cBioPortal Python API Docs | dltHub

cBioPortal is an open-access resource for interactive exploration of multidimensional cancer genomics data sets that provides a REST API for programmatic access to the data. The REST API base URL is https://www.cbioportal.org/api and all requests to protected API endpoints require an Authorization: Bearer header..

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 add "dlt[hub]" and start loading cBioPortal data in under 10 minutes.

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What data can I load from cBioPortal?

Here are some of the endpoints you can load from cBioPortal:

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How do I authenticate with the cBioPortal API?

Authentication is performed by including a Bearer token in the Authorization header. Users must obtain a data access token from their cBioPortal instance to use for authorized requests.

1. Get your credentials

To obtain a data access token for a private or authenticated cBioPortal instance, follow these steps: 1. Log in to the cBioPortal web interface. 2. Locate the user profile menu (labeled 'Logged in as...') in the top-right corner of the webpage. 3. Select 'Data Access Token' from the dropdown menu. If this option is not visible, the specific instance may not be configured to support tokens or may not require authentication.

2. Add them to .dlt/secrets.toml

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[sources.cbioportal_source]
cbioportal_token = "Bearer <your_token_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.

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How do I set up and run the pipeline?

Set up a virtual environment and install dlt:

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uv init
uv add "dlt[hub]"

1. Install the dlt AI harness:

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uv run dlthub 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:

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uv run dlthub ai toolkit install rest-api-pipeline

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 cBioPortal 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:

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uv run python cbioportal_pipeline.py

If everything is configured correctly, you'll see output like this:

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Pipeline cbioportal_pipeline load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset cbioportal_data
The duckdb destination used duckdb:/cbioportal.duckdb location to store data
Load package 1749667187.541553 is LOADED and contains no failed jobs

Inspect your pipeline and data:

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uv run dlthub show

This opens the Pipeline Dashboard where you can verify pipeline state, load metrics, schema (tables, columns, types), and query the loaded data directly.

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Python pipeline example

This example loads /studies and /clinicalattrs from the cBioPortal API into DuckDB. It mirrors the endpoint and data selector configuration from the table above:

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import dlt
from dlt.sources.rest_api import RESTAPIConfig, rest_api_resources

@dlt.source
def cbioportal_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.cbioportal.org/api",
            "auth": {"type": "bearer", "token": api_key},
        },
        "resources": [
            {"name": "studies", "endpoint": {"path": "api/studies"}},
            {"name": "generic_assay_meta", "endpoint": {"path": "api/generic-assay-meta"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="cbioportal_pipeline",
        destination="duckdb",
        dataset_name="cbioportal_data",
    )
    load_info = pipeline.run(cbioportal_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.

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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):

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import dlt

data = dlt.pipeline("cbioportal_pipeline").dataset()
sessions_df = data.studies.df()
print(sessions_df.head())

SQL (DuckDB example):

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SELECT * FROM cbioportal_data.studies LIMIT 10;

In a marimo or Jupyter notebook:

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import dlt

data = dlt.pipeline("cbioportal_pipeline").dataset()
data.studies.df().head()

See how to explore your data in marimo Notebooks and how to query your data in Python with dataset.

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What destinations can I load cBioPortal data to?

dlt supports loading into any of these destinations — only the destination parameter changes:

Change the destination in dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. See the full destinations list.

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Next steps

Continue your data engineering journey with the other toolkits of the dltHub AI harness:

• data-exploration — Build custom notebooks, charts, and dashboards for deeper analysis with marimo notebooks.
• dlthub-platform — Deploy, schedule, and monitor your pipeline in production.

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uv run dlthub ai toolkit install data-exploration
uv run dlthub ai toolkit install dlthub-platform

• How to deploy a pipeline
• How to explore your data in marimo Notebooks
• How to query your data in Python with dataset
• Join the dlt community on Slack