Trefle Python API Docs | dltHub

Trefle is a REST API providing botanical data for plants. It offers detailed information on plant species, including taxonomy and growing conditions. The API is free and open source. The REST API base URL is https://trefle.io/api/v1 and all requests require an access token (personal access token) passed as a query parameter or as the token 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 pip install "dlt[workspace]" and start loading Trefle data in under 10 minutes.

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What data can I load from Trefle?

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

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How do I authenticate with the Trefle API?

Trefle uses a personal access token. Examples in the docs show passing token as a query parameter (?token=YOUR_TREFLE_TOKEN) or as a header (Authorization: Bearer YOUR_TREFLE_TOKEN / token header). All requests are over HTTPS and return JSON.

1. Get your credentials

1. Create an account at https://trefle.io/users/sign_up
2. Confirm your email and log in to your profile at https://trefle.io/profile
3. Copy your personal access token (Trefle access token) from your profile/dashboard. Keep it secret.
4. Use the token in requests as ?token=YOUR_TREFLE_TOKEN or in the Authorization header (Bearer token) as supported by examples in the docs.

2. Add them to .dlt/secrets.toml

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[sources.trefle_source]
api_key = "YOUR_TREFLE_TOKEN"

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 venv && source .venv/bin/activate
uv pip install "dlt[workspace]"

1. Install the dlt AI Workbench:

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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:

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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 Trefle 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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python trefle_pipeline.py

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

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Pipeline trefle_pipeline load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset trefle_data
The duckdb destination used duckdb:/trefle.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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dlt pipeline trefle_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.

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Python pipeline example

This example loads plants and species from the Trefle 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 trefle_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://trefle.io/api/v1",
            "auth": {
                "type": "api_key",
                "api_key": api_key,
            },
        },
        "resources": [
            {"name": "plants", "endpoint": {"path": "api/v1/plants", "data_selector": "data"}},
            {"name": "species", "endpoint": {"path": "api/v1/species", "data_selector": "data"}}
        ],
    }
    yield from rest_api_resources(config)


def get_data() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="trefle_pipeline",
        destination="duckdb",
        dataset_name="trefle_data",
    )
    load_info = pipeline.run(trefle_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("trefle_pipeline").dataset()
sessions_df = data.plants.df()
print(sessions_df.head())

SQL (DuckDB example):

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SELECT * FROM trefle_data.plants LIMIT 10;

In a marimo or Jupyter notebook:

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import dlt

data = dlt.pipeline("trefle_pipeline").dataset()
data.plants.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 Trefle 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 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.

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dlt ai toolkit data-exploration install
dlt ai toolkit dlthub-runtime install

• 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