Load Galaxy Project data in Python using dltHub

Build a Galaxy Project-to-database or-dataframe pipeline in Python using dlt with automatic Cursor support.

In this guide, we'll set up a complete Galaxy Project data pipeline from API credentials to your first data load in just 10 minutes. You'll end up with a fully declarative Python pipeline based on dlt's REST API connector, like in the partial example code below:

Example code
@dlt.source
def galaxy_project_source(access_token=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://data.indores.fr/api/access/datafile/",
            "auth": {
                "type": "api_key",
                "key": "key",
                "value": api_key,
            },
        },
        "resources": [
            9756, 9777
        ],
    }
    [...]
    yield from rest_api_resources(config)


def get_data() -> None:
    # Connect to destination
    pipeline = dlt.pipeline(
        pipeline_name='galaxy_project_pipeline',
        destination='duckdb',
        dataset_name='galaxy_project_data', 
    )
    # Load the data
    load_info = pipeline.run(galaxy_project_source())
    print(load_info)

Why use dltHub Workspace with LLM Context to generate Python pipelines?

  • Accelerate pipeline development with AI-native context
  • Debug pipelines, validate schemas and data with the integrated Pipeline Dashboard
  • Build Python notebooks for end users of your data
  • Low maintenance thanks to Schema evolution with type inference, resilience and self documenting REST API connectors. A shallow learning curve makes the pipeline easy to extend by any team member
  • dlt is the tool of choice for Pythonic Iceberg Lakehouses, bringing mature data loading to pythonic Iceberg with or without catalogs

What you’ll do

We’ll show you how to generate a readable and easily maintainable Python script that fetches data from galaxy_project’s API and loads it into Iceberg, DataFrames, files, or a database of your choice. Here are some of the endpoints you can load:

  • Dataset Collections: Download and manage dataset collections with direct access to collection files
  • Occurrence Data: Retrieve species occurrence records and download compiled occurrence datasets
  • Data Files: Access and download individual data files from repositories with file-specific endpoints
  • FTP Access: Direct file transfer protocol access to biological databases and resources

You will then debug the Galaxy Project pipeline using our Pipeline Dashboard tool to ensure it is copying the data correctly, before building a Notebook to explore your data and build reports.

Setup & steps to follow

💡
Before getting started, let's make sure Cursor is set up correctly:

Now you're ready to get started!

  1. ⚙️ Set up dlt Workspace

    Install dlt with duckdb support:

    pip install dlt[workspace]

    Initialize a dlt pipeline with Galaxy Project support.

    dlt init dlthub:galaxy_project duckdb

    The init command will setup the necessary files and folders for the next step.

  2. 🤠 Start LLM-assisted coding

    Here’s a prompt to get you started:

    Prompt
    Please generate a REST API Source for Galaxy Project API, as specified in @galaxy_project-docs.yaml 
Start with endpoint(s) 9756 and 9777 and skip incremental loading for now. 
Place the code in galaxy_project_pipeline.py and name the pipeline galaxy_project_pipeline. 
If the file exists, use it as a starting point. 
Do not add or modify any other files. 
Use @dlt rest api as a tutorial. 
After adding the endpoints, allow the user to run the pipeline with python galaxy_project_pipeline.py and await further instructions.

  3. 🔒 Set up credentials

    API key authentication is required for dataset collection downloads. The API key must be supplied as a query parameter named "key" in the request URL. Example: https://usegalaxy.org/api/dataset_collections/d20ad3e1ccd4595de/download?key=MYSECRETAPIKEY

    To get the appropriate API keys, please visit the original source at training.galaxyproject.org. If you want to protect your environment secrets in a production environment, look into setting up credentials with dlt.

  4. 🏃‍♀️ Run the pipeline in the Python terminal in Cursor

    python galaxy_project_pipeline.py

    If your pipeline runs correctly, you’ll see something like the following:

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

  5. 📈 Debug your pipeline and data with the Pipeline Dashboard

    Now that you have a running pipeline, you need to make sure it’s correct, so you do not introduce silent failures like misconfigured pagination or incremental loading errors. By launching the dlt Workspace Pipeline Dashboard, you can see various information about the pipeline to enable you to test it. Here you can see:

    • Pipeline overview: State, load metrics
    • Data’s schema: tables, columns, types, hints
    • You can query the data itself
    dlt pipeline galaxy_project_pipeline show

  6. 🐍 Build a Notebook with data explorations and reports

    With the pipeline and data partially validated, you can continue with custom data explorations and reports. To get started, paste the snippet below into a new marimo Notebook and ask your LLM to go from there. Jupyter Notebooks and regular Python scripts are supported as well.

    import dlt

data = dlt.pipeline("galaxy_project_pipeline").dataset()
# get ["9756"] table as Pandas frame
data.["9756"].df().head()

Extra resources:

Next steps