Deps: Rails 8

[ericenns]

What does this PR do and why?

Describe in detail what your merge request does and why.

This PR upgrades our rails dependency to 8.0.1.

A few notables changes:

• Removed *DATABASE_URL env variables from config/database.yml
  • Note: Rails automatically supports overriding database config via *DATABASE_URL env variables (https://github.com/rails/rails/blob/ccf59d6d3a1d106e6ac44342fe2e8f89b61bc992/activerecord/lib/active_record/database_configurations.rb#L305)
• Changed identifier in rubyLsp.rubyVersionManager to auto, so that a developer doesn't need asdf if they don't want to use it (e.g. to support devcontainers better in the future)
• Dockerfile updated to match one generated by rails
• bin/docker-entrypoint updated to support using thruster (no change to use it yet though)
• Added bin/setup which is necessary for devcontainers
• Updated to use Rails 8.0 config defaults
• Changed logging to default to STDOUT, no file based logging for production (we already use STDOUT based logging with container deploy)
• Updated Capybara config to make it compatible for devcontainer later on

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How to set up and validate locally

Numbered steps to set up and validate the change are strongly suggested.

1. Ensure the tests pass
2. Ensure that the application is working as expected

PR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

• I have evaluated the PR acceptance checklist for this PR.

[deepsidhu85]

This looks good to me and works as expected. Tested it out with local storage, and with azurite (minus the workflow executions as sapporo nextflow doesn't recognize azurite)

[JeffreyThiessen]

Looks good. Tested a bunch of graphql queries/mutations as well as web ui functionality and everything seems to be working as expected.

Please update the schema files db/schema.rb and db/jobs_schema.rb which should have been updated to schema 8.0 and have enable_extension "pg_catalog.plpgsql"

[ChrisHuynh333]

Looks good!

[ericenns]

pg_catalog.plpgsql

I've ran bin/rails db:drop db:create db:migrate in 89b8cde which update both schemas.

[github-actions]

Code Metrics Report

Coverage	Test Execution Time
94.7%	10m58s

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Reported by octocov

[JeffreyThiessen]

Looks great!