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Self-hosted MySQL re-integration (Read 159 times)
Mar 6th, 2025 at 7:41pm

Rod   Offline
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Hi,

first of all, thank you so much for continuously developing this software!

I want to use UGene as our plasmid reference database and was wondering why the "Connect to UGENE shared database"-feature was removed. Are there any plans on reintegrating this feature?

Edit: The "Workspace" feature does not match our requirements for data safety and user access management.

Thanks and kind regards!
 
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Reply #1 - Mar 7th, 2025 at 9:37am

Dmitrii Sukhomlinov   Offline
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Hello,

> I want to use UGene as our plasmid reference database and was wondering why the "Connect to UGENE shared database"-feature was removed. Are there any plans on reintegrating this feature?

Unfortunatelly, no, we do not have plans on redeveloping this feature. It was removed because our statistics showed that very few users were using this feature. We replaced it with Workspace as an alternative.

> The "Workspace" feature does not match our requirements for data safety and user access management.

Could you tell us, please, what "data safety and user access management" Worspace doesn't match? Maybe, we will be able to fx that and make Workspace usable to you?

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
Support us: Patreon, Boosty.
 

Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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Reply #2 - Mar 9th, 2025 at 12:11am

Rod   Offline
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Quote:
Could you tell us, please, what "data safety and user access management" Worspace doesn't match? Maybe, we will be able to fx that and make Workspace usable to you?


Concerning access management, our users would each need to be given an individual combination (!) of the following privileges:
- See all sequence names and metadata in one folder
- Read some but not others of those sequences with annotations
- Add a new sequence to the folder
- Change sequences in the folder
(- Change annotations of those sequences)

Having a very brief look at the db structure created by Version 42.0, that seems achievable with different mysql user privileges per table (apart from maybe point 2).

The data safety part is a simply about (the necessity of) trust. I trust you more than I do benchling et al., but less than myself and my universities IT department. I can run UGene in a VM with Wireshark, but I can't audit the code running Workspace. I'm not dealing with state secrets, but leaked or compromised data could seriously harm our work.

Thanks for hearing me out and best regards!
 
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Reply #3 - Mar 10th, 2025 at 12:05pm

Yuliya Algaer   Offline
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Hi,

We have plans to enhance Workspace with user group support, access configuration, and—most importantly—a local installation option via a Docker container.

Our goal is to complete this work by the end of the year. However, we can already prepare the current version of Workspace for local installation as a Docker container. Implementing this will require additional resources on our side, and we are prepared to begin immediately if you are able to provide fund this project.

Please let us know if this option is of interest.

Thank you for your time and consideration.
 
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