Migrate to Spring 5

[arteymix]

Spring 4 has just reached end of life, so this is long overdue.

• Move to Spring 4 #508
• Update to Hibernate 5
• investigate if Spring Security 3 would still work (possibly! it still works with Spring 4 see Move to Spring 4 #508)
• get rid of HibernateDaoSupport, the session factory can be injected directly in BaseDao, and we can rely on Hibernate API directly like we currently do for nearly all use cases (this involves a few HibernateTemplate replacements)
• Migrate to Hibernate Search #661

I have started investigating Spring 4 to 5 migration in PavlidisLab/rdp#65 before the holidays. rgr shares numerous dependencies with Gemma and I think it would be preferable to migrate it first just to get an idea of the process at a smaller scale.

[ppavlidis]

See also https://github.com/PavlidisLab/Gemma/security/dependabot/pom.xml/org.springframework:spring-core/open

(I don't think any of the security issues are relevant to us)

[arteymix]

That was a long time ago, but the migration to Spring 5 for rgr went smoothly. The biggest concerns for Gemma is the breaking changes in spring-security from 3 to 4 and the lack of support for Hibernate 3.

Spring 4 still supports Hibernate 3 and would allow us to focus on security-related changes. Then migrating to Spring 5 would be a major overhaul of the DAO layer.

[arteymix]

Spring 3, 4 and 5 all support Hibernate 4 and with #351, we can relatively easily make this move as it will be just a matter of changing our bean configurations.

[arteymix]

I just finished and merged Spring 5 (via Spring Boot 2.6.8) migration for RDP PavlidisLab/rdp@ca4799d. I'll do a recap next dev meeting.

[arteymix]

Spring 3, 4 and 5 all support Hibernate 4 and with #351, we can relatively easily make this move as it will be just a matter of changing our bean configurations.

I stand corrected, Spring 5 requires Hibernate 5 as a minimum.