feat(backend): cache database and graphql api per user; move web -in/out from database to session

[mswertz]

demo:

• created a GraphqlSession that is lightweight because it uses a cache of GraphqlApi and Database instances per user/per schema
• removed Database.setActiveUser so users cannot be switched within database, to prevent accidental errors in that cache with wrong user assigned
• created runAsUser and runAsAdmin for use cases where database temporarily needs to run in different/elevated privileges

todo:

• removed Database.setActive user and replaced with runAsUser where it seems appriopriate
• replace raw use of Database/Graphql with using the GraphqlSession class with caching
• rework graphql tests to use this GraphqlSession so we can see the caching indeed works
• beacon needed a lot of changes as it used many of the 'raw' Database and Schema objects
• seems to be a bug around setSettings
• see if we can reduce the amount of changes needed (56 files is a bit much)

[Copilot]

Pull Request Overview

This PR introduces a per-user caching layer for Database and GraphQL API instances and shifts session/user tracking out of raw Database calls into a dedicated GraphqlSession class.

• Added GraphqlSession and GraphqlSessionFieldFactory to centralize session logic and cache heavy objects per user.
• Updated SqlDatabase and Database interfaces to replace setActiveUser/becomeAdmin with runAsUser/runAsAdmin.
• Refactored controllers, API factories, and almost all tests to use GraphqlSession or the new SqlDatabase(String, boolean) constructor.

Reviewed Changes

Copilot reviewed 56 out of 56 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
backend/molgenis-emx2/src/main/java/org/molgenis/emx2/DatabaseListener.java	Added databaseChanged flag and getter to track full-DB changes.
backend/molgenis-emx2/src/main/java/org/molgenis/emx2/Database.java / SqlDatabase.java	Removed setActiveUser/becomeAdmin, added runAsUser/runAsAdmin.
backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/MolgenisSessionManager.java / MolgenisSession.java	Switched from manual DB wrappers to MolgenisSession subclass of GraphqlSession.
backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSession.java	New session class with Caffeine caches for DB and GraphQL instances.
backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlApiFactory.java / GraphqlSessionFieldFactory.java	Adapted GraphQL factory to use GraphqlSession in field definitions.
Multiple test files	Updated imports and instantiation to use SqlDatabase or GraphqlSession.

Comments suppressed due to low confidence (3)

backend/molgenis-emx2/src/main/java/org/molgenis/emx2/DatabaseListener.java:29

• [nitpick] Rename getDatabaseChanged() to isDatabaseChanged() to follow standard boolean getter naming conventions.

  public boolean getDatabaseChanged() {

backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSession.java:33

• Using a static TaskService may lead to shared mutable state across sessions; consider making it instance-based or verifying thread-safety.

  private static TaskService taskService = new TaskServiceInMemory();

[Copilot]

Correct spelling in the comment: 'settigs' should be 'settings'.

Suggested change

	// set static settigs
	// set static settings

[connoratrug]

expose settings to (runtime) config