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[bioontology-support] Delay in implementing account creation or modifications of viewing/editing privileges

John Graybeal jgraybeal at
Fri Jun 5 15:27:24 PDT 2020


I discussed a similar question with our DevOps yesterday. He suggested that there may be an internal cache whose timeout is not being retriggered when the change is made to the ontology. In this case, there may be a 30-minute (or even 120-minute) delay in the availability of resources. Though I agree, public ontologies should be visible—the issue may be in the updating of account information within the system.

Also, sometimes the ontologies page fails to display if there is an ontology within it that has an internal inconsistency in BioPortal (so that the UI code thinks the ontology should display properly, but it does not). If this inconsistency resolves, for example by reparsing the ontology, the ontologies page displays properly again. It may be there is an internal condition that means the new user is not able to see the ontology but the UI thinks it should be visible.

We can have a look to see if we can actively trigger the refresh of any related caches, but I'm not sure when we will get to this—I'll contact you out of band to discuss your needs.

We'll also see if anyone else on the list has an idea of what might be happening.


On Jun 5, 2020, at 2:01 AM, Thomas Grivegnée <thomas.grivegnee at<mailto:thomas.grivegnee at>> wrote:


I am contacting you because we are experiencing a strange issue we are having a hard time diagnosing.

We are using the RC 3.0.1 and we created an OVF (Open Virtualization Format) image that we deployed on an Azure environment .

When we create an account, it' immediately recorded but when we login with this account, we get an error message when trying to navigate to the "Ontologies" tab.


This is already weird because some of the ontologies are public (like the default STY one.

If we connect with the "admin" account and grant viewing permissions to the account, and reconnect with the account, we still see the error message.

After some time, not sure how long, the changes are passed on but it is sometimes necessary to delete the cookies manually in order to see the ontologies having viewing permissions.

We could actually not really point what triggers the passing on of the changes.

Do you have any idea of what could be causing this error message in the first place (shouldn't we at least see the public ontologies)?

And secondly do you know what might be causing the delay in having the viewing permissions updated?

Thanks a lot



Thomas Grivegnée
Project Leader

Phone+32 478 23 78 54
Mailthomas.grivegnee at<mailto:thomas.grivegnee at>

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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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