any singularity container