Drop editor in favor of ord-app

.github/workflows/tests.yml

@@ -52,33 +52,27 @@ jobs:
         shell: bash -l {0}
         run: |
           uv run coverage erase
-          uv run pytest -vv --cov=ord_interface --durations=20 --ignore=ord_interface/editor
+          uv run pytest -vv --cov=ord_interface --durations=20
           uv run coverage report
 
   test_app:
     strategy:
       matrix:
         python-version: ["3.11", "3.12", "3.13", "3.14"]
     # NOTE(skearnes): Docker is not supported on macOS GitLab runners.
-    # NOTE(skearnes): ubuntu-latest AppArmor doesn't play nicely with puppeteer.
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
       - uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
         with:
           enable-cache: true
           python-version: ${{ matrix.python-version }}
-      - uses: actions/setup-node@820762786026740c76f36085b0efc47a31fe5020 # v7.0.0
       - name: actions-setup-redis
         uses: shogo82148/actions-setup-redis@59cda539fd5cc9be4c42bb07e4b28156951f37d6 # v1.55.0
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@bb05f3f5519dd87d3ba754cc423b652a5edd6d2c # v4.2.0
       - name: Install ord-interface
         run: uv sync --frozen
-      - name: Install non-python test dependencies
-        run: |
-          cd "${GITHUB_WORKSPACE}/ord_interface"
-          npm install puppeteer
       - name: Run tests
         run: |
           cd "${GITHUB_WORKSPACE}/ord_interface"

README.md

@@ -12,7 +12,6 @@ Web interface and FastAPI server for the [Open Reaction Database](https://open-r
   - `api/` — FastAPI server (search, view, queries)
   - `client/` — utilities for building the Postgres + rdkit-cartridge database
   - `visualization/` — Jinja filters and helpers for rendering reactions and molecules
-  - `editor/` — legacy reaction-submission UI (being removed)
 
 The React frontend talks to the FastAPI server, so both processes need to be running for the UI to work. On Windows, use WSL.
 
@@ -47,7 +46,6 @@ rest of the steps.
 ```shell
 cd ord_interface
 ./build_test_database.sh
-# Apple silicon: append `--build-arg="ARCH=aarch_64"`.
 docker build --file Dockerfile -t openreactiondatabase/ord-interface ..
 docker compose up
 ```

ord_interface/Dockerfile

@@ -18,46 +18,21 @@
 
 FROM python:3.11
 
-# default-jre is required for running the closure compiler linter.
-# For this next line, see:
-# https://github.com/geerlingguy/ansible-role-java/issues/64#issuecomment-597132394
-RUN mkdir -p /usr/share/man/man1/
 RUN apt-get update \
    && apt-get install -y \
    build-essential \
-   default-jre \
    nginx \
    npm \
    procps \
    unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*
 
-# Fetch and build editor dependencies.
+# Fetch the Ketcher distribution served by the SPA.
 # NOTE(kearnes): Do this before COPYing the local state so it can be cached.
 WORKDIR /app/ord-interface/ord_interface
 RUN wget https://github.com/epam/ketcher/releases/download/v2.5.1/ketcher-standalone-2.5.1.zip \
    && unzip ketcher-standalone-2.5.1.zip
-WORKDIR /app/ord-interface/ord_interface/editor
-RUN wget https://github.com/google/closure-library/archive/v20200517.tar.gz \
-   && tar -xzf v20200517.tar.gz \
-   && rm v20200517.tar.gz
-RUN wget https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protobuf-js-3.14.0.tar.gz \
-   && tar -xzf protobuf-js-3.14.0.tar.gz \
-   && rm protobuf-js-3.14.0.tar.gz
-ARG ARCH=x86_64
-RUN wget https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protoc-3.14.0-linux-${ARCH}.zip \
-   && unzip protoc-3.14.0-linux-${ARCH}.zip
-ENV PATH="/app/ord-interface/ord_interface/editor/bin:${PATH}"
-RUN wget https://raw.githubusercontent.com/google/closure-compiler/master/contrib/externs/jquery-3.3.js \
-   && mkdir -p externs \
-   && mv jquery-3.3.js externs
-RUN npm install google-closure-compiler@20220803
-WORKDIR /app
-RUN wget https://github.com/open-reaction-database/ord-schema/archive/refs/tags/v0.3.93.zip \
-   && unzip v0.3.93.zip \
-   && rm v0.3.93.zip \
-   && mv ord-schema-0.3.93 ord-schema
 
 # Install dependencies.
 WORKDIR /app/ord-interface
@@ -68,12 +43,6 @@ ENV UV_PROJECT_ENVIRONMENT=/usr/local \
 COPY pyproject.toml uv.lock README.md ./
 RUN uv sync --frozen --no-dev --no-install-project
 
-# Copy the local state.
-COPY ord_interface/editor/js/ ord_interface/editor/js/
-COPY ord_interface/editor/build.sh ord_interface/editor
-WORKDIR /app/ord-interface/ord_interface/editor
-RUN ./build.sh
-WORKDIR /app/ord-interface
 # Build the SPA (React + TypeScript + Vite).
 COPY app/ app/
 WORKDIR /app/ord-interface/app
@@ -88,10 +57,7 @@ RUN cp -r /app/ord-interface/ord_interface/standalone/ /app/ord-interface/app/pu
    && npm run build \
    && mv dist/ /app/ord-interface/spa
 WORKDIR /app/ord-interface
-# Copy the rest of the editor files.
-COPY ord_interface/editor/ ord_interface/editor/
 # Now copy everything else.
-COPY ord_interface/interface.py ord_interface/
 COPY ord_interface/api/ ord_interface/api/
 COPY ord_interface/visualization/ ord_interface/visualization/
 RUN uv sync --frozen --no-dev

ord_interface/api/main.py

@@ -15,7 +15,6 @@
 """Open Reaction Database API."""
 
 import os
-import re
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
@@ -33,8 +32,7 @@ async def lifespan(*args, **kwargs):
         from testing.postgresql import Postgresql
 
         with Postgresql() as postgres:
-            url = re.sub("postgresql://", "postgresql+psycopg://", postgres.url())
-            setup_test_postgres(url)
+            setup_test_postgres(postgres.url())
             os.environ["ORD_INTERFACE_POSTGRES"] = postgres.url()
             yield
     else:

ord_interface/api/testing.py

@@ -20,20 +20,28 @@
 from ord_schema.message_helpers import load_message
 from ord_schema.orm.database import add_dataset, prepare_database, update_derived_data
 from ord_schema.proto import dataset_pb2
-from sqlalchemy import create_engine
+from sqlalchemy import create_engine, make_url
 from sqlalchemy.orm import Session
 
 
 def setup_test_postgres(url: str) -> None:
-    """Adds test data to a postgres database."""
+    """Adds test data to a postgres database.
+
+    Args:
+        url: Postgres connection URL. Any driver it names is replaced with
+            psycopg (v3), the only Postgres driver we install; SQLAlchemy would
+            otherwise reach for psycopg2 on a bare ``postgresql://`` URL.
+    """
     datasets = [
         load_message(filename, dataset_pb2.Dataset)
         for filename in glob(
             os.path.join(os.path.dirname(__file__), "testdata", "*.pb.gz")
         )
     ]
     assert datasets
-    engine = create_engine(url, future=True)
+    engine = create_engine(
+        make_url(url).set(drivername="postgresql+psycopg"), future=True
+    )
     rdkit_cartridge = prepare_database(engine)
     with Session(engine) as session:
         for dataset in datasets:

ord_interface/build_test_database.sh

@@ -33,12 +33,6 @@ while [ $? -ne 0 ]; do
 done
 set -e
 
-# Editor.
-cd editor
-psql -p 5432 -h localhost -U postgres -f schema.sql
-python py/migrate.py
-cd ..
-
 # Client.
 psql -p 5432 -h localhost -U postgres -c 'CREATE DATABASE ord;'
 python client/build_database.py

ord_interface/docker-compose.yml

@@ -26,8 +26,6 @@ services:
       - POSTGRES_USER=postgres
       - POSTGRES_PASSWORD=postgres
       - POSTGRES_DATABASE=ord
-      - GH_CLIENT_ID=${GH_CLIENT_ID}
-      - GH_CLIENT_SECRET=${GH_CLIENT_SECRET}
     image: "openreactiondatabase/ord-interface:latest"
     ports:
       - "8080:8080"