Drop editor in favor of ord-app

[skearnes]

Summary

Removes the legacy Flask editor under ord_interface/editor/. Its job belongs to the standalone ord-app now, and the Contribute link in the header already points there.

Everything that existed only to serve the editor goes with it:

• ord_interface/editor/ and its Flask entrypoint ord_interface/interface.py.
• The flask gunicorn worker in start_app.sh, and the flask upstream + /editor/ proxy in nginx.conf.
• The closure-library / protobuf-js / protoc / closure-compiler / jquery-externs build chain in the Dockerfile, along with the default-jre install and the ord-schema v0.3.93 source download that fed it — and the ARCH build arg, which existed only to pick a protoc binary.
• The editor schema + migrate.py step in build_test_database.sh, and node editor/js/test.js in run_tests.sh.
• In CI: --ignore=ord_interface/editor, the npm install puppeteer step, and the setup-node step that served it. test_app moves from ubuntu-22.04 back to ubuntu-latest, since the pin was an AppArmor/puppeteer workaround.
• The flask and pygithub dependencies, and the ruff/ty excludes that kept the editor and its entrypoint out of the linters.
• The GH_CLIENT_ID/GH_CLIENT_SECRET passthrough in docker-compose.yml.

nginx 301s /editor and /editor/* to https://app.open-reaction-database.org/, so old bookmarks land on the new editor rather than a blank SPA shell.

Drive-by cleanups

• setup_test_postgres() normalizes its connection URL to the psycopg (v3) driver. SQLAlchemy was otherwise reaching for psycopg2 on the bare postgresql:// URL that testing.postgresql produces — the last psycopg2 caller in the repo — so psycopg2-binary comes out of the dependency list and main.py no longer has to patch the driver into the URL itself.
• Drops the *_pb2.py ruff/ty excludes: no generated protobuf wrappers are checked in or built here (the editor generated JS protos, not Python).

Retirement timeline

@bdeadman asked (below) that we not pull the editor out of production without giving the user community a clear deadline to retrieve their data. That happened in #178: since 2026-05-14 the editor's login and datasets pages have carried a banner announcing deactivation after July 31, 2026, pointing at the new editor and the announcement post, and giving help@open-reaction-database.org as a contact. That date has passed.

Deployment

The AWS Copilot manifest that pinned the front-end healthcheck to /editor/healthcheck is already gone from main (#174), and the Pulumi interface stack's target group uses the ALB default health check path (/), which the SPA serves. Nothing to change on the deployment side.

Follow-ups (out of scope for this PR)

• Delete the unused SSM parameters under /copilot/ord-editor/secrets/ (GH_CLIENT_ID, GH_CLIENT_SECRET) and the GitHub OAuth app behind them.
• Retire the editor database in ord-infrastructure (stacks/database/__main__.py) once the editor is off production.

Test plan

All of the below ran against d18ec48, the current head. CI is green on that commit as well: check_python, check_licenses, check_javascript, all 8 test_ord_interface jobs, and all 4 test_app jobs (which run ./run_tests.sh end to end).

• uv run pytest — 91 passed
• ruff check, ruff format --check, and ty check clean on ord_interface
• ./run_tests.sh — test database builds without the editor schema/migrate step, the slimmed-down image builds, and the app tests pass (75 passed)
• Container starts with only /run/fastapi.sock (no flask socket); gunicorn runs ord_interface.api.main:app alone, and the image has no ord_interface/editor/
• /, /browse, /search, /about, and /api/datasets return 200 through nginx; /ketcher takes nginx's directory redirect to /ketcher/ and then 200
• /editor, /editor/, /editor/foo, /editor/healthcheck all 301 to https://app.open-reaction-database.org/; /editorx falls through to the SPA

🤖 Generated with Claude Code

Greptile Summary

The PR removes the retired Flask editor and its build, runtime, test, and dependency infrastructure in favor of the standalone ORD app.

• Removes the editor implementation, Flask entrypoint, worker, database setup, and obsolete frontend content.
• Simplifies the Docker image, CI workflow, dependency lock, and startup scripts.
• Redirects legacy /editor URLs to the standalone application and updates deployment configuration accordingly.
• Normalizes test-database SQLAlchemy URLs to use the installed psycopg v3 driver.

Confidence Score: 5/5

The PR appears safe to merge, with the editor removal consistently reflected across routing, packaging, startup, tests, and deployment configuration.

No concrete changed-code failure remains after checking the retained database initialization and routing paths; the removed editor infrastructure is replaced by the documented external redirect.

Important Files Changed

Filename	Overview
ord_interface/nginx.conf	Removes the Flask upstream and redirects legacy editor paths while preserving SPA and FastAPI routing.
ord_interface/Dockerfile	Removes editor-only build dependencies and artifacts while retaining the SPA, Ketcher, and FastAPI image build.
ord_interface/start_app.sh	Removes the Flask gunicorn process so the container runs only nginx and FastAPI.
ord_interface/api/testing.py	Forces SQLAlchemy test connections onto the installed psycopg v3 driver without changing database semantics.
pyproject.toml	Removes editor-only Flask, GitHub, and psycopg2 dependencies and obsolete tool exclusions.
uv.lock	Refreshes the lockfile to remove dependency packages no longer required after deleting the editor.
.github/workflows/tests.yml	Removes editor-specific test setup and permits the application job to use the current Ubuntu runner.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  User[Browser request] --> Nginx
  Nginx -->|/editor or /editor/*| ORDApp[Standalone ORD app]
  Nginx -->|/api/*| FastAPI
  Nginx -->|Other paths| SPA[React SPA]
  FastAPI --> PostgreSQL

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_{Reviews (1): Last reviewed commit: "Point the test database at psycopg and d..." | Re-trigger Greptile}

[bdeadman]

@skearnes - yes we should do this to clean up the code, but I hesitate to rip the old editor out of the production instance without communicating a clear timeline for the user community to remove any important data. The latest statement we have made on the old editor is from the announcement of the new editor here https://www.linkedin.com/pulse/next-generation-reaction-editor-here-open-reaction-database-tfste.

[bdeadman]

My understanding is that this 'about' file no longer needed since the website uses this file (https://github.com/open-reaction-database/ord-interface/blob/8731895b44a960f0448a72042fa9981df2846c22/app/src/views/About.vue) instead for the about page.

[bdeadman]

Happy to approve the code changes as they are, but I'd like to have a conversation about how we manage the retirement of the legacy editor from the production instance.

[skearnes]

@bdeadman it's August 😄