[bioontology-support] Error when submitting a new ontology

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[bioontology-support] Error when submitting a new ontology

Georgeta Bordea
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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Re: [bioontology-support] Error when submitting a new ontology

Michael Dorf
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 <[hidden email]> 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
Could you please let us know how to address this issue?

Regards,
Georgeta Bordea

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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Re: [bioontology-support] Error when submitting a new ontology

Michael Dorf
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:


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

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 <[hidden email]> 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 <[hidden email]> 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
Could you please let us know how to address this issue?

Regards,
Georgeta Bordea

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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Re: [bioontology-support] Error when submitting a new ontology

Georgeta Bordea
In reply to this post by Georgeta Bordea
Dear BioPortal support team,

Thank you for helping us track down the previous issue related to submitting the FIDEO ontology [1]. Could you please let us know how to fix another issue, at the moment FIDEO classes are not properly retrieved and displayed.

The error message we get on BioPortal [2] is currently just:
"Problem retrieving classes"

Regards,
Georgeta Bordea

[1] https://gitub.u-bordeaux.fr/erias/fideo
[2] https://bioportal.bioontology.org/ontologies/FIDEO/?p=classes&conceptid=root



De: "Georgeta Bordea" <[hidden email]>
À: "support" <[hidden email]>
Envoyé: Jeudi 3 Septembre 2020 12:33:11
Objet: Error when submitting a new ontology

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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Re: [bioontology-support] Error when submitting a new ontology

John Graybeal-2
Georgeta,

It appears the document that was uploaded to BioPortal included an HTML document, not an ontology. I see that your link (https://gitub.u-bordeaux.fr/erias/fideo/-/raw/master/fideo_core.owl) appears to work in Protege, so I will have to check with my colleagues about why it might not be working in BioPortal. I'll try to do this today (before our Thanksgiving weekend), but I'm not sure if we'll be able to figure out it. (I suspect it may have to do with the networking again, but it could be tricky.)

Sorry for your trouble.

John




On Nov 25, 2020, at 9:05 AM, Georgeta Bordea <[hidden email]> wrote:

Dear BioPortal support team,

Thank you for helping us track down the previous issue related to submitting the FIDEO ontology [1]. Could you please let us know how to fix another issue, at the moment FIDEO classes are not properly retrieved and displayed.

The error message we get on BioPortal [2] is currently just:
"Problem retrieving classes"

Regards,
Georgeta Bordea




De: "Georgeta Bordea" <[hidden email]>
À: "support" <[hidden email]>
Envoyé: Jeudi 3 Septembre 2020 12:33:11
Objet: Error when submitting a new ontology

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

Regards,
Georgeta Bordea


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




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Re: [bioontology-support] Error when submitting a new ontology

Michael Dorf
Hi Georgeta,

Please accept my apologies for the late reply. I’ve checked FIDEO in BioPortal, and it appears to be displaying properly. Are you still seeing issues on your end?

Thank you,

Michael



On Nov 25, 2020, at 12:55 PM, John Graybeal <[hidden email]> wrote:

Georgeta,

It appears the document that was uploaded to BioPortal included an HTML document, not an ontology. I see that your link (https://gitub.u-bordeaux.fr/erias/fideo/-/raw/master/fideo_core.owl) appears to work in Protege, so I will have to check with my colleagues about why it might not be working in BioPortal. I'll try to do this today (before our Thanksgiving weekend), but I'm not sure if we'll be able to figure out it. (I suspect it may have to do with the networking again, but it could be tricky.)

Sorry for your trouble.

John




On Nov 25, 2020, at 9:05 AM, Georgeta Bordea <[hidden email]> wrote:

Dear BioPortal support team,

Thank you for helping us track down the previous issue related to submitting the FIDEO ontology [1]. Could you please let us know how to fix another issue, at the moment FIDEO classes are not properly retrieved and displayed.

The error message we get on BioPortal [2] is currently just:
"Problem retrieving classes"

Regards,
Georgeta Bordea




De: "Georgeta Bordea" <[hidden email]>
À: "support" <[hidden email]>
Envoyé: Jeudi 3 Septembre 2020 12:33:11
Objet: Error when submitting a new ontology

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

Regards,
Georgeta Bordea


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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