From e60e4182e55b310db2329e6d781d5a42425e0a9a Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Wed, 11 Jun 2025 16:04:09 -0400 Subject: [PATCH 01/10] added uv and pnpm, updated readme --- .env.example | 22 +- .gitignore | 1 + README.md | 399 ++-- docker-compose.yml | 27 + frontend/package.json | 3 +- frontend/pnpm-lock.yaml | 3910 ++++++++++++++++++++++++++++++++++ frontend/pnpm-workspace.yaml | 2 + frontend/tsconfig.app.json | 10 + frontend/tsconfig.json | 30 +- frontend/tsconfig.node.json | 24 - main.py | 6 + pyproject.toml | 20 + requirements.txt | 2 - setup.py | 0 uv.lock | 646 ++++++ 15 files changed, 4897 insertions(+), 205 deletions(-) create mode 100644 docker-compose.yml create mode 100644 frontend/pnpm-lock.yaml create mode 100644 frontend/pnpm-workspace.yaml create mode 100644 frontend/tsconfig.app.json delete mode 100644 frontend/tsconfig.node.json create mode 100644 main.py create mode 100644 pyproject.toml delete mode 100644 setup.py create mode 100644 uv.lock diff --git a/.env.example b/.env.example index c514d18..02ecf95 100644 --- a/.env.example +++ b/.env.example @@ -1,18 +1,26 @@ # Example Environment Variables - Copy to .env and fill in values -# --- Database --- -# Example format: postgresql://user:password@host:port/dbname +# --- PostgreSQL Configuration --- +POSTGRES_USER=moss_user +POSTGRES_PASSWORD=your_secure_password +POSTGRES_DB=moss_db +POSTGRES_HOST=localhost +POSTGRES_PORT=5432 + +# --- Redis Configuration --- +REDIS_HOST=localhost +REDIS_PORT=6379 + +# --- Application URLs (used directly by the Python application) --- 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) 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://localhost:8000/api/v1 \ No newline at end of file diff --git a/.gitignore b/.gitignore index 04fb7d5..f15df34 100644 --- a/.gitignore +++ b/.gitignore @@ -16,6 +16,7 @@ eggs/ .eggs/ lib/ lib64/ +logs/ parts/ sdist/ var/ diff --git a/README.md b/README.md index 5695c71..9ca5633 100644 --- a/README.md +++ b/README.md @@ -10,245 +10,314 @@ The system uses a FastAPI web framework for its API, PostgreSQL as the database, ## 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:** + * 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. ## 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. **Python:** Version 3.13 or higher. [Download Python](https://www.python.org/downloads/) + 2. **uv:** Python's package installer. [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) + 3. **Git:** For cloning the repository. [Download Git](https://git-scm.com/downloads) + 4. **Node.js and pnpm:** For the frontend. Download Node.js (LTS recommended). pnpm can be installed via various methods. pnpm - Installation + 5. **Docker and Docker Compose:** (Recommended for simplified setup of PostgreSQL and Redis). Install Docker and Docker Compose. + 6. **Alternatively, for manual setup of services:** + * **PostgreSQL:** Version 12+ recommended. Download PostgreSQL + * **Redis:** Download Redis ## Setup Instructions Follow these steps carefully to set up the MOSS backend application: -1. **Clone the Repository:** +1. **Clone the Repository:** Open your terminal or command prompt and run: - ```bash - git clone https://github.com/numfocus/MOSS.git - cd moss/ + + ```sh + git clone https://github.com/numfocus/MOSS/ + cd MOSS/ + ``` + +2. **Install uv** + As described here: [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) + + ```sh + curl -LsSf https://astral.sh/uv/install.sh | sh + ``` + + ```pwsh + winget install --id=astral-sh.uv -e ``` -2. **Create a Virtual Environment:** - It's highly recommended to use a virtual environment to isolate project dependencies. - ```bash - python -m venv venv +3. **Install pnpm** + As described here: [pnpm - Installation](https://pnpm.io/installation) + + ```sh + curl -fsSL https://get.pnpm.io/install.sh | sh - + ``` + + ```pwsh + winget install -e --id pnpm.pnpm + ``` + +4. **Create a Virtual Environment**: + Use uv to install setup virtual environment. + + ```sh + uv python install 3.13 # Install python + uv venv # create virtual environment in current folder ``` - *(This creates a `venv` directory in your project folder.)* -3. **Activate the Virtual Environment:** - * **On macOS/Linux:** - ```bash - source venv/bin/activate +5. **Activate the Virtual Environment:** + * **On macOS/Linux:** + + ```sh + source .venv/bin/activate ``` - * **On Windows:** - ```bash - .\venv\Scripts\activate + + * **On Windows:** + + ```pwsh + venv\Scripts\activate.bat ``` + *(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 +6. **Install Dependencies:** + Install all the required Python packages listed in `pyproject.toml`: + + ```sh + uv sync ``` -5. **Configure Environment Variables (`.env` file):** - * Copy the example environment file: - ```bash +7. **Configure Environment Variables (`.env` file):** + * Copy the example environment file: + + ```sh 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; + + * **Edit the `.env` file** using a text editor and fill in the required values: + * **PostgreSQL Configuration (for Docker Compose & App):** + * `POSTGRES_USER`: Username for PostgreSQL (e.g., `moss_user`). Used by Docker Compose to create the user. + * `POSTGRES_PASSWORD`: Password for the PostgreSQL user. Used by Docker Compose. + * `POSTGRES_DB`: Database name (e.g., `moss_db`). Used by Docker Compose to create the database. + * `POSTGRES_HOST`: Hostname for PostgreSQL (e.g., `localhost` when connecting from your app to the Docker container via mapped port). + * `POSTGRES_PORT`: Port for PostgreSQL (e.g., `5432`). Used by Docker Compose to map the port. + * **Redis Configuration (for Docker Compose & App):** + * `REDIS_HOST`: Hostname for Redis (e.g., `localhost` when connecting from your app to the Docker container via mapped port). + * `REDIS_PORT`: Port for Redis (e.g., `6379`). Used by Docker Compose to map the port. + * **Application Connection URLs (used by the Python application):** + * `DATABASE_URL`: Full connection string for PostgreSQL, used by SQLAlchemy. + * Example: `postgresql://moss_user:your_secure_password@localhost:5432/moss_db` + * This URL should be consistent with the `POSTGRES_USER`, `POSTGRES_PASSWORD`, `POSTGRES_DB`, `POSTGRES_HOST`, and `POSTGRES_PORT` variables. + * `CELERY_BROKER_URL`: Full URL for your Redis server, used by Celery for task queuing. + * Example: `redis://localhost:6379/0` (using Redis database 0). + * This URL should be consistent with `REDIS_HOST` and `REDIS_PORT`. + * `CELERY_RESULT_BACKEND_URL`: Full URL for your Redis server, used by Celery for storing task results. + * Example: `redis://localhost:6379/1` (using Redis database 1). + * This URL should be consistent with `REDIS_HOST` and `REDIS_PORT`. + * `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. + * Used for the OpenAlex API "polite pool" for potentially better rate limits. See OpenAlex documentation. + * Example: `your.email@example.com` + * `VITE_API_BASE_URL`: URL for the backend API, used by the frontend. + * Default: `http://localhost:8000/api/v1`. + +8. **Set Up PostgreSQL and Redis Services:** + + **Option 1: Using Docker (Recommended)** + This is the simplest way to get PostgreSQL and Redis running. Ensure Docker and Docker Compose are installed. + A `docker-compose.yml` file is provided in the project root. It uses the `POSTGRES_*` and `REDIS_*` variables from your `.env` file to configure the services. + Start the services in detached mode: + + ```sh + docker-compose up -d + ``` + + This will automatically create the PostgreSQL database and user specified in your `.env` file. + To stop the services: `docker-compose down` + + **Option 2: Manual Setup** + If you prefer to manage PostgreSQL and Redis manually: + + **PostgreSQL:** + * Ensure your PostgreSQL server is running. + * Connect to your PostgreSQL server (e.g., using `psql` or a GUI tool). + * Create the database (use the name from `POSTGRES_DB` in `.env`): + + ```sh + createdb your_db_name # Example: createdb moss_db ``` - * Create a user and grant privileges. **Use the username and password specified in `.env`**. + + Or using SQL: `CREATE DATABASE your_db_name;` + * Create a user and grant privileges (use credentials from `POSTGRES_USER` and `POSTGRES_PASSWORD` 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; + CREATE USER your_user WITH PASSWORD 'your_password'; + GRANT ALL PRIVILEGES ON DATABASE your_db_name TO your_user; + -- Optional: ALTER DATABASE your_db_name OWNER TO your_user; ``` - * *(**Note:** These are example commands. Adjust them based on your PostgreSQL setup and security practices.)* -7. **Run Database Migrations:** + * *(**Note:** Adjust commands based on your PostgreSQL setup and security practices.)* + + **Redis:** + * Ensure your Redis server is running and accessible on the host and port specified in `REDIS_HOST` and `REDIS_PORT` in your `.env` file. + +9. **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 + + ```sh python scripts/setup_db.py ``` - *(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.)* + + *(You should see output indicating migrations are being applied. If this fails, double-check your `.env` configuration and ensure PostgreSQL is running and accessible.)* + +10. **Install node and frontent dependencies:** + Install all the required node packages listed in `package.json`: + + ```sh + cd frontend/ + pnpm env use --global 24 + pnpm install + ``` ## Running the Application 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). -1. **Start the API Server (FastAPI with Uvicorn):** +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. -## Frontend Setup and Running + ```sh + ur run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 + ``` -The frontend application is typically developed and run separately from the backend API. + * `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. -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/ - ``` +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.** -2. **Install Frontend Dependencies:** - Install the necessary Node.js packages defined in `package.json`: - ```bash - npm install + ```sh + uv run celery -A backend.celery_app worker -l info ``` - *(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. + * `-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.). -4. **Start the Frontend Development Server:** +3. **Start the Frontend Development Server:** Run the development server script: - ```bash - npm run dev + + ```sh + pnpm dev ``` + *(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. +4. **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). **Summary of Running Terminals:** 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): -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`) +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`) *(Remember to have PostgreSQL and Redis running in the background as well).* + ## Running Database Migrations Manually 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 +2. **Apply the migration:** + + ```sh 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). +* `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). +* `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). +* `VITE_API_BASE_URL`: URL for the backend API diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..bb56948 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,27 @@ +services: + postgres: + image: postgres:16 + container_name: moss_postgres + environment: + POSTGRES_USER: ${POSTGRES_USER:-moss_user} + POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-your_secure_password} + POSTGRES_DB: ${POSTGRES_DB:-moss_db} + ports: + - "${POSTGRES_PORT:-5432}:5432" + volumes: + - moss_postgres_data:/var/lib/postgresql/data + restart: unless-stopped + + redis: + image: redis:7 + container_name: moss_redis + ports: + - "${REDIS_PORT:-6379}:6379" + volumes: + - moss_redis_data:/data + restart: unless-stopped + +volumes: + moss_postgres_data: + moss_redis_data: + diff --git a/frontend/package.json b/frontend/package.json index 757dfc6..ab748b8 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -13,7 +13,8 @@ "axios": "^1.8.4", "react": "^19.0.0", "react-dom": "^19.0.0", - "react-router-dom": "^7.5.0" + "react-router-dom": "^7.5.0", + "reactflow": "^11.11.4" }, "devDependencies": { "@eslint/js": "^9.21.0", diff --git a/frontend/pnpm-lock.yaml b/frontend/pnpm-lock.yaml new file mode 100644 index 0000000..c0d39b3 --- /dev/null +++ b/frontend/pnpm-lock.yaml @@ -0,0 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++++--------- frontend/package.json | 38 +- frontend/pnpm-lock.yaml | 675 +++++++++++++++-------------- frontend/src/services/apiClient.ts | 2 +- main.py | 6 - pyproject.toml | 43 +- requirements.txt | 32 -- uv.lock | 193 ++++++--- 9 files changed, 622 insertions(+), 670 deletions(-) delete mode 100644 main.py delete mode 100644 requirements.txt diff --git a/.env.example b/.env.example index 02ecf95..0d9dabc 100644 --- a/.env.example +++ b/.env.example @@ -1,17 +1,17 @@ -# Example Environment Variables - Copy to .env and fill in values +# Example Environment Variables -# --- PostgreSQL Configuration --- +# --- PostgreSQL Config --- POSTGRES_USER=moss_user POSTGRES_PASSWORD=your_secure_password POSTGRES_DB=moss_db POSTGRES_HOST=localhost POSTGRES_PORT=5432 -# --- Redis Configuration --- +# --- Redis Config --- REDIS_HOST=localhost REDIS_PORT=6379 -# --- Application URLs (used directly by the Python application) --- +# --- 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 @@ -23,4 +23,4 @@ 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 -VITE_API_BASE_URL=http://localhost:8000/api/v1 \ 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/README.md b/README.md index 9ca5633..36d1bb7 100644 --- a/README.md +++ b/README.md @@ -4,31 +4,30 @@ ## 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"). +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 it's intersection with academia and scientific publication. It aims to construct a knowledge graph system and reproducible framework for modeling public repositories, academic publications, and the contributing entities and relationships between them. This is accomplished by structured integration of data obtained through overlapping web traversal and graph construction strategies, grounded on existing schema and ontologies such as using context driven rules such as direct or mentioned DOI linking (`https://doi.org/10.1000/100` vs `

https://doi.org/10.1000/100

`), and care is taken to conform to existing schema based systems (OpenAlex topics, Schema.org entities) -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. +The Map of Open Source Science (MOSS) is a platform that reveals the hidden connections between research software and academic scholarship. It builds a rich knowledge graph of the research ecosystem by ingesting data about software repositories, scholarly publications, researchers, and institutions. By linking these entities, MOSS helps answer critical questions about the impact, sustainability, and collaborative nature of open source in science. + +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). + * **Repository Ingestion:** Ingest GitHub repositories directly via URL, asynchronously as workers with keyword searches, or discover through connection traversal * **Scholarly Linking:** - * Extracts DOIs from repository files (e.g., README). - * Resolves DOIs and fetches metadata from OpenAlex. - * Processes citation networks (references and citations). + * **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:** - * 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. + * **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 @@ -51,228 +50,133 @@ The system uses a FastAPI web framework for its API, PostgreSQL as the database, Before you begin, ensure you have the following installed on your system: - 1. **Python:** Version 3.13 or higher. [Download Python](https://www.python.org/downloads/) - 2. **uv:** Python's package installer. [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) - 3. **Git:** For cloning the repository. [Download Git](https://git-scm.com/downloads) - 4. **Node.js and pnpm:** For the frontend. Download Node.js (LTS recommended). pnpm can be installed via various methods. pnpm - Installation - 5. **Docker and Docker Compose:** (Recommended for simplified setup of PostgreSQL and Redis). Install Docker and Docker Compose. - 6. **Alternatively, for manual setup of services:** - * **PostgreSQL:** Version 12+ recommended. Download PostgreSQL - * **Redis:** Download Redis - -## Setup Instructions + 1. **uv:** Python package manager | [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) + 2. **pnpm:** Node package manager | [pnpm - Installation](https://pnpm.io/installation) + 3a. **Docker and Docker Compose:** (Recommended for simplified setup of PostgreSQL and Redis). Install Docker and Docker Compose. + 3b. **Alternatively, for manual setup of services:** + * **PostgreSQL:** Version 12+ + * **Redis:** Version 6+ -Follow these steps carefully to set up the MOSS backend application: +## Setup -1. **Clone the Repository:** - Open your terminal or command prompt and run: +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. ```sh - git clone https://github.com/numfocus/MOSS/ - cd MOSS/ + cp .env.example .env ``` -2. **Install uv** - As described here: [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) + * **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: (use "Tokens classic"). + * Grant the `public_repo` scope for read-only access to public repositories. - ```sh - curl -LsSf https://astral.sh/uv/install.sh | sh - ``` +2. **Start Background Services:** + This command starts PostgreSQL and Redis using Docker Compose. - ```pwsh - winget install --id=astral-sh.uv -e + ```sh + docker compose up -d ``` -3. **Install pnpm** - As described here: [pnpm - Installation](https://pnpm.io/installation) +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 - curl -fsSL https://get.pnpm.io/install.sh | sh - - ``` - - ```pwsh - winget install -e --id pnpm.pnpm + uv run poe setup ``` -4. **Create a Virtual Environment**: - Use uv to install setup virtual environment. +4. **Run the Application:** + * This single command starts the API server, Celery worker, and frontend development server concurrently in one terminal. ```sh - uv python install 3.13 # Install python - uv venv # create virtual environment in current folder + uv run poe start ``` -5. **Activate the Virtual Environment:** - * **On macOS/Linux:** + * To stop all services, press `Ctrl+C`. - ```sh - source .venv/bin/activate - ``` +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`). - * **On Windows:** +## Manual Setup & Configuration - ```pwsh - venv\Scripts\activate.bat - ``` +### Manual Python Environment Setup - *(Your terminal prompt should change to indicate the active environment, e.g., `(venv)`).* +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]`. -6. **Install Dependencies:** - Install all the required Python packages listed in `pyproject.toml`: +The manual steps are: - ```sh - uv sync - ``` - -7. **Configure Environment Variables (`.env` file):** - * Copy the example environment file: - - ```sh - cp .env.example .env - ``` - - * **Edit the `.env` file** using a text editor and fill in the required values: - * **PostgreSQL Configuration (for Docker Compose & App):** - * `POSTGRES_USER`: Username for PostgreSQL (e.g., `moss_user`). Used by Docker Compose to create the user. - * `POSTGRES_PASSWORD`: Password for the PostgreSQL user. Used by Docker Compose. - * `POSTGRES_DB`: Database name (e.g., `moss_db`). Used by Docker Compose to create the database. - * `POSTGRES_HOST`: Hostname for PostgreSQL (e.g., `localhost` when connecting from your app to the Docker container via mapped port). - * `POSTGRES_PORT`: Port for PostgreSQL (e.g., `5432`). Used by Docker Compose to map the port. - * **Redis Configuration (for Docker Compose & App):** - * `REDIS_HOST`: Hostname for Redis (e.g., `localhost` when connecting from your app to the Docker container via mapped port). - * `REDIS_PORT`: Port for Redis (e.g., `6379`). Used by Docker Compose to map the port. - * **Application Connection URLs (used by the Python application):** - * `DATABASE_URL`: Full connection string for PostgreSQL, used by SQLAlchemy. - * Example: `postgresql://moss_user:your_secure_password@localhost:5432/moss_db` - * This URL should be consistent with the `POSTGRES_USER`, `POSTGRES_PASSWORD`, `POSTGRES_DB`, `POSTGRES_HOST`, and `POSTGRES_PORT` variables. - * `CELERY_BROKER_URL`: Full URL for your Redis server, used by Celery for task queuing. - * Example: `redis://localhost:6379/0` (using Redis database 0). - * This URL should be consistent with `REDIS_HOST` and `REDIS_PORT`. - * `CELERY_RESULT_BACKEND_URL`: Full URL for your Redis server, used by Celery for storing task results. - * Example: `redis://localhost:6379/1` (using Redis database 1). - * This URL should be consistent with `REDIS_HOST` and `REDIS_PORT`. - * `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. - * Used for the OpenAlex API "polite pool" for potentially better rate limits. See OpenAlex documentation. - * Example: `your.email@example.com` - * `VITE_API_BASE_URL`: URL for the backend API, used by the frontend. - * Default: `http://localhost:8000/api/v1`. - -8. **Set Up PostgreSQL and Redis Services:** - - **Option 1: Using Docker (Recommended)** - This is the simplest way to get PostgreSQL and Redis running. Ensure Docker and Docker Compose are installed. - A `docker-compose.yml` file is provided in the project root. It uses the `POSTGRES_*` and `REDIS_*` variables from your `.env` file to configure the services. - Start the services in detached mode: +1. **Create Virtual Environment:** ```sh - docker-compose up -d + uv venv + source .venv/bin/activate ``` - This will automatically create the PostgreSQL database and user specified in your `.env` file. - To stop the services: `docker-compose down` - - **Option 2: Manual Setup** - If you prefer to manage PostgreSQL and Redis manually: - - **PostgreSQL:** - * Ensure your PostgreSQL server is running. - * Connect to your PostgreSQL server (e.g., using `psql` or a GUI tool). - * Create the database (use the name from `POSTGRES_DB` in `.env`): - - ```sh - createdb your_db_name # Example: createdb moss_db - ``` - - Or using SQL: `CREATE DATABASE your_db_name;` - * Create a user and grant privileges (use credentials from `POSTGRES_USER` and `POSTGRES_PASSWORD` in `.env`): - - ```sql - CREATE USER your_user WITH PASSWORD 'your_password'; - GRANT ALL PRIVILEGES ON DATABASE your_db_name TO your_user; - -- Optional: ALTER DATABASE your_db_name OWNER TO your_user; - ``` - - * *(**Note:** Adjust commands based on your PostgreSQL setup and security practices.)* - - **Redis:** - * Ensure your Redis server is running and accessible on the host and port specified in `REDIS_HOST` and `REDIS_PORT` in your `.env` file. - -9. **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. +2. **Install Dependencies:** ```sh - python scripts/setup_db.py + uv sync ``` - *(You should see output indicating migrations are being applied. If this fails, double-check your `.env` configuration and ensure PostgreSQL is running and accessible.)* - -10. **Install node and frontent dependencies:** - Install all the required node packages listed in `package.json`: +3. **Run Database Migrations:** ```sh - cd frontend/ - pnpm env use --global 24 - pnpm install + uv run python scripts/setup_db.py ``` -## Running the Application - -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). - -1. **Start the API Server (FastAPI with Uvicorn):** - This makes the REST API available. +4. **Install Frontend Dependencies:** ```sh - ur run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 + pnpm --dir frontend install ``` - * `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. +5. **Start the Services (in 3 separate terminals):** + * **Terminal 1: API Server** -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.** + ```sh + uv run uvicorn backend.main:app --reload --host 0.0.0.0 --port 8000 + ``` - ```sh - uv run celery -A backend.celery_app worker -l info - ``` + * **Terminal 2: Celery Worker** - * `-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.). + ```sh + uv run celery -A backend.celery_app worker -l info + ``` -3. **Start the Frontend Development Server:** - Run the development server script: + * **Terminal 3: Frontend Server** - ```sh - pnpm dev - ``` + ```sh + pnpm --dir frontend dev + ``` - *(This command typically starts a local web server for the frontend with features like automatic reloading when you change frontend code.)* +### Manual Service Setup (PostgreSQL & Redis) -4. **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). +If you are not using Docker, ensure PostgreSQL and Redis are installed and running, then: -**Summary of Running Terminals:** +* **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`. -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): +### Environment Variable Details (`.env`) -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`) +The `.env` file is crucial for configuring the application. Here is a detailed breakdown: -*(Remember to have PostgreSQL and Redis running in the background as well).* +* **`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. -## Running Database Migrations Manually +## Manual Database Migrations If you make changes to the database models (`backend/data/models/`) later, you will need to: @@ -287,7 +191,7 @@ If you make changes to the database models (`backend/data/models/`) later, you w 2. **Apply the migration:** ```sh - python scripts/setup_db.py + uv run python scripts/setup_db.py ``` *(Alternatively, you can use `alembic upgrade head`)* @@ -310,14 +214,3 @@ A high-level overview of the project structure: * `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). -* `VITE_API_BASE_URL`: URL for the backend API diff --git a/frontend/package.json b/frontend/package.json index ab748b8..c8f628d 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -10,29 +10,29 @@ "preview": "vite preview" }, "dependencies": { - "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", - 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vite: 6.3.5 + vite: 7.0.0 transitivePeerDependencies: - supports-color @@ -2639,7 +2642,7 @@ snapshots: dependencies: possible-typed-array-names: 1.1.0 - axios@1.9.0: + axios@1.10.0: dependencies: follow-redirects: 1.15.9 form-data: 4.0.3 @@ -2662,12 +2665,12 @@ snapshots: dependencies: fill-range: 7.1.1 - browserslist@4.25.0: + browserslist@4.25.1: dependencies: - caniuse-lite: 1.0.30001722 - electron-to-chromium: 1.5.166 + caniuse-lite: 1.0.30001726 + electron-to-chromium: 1.5.176 node-releases: 2.0.19 - update-browserslist-db: 1.1.3(browserslist@4.25.0) + update-browserslist-db: 1.1.3(browserslist@4.25.1) call-bind-apply-helpers@1.0.2: dependencies: @@ -2688,7 +2691,7 @@ snapshots: callsites@3.1.0: {} - caniuse-lite@1.0.30001722: {} + caniuse-lite@1.0.30001726: {} chalk@4.1.2: dependencies: @@ -2805,7 +2808,7 @@ snapshots: es-errors: 1.3.0 gopd: 1.2.0 - electron-to-chromium@1.5.166: {} + electron-to-chromium@1.5.176: {} es-abstract@1.24.0: dependencies: @@ -2940,28 +2943,28 @@ snapshots: escape-string-regexp@4.0.0: {} - eslint-config-prettier@10.1.5(eslint@9.28.0): + eslint-config-prettier@10.1.5(eslint@9.29.0): dependencies: - eslint: 9.28.0 + eslint: 9.29.0 - eslint-plugin-prettier@5.4.1(eslint-config-prettier@10.1.5(eslint@9.28.0))(eslint@9.28.0)(prettier@3.5.3): + eslint-plugin-prettier@5.5.1(eslint-config-prettier@10.1.5(eslint@9.29.0))(eslint@9.29.0)(prettier@3.6.1): dependencies: - eslint: 9.28.0 - prettier: 3.5.3 + eslint: 9.29.0 + prettier: 3.6.1 prettier-linter-helpers: 1.0.0 synckit: 0.11.8 optionalDependencies: - eslint-config-prettier: 10.1.5(eslint@9.28.0) + eslint-config-prettier: 10.1.5(eslint@9.29.0) - eslint-plugin-react-hooks@5.2.0(eslint@9.28.0): + eslint-plugin-react-hooks@5.2.0(eslint@9.29.0): dependencies: - eslint: 9.28.0 + eslint: 9.29.0 - eslint-plugin-react-refresh@0.4.20(eslint@9.28.0): + eslint-plugin-react-refresh@0.4.20(eslint@9.29.0): dependencies: - eslint: 9.28.0 + eslint: 9.29.0 - eslint-plugin-react@7.37.5(eslint@9.28.0): + eslint-plugin-react@7.37.5(eslint@9.29.0): dependencies: array-includes: 3.1.9 array.prototype.findlast: 1.2.5 @@ -2969,7 +2972,7 @@ snapshots: array.prototype.tosorted: 1.1.4 doctrine: 2.1.0 es-iterator-helpers: 1.2.1 - eslint: 9.28.0 + eslint: 9.29.0 estraverse: 5.3.0 hasown: 2.0.2 jsx-ast-utils: 3.3.5 @@ -2992,16 +2995,16 @@ snapshots: eslint-visitor-keys@4.2.1: {} - eslint@9.28.0: + eslint@9.29.0: dependencies: - '@eslint-community/eslint-utils': 4.7.0(eslint@9.28.0) + '@eslint-community/eslint-utils': 4.7.0(eslint@9.29.0) '@eslint-community/regexpp': 4.12.1 - '@eslint/config-array': 0.20.0 - '@eslint/config-helpers': 0.2.2 + '@eslint/config-array': 0.20.1 + '@eslint/config-helpers': 0.2.3 '@eslint/core': 0.14.0 '@eslint/eslintrc': 3.3.1 - '@eslint/js': 9.28.0 - '@eslint/plugin-kit': 0.3.1 + '@eslint/js': 9.29.0 + '@eslint/plugin-kit': 0.3.3 '@humanfs/node': 0.16.6 '@humanwhocodes/module-importer': 1.0.1 '@humanwhocodes/retry': 0.4.3 @@ -3162,7 +3165,7 @@ snapshots: globals@14.0.0: {} - globals@15.15.0: {} + globals@16.2.0: {} globalthis@1.0.4: dependencies: @@ -3486,7 +3489,7 @@ snapshots: possible-typed-array-names@1.1.0: {} - postcss@8.5.5: + postcss@8.5.6: dependencies: nanoid: 3.3.11 picocolors: 1.1.1 @@ -3498,7 +3501,7 @@ snapshots: dependencies: fast-diff: 1.3.0 - prettier@3.5.3: {} + prettier@3.6.1: {} prop-types@15.8.1: dependencies: @@ -3581,30 +3584,30 @@ snapshots: reusify@1.1.0: {} - rollup@4.43.0: + rollup@4.44.1: dependencies: - '@types/estree': 1.0.7 + '@types/estree': 1.0.8 optionalDependencies: - '@rollup/rollup-android-arm-eabi': 4.43.0 - '@rollup/rollup-android-arm64': 4.43.0 - '@rollup/rollup-darwin-arm64': 4.43.0 - '@rollup/rollup-darwin-x64': 4.43.0 - '@rollup/rollup-freebsd-arm64': 4.43.0 - '@rollup/rollup-freebsd-x64': 4.43.0 - '@rollup/rollup-linux-arm-gnueabihf': 4.43.0 - '@rollup/rollup-linux-arm-musleabihf': 4.43.0 - '@rollup/rollup-linux-arm64-gnu': 4.43.0 - '@rollup/rollup-linux-arm64-musl': 4.43.0 - '@rollup/rollup-linux-loongarch64-gnu': 4.43.0 - '@rollup/rollup-linux-powerpc64le-gnu': 4.43.0 - '@rollup/rollup-linux-riscv64-gnu': 4.43.0 - '@rollup/rollup-linux-riscv64-musl': 4.43.0 - '@rollup/rollup-linux-s390x-gnu': 4.43.0 - '@rollup/rollup-linux-x64-gnu': 4.43.0 - '@rollup/rollup-linux-x64-musl': 4.43.0 - '@rollup/rollup-win32-arm64-msvc': 4.43.0 - '@rollup/rollup-win32-ia32-msvc': 4.43.0 - '@rollup/rollup-win32-x64-msvc': 4.43.0 + '@rollup/rollup-android-arm-eabi': 4.44.1 + '@rollup/rollup-android-arm64': 4.44.1 + '@rollup/rollup-darwin-arm64': 4.44.1 + '@rollup/rollup-darwin-x64': 4.44.1 + '@rollup/rollup-freebsd-arm64': 4.44.1 + '@rollup/rollup-freebsd-x64': 4.44.1 + '@rollup/rollup-linux-arm-gnueabihf': 4.44.1 + '@rollup/rollup-linux-arm-musleabihf': 4.44.1 + '@rollup/rollup-linux-arm64-gnu': 4.44.1 + '@rollup/rollup-linux-arm64-musl': 4.44.1 + '@rollup/rollup-linux-loongarch64-gnu': 4.44.1 + '@rollup/rollup-linux-powerpc64le-gnu': 4.44.1 + '@rollup/rollup-linux-riscv64-gnu': 4.44.1 + '@rollup/rollup-linux-riscv64-musl': 4.44.1 + '@rollup/rollup-linux-s390x-gnu': 4.44.1 + '@rollup/rollup-linux-x64-gnu': 4.44.1 + '@rollup/rollup-linux-x64-musl': 4.44.1 + '@rollup/rollup-win32-arm64-msvc': 4.44.1 + '@rollup/rollup-win32-ia32-msvc': 4.44.1 + '@rollup/rollup-win32-x64-msvc': 4.44.1 fsevents: 2.3.3 run-parallel@1.2.0: @@ -3766,9 +3769,9 @@ snapshots: dependencies: is-number: 7.0.0 - ts-api-utils@2.1.0(typescript@5.7.3): + ts-api-utils@2.1.0(typescript@5.8.3): dependencies: - typescript: 5.7.3 + typescript: 5.8.3 type-check@0.4.0: dependencies: @@ -3807,17 +3810,17 @@ snapshots: possible-typed-array-names: 1.1.0 reflect.getprototypeof: 1.0.10 - typescript-eslint@8.34.0(eslint@9.28.0)(typescript@5.7.3): + typescript-eslint@8.35.0(eslint@9.29.0)(typescript@5.8.3): dependencies: - '@typescript-eslint/eslint-plugin': 8.34.0(@typescript-eslint/parser@8.34.0(eslint@9.28.0)(typescript@5.7.3))(eslint@9.28.0)(typescript@5.7.3) - '@typescript-eslint/parser': 8.34.0(eslint@9.28.0)(typescript@5.7.3) - '@typescript-eslint/utils': 8.34.0(eslint@9.28.0)(typescript@5.7.3) - eslint: 9.28.0 - typescript: 5.7.3 + '@typescript-eslint/eslint-plugin': 8.35.0(@typescript-eslint/parser@8.35.0(eslint@9.29.0)(typescript@5.8.3))(eslint@9.29.0)(typescript@5.8.3) + '@typescript-eslint/parser': 8.35.0(eslint@9.29.0)(typescript@5.8.3) + '@typescript-eslint/utils': 8.35.0(eslint@9.29.0)(typescript@5.8.3) + eslint: 9.29.0 + typescript: 5.8.3 transitivePeerDependencies: - supports-color - typescript@5.7.3: {} + typescript@5.8.3: {} unbox-primitive@1.1.0: dependencies: @@ -3826,9 +3829,9 @@ snapshots: has-symbols: 1.1.0 which-boxed-primitive: 1.1.1 - update-browserslist-db@1.1.3(browserslist@4.25.0): + update-browserslist-db@1.1.3(browserslist@4.25.1): dependencies: - browserslist: 4.25.0 + browserslist: 4.25.1 escalade: 3.2.0 picocolors: 1.1.1 @@ -3840,13 +3843,13 @@ snapshots: dependencies: react: 19.1.0 - vite@6.3.5: + vite@7.0.0: dependencies: esbuild: 0.25.5 fdir: 6.4.6(picomatch@4.0.2) picomatch: 4.0.2 - postcss: 8.5.5 - rollup: 4.43.0 + postcss: 8.5.6 + rollup: 4.44.1 tinyglobby: 0.2.14 optionalDependencies: fsevents: 2.3.3 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/main.py b/main.py deleted file mode 100644 index ac4f143..0000000 --- a/main.py +++ /dev/null @@ -1,6 +0,0 @@ -def main(): - print("Hello from moss!") - - -if __name__ == "__main__": - main() diff --git a/pyproject.toml b/pyproject.toml index 71e8319..16900a2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,17 +4,52 @@ 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 = 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insertion(+), 2 deletions(-) diff --git a/frontend/package.json b/frontend/package.json index c8f628d..58ab309 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -13,8 +13,7 @@ "axios": "^1.10.0", "react": "^19.1.0", "react-dom": "^19.1.0", - "react-router-dom": "^7.6.2", - "reactflow": "^11.11.4" + "react-router-dom": "^7.6.2" }, "devDependencies": { "@eslint/js": "^9.29.0", From c9fe76a37d0816200353d2e684d671e45f674a81 Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 10:52:35 -0400 Subject: [PATCH 04/10] new token link, add docker install link, fix overview --- .env.example | 4 ++-- README.md | 23 +++++++++-------------- 2 files changed, 11 insertions(+), 16 deletions(-) diff --git a/.env.example b/.env.example index 0d9dabc..dddc66f 100644 --- a/.env.example +++ b/.env.example @@ -17,8 +17,8 @@ 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 diff --git a/README.md b/README.md index 36d1bb7..6b130eb 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,7 @@ ## Overview -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 it's intersection with academia and scientific publication. It aims to construct a knowledge graph system and reproducible framework for modeling public repositories, academic publications, and the contributing entities and relationships between them. This is accomplished by structured integration of data obtained through overlapping web traversal and graph construction strategies, grounded on existing schema and ontologies such as using context driven rules such as direct or mentioned DOI linking (`https://doi.org/10.1000/100` vs `

https://doi.org/10.1000/100

`), and care is taken to conform to existing schema based systems (OpenAlex topics, Schema.org entities) - -The Map of Open Source Science (MOSS) is a platform that reveals the hidden connections between research software and academic scholarship. It builds a rich knowledge graph of the research ecosystem by ingesting data about software repositories, scholarly publications, researchers, and institutions. By linking these entities, MOSS helps answer critical questions about the impact, sustainability, and collaborative nature of open source in science. +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. 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. @@ -50,12 +48,9 @@ This repository contains the backend services, API, and frontend application for Before you begin, ensure you have the following installed on your system: - 1. **uv:** Python package manager | [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) - 2. **pnpm:** Node package manager | [pnpm - Installation](https://pnpm.io/installation) - 3a. **Docker and Docker Compose:** (Recommended for simplified setup of PostgreSQL and Redis). Install Docker and Docker Compose. - 3b. **Alternatively, for manual setup of services:** - * **PostgreSQL:** Version 12+ - * **Redis:** Version 6+ + 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 @@ -68,8 +63,8 @@ This repository contains the backend services, API, and frontend application for * **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: (use "Tokens classic"). - * Grant the `public_repo` scope for read-only access to public repositories. + * Generate one at: + * Select the "Public repositories" option for repository access 2. **Start Background Services:** This command starts PostgreSQL and Redis using Docker Compose. @@ -100,7 +95,7 @@ This repository contains the backend services, API, and frontend application for ## Manual Setup & Configuration -### Manual Python Environment Setup +### Python Environment Setup 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]`. @@ -150,7 +145,7 @@ The manual steps are: pnpm --dir frontend dev ``` -### Manual Service Setup (PostgreSQL & Redis) +### Service Setup (PostgreSQL & Redis) If you are not using Docker, ensure PostgreSQL and Redis are installed and running, then: @@ -176,7 +171,7 @@ The `.env` file is crucial for configuring the application. Here is a detailed b * **`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. -## Manual Database Migrations +## Database Migrations If you make changes to the database models (`backend/data/models/`) later, you will need to: From 0dece64692d75bf2cb931439847b2a7d786b6a48 Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 11:12:42 -0400 Subject: [PATCH 05/10] add docker-compose.yml comment --- docker-compose.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/docker-compose.yml b/docker-compose.yml index bb56948..2fb5591 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,3 +1,16 @@ +# +# 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` +# services: postgres: image: postgres:16 From f8159cb092ee508785f4fdcdf29dd05b134921fe Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 12:03:52 -0400 Subject: [PATCH 06/10] added lock files, removed .python-version from .gitignore --- .gitignore | 195 +- .python-version | 1 + frontend/.gitignore | 41 - frontend/package-lock.json | 5412 ------------------------------------ uv.lock | 705 ----- 5 files changed, 90 insertions(+), 6264 deletions(-) create mode 100644 .python-version delete mode 100644 frontend/.gitignore delete mode 100644 frontend/package-lock.json delete mode 100644 uv.lock diff --git a/.gitignore b/.gitignore index f15df34..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/ @@ -16,7 +49,6 @@ eggs/ .eggs/ lib/ lib64/ -logs/ parts/ sdist/ var/ @@ -28,124 +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/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* - 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{ url = "https://files.pythonhosted.org/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859", size = 34166, upload-time = "2024-01-06T02:10:55.763Z" }, -] From 66aebe887d88c3f0c12f8b2280e7422dcbba6d17 Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 12:16:11 -0400 Subject: [PATCH 07/10] added packages param to pnpm-workspace.yaml --- frontend/pnpm-workspace.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/frontend/pnpm-workspace.yaml b/frontend/pnpm-workspace.yaml index efc037a..4dca4c0 100644 --- a/frontend/pnpm-workspace.yaml +++ b/frontend/pnpm-workspace.yaml @@ -1,2 +1,5 @@ +packages: + - 'frontend' + onlyBuiltDependencies: - esbuild From 54279c2ae83ba76b265799a5d6ed93ab921e0b7f Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 12:35:58 -0400 Subject: [PATCH 08/10] fixed docker lint warnings --- docker-compose.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 2fb5591..ae76ffa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -11,30 +11,33 @@ # - 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: ${POSTGRES_DB:-moss_db} ports: - - "${POSTGRES_PORT:-5432}:5432" - volumes: - - moss_postgres_data:/var/lib/postgresql/data + - '127.0.0.1:${POSTGRES_PORT:-5432}:5432' restart: unless-stopped redis: image: redis:7 container_name: moss_redis - ports: - - "${REDIS_PORT:-6379}:6379" volumes: - moss_redis_data:/data + ports: + - '127.0.0.1:${REDIS_PORT:-6379}:6379' restart: unless-stopped volumes: moss_postgres_data: moss_redis_data: + From f368a7b542f8957047135efddade4c43fb44b7fa Mon Sep 17 00:00:00 2001 From: Max <7529314+vasilmax@users.noreply.github.com> Date: Tue, 8 Jul 2025 12:36:52 -0400 Subject: [PATCH 09/10] removed pnpm lock file --- frontend/pnpm-lock.yaml | 3913 --------------------------------------- 1 file changed, 3913 deletions(-) delete mode 100644 frontend/pnpm-lock.yaml diff --git a/frontend/pnpm-lock.yaml b/frontend/pnpm-lock.yaml deleted file mode 100644 index 91ec578..0000000 --- a/frontend/pnpm-lock.yaml +++ /dev/null @@ -1,3913 +0,0 @@ -lockfileVersion: '9.0' - 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"react-router-dom": "^7.6.2" + "react-router-dom": "^7.6.2", + "reactflow": "^11.11.4" }, "devDependencies": { "@eslint/js": "^9.29.0",