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Python Data Loading from mongodb to clickhouse using dlt

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Welcome to the technical documentation page for data loading from mongodb to clickhouse using the open-source Python library, dlt. mongodb, a leading modern database, accelerates your path from idea to market by simplifying data handling. On the other end, clickhouse is a swift, open-source, column-oriented database management system, enabling real-time analytical data report generation through SQL queries. With dlt, we bridge the gap between these two powerful platforms, facilitating seamless data transfer and manipulation. For more information on mongodb, please visit MongoDB.

dlt Key Features​

  • Data Types Support: dlt supports a variety of data types such as text, double, bool, timestamp, date, time, bigint, binary, complex, decimal, and wei. This allows for a wide range of data manipulation and storage options. More details can be found here.
  • Governance Support: dlt provides robust governance support through pipeline metadata utilization, schema enforcement and curation, and schema change alerts. This contributes to better data management practices, compliance adherence, and overall data governance. Read more here.
  • Authentication Types: dlt supports multiple authentication types for Snowflake destination including password authentication, key pair authentication, and external authentication. This provides flexibility and security in data access. More information can be found here.
  • Normalization and Loading: dlt extracts JSON data, normalizes it to a schema, and loads it to the chosen destination. This process ensures data consistency, traceability, and control throughout the data processing lifecycle. Learn more about how dlt works here.
  • Supports DuckDB Destination: dlt supports DuckDB as a destination with all write dispositions. It loads data using large INSERT VALUES statements by default and supports multiple file formats. More details can be found here.

Getting started with your pipeline locally​

0. Prerequisites​

dlt requires Python 3.8 or higher. Additionally, you need to have the pip package manager installed, and we recommend using a virtual environment to manage your dependencies. You can learn more about preparing your computer for dlt in our installation reference.

1. Install dlt​

First you need to install the dlt library with the correct extras for ClickHouse:

pip install "dlt[clickhouse]"

The dlt cli has a useful command to get you started with any combination of source and destination. For this example, we want to load data from MongoDB to ClickHouse. You can run the following commands to create a starting point for loading data from MongoDB to ClickHouse:

# create a new directory
mkdir mongodb_pipeline
cd mongodb_pipeline
# initialize a new pipeline with your source and destination
dlt init mongodb clickhouse
# install the required dependencies
pip install -r requirements.txt

The last command will install the required dependencies for your pipeline. The dependencies are listed in the requirements.txt:


pymongo>=4.3.3
dlt[clickhouse]>=0.3.5

You now have the following folder structure in your project:

mongodb_pipeline/
├── .dlt/
│   ├── config.toml          # configs for your pipeline
│   └── secrets.toml         # secrets for your pipeline
├── mongodb/                   # folder with source specific files
│   └── ...
├── mongodb_pipeline.py        # your main pipeline script
├── requirements.txt         # dependencies for your pipeline
└── .gitignore               # ignore files for git (not required)

2. Configuring your source and destination credentials​

The dlt cli will have created a .dlt directory in your project folder. This directory contains a config.toml file and a secrets.toml file that you can use to configure your pipeline. The automatically created version of these files look like this:

generated config.toml​

# put your configuration values here

[runtime]
log_level="WARNING"  # the system log level of dlt
# use the dlthub_telemetry setting to enable/disable anonymous usage data reporting, see https://dlthub.com/docs/telemetry
dlthub_telemetry = true

generated secrets.toml​

# put your secret values and credentials here. do not share this file and do not push it to github

[sources.mongodb]
connection_url = "connection_url" # please set me up!

[destination.clickhouse]
dataset_name = "dataset_name" # please set me up!

[destination.clickhouse.credentials]
database = "default"
password = "password" # please set me up!
username = "default"
host = "host" # please set me up!
port = 9440
http_port = 8443

2.1. Adjust the generated code to your usecase​

Further help setting up your source and destinations
  • Read more about setting up the MongoDB source in our docs.
  • Read more about setting up the ClickHouse destination in our docs.

3. Running your pipeline for the first time​

The dlt cli has also created a main pipeline script for you at mongodb_pipeline.py, as well as a folder mongodb that contains additional python files for your source. These files are your local copies which you can modify to fit your needs. In some cases you may find that you only need to do small changes to your pipelines or add some configurations, in other cases these files can serve as a working starting point for your code, but will need to be adjusted to do what you need them to do.

The main pipeline script will look something like this:


from typing import List

import dlt
from dlt.common import pendulum
from dlt.common.pipeline import LoadInfo
from dlt.common.typing import TDataItems
from dlt.pipeline.pipeline import Pipeline

# As this pipeline can be run as standalone script or as part of the tests, we need to handle the import differently.
try:
    from .mongodb import mongodb, mongodb_collection  # type: ignore
except ImportError:
    from mongodb import mongodb, mongodb_collection


def load_select_collection_db(pipeline: Pipeline = None) -> LoadInfo:
    """Use the mongodb source to reflect an entire database schema and load select tables from it.

    This example sources data from a sample mongo database data from [mongodb-sample-dataset](https://github.com/neelabalan/mongodb-sample-dataset).
    """
    if pipeline is None:
        # Create a pipeline
        pipeline = dlt.pipeline(
            pipeline_name="local_mongo",
            destination='clickhouse',
            dataset_name="mongo_select",
        )

    # Configure the source to load a few select collections incrementally
    mflix = mongodb(incremental=dlt.sources.incremental("date")).with_resources(
        "comments"
    )

    # Run the pipeline. The merge write disposition merges existing rows in the destination by primary key
    info = pipeline.run(mflix, write_disposition="merge")

    return info


def load_select_collection_db_items(parallel: bool = False) -> TDataItems:
    """Get the items from a mongo collection in parallel or not and return a list of records"""
    comments = mongodb(
        incremental=dlt.sources.incremental("date"), parallel=parallel
    ).with_resources("comments")
    return list(comments)


def load_select_collection_db_filtered(pipeline: Pipeline = None) -> LoadInfo:
    """Use the mongodb source to reflect an entire database schema and load select tables from it.

    This example sources data from a sample mongo database data from [mongodb-sample-dataset](https://github.com/neelabalan/mongodb-sample-dataset).
    """
    if pipeline is None:
        # Create a pipeline
        pipeline = dlt.pipeline(
            pipeline_name="local_mongo",
            destination='clickhouse',
            dataset_name="mongo_select_incremental",
        )

    # Configure the source to load a few select collections incrementally
    movies = mongodb_collection(
        collection="movies",
        incremental=dlt.sources.incremental(
            "lastupdated", initial_value=pendulum.DateTime(2016, 1, 1, 0, 0, 0)
        ),
    )

    # Run the pipeline. The merge write disposition merges existing rows in the destination by primary key
    info = pipeline.run(movies, write_disposition="merge")

    return info


def load_select_collection_hint_db(pipeline: Pipeline = None) -> LoadInfo:
    """Use the mongodb source to reflect an entire database schema and load select tables from it.

    This example sources data from a sample mongo database data from [mongodb-sample-dataset](https://github.com/neelabalan/mongodb-sample-dataset).
    """
    if pipeline is None:
        # Create a pipeline
        pipeline = dlt.pipeline(
            pipeline_name="local_mongo",
            destination='clickhouse',
            dataset_name="mongo_select_hint",
        )

    # Load a table incrementally with append write disposition
    # this is good when a table only has new rows inserted, but not updated
    airbnb = mongodb().with_resources("listingsAndReviews")
    airbnb.listingsAndReviews.apply_hints(
        incremental=dlt.sources.incremental("last_scraped")
    )

    info = pipeline.run(airbnb, write_disposition="append")

    return info


def load_entire_database(pipeline: Pipeline = None) -> LoadInfo:
    """Use the mongo source to completely load all collection in a database"""
    if pipeline is None:
        # Create a pipeline
        pipeline = dlt.pipeline(
            pipeline_name="local_mongo",
            destination='clickhouse',
            dataset_name="mongo_database",
        )

    # By default the mongo source reflects all collections in the database
    source = mongodb()

    # Run the pipeline. For a large db this may take a while
    info = pipeline.run(source, write_disposition="replace")

    return info


if __name__ == "__main__":
    # Credentials for the sample database.
    # Load selected tables with different settings
    print(load_select_collection_db())
    # print(load_select_collection_db_filtered())

    # Load all tables from the database.
    # Warning: The sample database is large
    # print(load_entire_database())

Provided you have set up your credentials, you can run your pipeline like a regular python script with the following command:

python mongodb_pipeline.py

4. Inspecting your load result​

You can now inspect the state of your pipeline with the dlt cli:

dlt pipeline local_mongo info

You can also use streamlit to inspect the contents of your ClickHouse destination for this:

# install streamlit
pip install streamlit
# run the streamlit app for your pipeline with the dlt cli:
dlt pipeline local_mongo show

5. Next steps to get your pipeline running in production​

One of the beauties of dlt is, that we are just a plain Python library, so you can run your pipeline in any environment that supports Python >= 3.8. We have a couple of helpers and guides in our docs to get you there:

The Deploy section will show you how to deploy your pipeline to​

  • Deploy with Github Actions: dlt provides the ability to deploy your pipelines using Github Actions. This is a CI/CD runner that you can use for free.
  • Deploy with Airflow: You can also deploy your dlt pipelines using Airflow, a platform to programmatically author, schedule and monitor workflows.
  • Deploy with Google Cloud Functions: dlt allows the deployment of pipelines using Google Cloud Functions, a serverless execution environment for building and connecting cloud services.
  • Other Deployment Options: There are various other ways to deploy your dlt pipelines. You can learn more about these options here.

The running in production section will teach you about:​

  • Monitor Your Pipeline: With dlt, you can easily monitor your pipeline's performance and status. This allows you to keep track of your pipeline's progress and quickly identify any issues that may arise. Learn more about it here.
  • Set Up Alerts: dlt allows you to set up alerts to notify you of any significant events or changes in your pipeline. This feature ensures that you are always aware of your pipeline's status and can quickly react to any issues. Find out how to set up alerts here.
  • Set Up Tracing: Tracing is a powerful feature in dlt that allows you to track the execution of your pipeline. This can be incredibly useful for debugging and performance optimization. Learn more about setting up tracing here.

Additional pipeline guides​

This demo works on codespaces. Codespaces is a development environment available for free to anyone with a Github account. You'll be asked to fork the demo repository and from there the README guides you with further steps.
The demo uses the Continue VSCode extension.

Off to codespaces!

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