Load Tapis PgREST data in Python using dltHub

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

In this guide, we'll set up a complete Tapis PgREST 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 tapis_pgrest_source(access_token=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://${tenant_id}.tapis.io/v3/",
            "auth": {
                "type": "bearer",
                "token": access_token,
            },
        },
        "resources": [
            sites, oauth2
        ],
    }
    [...]
    yield from rest_api_resources(config)


def get_data() -> None:
    # Connect to destination
    pipeline = dlt.pipeline(
        pipeline_name='tapis_pgrest_pipeline',
        destination='duckdb',
        dataset_name='tapis_pgrest_data', 
    )
    # Load the data
    load_info = pipeline.run(tapis_pgrest_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 tapis_pgrest’s API and loads it into Iceberg, DataFrames, files, or a database of your choice. Here are some of the endpoints you can load:

  • Sites Management: Retrieve and manage site configurations across Tapis instances
  • OAuth2: Handle authentication and authorization flows
  • Security: Manage security policies and configurations
  • Tenants: Administer tenant information and settings
  • Tokens: Create, manage, and validate authentication tokens
  • Systems: List, search, and manage compute and storage systems

You will then debug the Tapis PgREST 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 Tapis PgREST support.

    dlt init dlthub:tapis_pgrest 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 Tapis PgREST API, as specified in @tapis_pgrest-docs.yaml 
Start with endpoint(s) sites and oauth2 and skip incremental loading for now. 
Place the code in tapis_pgrest_pipeline.py and name the pipeline tapis_pgrest_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 tapis_pgrest_pipeline.py and await further instructions.

  3. 🔒 Set up credentials

    The Tapis framework uses OAuth2-based authentication. Users authenticate via the /v3/oauth2 endpoints with the password grant flow to generate tokens for themselves. The specific authenticator URL varies by tenant, for example https://tacc.tapis.io/v3/oauth2 for the tacc tenant and https://dev.tapis.io/v3/oauth2 for the dev tenant.

    To get the appropriate API keys, please visit the original source at tapis.readthedocs.io. 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 tapis_pgrest_pipeline.py

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

    Pipeline tapis_pgrest load step completed in 0.26 seconds
1 load package(s) were loaded to destination duckdb and into dataset tapis_pgrest_data
The duckdb destination used duckdb:/tapis_pgrest.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 tapis_pgrest_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("tapis_pgrest_pipeline").dataset()
# get sites table as Pandas frame
data.sites.df().head()

Extra resources:

Next steps