BI-2540 - Update bi_user Table for Alternate OAuth Provider(s)

[mlm483]

Description

Story: BI-2540

Most of the changes are renaming ORCID to OAuthID. Non-trivial changes are:

• In UserService.java, biUser.setOauthProvider(oAuthProvider); sets the OAuth provider on the bi_user when the account is activated.
• The migration, V1.34.0__rename-orcid.sql, renames orcid to oauth_id and adds a column oauth_provider that defaults to 'orcid'.
• I added GitHub OAuth variables to .env.template and docker-compose.yml, you'll need to add and populate them in .env for testing.
• In application.yml, I disabled flyway's out-of-order migrations, as this was causing some issues. I reverted this change, the pom.xml change below should make this unnecessary.
• I also added configuration in pom.xml for the flyway maven plugin so that is knows to run both our SQL-based migrations and Java-based migrations. Because it's used in two places, I added the locations value to .env.template.

These changes go along with the bi-web PR for BI-2539, and this PR includes the changes from the bi-api PR for BI-2539.

bi-docker-stack PR: Breeding-Insight/bi-docker-stack#58

Dependencies

The feature/BI-2539 branch of bi-web, which adds UI elements to sign in with GitHub.

Testing

Make sure bi-web is running with VUE_APP_ALTERNATE_AUTHENTICATION_ENABLED=true.
Add the following variables for bi-api.

# GitHub OAuth variables. Only required if using GitHub as an alternative to ORCID.
GITHUB_OAUTH_CLIENT_ID=<Client ID of GitHub OAuth app.>
GITHUB_OAUTH_CLIENT_SECRET=<Client Secret of GitHub Oauth app.>

Try adding new users and opening the activation link (found in the email or debug logs) in a private window or separate browser. Test signing in with GitHub and ORCID.

Check the bi_user table, ensure that the oauth_provider column contains 'github' or 'orcid' as expected.

Checklist:

• I have performed a self-review of my own code
• I have tested my code and ensured it meets the acceptance criteria of the story
• I have tested that my code works with both the brapi-java-server and BreedBase
• I have create/modified unit tests to cover this change
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to documentation
• I have run TAF: <please include a link to TAF run>

[dmeidlin]

The Micronaut server fails to start up because the ProgramDAO is not recognized as a bean when the GermplasmDAO tries to inject it. Prior to this a maven clean install was done with the flyway migration, which correctly picked up the orcid_id to oauth_id column change in the bi_user table. After seeing the error, I wiped the bi_api docker volume as a precaution and tried again with a fresh install, same error with the Micronaut server. Also, the error goes away when reverting back to a different branch.

Not sure where the error lies, especially since neither ProgramDAOImpl.java class or ProgramDAO.java interface have been modified.

[mlm483]

The Micronaut server fails to start up because the ProgramDAO is not recognized as a bean when the GermplasmDAO tries to inject it. Prior to this a maven clean install was done with the flyway migration, which correctly picked up the orcid_id to oauth_id column change in the bi_user table. After seeing the error, I wiped the bi_api docker volume as a precaution and tried again with a fresh install, same error with the Micronaut server. Also, the error goes away when reverting back to a different branch.

Not sure where the error lies, especially since neither ProgramDAOImpl.java class or ProgramDAO.java interface have been modified.

Thanks for testing, I'll try to reproduce and troubleshoot this issue.

[mlm483]

@dmeidlin 0cf53b8 fixes an issue with migrations where the flyway maven plugin was not configured to find the Java-based migrations, this was causing various issues building the project.

Now that it's fixed, could you try building and running again?

[dmeidlin]

With the change made to FLYWAY_LOCATIONS=filesystem:src/main/java/org/breedinginsight/db/migration,filesystem:src/main/resources/db/migration bi-api was able to compile after the flyway migrations. The login flow using Github via the Deltabreed UI works as expected.

[mlm483]

Passed: https://github.com/Breeding-Insight/bi-api/actions/runs/17103770331