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README.md

Amazon DocumentDB with Jupyter Notebooks

documentdb-sagemaker-arch

This is a sample project for Python development with CDK.

The cdk.json file tells the CDK Toolkit how to execute your app.

This project is set up like a standard Python project. The initialization process also creates a virtualenv within this project, stored under the .venv directory. To create the virtualenv it assumes that there is a python3 (or python for Windows) executable in your path with access to the venv package. If for any reason the automatic creation of the virtualenv fails, you can create the virtualenv manually.

To manually create a virtualenv on MacOS and Linux:

$ python3 -m venv .venv

After the init process completes and the virtualenv is created, you can use the following step to activate your virtualenv.

$ source .venv/bin/activate

If you are a Windows platform, you would activate the virtualenv like this:

% .venv\Scripts\activate.bat

Once the virtualenv is activated, you can install the required dependencies.

$ pip install -r requirements.txt

At this point you can now synthesize the CloudFormation template for this code.

$ export CDK_DEFAULT_ACCOUNT=$(aws sts get-caller-identity --query Account --output text)
$ export CDK_DEFAULT_REGION=$(aws configure get region)
$ cdk synth --all

Use cdk deploy command to create the stack shown above,

$ cdk deploy --all

then load and run the Jupyter notebook in your Sagemaker instance.

Useful commands

  • cdk ls list all stacks in the app
  • cdk synth emits the synthesized CloudFormation template
  • cdk deploy deploy this stack to your default AWS account/region
  • cdk diff compare deployed stack with current state
  • cdk docs open CDK documentation

Enjoy!

Troubleshooting

When you run the Jupyter notebook in your Sagemaker instance, you need to change some codes (1) You should assign secret_name variable to your AWS Secrets to access DocumentDB

# Get DocumentDB credentials stored in Secrets Manager
def get_secret(secret_name):

    # Create a Secrets Manager client
    session = boto3.session.Session()
    client = session.client(
        service_name='secretsmanager',
        region_name=session.region_name
    )

    get_secret_value_response = client.get_secret_value(SecretId=secret_name)
    secret = get_secret_value_response['SecretString']

    return json.loads(secret)

You can find AWS Secrets as runing the following codes.

$ python
Python 3.9.1 (default, Dec 17 2020, 03:41:37)
[Clang 12.0.0 (clang-1200.0.32.27)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import boto3
>>> cf_client = boto3.client('cloudformation', region_name='us-east-1')
>>> cf_stackname = 'AmazonDocDBStack'
>>> response = cf_client.describe_stacks(StackName=cf_stackname)
>>> outputs = response["Stacks"][0]["Outputs"]
>>> secrets = [e for e in outputs if e['OutputKey'] == 'DocDBSecret'][0]
>>> secrets
{'OutputKey': 'DocDBSecret', 'OutputValue': 'DocDBSecret3B817195-ZPE9J6tmnLtd', 'ExportName': 'DocDBSecret'}
>>> secret_name = secrets['OutputValue']
>>> secret_name
'DocDBSecret3B817195-ZPE9J6tmnLtd'
>>>

(2) You should apply URL encoding for DocumentDB password. DocumentDB password has been genenerated by CloudFormation so that it may contain invalid characters in URL.

  • As-Is

    # Sets up a connection to the Amazon DocumentDB database
secret = get_secret(secret_name)

db_username = secret['username']
db_password = secret['password']
db_port = secret['port']
db_host = secret['host']

  • To-Be

    # Sets up a connection to the Amazon DocumentDB database
secret = get_secret(secret_name)

import urllib
db_username = secret['username']
db_password = urllib.parse.quote_plus(secret['password'])
db_port = secret['port']
db_host = secret['host']

References