Loading Data from MySQL
to AlloyDB
with dlt
in Python
We will be using the dlt PostgreSQL destination to connect to AlloyDB. You can get the connection string for AlloyDB from the GCP AlloyDB Console.
Join our Slack community or book a call with our support engineer Violetta.
MySQL
is a widely used relational database management system (RDBMS) that is free and open-source. It is suitable for both small and large applications. AlloyDB
for PostgreSQL is a fully managed, PostgreSQL-compatible database service designed for demanding workloads, including hybrid transactional and analytical processing. It combines a Google-built database engine with a cloud-based, multi-node architecture to deliver enterprise-grade performance, reliability, and availability. This documentation provides guidance on loading data from MySQL
to AlloyDB
using the open-source Python library dlt
. For more information about MySQL
, visit here.
dlt
Key Features
- Pipeline Metadata:
dlt
pipelines leverage metadata to provide governance capabilities, including load IDs for incremental transformations and data lineage. Learn more. - Schema Enforcement and Curation:
dlt
empowers users to enforce and curate schemas, ensuring data consistency and quality. Learn more. - Schema Evolution:
dlt
alerts users to schema changes, allowing them to take necessary actions like reviewing changes or updating downstream processes. Learn more. - Scaling and Finetuning:
dlt
offers several mechanisms and configuration options to scale up and fine-tune pipelines, including parallel execution and memory buffer adjustments. Learn more. - Naming Convention:
dlt
uses a standard snake_case naming convention for table and column identifiers across all destinations, ensuring consistency. Learn more.
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 AlloyDB
:
pip install "dlt[postgres]"
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 MySQL
to AlloyDB
. You can run the following commands to create a starting point for loading data from MySQL
to AlloyDB
:
# create a new directory
mkdir sql_database_mysql_pipeline
cd sql_database_mysql_pipeline
# initialize a new pipeline with your source and destination
dlt init sql_database postgres
# 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
:
sqlalchemy>=1.4
dlt[postgres]>=0.4.7
You now have the following folder structure in your project:
sql_database_mysql_pipeline/
├── .dlt/
│ ├── config.toml # configs for your pipeline
│ └── secrets.toml # secrets for your pipeline
├── sql_database/ # folder with source specific files
│ └── ...
├── sql_database_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.sql_database.credentials]
drivername = "drivername" # please set me up!
database = "database" # please set me up!
password = "password" # please set me up!
username = "username" # please set me up!
host = "host" # please set me up!
port = 0 # please set me up!
[destination.postgres]
dataset_name = "dataset_name" # please set me up!
[destination.postgres.credentials]
database = "database" # please set me up!
password = "password" # please set me up!
username = "username" # please set me up!
host = "host" # please set me up!
port = 5432
connect_timeout = 15
2.1. Adjust the generated code to your usecase
The default sql_database
pipeline is configured to connect to an example postgres database. The sql_database
source supports all sql dialects
supported by SQLAlchemy. Please refer to the MySQL Section
of the SQLAlchemy docs for additional info about SQLAlchemy and MySQL.
To connect to MySQL with this example pipeline, you'll need to install an MySQL Python DB API driver:
pip install mysqlclient
And use an MySQL connection String in your code:
credentials = ConnectionStringCredentials(
"mysql+mysqldb://username:password@host:3306/database"
)
Or your secrets.toml
:
[sources.sql_database.credentials]
drivername = "mysql+mysqldb"
database = "database"
password = "password"
username = "username"
host = "host"
port = 3306
3. Running your pipeline for the first time
The dlt
cli has also created a main pipeline script for you at sql_database_pipeline.py
, as well as a folder sql_database
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:
import sqlalchemy as sa
import humanize
import dlt
from dlt.common import pendulum
from dlt.sources.credentials import ConnectionStringCredentials
from sql_database import sql_database, sql_table, Table
def load_select_tables_from_database() -> None:
"""Use the sql_database source to reflect an entire database schema and load select tables from it.
This example sources data from the public Rfam MySQL database.
"""
# Create a pipeline
pipeline = dlt.pipeline(
pipeline_name="rfam", destination='postgres', dataset_name="rfam_data"
)
# Credentials for the sample database.
# Note: It is recommended to configure credentials in `.dlt/secrets.toml` under `sources.sql_database.credentials`
credentials = ConnectionStringCredentials(
"mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam"
)
# To pass the credentials from `secrets.toml`, comment out the above credentials.
# And the credentials will be automatically read from `secrets.toml`.
# Configure the source to load a few select tables incrementally
source_1 = sql_database(credentials).with_resources("family", "clan")
# Add incremental config to the resources. "updated" is a timestamp column in these tables that gets used as a cursor
source_1.family.apply_hints(incremental=dlt.sources.incremental("updated"))
source_1.clan.apply_hints(incremental=dlt.sources.incremental("updated"))
# Run the pipeline. The merge write disposition merges existing rows in the destination by primary key
info = pipeline.run(source_1, write_disposition="merge")
print(info)
# Load some other tables with replace write disposition. This overwrites the existing tables in destination
source_2 = sql_database(credentials).with_resources("features", "author")
info = pipeline.run(source_2, write_disposition="replace")
print(info)
# Load a table incrementally with append write disposition
# this is good when a table only has new rows inserted, but not updated
source_3 = sql_database(credentials).with_resources("genome")
source_3.genome.apply_hints(incremental=dlt.sources.incremental("created"))
info = pipeline.run(source_3, write_disposition="append")
print(info)
def load_entire_database() -> None:
"""Use the sql_database source to completely load all tables in a database"""
pipeline = dlt.pipeline(
pipeline_name="rfam", destination='postgres', dataset_name="rfam_data"
)
# By default the sql_database source reflects all tables in the schema
# The database credentials are sourced from the `.dlt/secrets.toml` configuration
source = sql_database()
# Run the pipeline. For a large db this may take a while
info = pipeline.run(source, write_disposition="replace")
print(
humanize.precisedelta(
pipeline.last_trace.finished_at - pipeline.last_trace.started_at
)
)
print(info)
def load_standalone_table_resource() -> None:
"""Load a few known tables with the standalone sql_table resource, request full schema and deferred
table reflection"""
pipeline = dlt.pipeline(
pipeline_name="rfam_database",
destination='postgres',
dataset_name="rfam_data",
full_refresh=True,
)
# Load a table incrementally starting at a given date
# Adding incremental via argument like this makes extraction more efficient
# as only rows newer than the start date are fetched from the table
# we also use `detect_precision_hints` to get detailed column schema
# and defer_table_reflect to reflect schema only during execution
family = sql_table(
credentials="mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam",
table="family",
incremental=dlt.sources.incremental(
"updated",
),
detect_precision_hints=True,
defer_table_reflect=True,
)
# columns will be empty here due to defer_table_reflect set to True
print(family.compute_table_schema())
# Load all data from another table
genome = sql_table(
credentials="mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam",
table="genome",
detect_precision_hints=True,
defer_table_reflect=True,
)
# Run the resources together
info = pipeline.extract([family, genome], write_disposition="merge")
print(info)
# Show inferred columns
print(pipeline.default_schema.to_pretty_yaml())
def select_columns() -> None:
"""Uses table adapter callback to modify list of columns to be selected"""
pipeline = dlt.pipeline(
pipeline_name="rfam_database",
destination='postgres',
dataset_name="rfam_data_cols",
full_refresh=True,
)
def table_adapter(table: Table) -> None:
print(table.name)
if table.name == "family":
# this is SqlAlchemy table. _columns are writable
# let's drop updated column
table._columns.remove(table.columns["updated"])
family = sql_table(
credentials="mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam",
table="family",
chunk_size=10,
detect_precision_hints=True,
table_adapter_callback=table_adapter,
)
# also we do not want the whole table, so we add limit to get just one chunk (10 records)
pipeline.run(family.add_limit(1))
# only 10 rows
print(pipeline.last_trace.last_normalize_info)
# no "updated" column in "family" table
print(pipeline.default_schema.to_pretty_yaml())
def select_with_end_value_and_row_order() -> None:
"""Gets data from a table withing a specified range and sorts rows descending"""
pipeline = dlt.pipeline(
pipeline_name="rfam_database",
destination='postgres',
dataset_name="rfam_data",
full_refresh=True,
)
# gets data from this range
start_date = pendulum.now().subtract(years=1)
end_date = pendulum.now()
family = sql_table(
credentials="mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam",
table="family",
incremental=dlt.sources.incremental( # declares desc row order
"updated", initial_value=start_date, end_value=end_date, row_order="desc"
),
chunk_size=10,
)
# also we do not want the whole table, so we add limit to get just one chunk (10 records)
pipeline.run(family.add_limit(1))
# only 10 rows
print(pipeline.last_trace.last_normalize_info)
def my_sql_via_pyarrow() -> None:
"""Uses pyarrow backend to load tables from mysql"""
# uncomment line below to get load_id into your data (slows pyarrow loading down)
# dlt.config["normalize.parquet_normalizer.add_dlt_load_id"] = True
# Create a pipeline
pipeline = dlt.pipeline(
pipeline_name="rfam_cx",
destination='postgres',
dataset_name="rfam_data_arrow_4",
)
def _double_as_decimal_adapter(table: sa.Table) -> None:
"""Return double as double, not decimals"""
for column in table.columns.values():
if isinstance(column.type, sa.Double):
column.type.asdecimal = False
sql_alchemy_source = sql_database(
"mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam?&binary_prefix=true",
backend="pyarrow",
table_adapter_callback=_double_as_decimal_adapter,
).with_resources("family", "genome")
info = pipeline.run(sql_alchemy_source)
print(info)
def create_unsw_flow() -> None:
"""Uploads UNSW_Flow dataset to postgres via csv stream skipping dlt normalizer.
You need to download the dataset from https://github.com/rdpahalavan/nids-datasets
"""
from pyarrow.parquet import ParquetFile
# from dlt.destinations import postgres
# use those config to get 3x speedup on parallelism
# [sources.data_writer]
# file_max_bytes=3000000
# buffer_max_items=200000
# [normalize]
# workers=3
data_iter = ParquetFile("UNSW-NB15/Network-Flows/UNSW_Flow.parquet").iter_batches(
batch_size=128 * 1024
)
pipeline = dlt.pipeline(
pipeline_name="unsw_upload",
# destination=postgres("postgres://loader:loader@localhost:5432/dlt_data"),
destination='postgres',
progress="log",
)
pipeline.run(
data_iter,
dataset_name="speed_test",
table_name="unsw_flow_7",
loader_file_format="csv",
)
def test_connectorx_speed() -> None:
"""Uses unsw_flow dataset (~2mln rows, 25+ columns) to test connectorx speed"""
import os
# from dlt.destinations import filesystem
unsw_table = sql_table(
"postgresql://loader:loader@localhost:5432/dlt_data",
"unsw_flow_7",
"speed_test",
# this is ignored by connectorx
chunk_size=100000,
backend="connectorx",
# keep source data types
detect_precision_hints=True,
# just to demonstrate how to setup a separate connection string for connectorx
backend_kwargs={"conn": "postgresql://loader:loader@localhost:5432/dlt_data"},
)
pipeline = dlt.pipeline(
pipeline_name="unsw_download",
destination='postgres',
# destination=filesystem(os.path.abspath("../_storage/unsw")),
progress="log",
full_refresh=True,
)
info = pipeline.run(
unsw_table,
dataset_name="speed_test",
table_name="unsw_flow",
loader_file_format="parquet",
)
print(info)
def test_pandas_backend_verbatim_decimals() -> None:
pipeline = dlt.pipeline(
pipeline_name="rfam_cx",
destination='postgres',
dataset_name="rfam_data_pandas_2",
)
def _double_as_decimal_adapter(table: sa.Table) -> None:
"""Emits decimals instead of floats."""
for column in table.columns.values():
if isinstance(column.type, sa.Float):
column.type.asdecimal = True
sql_alchemy_source = sql_database(
"mysql+pymysql://rfamro@mysql-rfam-public.ebi.ac.uk:4497/Rfam?&binary_prefix=true",
backend="pandas",
table_adapter_callback=_double_as_decimal_adapter,
chunk_size=100000,
# set coerce_float to False to represent them as string
backend_kwargs={"coerce_float": False, "dtype_backend": "numpy_nullable"},
# preserve full typing info. this will parse
detect_precision_hints=True,
).with_resources("family", "genome")
info = pipeline.run(sql_alchemy_source)
print(info)
if __name__ == "__main__":
# Load selected tables with different settings
load_select_tables_from_database()
# load a table and select columns
# select_columns()
# load_entire_database()
# select_with_end_value_and_row_order()
# Load tables with the standalone table resource
# load_standalone_table_resource()
# Load all tables from the database.
# Warning: The sample database is very large
# 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 sql_database_pipeline.py
4. Inspecting your load result
You can now inspect the state of your pipeline with the dlt
cli:
dlt pipeline sql_database info
You can also use streamlit to inspect the contents of your AlloyDB
destination for this:
# install streamlit
pip install streamlit
# run the streamlit app for your pipeline with the dlt cli:
dlt pipeline sql_database 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: Learn how to deploy your
dlt
pipeline using GitHub Actions for automated CI/CD workflows. Github Actions - Deploy with Airflow and Google Composer: Follow this guide to deploy your
dlt
pipeline using Airflow, a popular workflow orchestration tool, managed by Google Composer. Airflow - Deploy with Google Cloud Functions: Discover how to deploy your
dlt
pipeline using Google Cloud Functions for serverless execution. Google cloud functions - Other Deployment Options: Explore additional methods and tools for deploying your
dlt
pipeline in various environments. and others...
The running in production section will teach you about:
- How to Monitor your pipeline: Learn how to effectively monitor your
dlt
pipeline in production to ensure smooth operations. How to Monitor your pipeline - Set up alerts: Set up alerts to get notified about important events and issues in your
dlt
pipeline. Set up alerts - Set up tracing: Implement tracing to track and analyze the flow of data through your
dlt
pipeline. And set up tracing
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