Flask>=3 requires changes to flask-jwt-extended usage

[kkaris]

Upgrading to Flask>=3,<4 comes with a second order consequence: currently we use flask-jwt-extended<4, which requires Flask<2.0,>=1.0. However, upgrading flask-jwt-extended to be compatible with Flask>=3,<4 comes with an api change documented here: https://flask-jwt-extended.readthedocs.io/en/stable/v4_upgrade_guide.html#api-changes

In short, we need to replace all instances of the decorator @jwt_optional with @jwt_required(optional=True) wherever we update to Flask>=3,<4.

Related: https://github.com/gyorilab/gilda/issues/137

I'll try to list all places in downstream repositories in sorger/gyorilab where we would need to make the change:

• [x] emmaa/emmaa_service/api.py - 9 instances
• [x] indra_cogex/apps/curator/curator_blueprint.py - 16 instances
• [x] indra_cogex/apps/data_display/init.py - 3 instances
• [x] ui_util/indralab_auth_tools/indralab_auth_tools/auth.py - 1 instance
• [x] indra_db/indra_db_service/config.py - 1 instance

To test the upgrade

• Use e.g. CoGEx with the updates provided in https://github.com/gyorilab/indra_cogex/pull/172 as a test case
• Build the CoGEx docker locally and ensure the docker builds from the branch for CoGEx and for indralab_auth_tools to provide the full updates. Make sure the build is tagged with something else than latest to not overwrite the current running service.
• Run the docker locally and check that login and curation capabilities work as expected (although actually logging in probably won't work as login typically requires https) as well as looking for any other issues that come from updates.
• Repeat the build and deploy steps for the current service and check again that everything works (especially the actual login functionality).
• Repeat the whole process for emmaa (which runs on a separate server) and indra_db (which uses lambda + api gateway)

Testing

• [x] Test with CoGEx - see https://github.com/gyorilab/indra_cogex/pull/172
• [x] Test with EMMAA - see https://github.com/gyorilab/emmaa/pull/280
• [x] Test with new indra db deployment - https://github.com/gyorilab/indra_db/pull/222

[kkaris]

Remaining things:

• [x] Redeploy Indra CoGEx to use the updated key in ui_util
• [x] Redeploy EMMAA to use the updated key in ui_util