diff --git a/.env.example b/.env.example index c514d18..dddc66f 100644 --- a/.env.example +++ b/.env.example @@ -1,18 +1,26 @@ -# Example Environment Variables - Copy to .env and fill in values +# Example Environment Variables -# --- Database --- -# Example format: postgresql://user:password@host:port/dbname +# --- PostgreSQL Config --- +POSTGRES_USER=moss_user +POSTGRES_PASSWORD=your_secure_password +POSTGRES_DB=moss_db +POSTGRES_HOST=localhost +POSTGRES_PORT=5432 + +# --- Redis Config --- +REDIS_HOST=localhost +REDIS_PORT=6379 + +# --- Application URLs (for internal use) --- DATABASE_URL=postgresql://moss_user:your_secure_password@localhost:5432/moss_db +CELERY_BROKER_URL=redis://localhost:6379/0 +CELERY_RESULT_BACKEND_URL=redis://localhost:6379/1 # --- External APIs --- -# GitHub Personal Access Token (PAT) with 'public_repo' scope recommended -# Generate one at: https://github.com/settings/tokens (Tokens classic) +# Select the "Public repositories" option for repository access +# Generate one at: https://github.com/settings/personal-access-tokens GITHUB_API_TOKEN=ghp_YourGitHubTokenHere - # Email address for OpenAlex polite pool (helps with rate limits) # See: https://docs.openalex.org/how-to-use-the-api/rate-limits-and-authentication#the-polite-pool OPENALEX_EMAIL=your.email@example.com - -# Celery Configuration (using Redis as example) -CELERY_BROKER_URL=redis://localhost:6379/0 -CELERY_RESULT_BACKEND_URL=redis://localhost:6379/1 \ No newline at end of file +VITE_API_BASE_URL=http://0.0.0.0:8000/api/v1 \ No newline at end of file diff --git a/.gitignore b/.gitignore index 04fb7d5..1509e01 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,45 @@ -# Byte-compiled / optimized / DLL files +# --- Environments --- +.venv +venv/ +env/ +ENV/ +env.bak/ +venv.bak/ +__pypackages__/ +.env +.env.*.local +.env.local +.env.*.test +.env.test +.env.*.production +.env.production +# Example Env Vars +!.env.example + +# --- Lock Files --- +Pipfile.lock +uv.lock +pnpm-lock.yaml + +# --- Python Cache & Compiled Files --- __pycache__/ *.py[cod] *$py.class - -# C extensions *.so +.coverage +.coverage.* +.cache +.hypothesis/ +.pytest_cache/ +.ropeproject +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json +# Pyre type checker +.pyre/ -# Distribution / packaging +# Python Distribution & Packaging .Python build/ develop-eggs/ @@ -27,124 +60,75 @@ share/python-wheels/ *.egg MANIFEST -# PyInstaller -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log +# --- Python Tools & Libraries --- +# Celery +celerybeat-schedule +celerybeat.pid +# Django local_settings.py db.sqlite3 db.sqlite3-journal - -# Flask stuff: +# Flask instance/ .webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - # IPython profile_default/ ipython_config.py - -# pyenv -.python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# Pipfile.lock - -# PEP 582; used by PDM, Flit and potentially other management tools -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files +# Jupyter +.ipynb_checkpoints +# pip +pip-log.txt +pip-delete-this-directory.txt +# mkdocs +/site +# PyBuilder +target/ +# PyInstaller +*.manifest +*.spec +# SageMath *.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings +# Scrapy +.scrapy +# Sphinx +docs/_build/ +# Spyder .spyderproject .spyproject -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# OS specific files +# --- General --- +# Logs +logs/ +*.log +# Test & Coverage Reports +htmlcov/ +.tox/ +.nox/ +nosetests.xml +coverage.xml +*.cover +*.py,cover +coverage/ +# OS generated files .DS_Store Thumbs.db - -# Frontend Dependencies / Build artifacts -frontend/node_modules/ -frontend/dist/ -frontend/.env*.local -frontend/coverage/ -frontend/.DS_Store - -# Log files -*.log -npm-debug.log* -yarn-debug.log* -yarn-error.log* - -# IDE files +# IDE & Editor Config .idea/ .vscode/ *.suo *.ntvs* *.njsproj *.sln -*.sw? \ No newline at end of file +*.sw? +# Translations +*.mo +*.pot + +# --- Frontend (Node.js/pnpm) --- +node_modules/ +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..3523e81 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.13.5 \ No newline at end of file diff --git a/README.md b/README.md index 5695c71..6b130eb 100644 --- a/README.md +++ b/README.md @@ -4,251 +4,208 @@ ## Overview -MOSS (Map of Open Source Science) is a backend application designed to build a knowledge graph about open source scientific software. It ingests data about repositories (primarily from GitHub), links them to scholarly works (using DOIs and OpenAlex), identifies contributors and institutions, and provides an API to query these relationships. It also supports running custom analysis and discovery algorithms ("recipes"). +The Map of Open Source Science (MOSS) is an open-source application and collaborative effort to model and map the domain of open-source research software and its intersection with academic scholarship. It aims to reveal the hidden connections within this ecosystem by constructing a rich knowledge graph that links software repositories, scholarly publications, researchers, and institutions. This is accomplished through a reproducible framework that uses structured data integration, overlapping web traversal, and graph construction strategies. The system is grounded in existing ontologies (e.g., OpenAlex topics, Schema.org entities) and uses context-driven rules to establish relationships, ensuring data provenance and consistency. By making these connections visible, MOSS helps answer critical questions about the impact, sustainability, and collaborative nature of open source in science. -The system uses a FastAPI web framework for its API, PostgreSQL as the database, Celery for background task processing (like keyword-based discovery and DOI processing), and Redis as the message broker for Celery. +This repository contains the backend services, API, and frontend application for the MOSS platform. It provides the tools to ingest data from sources like GitHub and OpenAlex, store it in a structured database, and expose it for analysis and exploration. ## Key Features -* **Data Ingestion:** - * Ingest GitHub repositories via direct URL. - * Discover and ingest repositories based on keyword searches (asynchronous). -* **Scholarly Linking:** - * Extracts DOIs from repository files (e.g., README). - * Resolves DOIs and fetches metadata from OpenAlex. - * Processes citation networks (references and citations). -* **Entity Tracking:** - * Stores detailed information about Repositories, Owners (Users/Orgs), Contributors. - * Stores Scholarly Works, Persons (Authors), Institutions. - * Tracks affiliations between authors and institutions. - * Tracks dependencies listed in common package files (`requirements.txt`, `package.json`). - * Tracks GitHub Issues, Pull Requests, and associated comments. -* **Provenance:** Uses a `DiscoveryChain` system to track how data was found and linked. -* **Extensibility:** Supports custom "recipes" for: - * Affiliation detection between repositories and institutions. - * Data analysis queries. - * Repository discovery algorithms. -* **API:** Provides a RESTful API (built with FastAPI) for interacting with the ingested data and triggering processes. +* **Data Ingestion:** + * **Repository Ingestion:** Ingest GitHub repositories directly via URL, asynchronously as workers with keyword searches, or discover through connection traversal +* **Scholarly Linking:** + * **DOI Extraction:** Automatically extracts DOIs from repository files like `README.md` and `CITATION.cff`. + * **Publication Mapping:** Resolves DOIs using the OpenAlex API to fetch detailed publication metadata. + * **Citation Traversal:** Recursively processes citation networks (references and citations) to build a deeper graph. +* **Entity Tracking:** + * **Comprehensive Modeling:** Stores detailed information for repositories, repository owners (users/organizations), contributors, scholarly works, authors, and institutions. + * **Relationship Tracking:** Models affiliations between authors and institutions, and dependencies from common package manager files (e.g., `requirements.txt`, `package.json`). +* **Data Provenance:** + * **Discovery Chains:** A robust `DiscoveryChain` system tracks the origin of every piece of data, recording how it was discovered and linked. This ensures transparency and reproducibility. +* **Asynchronous Processing:** + * **Background Tasks:** Leverages Celery and Redis to handle long-running processes like repository discovery and citation traversal without blocking the API. +* **Modern API:** + * **FastAPI Backend:** A high-performance RESTful API provides endpoints for triggering ingestion and querying the knowledge graph. + * **Interactive Docs:** Automatic API documentation is available via Swagger UI and ReDoc. ## Technology Stack -* **Backend Framework:** FastAPI -* **Database:** PostgreSQL -* **ORM:** SQLAlchemy -* **Migrations:** Alembic -* **Background Tasks:** Celery -* **Message Broker / Cache:** Redis -* **HTTP Client:** Requests -* **Logging:** Python `logging`, `concurrent-log-handler` -* **Configuration:** `python-dotenv` -* **API Clients:** Custom clients for GitHub API v3 and OpenAlex API -* **Analysis (Optional):** NetworkX, python-louvain +* **Backend:** Python + uvicorn + FastAPI +* **Frontend:** Node + React (Vite) +* **Package Managers:** uv + pnpm +* **Database:** PostgreSQL +* **Background Tasks:** Celery +* **Message Broker / Cache:** Redis - ## Prerequisites +* **ORM:** SQLAlchemy +* **Migrations:** Alembic +* **HTTP Client:** Requests +* **Logging:** Python `logging`, `concurrent-log-handler` +* **Configuration:** `python-dotenv` +* **API Clients:** Custom clients for GitHub API v3 and OpenAlex API +* **Analysis (Optional):** NetworkX, python-louvain + +## Prerequisites Before you begin, ensure you have the following installed on your system: - 1. **Python:** Version 3.10 or higher is recommended. [Download Python](https://www.python.org/downloads/) - 2. **pip:** Python's package installer (usually comes with Python). - 3. **Git:** For cloning the repository. [Download Git](https://git-scm.com/downloads) - 4. **PostgreSQL:** A running PostgreSQL database server (version 12+ recommended). You'll need the ability to create a database and a user. [Download PostgreSQL](https://www.postgresql.org/download/) - 5. **Redis:** A running Redis server. Celery uses this to manage background tasks. [Download Redis](https://redis.io/docs/getting-started/installation/) or use Docker. -+6. **Node.js and npm:** For running the frontend application. Npm usually comes bundled with Node.js. [Download Node.js](https://nodejs.org/) (LTS version recommended). You can check your installation by running `node -v` and `npm -v` in your terminal. + 1. **uv:** Python package manager | [uv - Install](https://docs.astral.sh/uv/getting-started/installation/) + 2. **pnpm:** Node package manager | [pnpm - Install](https://pnpm.io/installation) + 3. **Docker:** Containerization platform | [Docker - Install](https://docs.docker.com/engine/install/) (Recommended for simplified setup of PostgreSQL and Redis) -## Setup Instructions +## Setup -Follow these steps carefully to set up the MOSS backend application: +1. **Configure Environment:** + * Copy `.env.example` to `.env` and add your `GITHUB_API_TOKEN`. This is the only variable you need to change to get started. -1. **Clone the Repository:** - Open your terminal or command prompt and run: - ```bash - git clone https://github.com/numfocus/MOSS.git - cd moss/ + ```sh + cp .env.example .env ``` -2. **Create a Virtual Environment:** - It's highly recommended to use a virtual environment to isolate project dependencies. - ```bash - python -m venv venv + * **Edit `.env` and add your GitHub Token.** This is the only variable you need to change to get started. + * `GITHUB_API_TOKEN`: Your GitHub Personal Access Token (PAT). + * Generate one at: + * Select the "Public repositories" option for repository access + +2. **Start Background Services:** + This command starts PostgreSQL and Redis using Docker Compose. + + ```sh + docker compose up -d ``` - *(This creates a `venv` directory in your project folder.)* - -3. **Activate the Virtual Environment:** - * **On macOS/Linux:** - ```bash - source venv/bin/activate - ``` - * **On Windows:** - ```bash - .\venv\Scripts\activate - ``` - *(Your terminal prompt should change to indicate the active environment, e.g., `(venv)`).* - -4. **Install Dependencies:** - Install all the required Python packages listed in `requirements.txt`: - ```bash - pip install -r requirements.txt + +3. **Set up the Database & Frontend:** + * This command, powered by `poethepoet`, runs database migrations and installs all frontend dependencies. It uses `uv run` to execute `poe` from the virtual environment without needing to activate it. + + ```sh + uv run poe setup ``` -5. **Configure Environment Variables (`.env` file):** - * Copy the example environment file: - ```bash - cp .env.example .env - ``` - * **Edit the `.env` file** using a text editor and fill in the required values: - * `DATABASE_URL`: The connection string for your PostgreSQL database. - * Format: `postgresql://:@:/` - * Example: `postgresql://moss_user:your_secure_password@localhost:5432/moss_db` - * Make sure the user (`moss_user`) and database (`moss_db`) exist and the user has privileges (see next step). - * `GITHUB_API_TOKEN`: Your GitHub Personal Access Token (PAT). - * This is needed to interact with the GitHub API (fetching repository info, etc.). - * Generate one at: [https://github.com/settings/tokens](https://github.com/settings/tokens) (use "Tokens classic"). - * Grant the `public_repo` scope for read-only access to public repositories. Keep this token secure! - * Example: `ghp_YourGitHubTokenHere` - * `OPENALEX_EMAIL`: Your email address. - * This is used to identify your requests to the OpenAlex API, placing you in their "polite pool" which might offer better rate limits. It's recommended but the application might work without it (with lower limits). - * Example: `your.email@example.com` - * `CELERY_BROKER_URL`: URL for your Redis server (used by Celery for task queuing). - * Default assumes Redis running locally on default port: `redis://localhost:6379/0` (using database 0). Adjust if your Redis is different. - * `CELERY_RESULT_BACKEND_URL`: URL for your Redis server (used by Celery to store task results). - * Default: `redis://localhost:6379/1` (using database 1, different from the broker). Adjust if needed. - -6. **Set Up PostgreSQL Database:** - * Connect to your PostgreSQL server (e.g., using `psql` or a GUI tool). - * Create the database (if it doesn't exist). **Use the name you specified in `.env`**. - ```sql - CREATE DATABASE moss_db; - ``` - * Create a user and grant privileges. **Use the username and password specified in `.env`**. - ```sql - CREATE USER moss_user WITH PASSWORD 'your_secure_password'; - GRANT ALL PRIVILEGES ON DATABASE moss_db TO moss_user; - -- Optional: Make the user the owner if needed - -- ALTER DATABASE moss_db OWNER TO moss_user; - ``` - * *(**Note:** These are example commands. Adjust them based on your PostgreSQL setup and security practices.)* - -7. **Run Database Migrations:** - This step creates all the necessary tables in your database based on the application's models. We use Alembic, managed via a script. - ```bash - python scripts/setup_db.py +4. **Run the Application:** + * This single command starts the API server, Celery worker, and frontend development server concurrently in one terminal. + + ```sh + uv run poe start ``` - *(You should see output indicating migrations are being applied. If this fails, double-check your `DATABASE_URL` in `.env` and ensure PostgreSQL is running and accessible.)* -## Running the Application + * To stop all services, press `Ctrl+C`. -The application consists of two main parts that need to run concurrently: the **API Server** and the **Celery Workers**. You will typically run these in separate terminal windows (make sure the virtual environment is activated in each). +5. **Access the Application:** + * The API documentation will be available at `http://localhost:8000/docs`. + * The frontend will be available at the URL provided by the `pnpm dev` command (usually `http://localhost:5173`). -1. **Start the API Server (FastAPI with Uvicorn):** - This makes the REST API available. - ```bash - uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 - ``` - * `backend.main:app`: Tells Uvicorn where to find the FastAPI app instance. - * `--reload`: Automatically restarts the server when code changes (useful for development). Remove this flag in production. - * `--host 0.0.0.0`: Makes the server accessible from other devices on your network (not just `localhost`). - * `--port 8000`: Specifies the port the server will listen on. - * You should see output indicating the server is running, often including `Application startup complete.` - * You can access the API documentation at `http://localhost:8000/docs` in your browser. - -2. **Start the Celery Workers:** - These processes handle background tasks like keyword discovery and DOI processing. **Make sure Redis is running before starting the workers.** - ```bash - celery -A backend.celery_app worker -l info -P eventlet -c 4 - ``` - * `-A backend.celery_app`: Points to the Celery application instance. - * `worker`: Specifies that this process should run as a worker. - * `-l info`: Sets the logging level to INFO (can be changed to DEBUG, WARNING, etc.). - * `-P eventlet`: (**Optional, Recommended**) Specifies the concurrency pool type. `eventlet` is good for I/O-bound tasks (like API calls). Requires `pip install eventlet`. If omitted, Celery might use a process-based pool. - * `-c 4`: (**Optional**) Sets the number of concurrent worker processes/threads to 4. Adjust based on your machine's resources. - * You should see output indicating the worker has connected to the broker (Redis) and is ready to receive tasks. Log messages from tasks will appear here. +## Manual Setup & Configuration + +### Python Environment Setup -## Frontend Setup and Running +This project uses `poethepoet` for task automation, which simplifies the setup process. The recommended setup above is the easiest path. If you wish to run commands manually, you can inspect the tasks defined in `pyproject.toml` under `[tool.poe.tasks]`. -The frontend application is typically developed and run separately from the backend API. +The manual steps are: -1. **Navigate to Frontend Directory:** - Open a **new terminal window** (separate from the backend server and Celery worker terminals) and navigate into the frontend directory: - ```bash - cd frontend/ +1. **Create Virtual Environment:** + + ```sh + uv venv + source .venv/bin/activate ``` -2. **Install Frontend Dependencies:** - Install the necessary Node.js packages defined in `package.json`: - ```bash - npm install +2. **Install Dependencies:** + + ```sh + uv sync + ``` + +3. **Run Database Migrations:** + + ```sh + uv run python scripts/setup_db.py ``` - *(This command downloads all the libraries the frontend needs. It might take a few minutes the first time.)* - -3. **Configure Frontend Environment (Optional):** - * The frontend might require its own environment variables (e.g., the URL of the backend API). Look for a file named `.env.development.local` or similar example files in the `frontend/` directory. - * If an example file exists (like `.env.development.local.example`), copy it: - ```bash - cp .env.development.local.example .env.development.local - ``` - * Edit the `.env.development.local` file and adjust any necessary settings, such as `VITE_API_BASE_URL` if the backend isn't running on `http://localhost:8000`. By default, it should usually point to where the backend API server is running. - -4. **Start the Frontend Development Server:** - Run the development server script: - ```bash - npm run dev + +4. **Install Frontend Dependencies:** + + ```sh + pnpm --dir frontend install ``` - *(This command typically starts a local web server for the frontend with features like automatic reloading when you change frontend code.)* -5. **Access the Frontend:** - * Once the server starts, it will usually print a URL in the terminal. Open this URL in your web browser. - * Common URLs are `http://localhost:5173` (Vite default) or `http://localhost:3000` (Create React App default). Check the terminal output for the correct one. +5. **Start the Services (in 3 separate terminals):** + * **Terminal 1: API Server** + + ```sh + uv run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 + ``` + + * **Terminal 2: Celery Worker** + + ```sh + uv run celery -A backend.celery_app worker -l info + ``` + + * **Terminal 3: Frontend Server** + + ```sh + pnpm --dir frontend dev + ``` -**Summary of Running Terminals:** +### Service Setup (PostgreSQL & Redis) -To run the full MOSS application locally for development, you will typically need **three separate terminals** running concurrently (ensure the Python virtual environment is activated in the backend terminals): +If you are not using Docker, ensure PostgreSQL and Redis are installed and running, then: -1. **Terminal 1:** Backend API Server (`uvicorn backend.main:app ...`) -2. **Terminal 2:** Celery Worker (`celery -A backend.celery_app worker ...`) -3. **Terminal 3:** Frontend Development Server (`cd frontend && npm run dev`) +* **PostgreSQL:** + 1. Create a database (e.g., `moss_db`). + 2. Create a user and password (e.g., `moss_user`). + 3. Grant the user privileges on the database. + 4. Update the `POSTGRES_*` variables and the `DATABASE_URL` in your `.env` file to match. +* **Redis:** + 1. Ensure the Redis server is running. + 2. Update `REDIS_HOST`, `REDIS_PORT`, `CELERY_BROKER_URL`, and `CELERY_RESULT_BACKEND_URL` in `.env` if your server is not on the default `localhost:6379`. -*(Remember to have PostgreSQL and Redis running in the background as well).* -## Running Database Migrations Manually +### Environment Variable Details (`.env`) + +The `.env` file is crucial for configuring the application. Here is a detailed breakdown: + +* **`POSTGRES_USER`, `POSTGRES_PASSWORD`, `POSTGRES_DB`, `POSTGRES_HOST`, `POSTGRES_PORT`**: These are used by Docker Compose to initialize the PostgreSQL container. They are also used to construct the `DATABASE_URL`. +* **`REDIS_HOST`, `REDIS_PORT`**: Used by Docker Compose and to construct the Celery URLs. +* **`DATABASE_URL`**: The full connection string for PostgreSQL, used by SQLAlchemy. Must be consistent with the `POSTGRES_*` variables. +* **`CELERY_BROKER_URL`**: The URL for your Redis server (or other message broker) for task queuing. +* **`CELERY_RESULT_BACKEND_URL`**: The URL for your Redis server to store task results. +* **`GITHUB_API_TOKEN`**: **(Required)** Your GitHub Personal Access Token (PAT) for interacting with the GitHub API. +* **`OPENALEX_EMAIL`**: **(Recommended)** Your email address for the OpenAlex API "polite pool" to get better rate limits. +* **`VITE_API_BASE_URL`**: The base URL for the backend API, used by the frontend. + +## Database Migrations If you make changes to the database models (`backend/data/models/`) later, you will need to: -1. **Generate a new migration script:** - ```bash +1. **Generate a new migration script:** + + ```sh alembic revision --autogenerate -m "Short description of changes" ``` + *(Review the generated script in `backend/data/migrations/versions/`)* -2. **Apply the migration:** - ```bash - python scripts/setup_db.py +2. **Apply the migration:** + + ```sh + uv run python scripts/setup_db.py ``` + *(Alternatively, you can use `alembic upgrade head`)* ## Directory Structure A high-level overview of the project structure: -* `moss/`: Project root. - * `backend/`: Contains all the backend code (API, services, data layer). - * `api/`: FastAPI endpoints and dependencies. - * `config/`: Configuration loading (`settings.py`) and logging (`logging_config.py`). - * `data/`: Database interaction (models, repositories, migrations). - * `external/`: Clients for external APIs (GitHub, OpenAlex). - * `schemas/`: Pydantic models for API request/response validation. - * `services/`: Business logic layer. - * `tasks/`: Celery background task definitions. - * `utils/`: Shared utility functions. - * `contrib/`: Location for contributed "recipe" scripts (analysis, affiliation, discovery). - * `frontend/`: Contains the React frontend code (setup instructions not covered here). - * `logs/`: Where log files (`moss_api.log`, `moss_celery.log`) are stored. - * `scripts/`: Helper scripts (database setup). - -## Configuration Summary (`.env`) - -The `.env` file is crucial for configuring the application. Key variables: - -* `DATABASE_URL`: Connection string for PostgreSQL. -* `GITHUB_API_TOKEN`: Essential for interacting with GitHub. -* `OPENALEX_EMAIL`: Recommended for better OpenAlex API access. -* `CELERY_BROKER_URL`: Connection URL for Redis (or other broker). -* `CELERY_RESULT_BACKEND_URL`: Connection URL for Redis (or other backend). +* `moss/`: Project root. + * `backend/`: Contains all the backend code (API, services, data layer). + * `api/`: FastAPI endpoints and dependencies. + * `config/`: Configuration loading (`settings.py`) and logging (`logging_config.py`). + * `data/`: Database interaction (models, repositories, migrations). + * `external/`: Clients for external APIs (GitHub, OpenAlex). + * `schemas/`: Pydantic models for API request/response validation. + * `services/`: Business logic layer. + * `tasks/`: Celery background task definitions. + * `utils/`: Shared utility functions. + * `contrib/`: Location for contributed "recipe" scripts (analysis, affiliation, discovery). + * `frontend/`: Contains the React frontend code (setup instructions not covered here). + * `logs/`: Where log files (`moss_api.log`, `moss_celery.log`) are stored. + * `scripts/`: Helper scripts (database setup). diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..ae76ffa --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,43 @@ +# +# MOSS - Background Services +# +# This file defines the background services required for the MOSS application, +# which are managed by Docker Compose. It sets up PostgreSQL for the database +# and Redis to serve as the Celery message broker and result backend. +# +# Environment variables are sourced from the `.env` file. +# +# Usage: +# - Start services: `docker compose up -d` +# - Stop services: `docker compose down` +# +name: moss + +services: + postgres: + image: postgres:16 + container_name: moss_postgres + volumes: + - moss_postgres_data:/var/lib/postgresql/data + environment: + POSTGRES_USER: ${POSTGRES_USER:-moss_user} + POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-your_secure_password} + POSTGRES_DB: ${POSTGRES_DB:-moss_db} + ports: + - '127.0.0.1:${POSTGRES_PORT:-5432}:5432' + restart: unless-stopped + + redis: + image: redis:7 + container_name: moss_redis + volumes: + - moss_redis_data:/data + ports: + - '127.0.0.1:${REDIS_PORT:-6379}:6379' + restart: unless-stopped + +volumes: + moss_postgres_data: + moss_redis_data: + + diff --git a/frontend/.gitignore b/frontend/.gitignore deleted file mode 100644 index f8c145c..0000000 --- a/frontend/.gitignore +++ /dev/null @@ -1,41 +0,0 @@ -# Dependencies -/node_modules/ - -# Build output -/dist/ -/build/ -# Add other build output folders if applicable - -# Logs -logs -*.log -npm-debug.log* -yarn-debug.log* -yarn-error.log* -pnpm-debug.log* -lerna-debug.log* - -# Environment variables -.env.*.local -.env.local -.env.*.test -.env.test -.env.*.production -.env.production - -# Editor directories and files -.vscode/* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -.idea -*.suo -*.ntvs* -*.njsproj -*.sln -*.sw? - -# OS generated files -.DS_Store -Thumbs.db \ No newline at end of file diff --git a/frontend/package-lock.json b/frontend/package-lock.json deleted file mode 100644 index 4efaa2f..0000000 --- a/frontend/package-lock.json +++ /dev/null @@ -1,5412 +0,0 @@ -{ - "name": "frontend", - "version": "0.0.0", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "frontend", - "version": "0.0.0", - "dependencies": { - "axios": "^1.8.4", - "react": "^19.0.0", - "react-dom": "^19.0.0", - "react-router-dom": "^7.5.0" - 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"axios": "^1.8.4", - "react": "^19.0.0", - "react-dom": "^19.0.0", - "react-router-dom": "^7.5.0" + "axios": "^1.10.0", + "react": "^19.1.0", + "react-dom": "^19.1.0", + "react-router-dom": "^7.6.2", + "reactflow": "^11.11.4" }, "devDependencies": { - "@eslint/js": "^9.21.0", - "@types/react": "^19.0.10", - "@types/react-dom": "^19.0.4", - "@typescript-eslint/eslint-plugin": "^8.29.1", - "@typescript-eslint/parser": "^8.29.1", - "@vitejs/plugin-react": "^4.3.4", - "eslint": "^9.24.0", - "eslint-config-prettier": "^10.1.1", - "eslint-plugin-prettier": "^5.2.6", + "@eslint/js": "^9.29.0", + "@types/react": "^19.1.8", + "@types/react-dom": "^19.1.6", + "@typescript-eslint/eslint-plugin": "^8.35.0", + "@typescript-eslint/parser": "^8.35.0", + "@vitejs/plugin-react": "^4.6.0", + "eslint": "^9.29.0", + "eslint-config-prettier": "^10.1.5", + "eslint-plugin-prettier": "^5.5.1", "eslint-plugin-react": "^7.37.5", "eslint-plugin-react-hooks": "^5.2.0", - "eslint-plugin-react-refresh": "^0.4.19", - "globals": "^15.15.0", - "prettier": "^3.5.3", - "typescript": "~5.7.2", - "typescript-eslint": "^8.24.1", - "vite": "^6.2.0" + "eslint-plugin-react-refresh": "^0.4.20", + "globals": "^16.2.0", + "prettier": "^3.6.1", + "typescript": "~5.8.3", + "typescript-eslint": "^8.35.0", + "vite": "^7.0.0" } } diff --git a/frontend/pnpm-workspace.yaml b/frontend/pnpm-workspace.yaml new file mode 100644 index 0000000..4dca4c0 --- /dev/null +++ b/frontend/pnpm-workspace.yaml @@ -0,0 +1,5 @@ +packages: + - 'frontend' + +onlyBuiltDependencies: + - esbuild diff --git a/frontend/src/services/apiClient.ts b/frontend/src/services/apiClient.ts index 6e30fb0..7c1601a 100644 --- a/frontend/src/services/apiClient.ts +++ b/frontend/src/services/apiClient.ts @@ -12,7 +12,7 @@ import axios, { AxiosError } from 'axios'; // --- Axios Client Configuration --- /** Base URL for the MOSS API. Reads from environment variable VITE_API_BASE_URL or defaults to /api/v1. */ -const API_BASE_URL = import.meta.env.VITE_API_BASE_URL || '/api/v1'; +const API_BASE_URL = import.meta.env.VITE_API_BASE_URL || 'http://0.0.0.0:8000/api/v1'; /** Configured Axios instance for API requests. */ const apiClient = axios.create({ diff --git a/frontend/tsconfig.app.json b/frontend/tsconfig.app.json new file mode 100644 index 0000000..edd794f --- /dev/null +++ b/frontend/tsconfig.app.json @@ -0,0 +1,10 @@ +{ + "extends": "./tsconfig.json", + "compilerOptions": { + "composite": true, + "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.app.tsbuildinfo" + }, + "include": [ + "src" + ] +} diff --git a/frontend/tsconfig.json b/frontend/tsconfig.json index 1ffef60..95988c0 100644 --- a/frontend/tsconfig.json +++ b/frontend/tsconfig.json @@ -1,7 +1,25 @@ { - "files": [], - "references": [ - { "path": "./tsconfig.app.json" }, - { "path": "./tsconfig.node.json" } - ] -} + "compilerOptions": { + "target": "ESNext", + "useDefineForClassFields": true, + "lib": ["ESNext", "DOM", "DOM.Iterable"], + "module": "ESNext", + "skipLibCheck": true, + + /* Bundler mode */ + "moduleResolution": "bundler", + "allowImportingTsExtensions": true, + "resolveJsonModule": true, + "isolatedModules": true, + "noEmit": true, + "jsx": "react-jsx", + + /* Linting */ + "strict": true, + "noUnusedLocals": true, + "noUnusedParameters": true, + "noFallthroughCasesInSwitch": true + }, + "include": ["src", "vite.config.ts"], + "references": [{ "path": "./tsconfig.app.json" }] +} \ No newline at end of file diff --git a/frontend/tsconfig.node.json b/frontend/tsconfig.node.json deleted file mode 100644 index db0becc..0000000 --- a/frontend/tsconfig.node.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "compilerOptions": { - "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo", - "target": "ES2022", - "lib": ["ES2023"], - "module": "ESNext", - "skipLibCheck": true, - - /* Bundler mode */ - "moduleResolution": "bundler", - "allowImportingTsExtensions": true, - "isolatedModules": true, - "moduleDetection": "force", - "noEmit": true, - - /* Linting */ - "strict": true, - "noUnusedLocals": true, - "noUnusedParameters": true, - "noFallthroughCasesInSwitch": true, - "noUncheckedSideEffectImports": true - }, - "include": ["vite.config.ts"] -} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..16900a2 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,55 @@ +[project] +name = "moss" +version = "0.1.0" +description = "MOSS (Map of Open Source Science) is a backend application designed to build a knowledge graph about open source scientific software" +readme = "README.md" +requires-python = ">=3.13" +license = { text = "Apache-2.0" } +authors = [ + { name = "The MOSS Authors", email = "jon@numfocus.org" }, +] +keywords = ["knowledge-graph", "open-source", "research software", "science", "github", "openalex"] +dependencies = [ + "alembic>=1.16.1", + "celery[redis]>=5.5.3", + "concurrent-log-handler>=0.9.26", + "fastapi>=0.115.12", + "psycopg2-binary>=2.9.10", + "python-dotenv>=1.1.0", + "requests>=2.32.3", + "sqlalchemy>=2.0.41", + "uvicorn>=0.34.3", +] + +[project.urls] +Homepage = "https://www.opensource.science" +Repository = "https://github.com/numfocus/MOSS" +"Bug Tracker" = "https://github.com/numfocus/MOSS/issues" + +[dependency-groups] +dev = [ + "poethepoet>=0.36.0", +] +analysis = [ + "networkx>=3.5", + "python-louvain>=0.16", +] + +[tool.poe.tasks] +# --- Setup Tasks --- +setup-db = { cmd = "uv run python scripts/setup_db.py", help = "Run database migrations to set up the schema." } +install-frontend = { cmd = "pnpm --dir frontend install", help = "Install frontend dependencies." } +setup = { sequence = ["install-frontend", "setup-db"], help = "Set up the database and install frontend dependencies." } + +# --- Individual Services --- +api = { cmd = "uv run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000", help = "Run the FastAPI API server." } +worker = { cmd = "uv run celery -A backend.celery_app worker -l info", help = "Run the Celery background worker." } +frontend = { cmd = "pnpm --dir frontend dev", help = "Run the frontend development server." } + +# --- Concurrent Development Server --- +start = { shell = """ +uv run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 & +uv run celery -A backend.celery_app worker -l info & +pnpm --dir frontend dev & +wait +""", help = "Run the API, worker, and frontend concurrently for development." } diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 27a278d..0000000 --- a/requirements.txt +++ /dev/null @@ -1,34 +0,0 @@ -# --- UPDATED FILE: requirements.txt --- - -# Configuration -python-dotenv - -# Database ORM and Migrations -SQLAlchemy -psycopg2-binary # For PostgreSQL connection (use non-binary in production if needed) -alembic - -# HTTP Requests -requests - -# UUID Generation (Needed for DiscoveryChain ID) - Standard library 'uuid' used. - -# --- ADDED FOR PHASE 2 API --- -# Web Framework -fastapi - -concurrent-log-handler>=0.9.23 # Or latest version - -# ASGI Server -uvicorn[standard] # Includes standard extras like httptools, websockets -# --- END ADDED FOR PHASE 2 API --- - -# Background Task Queue -celery>=5.3.6 # Use a specific recent version -redis>=5.0.4 - -# --- ADDED FOR PHASE 17 Analysis --- -# Graph Analysis -networkx>=3.0 # Use version 3+ -python-louvain # For Louvain community detection -# --- END ADDED FOR PHASE 17 Analysis --- \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index e69de29..0000000