diff --git a/.dockerignore b/.dockerignore index dc12cb7..1a9663e 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,2 +1,6 @@ .env -__pycache__ \ No newline at end of file +__pycache__ +.venv +.data +.pytest_cache +.ruff_cache \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 932f3e7..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,25 +0,0 @@ -name: CI - -permissions: - contents: read - -on: - push: - branches: - - '**' - -jobs: - CI: - runs-on: ubuntu-24.04 - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Docker Build - uses: docker/setup-buildx-action@f7ce87c1d6bead3e36075b2ce75da1f6cc28aaca # v3.9.0 - # update w/ git ls-remote https://github.com/docker/setup-buildx-action.git | grep refs/tags/v - - - name: Build current Docker image with tests - run: | - docker build --target test -t zephir-api2:test . diff --git a/.github/workflows/code-analysis.yml b/.github/workflows/code-analysis.yml index bc81f99..dfab911 100644 --- a/.github/workflows/code-analysis.yml +++ b/.github/workflows/code-analysis.yml @@ -16,42 +16,39 @@ jobs: - name: Checkout code uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v5.1.1 - with: - python-version: 3.x + - name: Install uv + uses: astral-sh/setup-uv@v5 - name: Display Python version run: | - python --version + uv run python --version - name: Install dependencies run: | - pip install poetry - poetry install --no-root --with dev + uv sync --frozen - name: Check for outdated dependencies if: env.skip-job != 'true' run: | - poetry show --outdated --only main + uv tree --outdated - name: Run tests with coverage in latest stable 3.x run: | - poetry run pytest --cov=app --cov-report=term-missing + uv run pytest --cov=app --cov-report=term-missing continue-on-error: false - name: Run Bandit for security analysis run: | - poetry run bandit -r app + uv run bandit -r app continue-on-error: false - name: Run Ruff for linting run: | - poetry run ruff check . + uv run ruff check . continue-on-error: false - name: Run Vulture for dead code analysis run: | - poetry run vulture . --min-confidence 70 + uv run vulture . --min-confidence 70 --exclude .venv continue-on-error: false diff --git a/.github/workflows/compatability-matrix.yml b/.github/workflows/compatability-matrix.yml deleted file mode 100644 index 87ba7b1..0000000 --- a/.github/workflows/compatability-matrix.yml +++ /dev/null @@ -1,67 +0,0 @@ -name: Compatibility Matrix - -permissions: - contents: read - -on: - workflow_dispatch: - -jobs: - CompatibilityMatrix: - runs-on: ubuntu-24.04 - - strategy: - fail-fast: false - matrix: - python-version: ['3.13', '3.14.0-alpha.5'] - update-strategy: [minor, major] - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v5.1.1 - with: - python-version: ${{ matrix.python-version }} - - - name: Get Python version - id: python_version - run: | - python --version - - - name: Install Poetry - run: | - pip install poetry - - - name: Backup lock file - run: | - if [ -f poetry.lock ]; then - mv poetry.lock poetry.lock.backup - fi - - - name: Install and update dependencies - run: | - if [[ "${{ matrix.update-strategy }}" == "minor" ]]; then - echo "Updating to minor versions" - poetry install --no-root --with dev - poetry update - elif [[ "${{ matrix.update-strategy }}" == "major" ]]; then - echo "Updating to major versions" - cp pyproject.toml pyproject.toml.backup - sed -i 's/\^/>=/g' pyproject.toml # Adjust constraints to allow major updates - poetry install --no-root --with dev - mv pyproject.toml.backup pyproject.toml - fi - - - - name: Restore lock file - run: | - if [ -f poetry.lock.backup ]; then - mv poetry.lock.backup poetry.lock - fi - - - name: Run tests - run: | - poetry run pytest - continue-on-error: false # Set to true if you want to continue on test failures diff --git a/.github/workflows/docker-matrix.yml b/.github/workflows/docker-matrix.yml deleted file mode 100644 index a49dcef..0000000 --- a/.github/workflows/docker-matrix.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: Docker Matrix - -permissions: - contents: read - -on: - workflow_dispatch: - -jobs: - DockerMatrix: - runs-on: ubuntu-24.04 - - strategy: - fail-fast: false - matrix: - image-tag: ['3.13-slim-bullseye', '3.14-rc-bullseye'] - update-strategy: [default, minor] - - steps: - - name: Checkout code - uses: actions/checkout@v4 - - - name: Set up Docker Build - uses: docker/setup-buildx-action@f7ce87c1d6bead3e36075b2ce75da1f6cc28aaca # v3.9.0 - # update w/ git ls-remote https://github.com/docker/setup-buildx-action.git | grep refs/tags/v - - - name: Build current Docker image with tests - run: | - docker build --target test -t zephir-api2:test . - - - name: Install and update dependencies - run: | - if [[ "${{ matrix.update-strategy }}" == "default" ]]; then - - echo "Running normal test suite" - docker build --build-arg IMAGE_TAG=${{ matrix.image-tag }} --target test -t zephir-api2:test . - - elif [[ "${{ matrix.update-strategy }}" == "minor" ]]; then - - echo "Minor version update" - docker build --build-arg IMAGE_TAG=${{ matrix.image-tag }} --target test-minor-update -t zephir-api2:test . - - fi diff --git a/.gitignore b/.gitignore index ea9c7b4..ceb70cc 100644 --- a/.gitignore +++ b/.gitignore @@ -82,24 +82,7 @@ target/ profile_default/ ipython_config.py -# pyenv -# For a library or package, you might want to ignore these files since the code is -# intended to run in multiple environments; otherwise, check them in: -# .python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# poetry -# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. -# This is especially recommended for binary packages to ensure reproducibility, and is more -# commonly ignored for libraries. -# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control -#poetry.lock + # PEP 582; used by e.g. github.com/David-OConnor/pyflow __pypackages__/ @@ -120,6 +103,9 @@ ENV/ env.bak/ venv.bak/ +# Local Docker volume data +.data/ + # Spyder project settings .spyderproject .spyproject diff --git a/.python-version b/.python-version deleted file mode 100644 index 3e388a4..0000000 --- a/.python-version +++ /dev/null @@ -1 +0,0 @@ -3.13.2 diff --git a/Dockerfile b/Dockerfile index 86fbccc..2581ad7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,76 +1,64 @@ ARG IMAGE_TAG=3.13-slim-bullseye -FROM python:${IMAGE_TAG} AS base -# Allowing the argumenets to be read into the dockerfile. Ex: .env > compose.yml > Dockerfile -ARG UID=1000 -ARG GID=1000 +# +# Python dependencies stage +# +FROM python:${IMAGE_TAG} AS deps -# Create the user and usergroup -RUN groupadd -g ${GID} -o app -RUN useradd -m -d /app -u ${UID} -g ${GID} -o -s /bin/bash app +# Copy uv binary for dependency management +COPY --from=ghcr.io/astral-sh/uv:0.8.4 /uv /usr/local/bin/uv -# Set the working directory to /app WORKDIR /app -# Both build and development need poetry, so it is its own step. -FROM base AS poetry -RUN pip install poetry - -# Use this page as a reference for python and poetry environment variables: -# https://docs.python.org/3/using/cmdline.html#envvar-PYTHONUNBUFFERED Ensure -# the stdout and stderr streams are sent straight to terminal, then you can see -# the output of your application -ENV PYTHONUNBUFFERED=1\ - # Avoid the generation of .pyc files during package install - # Disable pip's cache, then reduce the size of the image - PIP_NO_CACHE_DIR=off \ - # Save runtime because it is not look for updating pip version - PIP_DISABLE_PIP_VERSION_CHECK=on \ - PIP_DEFAULT_TIMEOUT=100 \ - # Disable poetry interaction - POETRY_NO_INTERACTION=1 \ - POETRY_VIRTUALENVS_CREATE=1 \ - POETRY_VIRTUALENVS_IN_PROJECT=1 \ - POETRY_CACHE_DIR=/tmp/poetry_cache - -FROM poetry AS build -COPY pyproject.toml poetry.lock ./ -RUN poetry install --no-root --without dev && rm -rf ${POETRY_CACHE_DIR}; - -# FROM poetry AS build-minor-update -# # Install minor version updates in the absence of poetry.lock file -# COPY pyproject.toml poetry.lock ./ -# RUN poetry install --no-root --without dev && rm -rf ${POETRY_CACHE_DIR}; - -FROM build AS test -# Install dev dependencies -RUN poetry install --only dev --no-root && rm -rf ${POETRY_CACHE_DIR}; -COPY . . -# Run tests -USER app -RUN poetry run pytest tests +ENV PYTHONUNBUFFERED=1 \ + # Compile Python bytecode for faster startup + UV_COMPILE_BYTECODE=1 \ + # Use copy mode (required in Docker; hardlinks don't work across layers) + UV_LINK_MODE=copy + +# Install production dependencies +COPY pyproject.toml uv.lock ./ +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --no-install-project --no-dev + +# +# Test stage +# +FROM deps AS test -FROM build AS test-minor-update # Install dev dependencies -RUN poetry install --only dev --no-root && rm -rf ${POETRY_CACHE_DIR}; -RUN poetry update +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --no-install-project + COPY . . -# Run tests -USER app -RUN poetry run pytest tests +CMD ["uv", "run", "pytest", "tests"] -FROM base AS production -RUN mkdir -p /venv && chown ${UID}:${GID} /venv +# +# Production stage +# +FROM python:${IMAGE_TAG} AS production -# By adding /venv/bin to the PATH, the dependencies in the virtual environment -# are used -ENV VIRTUAL_ENV=/venv \ - PATH="/venv/bin:$PATH" +# Copy uv binary for runtime +COPY --from=ghcr.io/astral-sh/uv:0.8.4 /uv /usr/local/bin/uv -COPY --chown=${UID}:${GID} . /app -COPY --chown=${UID}:${GID} --from=build "/app/.venv" ${VIRTUAL_ENV} -COPY . . +# Create an unprivileged user and group to run the application +RUN groupadd --gid 1001 app && \ + useradd --uid 1001 --gid app --no-create-home app + +WORKDIR /app + +ENV PYTHONUNBUFFERED=1 \ + # Deps are pre-installed in the venv; no cache needed at runtime + UV_NO_CACHE=1 + +# Copy the virtualenv from the deps stage with correct ownership +COPY --from=deps --chown=app:app /app/.venv /app/.venv + +# Copy application source with correct ownership +COPY --chown=app:app . . + +# Switch to the unprivileged user before starting the process +USER app -# Switch to the app user -USER app \ No newline at end of file +CMD ["uv", "run", "python", "-m", "gunicorn", "-c", "gunicorn_config.py"] \ No newline at end of file diff --git a/README.md b/README.md index 67daed8..3e68041 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,110 @@ # zephir_api2 ![CI](https://github.com/cdlib/zephir-api2/actions/workflows/ci.yml/badge.svg) + +The Zephir Item API provides item-level MARC metadata records for all items submitted to HathiTrust. +See [API.md](API.md) for full endpoint documentation. + +## Getting Started + +### Prerequisites + +Install [uv](https://docs.astral.sh/uv/) — it manages both Python and project dependencies: + +```sh +brew install uv +``` + +### Local Development + +**Install dependencies:** + +```sh +uv sync +``` + +**Set required environment variables** (see [Database configuration](#database-configuration) below), then **run the app:** + +Copy `env.template` to `.env` and update the `DATABASE_URI` variable. + +```sh +uv run python -m gunicorn -c gunicorn_config.py +``` + +The API will be available at `http://localhost:8000/api/`. + +**Run tests:** + +```sh +uv run pytest tests +``` + +Tests use a bundled SQLite fixture (`tests/test_zephir_api/`) and do not require a live database connection. + +**Run linting and analysis tools:** + +```sh +uv run ruff check . +uv run bandit -r app +uv run vulture . --min-confidence 70 --exclude .venv +uv run pytest --cov=app --cov-report=term-missing +``` + +### Docker + +The Dockerfile has three useful targets: + +| Target | What it does | +|---|---| +| `test` | Installs all deps, copies source, runs `pytest tests` on start | +| `test-minor-update` | Same as `test` but upgrades deps to latest compatible versions first | +| `production` | Installs prod deps only, starts Gunicorn on start | + +**Run a single target directly:** + +```sh +# Run the test suite +docker run $(docker build -q --target test .) + +# Build and run the production image +docker run -p 8000:8000 \ + -e DATABASE_URI=mysql+mysqlconnector://user:pass@host/dbname \ + $(docker build -q --target production .) +``` + +**Run with Docker Compose:** + +Docker Compose will automatically bootstrap a MySQL instance with test data from `tests/sample_data.csv`. + +```sh +docker compose up +``` + +The API will be available at `http://localhost:8000/api/` once the MySQL service has finished bootstrapping. + +--- + +## Database Configuration + +The app resolves the database connection from environment variables in priority order: + +| Variable | When to use | +|---|---| +| `DATABASE_URI` | Full SQLAlchemy URI — simplest for local dev | +| `DATABASE_CREDENTIALS_SECRET_NAME` + AWS vars | Pull credentials from AWS Secrets Manager | +| `DB_USERNAME` + `DB_PASSWORD` + `DB_HOST` + `DB_DATABASE` | Individual credential env vars | + +--- + +## Dependency Management + +This project uses [uv](https://docs.astral.sh/uv/) for dependency management. + +| Command | Purpose | +|---|---| +| `uv sync` | Install all dependencies (prod + dev) | +| `uv sync --no-dev` | Install production dependencies only | +| `uv add ` | Add a new runtime dependency | +| `uv add --dev ` | Add a new dev dependency | +| `uv lock --upgrade` | Update all dependencies within version constraints | +| `uv tree --outdated` | List dependencies with available updates | diff --git a/app/config.py b/app/config.py index 3178acb..bcdea50 100644 --- a/app/config.py +++ b/app/config.py @@ -62,7 +62,7 @@ def get_database_uri(): class Config: - LOG_LEVEL = os.getenv("LOG_LEVEL") + LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO").upper() SQLALCHEMY_DATABASE_URI = get_database_uri() SQLALCHEMY_TRACK_MODIFICATIONS = False SQLALCHEMY_ENGINE_OPTIONS = { diff --git a/app/routes.py b/app/routes.py index cccaedb..27ae74f 100644 --- a/app/routes.py +++ b/app/routes.py @@ -1,3 +1,5 @@ +from urllib.parse import urlparse + import markdown from flask import Blueprint, current_app, jsonify, make_response, redirect, request, url_for from markupsafe import Markup @@ -39,11 +41,17 @@ def documentation(): with open('API.md', 'r') as file: content = file.read() + # Sanitize the URL root by reconstructing it from only the scheme and netloc + # This avoids a (very unlikely) injection vulnerability + parsed = urlparse(request.url_root) + safe_url_root = f"{parsed.scheme}://{parsed.netloc}/" + # Convert Markdown to HTML - html_content = markdown.markdown(content.replace('http://localhost/', request.url_root)) + html_content = markdown.markdown(content.replace('http://localhost/', safe_url_root)) - # Return HTML content. The Markup class prevents Flask from escaping HTML content. - return Markup(html_content) + # Ignore Bandit security warning + # The content is safe: it comes from a controlled Markdown file and the URL is sanitized. + return Markup(html_content) # nosec B704 @blueprint.route('/ping') diff --git a/bootstrap_db.py b/bootstrap_db.py new file mode 100644 index 0000000..faea3fd --- /dev/null +++ b/bootstrap_db.py @@ -0,0 +1,55 @@ +""" +Seed the database with sample data from a CSV file. + +Usage: + uv run python bootstrap_db.py [CSV_FILE] + +CSV_FILE defaults to tests/sample_data.csv. Rows whose id already exists are +skipped (upsert-on-conflict is not performed, to preserve any live data). + +Required environment variables (same as the app): + DATABASE_URI or DB_USERNAME / DB_PASSWORD / DB_HOST / DB_DATABASE +""" + +import csv +import sys + +from app import create_app +from app.extensions import db +from app.models import ZephirFiledata + +CSV_DEFAULT = "tests/sample_data.csv" + + +def seed(csv_path: str) -> None: + app = create_app() + with app.app_context(): + db.create_all() + + with open(csv_path, newline="", encoding="utf-8") as f: + reader = csv.DictReader(f) + inserted = skipped = 0 + + for row in reader: + htid = row["id"] + if db.session.get(ZephirFiledata, htid) is not None: + print(f" skip {htid} (already exists)") + skipped += 1 + continue + + db.session.add(ZephirFiledata( + htid=htid, + metadata_xml=row["metadata"], + metadata_json=row.get("metadata_json"), + )) + print(f" insert {htid}") + inserted += 1 + + db.session.commit() + + print(f"\nDone. {inserted} inserted, {skipped} skipped.") + + +if __name__ == "__main__": + path = sys.argv[1] if len(sys.argv) > 1 else CSV_DEFAULT + seed(path) diff --git a/docker-compose.yml b/docker-compose.yml index f1b02ce..4bbf881 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,33 +1,48 @@ +# Full local stack (MySQL + zephir-api): +# +# docker compose up + services: - zephir-api: + mysql: + image: mysql:8.4 + container_name: zephir_mysql + environment: + MYSQL_ROOT_PASSWORD: devpassword + MYSQL_DATABASE: zephir_dev + ports: + - "3306:3306" + volumes: + - .data/mysql:/var/lib/mysql + healthcheck: + test: ["CMD", "mysqladmin", "ping", "-h", "localhost", "-u", "root", "-pdevpassword"] + interval: 5s + timeout: 5s + retries: 10 + start_period: 10s + + bootstrap: build: context: . target: production - command: ["python", "-m", "gunicorn", "-c", "gunicorn_config.py"] - ports: - - "${APP_PORT}:${APP_PORT}" environment: - # Required - - FLASK_ENV - - APP_PORT - - LOG_LEVEL - - # One of the following must be set - - DATABASE_URI - - - DATABASE_CREDENTIALS_SECRET_NAME - - AWS_DEFAULT_REGION - - AWS_ACCESS_KEY_ID - - AWS_SECRET_ACCESS_KEY - - AWS_SESSION_TOKEN - - - DB_USERNAME - - DB_PASSWORD - - DB_HOST - - DB_DATABASE + - DATABASE_URI=mysql+mysqlconnector://root:devpassword@mysql/zephir_dev + command: ["uv", "run", "python", "bootstrap_db.py"] depends_on: - - test - test: + mysql: + condition: service_healthy + + zephir-api: build: context: . - target: test \ No newline at end of file + target: production + ports: + - "${APP_PORT:-8000}:${APP_PORT:-8000}" + environment: + - APP_PORT=${APP_PORT:-8000} + - LOG_LEVEL=${LOG_LEVEL:-info} + - DATABASE_URI=mysql+mysqlconnector://root:devpassword@mysql/zephir_dev + depends_on: + mysql: + condition: service_healthy + bootstrap: + condition: service_completed_successfully \ No newline at end of file diff --git a/env.template b/env.template new file mode 100644 index 0000000..52a72ab --- /dev/null +++ b/env.template @@ -0,0 +1,3 @@ +APP_PORT=8000 +LOG_LEVEL=INFO +DATABASE_URI=mysql+mysqlconnector://user:password@host/database \ No newline at end of file diff --git a/gunicorn_config.py b/gunicorn_config.py index de52ddd..e033a74 100644 --- a/gunicorn_config.py +++ b/gunicorn_config.py @@ -1,8 +1,11 @@ import os -APP_PORT = os.getenv("APP_PORT") -LOG_LEVEL = os.getenv("LOG_LEVEL") +APP_PORT = os.getenv("APP_PORT", 8000) +LOG_LEVEL = os.getenv("LOG_LEVEL", "INFO").upper() bind = f"0.0.0.0:{APP_PORT}" wsgi_app = "app:create_app()" -loglevel = LOG_LEVEL \ No newline at end of file +loglevel = LOG_LEVEL + +accesslog = "-" +errorlog = "-" \ No newline at end of file diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 3a8e08f..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1015 +0,0 @@ -# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. - 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Item API" authors = [] readme = "README.md" +requires-python = ">=3.13,<3.14" +dependencies = [ + "flask~=3.1", + "flask-sqlalchemy~=3.1", + "mysql-connector-python~=9.6", + "markdown~=3.10", + "markupsafe~=3.0", + "gunicorn~=25.1", + "boto3~=1.42", +] -[tool.poetry.dependencies] -python = "^3.13" -flask = "^3.1" -flask_sqlalchemy = "^3.1.1" -mysql-connector-python = "^9.2.0" -markdown = "^3.7" -markupsafe = "^3.0.2" -gunicorn = "^23.0.0" -boto3 = "^1.36.16" - -[tool.poetry.group.dev.dependencies] -pytest = "^8.3.4" -pytest-flask = "^1.3.0" -bandit = "^1.8.2" -ruff = "^0.6.1" -pytest-cov = "^6.0.0" -vulture = "^2.14" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" \ No newline at end of file +[dependency-groups] +dev = [ + "pytest~=9.0", + "pytest-flask~=1.3", + "bandit~=1.9", + "ruff~=0.15", + "pytest-cov~=7.0", + "vulture~=2.15", +] diff --git a/tests/sample_data.csv b/tests/sample_data.csv new file mode 100644 index 0000000..f56530d --- 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