Fully Local Data Transformation with dbt and DuckDB

Petrica Leuca
Published on 2025-04-04

TL;DR: In this post, we implement data transformation and reverse ETL pipelines with DuckDB and dbt using the dbt-duckdb adapter.

Introduction

The Data Build Tool, dbt, is an open-source transformation framework, which enables data teams to adopt software engineering best practices in the code they deliver, such as Git workflow and unit testing. Other notable features of dbt are data lineage, documentation and data testing as part of the execution pipeline.

In this article we will demonstrate how to perform fully local data transformations with dbt and DuckDB. To this end, we'll use the dbt-duckdb adapter, which integrates the dbt standard and with DuckDB's processing power.

Data Model

We use two open datasets in this post: railway services, provided by the team behind the Rijden de Treinen (Are the trains running?) application and cartography information about the Netherlands provided by cartomap. The datasets are organized into:

  • a persisted DuckDB database, in which we store the railway services data from 2024, hosted on Cloudflare;
  • a provinces GeoJSON file, containing the geographic information about the Dutch provinces, hosted on GitHub;
  • a municipalities GeoJSON file, containing the geographic information about Dutch municipalities, stored together with the code.

After doing an initial exploration of the above data, we can observe that a province can have one or many municipalities, a municipality can have none or many train stations and a train service record is connected to one and only one train station. Therefore we decide on the following data model:

  • a dimension table, dim_nl_provinces, to hold information about the Dutch provinces;
  • a dimension table, dim_nl_municipalities, to hold information about the Dutch municipalities, linked to dim_nl_provinces;
  • a dimension table, dim_nl_train_stations, to hold information about the train stations in the Netherlands, linked to dim_nl_municipalities;
  • a fact table, fact_services, to hold information about the train services, linked to dim_nl_train_stations.

The purpose of processing the train services and the Netherlands cartography data is to organize the data in a structure which can easily be used in future railway data analysis use cases. Such curated data structures are often called data marts.

Tip The following code is available on GitHub.

Processing Data with DuckDB and dbt

After we have initialized our project, we configure the connection details for DuckDB in the profiles.yml file. Along with specifying if the database should be in memory or persisted to disk, we also specify:

  • which extensions are required for the data processing, e.g., spatial;
  • external databases, attached from the local disk or other storage solutions.
dutch_railway_network:

  outputs:
    dev:
      type: duckdb
      path: data/dutch_railway_network.duckdb
      extensions:
        - spatial
        - httpfs
      threads: 5
      attach:
        - path: 'https://blobs.duckdb.org/nl-railway/train_stations_and_services.duckdb'
          type: duckdb
          alias: external_db
  target: dev

We then configure the sources.yml file under the models directory by specifying external sources (such as files) and table definitions from the attached database(s):

version: 2
sources:
  - name: geojson_external
    tables:
      - name: nl_provinces
        config:
          external_location: "https://cartomap.github.io/nl/wgs84/provincie_2025.geojson"
      - name: nl_municipalities
        config:
          external_location: "seeds/gemeente_2025.geojson"
  - name: external_db
    database: external_db
    schema: main
    tables:
      - name: stations
      - name: services

The external_location can point to CSV, Parquet or JSON files. Both the local file system and remote endpoints (e.g., HTTP or S3) are supported.

With both the profile and source defined, we can now load the data.

Loading Data to DuckDB

In dbt the way of storing the data in the target system is called materialization. The dbt-duckdb adapter provides the following materialization options:

  • table, replacing the target table at each run;
  • incremental, with append and delete+insert options, modifying the data in the table, but not the table itself (if it exists);
  • snapshot, implementing a Slowly Changing Dimension Type 2 table with time validity intervals;
  • view, replacing the target view at each run.

Another feature of using the above adapter is that the SQL dialect used in the data processing scripts has all the friendly SQL extensions DuckDB has to offer.

To refresh the data in the dim_nl_provinces table, we use the st_read spatial function, which reads and parses automatically the nl_provinces GeoJSON file, defined in sources.yml.

{{ config(materialized='table') }}

SELECT
    {{ dbt_utils.generate_surrogate_key(['id']) }} AS province_sk,
    id AS province_id,
    statnaam AS province_name,
    geom AS province_geometry,
    {{ common_columns() }}
FROM st_read({{ source("geojson_external", "nl_provinces") }}) AS src;

Similarly, we fully refresh the data for dim_nl_municipalities and fact_services.

To build the relation between a train station location and a municipality, we use the st_contains spatial function, which returns true when a geometry contains another geometry:

{{ config(materialized='table') }}

SELECT
    {{ dbt_utils.generate_surrogate_key(['tr_st.code']) }} AS station_sk,
    tr_st.id AS station_id,
    tr_st.code AS station_code,
    tr_st.name_long AS station_name,
    tr_st.type AS station_type,
    st_point(tr_st.geo_lng, tr_st.geo_lat) AS station_geo_location,
    coalesce(dim_mun.municipality_sk, 'unknown') AS municipality_sk,
    {{ common_columns() }}
FROM {{ source("external_db", "stations") }} AS tr_st
LEFT JOIN {{ ref ("dim_nl_municipalities") }} AS dim_mun
       ON st_contains(
           dim_mun.municipality_geometry,
           st_point(tr_st.geo_lng, tr_st.geo_lat)
       )
WHERE tr_st.country = 'NL';

To read from the external sources, we reference the source by providing the source and table names.

Exporting Data from DuckDB

One major benefit of using DuckDB for data processing is the ability to export data to files (such as CSV, JSON and Parquet) and to refresh data directly in PostgreSQL or MySQL databases.

External Files

The feature of exporting data to files is enabled by the dbt-duckdb adapter with the external materialization. With the external materialization, we are able to export data to CSV, JSON and Parquet file types to a specified storage location (local or external). The load type is full refresh, therefore existing files are overwritten.

In the following processing step, we export aggregated train service data at month level, to a Parquet file, partitioned by year and month:

{{
    config(
        materialized='external',
        location="data/exports/nl_train_services_aggregate",
        options={
            "partition_by": "service_year, service_month",
            "overwrite": True
        }
    )
}}

SELECT
    year(service_date) AS service_year,
    month(service_date) AS service_month,
    service_type,
    service_company,
    tr_st.station_sk,
    tr_st.station_name,
    m.municipality_sk,
    m.municipality_name,
    p.province_sk,
    p.province_name,
    count(*) AS number_of_rides
FROM {{ ref ("fact_services") }} AS srv
INNER JOIN {{ ref("dim_nl_train_stations") }} AS tr_st
        ON srv.station_sk = tr_st.station_sk
INNER JOIN {{ ref("dim_nl_municipalities") }} AS m
        ON tr_st.municipality_sk = m.municipality_sk
INNER JOIN {{ ref("dim_nl_provinces") }} AS p
        ON m.province_sk = p.province_sk
WHERE service_year = {{ var('execution_year') }}
GROUP BY ALL

The exported files are placed in Hive partitioned directory structure.

./service_year=2024/service_month=1:
49255 Apr  2 14:54 data_0.parquet

...

./service_year=2024/service_month=12:
48031 Apr  2 14:54 data_0.parquet

PostgreSQL

After we process the data into our railway services data mart, we can generate from it a daily aggregate at train station level, organized into a star schema model, by having the dimension keys part of the data:

{{
    config(
        materialized='incremental',
        incremental_strategy='delete+insert',
        unique_key="""
            service_date,
            service_type,
            service_company,
            station_sk
        """
    )
}}

SELECT
    service_date,
    service_type,
    service_company,
    srv.station_sk,
    mn.municipality_sk,
    province_sk,
    count(*) AS number_of_rides,
    {{ common_columns() }}
FROM {{ ref ("fact_services") }} AS srv
INNER JOIN {{ ref("rep_dim_nl_train_stations") }} AS tr_st
        ON srv.station_sk = tr_st.station_sk
INNER JOIN {{ ref("rep_dim_nl_municipalities") }} AS mn
        ON tr_st.municipality_sk = mn.municipality_sk
WHERE NOT service_arrival_cancelled

  {% if is_incremental() %}
    AND srv.invocation_id = (
        SELECT invocation_id
        FROM {{ ref("fact_services") }}
        ORDER BY last_updated_dt DESC
        LIMIT 1
    )
  {% endif %}
GROUP BY ALL

Thanks to DuckDB's ability to connect and write to a PostgreSQL database, we can add the above processing step to our dbt project, under the directory models/reverse_etl.

To connect to a PostgreSQL database, we need to specify in profiles.yml:

dutch_railway_network:

  outputs:
    dev:
      type: duckdb
      path: data/dutch_railway_network.duckdb
      extensions:
        - ...
        - postgres
      threads: 5
      attach:
        - ...
        - path: "postgresql://postgres:{{ env_var('DBT_DUCKDB_PG_PWD') }}@localhost:5466/postgres"
          type: postgres
          alias: postgres_db
  target: dev

We also have to configure the model's database details in dbt_project.yml:

models:
  dutch_railway_network:
    transformation:
      schema: main
      +docs:
        node_color: 'silver'
    reverse_etl:
      database: postgres_db
      schema: public
      +docs:
        node_color: '#d5b85a'

With this configuration, all the models from the transformation directory will be executed on the main_main schema, while the models from reverse_etl will be executed on the main_public schema.

After executing the models with dbt run --model +reverse_etl, the data is available to query from PostgreSQL:

psql -U postgres

SELECT count(*), sum(number_of_rides)
FROM main_public.rep_fact_train_services_daily_agg;

 count  |   sum    
--------+----------
 240826 | 17438151

It is important to mention that while PostgreSQL is the target database and dbt provides merge as an incremental strategy for it; the execution of the above pipeline is happening in DuckDB, therefore the incremental load can be done only with append or delete+insert strategies.

Execution Details

The above implementation consists of 10 models and 20 data tests, processing 400 MB of data from the attached DuckDB database, together with small data organized in GeoJSON files. The total execution time, on a single thread and on a MacBook Pro of 12 GB, is between 40 and 45 seconds. From the total execution time, approximatively 30 seconds are spent to process the train services data and 4 seconds to write the aggregated data to PostgreSQL:

05:48:07  Running with dbt=1.9.3
05:48:08  Registered adapter: duckdb=1.9.2
05:48:08  Found 10 models, 20 data tests, 4 sources, 565 macros
05:48:08  
05:48:08  Concurrency: 1 threads (target='dev')
...
05:48:45  19 of 30 OK created sql table model main_main.fact_services .................... [OK in 32.60s]
...
05:48:50  26 of 30 OK created sql incremental model postgres_db.main_public.rep_fact_train_services_daily_agg  [OK in 3.74s]
...
05:48:51  Finished running 2 external models, 1 incremental model, 7 table models, 20 data tests in 0 hours 0 minutes and 42.63 seconds (42.63s).
05:48:51  
05:48:51  Completed successfully
05:48:51  
05:48:51  Done. PASS=30 WARN=0 ERROR=0 SKIP=0 TOTAL=30

Conclusion

In this post we have demonstrated how DuckDB integrates with dbt and how it is part of the data processing ecosystem by showcasing data mart creation, file exports and reverse ETL to a PostgreSQL database.

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