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[bioontology-support] Error when submitting a new ontology

Michael Dorf mdorf at stanford.edu
Fri Sep 4 13:59:44 PDT 2020


Hi Georgeta,

I’ve finally tracked down the issue that’s causing the error you are seeing with your remote file location. The error is a bit misleading here, pointing to a missing file, when in reality the file is there. The real issue, which, unfortunately, isn’t surfaced to the user is this:

OpenSSL::SSL::SSLError: SSL_connect returned=1 errno=0 state=error: certificate verify failed (unable to get local issuer certificate)

The certificate appears to be valid when viewing the URL (https://gitub.u-bordeaux.fr/erias/fideo/-/raw/master/fideo_core.owl) in browser, but a more thorough check reveals an issue with the certificate chain:

https://www.ssllabs.com/ssltest/analyze.html?d=gitub.u-bordeaux.fr

This is what my sysadmin had to say about this:

they need to include TERENA SSL CA 3 in the chain... Modern browsers fetch those missing certs in the chain themselves but perhaps ruby doesn't?

If you run this in your Terminal:


openssl s_client -showcerts -connect gitub.u-bordeaux.fr:443<http://gitub.u-bordeaux.fr:443>

you will see this error:


verify error:num=21:unable to verify the first certificate

Another utility check on our end yielded this:

ERROR:  SSL verification error at depth 0: unable to get local issuer certificate (20)
ERROR:  You must add /C=NL/ST=Noord-Holland/L=Amsterdam/O=TERENA/CN=TERENA SSL CA 3 to your local trusted store


I’d run these errors by your sysadmin, so they can check and fix your server’s SSL cert. Once fixed, you should be able to submit your ontology.

Michael





On Sep 3, 2020, at 3:41 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Georgeta,

Thank you for contacting us. I was able to reproduce this issue in our own staging environment, but at this point I don’t have a solution for you. I need to do some further troubleshooting to figure out what causes this issue. The file is clearly present at the remote location, but the error is still being triggered.

I’ll keep you posted as soon as I get to the bottom of this issue. Thank you for your patience.

Michael



On Sep 3, 2020, at 3:33 AM, Georgeta Bordea <georgeta.bordea at u-bordeaux.fr<mailto:georgeta.bordea at u-bordeaux.fr>> wrote:

Hi,

We are trying to submit a new ontology on BioPortal with the main public file located here [1] but there's the following error message:

Errors On Form

  *   [:error, #<OpenStruct links=nil, context=nil, pullLocation=["File at https://gitub.u-bordeaux.fr/erias/fideo/-/raw/master/fideo_core.owl does not exist"]>]

Could you please let us know how to address this issue?

Regards,
Georgeta Bordea

[1] https://gitub.u-bordeaux.fr/erias/fideo/-/raw/master/fideo_core.owl
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