SchemaLink

Web-based tool for drawing schemas.

Run locally

1. Git clone/Download and unzip ​schemalink-webapp​ and ​schemalink-api​.

2. Install and start postgres on port 5432. For instance, on MacOS:

   • brew install postgresql
   • brew services start postgresql
   • dropdb Authentication
   • createdb Authentication
   • psql -d Authentication -f schemalink-api/authentication_database.sql
   • createuser -s postgres
   • psql -d postgres
   • ALTER USER postgres WITH password 'unimi';
   • \q

   Note: Ensure postgres runs on port 5432 (check that the port is free).

3. Install and start ChromaDB. For instance, on MacOS:

   • brew install sqlite3
   • pip install -r schemalink-api/requirements.txt
   • sqlite3 schemalink-api/chroma_data/chroma.sqlite3 < schemalink-api/vector_store.sql
   • chroma run --port 8001 --path schemalink-api/chroma_data

   Note: Ensure ChromaDB runs on port 8001 (check that the port is free).

4. Open a new shell tab, and start the SchemaLink extraction engine:

   • git clone https://github.com/BioDataUniMI/schemalink-engine.git (or download and unzip it)
   • cd schemalink-engine
   • pip install -r requirements.txt
   • export OPENAI_API_KEY=sk-your-key-here
   • python production_server.py

   Note: Ensure the engine runs on port 15002 (check that the port is free).

   The engine is required for extractions. On the first extraction, it will automatically download the OAK ontology SQLite databases needed by the schema (e.g. MONDO, CHEBI) from the bbop-sqlite S3 bucket and cache them in ~/.data/oaklib/. This may take a few minutes depending on the schema. Subsequent extractions are instant.

5. Open a new shell tab, and start the API:

   • cd schemalink-api
   • cp .env.template .env
   • Open .env and fill in your values:
     • OPENAI_API_KEY — required for intelligent operations
     • ADMIN_EMAIL and EMAIL_PASSWORD — required for gmail-based functionalities (app password can be generated at: https://myaccount.google.com/apppasswords)
     • SCHEMALINK_ENGINE_URL — set to http://localhost:15002/engine/api/v1/extract
   • python -m uvicorn main:app --port 8000

   Note: Ensure the API runs on port 8000 (check that the port is free).

6. Open a new shell tab, and start the webapp:

   • cd schemalink-webapp
   • npm install
   • npm audit fix
   • npx nx serve arrows-ts

   Note: Ensure the webapp runs on port 4200 (check that the port is free).

7. Log-in webapp (browser --> localhost:4200) with admin credentials (can be edited): usr="schemalink"; pwd="Admin123!". Edit admin e-mail to exploit gmail-based functionalities.

Issues and Feedback

To report a problem that needs fixing, please create an issue.

For suggestions and feedback, please start a discussion.