Overture Bio Python API Docs | dltHub
Build a Overture Bio-to-database pipeline in Python using dlt with AI Workbench support for Claude Code, Cursor, and Codex.
Last updated:
Overture Bio is a platform that provides APIs (Song, Score, Maestro) for managing and querying file metadata, programmatically transferring files to and from object storage, and handling data indexing operations. The REST API base URL is https://score.demo.overture.bio and All requests require an API key provided as a Bearer token for authentication..
dlt is an open-source Python library that handles authentication, pagination, and schema evolution automatically. dlthub provides AI context files that enable code assistants to generate production-ready pipelines. Install with uv pip install "dlt[workspace]" and start loading Overture Bio data in under 10 minutes.
What data can I load from Overture Bio?
Here are some of the endpoints you can load from Overture Bio:
| Resource | Endpoint | Method | Data selector | Description |
|---|---|---|---|---|
| song_api | (See Swagger UI) | GET/POST/PUT/DELETE | (See Swagger UI) | Manage and query file metadata (studies, analyses, donors, specimens, samples) |
| score_api | (See Swagger UI) | GET/POST/PUT/DELETE | (See Swagger UI) | Query Score server and programmatically transfer files to and from object storage |
| maestro_api | (See Swagger UI) | GET/POST/PUT/DELETE | (See Swagger UI) | Data indexing operations |
How do I authenticate with the Overture Bio API?
Authentication requires an API key to be included in the Authorization header of each request, formatted as Authorization: Bearer YOUR_API_KEY.
1. Get your credentials
The documentation does not provide specific step-by-step instructions for obtaining API credentials from a dashboard. It only states that an API key is required for authentication in production environments.
2. Add them to .dlt/secrets.toml
[sources.overture_bio_source] api_key = "your_api_key_here"
dlt reads this automatically at runtime — never hardcode tokens in your pipeline script. For production environments, see setting up credentials with dlt for environment variable and vault-based options.
How do I set up and run the pipeline?
Set up a virtual environment and install dlt:
uv venv && source .venv/bin/activate uv pip install "dlt[workspace]"
1. Install the dlt AI Workbench:
dlt ai init --agent <your-agent> # <agent>: claude | cursor | codex
This installs project rules, a secrets management skill, appropriate ignore files, and configures the dlt MCP server for your agent. Learn more →
2. Install the rest-api-pipeline toolkit:
dlt ai toolkit rest-api-pipeline install
This loads the skills and context about dlt the agent uses to build the pipeline iteratively, efficiently, and safely. The agent uses MCP tools to inspect credentials — it never needs to read your secrets.toml directly. Learn more →
3. Start LLM-assisted coding:
Use /find-source to load data from the Overture Bio API into DuckDB.
The rest-api-pipeline toolkit takes over from here — it reads relevant API documentation, presents you with options for which endpoints to load, and follows a structured workflow to scaffold, debug, and validate the pipeline step by step.
4. Run the pipeline:
python overture_bio_pipeline.py
If everything is configured correctly, you'll see output like this:
Pipeline overture_bio_pipeline load step completed in 0.26 seconds 1 load package(s) were loaded to destination duckdb and into dataset overture_bio_data The duckdb destination used duckdb:/overture_bio.duckdb location to store data Load package 1749667187.541553 is LOADED and contains no failed jobs
Inspect your pipeline and data:
dlt pipeline overture_bio_pipeline show
This opens the Pipeline Dashboard where you can verify pipeline state, load metrics, schema (tables, columns, types), and query the loaded data directly.
Python pipeline example
This example loads song_api and score_api from the Overture Bio API into DuckDB. It mirrors the endpoint and data selector configuration from the table above:
import dlt from dlt.sources.rest_api import RESTAPIConfig, rest_api_resources @dlt.source def overture_bio_source(api_key=dlt.secrets.value): config: RESTAPIConfig = { "client": { "base_url": "https://score.demo.overture.bio", "auth": { "type": "bearer", "api_key": api_key, }, }, "resources": [ {"name": "song_api", "endpoint": {"path": "(See Swagger UI)"}}, {"name": "score_api", "endpoint": {"path": "(See Swagger UI)"}} ], } yield from rest_api_resources(config) def get_data() -> None: pipeline = dlt.pipeline( pipeline_name="overture_bio_pipeline", destination="duckdb", dataset_name="overture_bio_data", ) load_info = pipeline.run(overture_bio_source()) print(load_info)
To add more endpoints, append entries from the resource table to the "resources" list using the same name, path, and data_selector pattern.
How do I query the loaded data?
Once the pipeline runs, dlt creates one table per resource. You can query with Python or SQL.
Python (pandas DataFrame):
import dlt data = dlt.pipeline("overture_bio_pipeline").dataset() sessions_df = data.song_api.df() print(sessions_df.head())
SQL (DuckDB example):
SELECT * FROM overture_bio_data.song_api LIMIT 10;
In a marimo or Jupyter notebook:
import dlt data = dlt.pipeline("overture_bio_pipeline").dataset() data.song_api.df().head()
See how to explore your data in marimo Notebooks and how to query your data in Python with dataset.
What destinations can I load Overture Bio data to?
dlt supports loading into any of these destinations — only the destination parameter changes:
| Destination | Example value |
|---|---|
| DuckDB (local, default) | "duckdb" |
| PostgreSQL | "postgres" |
| BigQuery | "bigquery" |
| Snowflake | "snowflake" |
| Redshift | "redshift" |
| Databricks | "databricks" |
| Filesystem (S3, GCS, Azure) | "filesystem" |
Change the destination in dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. See the full destinations list.
Troubleshooting
Authentication Failures
In production environments, all requests to the Overture Bio APIs (e.g., Song API) require authentication using an API key. If requests are failing, ensure that your API key is correctly included in the Authorization header of each request, formatted as Authorization: Bearer YOUR_API_KEY.
Ensure that the API key is valid to avoid 401 Unauthorized errors. Also, verify endpoint paths and parameters to avoid 404 Not Found errors.
Next steps
Continue your data engineering journey with the other toolkits of the dltHub AI Workbench:
data-exploration— Build custom notebooks, charts, and dashboards for deeper analysis with marimo notebooks.dlthub-runtime— Deploy, schedule, and monitor your pipeline in production.
dlt ai toolkit data-exploration install dlt ai toolkit dlthub-runtime install
Was this page helpful?
Community Hub
Need more dlt context for Overture Bio?
Request dlt skills, commands, AGENT.md files, and AI-native context.