Push Data by Using SSPs: Send Data to an AI/ML Platform

You can create self-service Tetra Data pipelines (SSPs) to send data to many downstream systems. For example, you can use an SSP to push data to an electronic lab notebook (ELN), laboratory information management system (LIMS), or an artificial intelligence (AI) / machine learning (ML) platform.

This topic provides an example setup for sending data from the Tetra Scientific Data Cloud to a downstream AI/ML platform.

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NOTE

Itโ€™s common for AI/ML applications to pull data from an existing database, rather than having data pushed to them. If the AI/ML tool that youโ€™re using requires you to pull data from the Tetra Data Platform (TDP), see Use Third-Party Tools to Connect to Athena Tables.

Also, the following topic shows how to push data to Kaggle specifically. However, you can use a similar process to push Tetra Data to other AI/ML platforms, because most have software development kits (SDKs) and APIs that allow you to push and pull datasets.

Architecture

The following diagram shows an example SSP workflow for sending data from the Tetra Scientific Data Cloud to a downstream AI/ML platform:

Example SSP workflow for pushing data

Example SSP workflow for pushing data to another system

The diagram shows the following workflow:

  1. Required third-party API credentials are identified.
  2. The API credentials are stored as Shared Settings and Secrets in the TDP.
  3. The โ€œHello, World!โ€ SSP Example sspdemo-taskscript task script version is updated to v5.0.0. The config.json file has five exposed functions:
  • print-hello-world (main.print_hello_world), which is the print_hello_world function found in the main.py file.
  • decorate-input-file (main.decorate_input_file), which is the decorate_input_file function found in the main.py file.
  • harmonize-input-file (main.harmonize_input_file), which is the harmonize_input_file function found in the main.py file.
  • enrich-input-file (main.enrich_input_file), which is the enrich_input_file function found in the main.py file.
  • push-step (main.push_data), which is the push_data function found in the main.py file that uses the third-party API credentials to push data.
  1. A protocol named v3-push (v1.0.0) is created. The protocol.yml file provides the protocol name, description, and two configuration items named kaggle_username and kaggle_api_key. It also outlines one step: push-step. This step points to the sspdemo-taskscript task script and the exposed function, v3-push. The inputs to this function are the input file that kicked off the pipeline workflow, the kaggle_username, and the kaggle_api_key.

Store Third-Party API Authentication Credentials in the TDP

To use third-party API authentication credentials in your protocol configuration elements and task script Python functions, do the following:

  1. Get the required authentication credentials from your target system. To get Kaggle credentials, do the following:
    • Open Kaggle. Then, choose Settings.
    • In the API section, choose Create New Token.
    • Save the Username and API Key so that you can save them in the TDP.
  2. Sign in to the TDP as an admin.
  3. In the left navigation menu, select the hamburger menu icon.
  4. Choose Administration. Then, choose Shared Settings. The Shared Settings page appears.
  5. Add the username from the target system as a Shared Setting. For instructions, see Add a Shared Setting.
  6. Add the API key from the target system as a Secret. For instructions, see Add a Secret.

Identify the Required Third-Party SDK and API Endpoints

Each AI/ML platform has a different SDK and API endpoints. Learn how your target system works, and then find the relevant API calls that allow you to send data to your target platform.

For this example setup, Kaggleโ€™s API works by having Kaggle software on a local machine, saving environment variables with your username and API key, and then running a command on the command line to create a new dataset on the Kaggle platform. The example task script in this topic follows this process.

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NOTE

You will add these required SDK and API endpoints to a task script in the Create and Deploy a Task Script section of this topic.

Create and Deploy the Task Script

Task scripts are the building blocks of protocols, so you must build and deploy your task scripts before you can deploy a protocol that uses them.

Task scripts require the following:

  • A config.json file that contains configuration information that exposes and makes your Python functions accessible so that protocols can use them.
  • A Python file that contains python functions (main.py in the following examples) that include the code thatโ€™s used in file processing.
  • A requirements.txt file that either specifies any required third-party Python modules, or that is left empty if no modules are needed.

To create a task script that programmatically sends data from the Tetra Scientific Data Cloud to a downstream AI/ML platform, do the following.

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NOTE

For more information about creating custom task scripts, see Task Script Files. For information about testing custom task scripts locally, see Create and Test Custom Task Scripts.

Create a config.json File

Create a config.json file in your code editor by using the following code snippet:

{
    "language": "python",
    "functions": [
        {
            "slug": "print-hello-world",
            "function": "main.print_hello_world"
        },
        {
            "slug": "decorate-input-file",
            "function": "main.decorate_input_file"
        },
        {
            "slug": "harmonize-input-file",
            "function": "main.harmonize_input_file"
        },
        {
            "slug": "enrich-input-file",
            "function": "main.enrich_input_file"
        },
        {
            "slug": "push-data",
            "function": "main.push_data"
        }
    ]
}

Update Your main.py File

Using the task script from Enrich Data by Using SSPs: Add Extra Data to Files, add the following elements to your task script:

# Add new import statement
import os

...

# Add this new function
def push_data(input: dict, context: Context) -> dict:

    print("Starting push to 3rd party")

    # Pull out the arguments to the function
    input_file_pointer = input["input_file_pointer"]
    kaggle_username = input["kaggle_username"]
    kaggle_api_key_secret = input["kaggle_api_key"]
    kaggle_api_key = context.resolve_secret(kaggle_api_key_secret)

    print("Get Processed file data")
    # Open the file and import json
    f = context.read_file(input_file_pointer, form='file_obj')
    processed_data = f['file_obj'].read().decode("utf-8")
    processed_json = json.loads(processed_data)

    print("Start Kaggle content")
    # Kaggle Specific
    # Add username and API Key to OS environment
    os.environ['KAGGLE_USERNAME'] = kaggle_username
    os.environ['KAGGLE_KEY'] = kaggle_api_key

    # Kaggle Specific
    # Pull out the data from the PROCESSED file and save as a temporary file
    data = {}
    data["data"] = processed_json["extra_data"]

    with open('data.json', 'w') as outfile:
        json.dump(data, outfile)

    # Kaggle Specific
    # Create dataset metadata and save as a temporary file
    dataset_name = "exampledataset"
    dataset_metadata = {
                        "title": dataset_name,
                        "id": kaggle_username+"/"+dataset_name,
                        "licenses": [
                                {
                                "name": "CC0-1.0"
                                }
                            ]
                        }
    with open('dataset-metadata.json', 'w') as outfile:
        json.dump(dataset_metadata, outfile)


    # Kaggle Specific
    # Upload data to Kaggle. Uses OS environment variables
    os.system("kaggle datasets create -p .")

Context API

In the Python code provided in this example setup, the Context API is used by importing it in the main.py file (from ts_sdk.task.__task_script_runner import Context). The Context section provides the necessary APIs for the task script to interact with the TDP.

This example setup uses the following Context API endpoint:

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NOTE

The context.resolve_secret function converts the AWS Systems Manager (SSM) reference to the actual secret value.

Install Any Required Third-Party Packages

You may need to install a third-party package in your Docker image so your task script can use the installed package (for example, Kaggle or OpenJDK). This example procedure uses Kaggle.

To install a third-party package in the Docker image, do the following:

  1. Create a folder called init in your task local task script folder.
  2. Create a new file locally in the init folder named before_install. Then, add install command line statements that use your specific package management system.

Kaggle Install Command Example

pip install kaggle

OpenJDK Install Command Example

apt-get update && apt-get install -y openjdk-11-jdk
  1. Open your task scriptโ€™s root folder, and then add the before_install file by using the following SSP folder structure:

SSP Folder Structure Example that Includes a ./init/before_install File

protocol
โ””โ”€โ”€ protocol.yml
task-script
โ”œโ”€โ”€ init
|   โ””โ”€โ”€ before_install
โ”œโ”€โ”€ config.json
โ””โ”€โ”€ main.py

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NOTE

The code runs when the task script Docker image builds.

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IMPORTANT

The executable attributes of task script files on your local machine are not preserved. If a file is executable on your local machine, that doesnโ€™t mean itโ€™s executable during the Docker image build step.

To execute your files during the Docker image build step and have your task script files run them from your code, you must include the following command in your before_install script:

chmod a+x ./path-to-your-exec-file

Create a Python Package

Within the task script folder that contains the config.json and main.py files, use Python Poetry to create a Python package and the necessary files to deploy them to the TDP.

Poetry Command Example to Create a Python Package

poetry init
poetry add datetime
poetry export --without-hashes --format=requirements.txt > requirements.txt

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NOTE

If no packages are added, this poetry export command example produces text in requirements.txt that you must delete to create an empty requirements.txt file. However, for this example setup, thereโ€™s a datetime package, so requirements.txt shouldn't be empty. A requirements.txt file is required to deploy the package to the TDP.

Deploy the Task Script

To the deploy the task script, run the following command from your command line (for example, bash):

ts-sdk put task-script private-{TDP ORG} sspdemo-taskscript v5.0.0 {task-script-folder} -c {auth-folder}/auth.json

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NOTE

Make sure to replace {TDP ORG} with your organization slug, {task-script-folder} with the local folder that contains your protocol code, and {auth-folder} with the local folder that contains your authentication information.

Also, when creating a new version of a task script and deploying it to the TDP, you must increase the version number. In this example command, the version is increased to v5.0.0.

Create and Deploy a Protocol

Protocols define the business logic of your pipeline by specifying the steps and the functions within task scripts that execute those steps. For more information about how to create a protocol, see Protocol YAML Files.

In the following example, thereโ€™s one step: push-step. This step uses the push-data function thatโ€™s in the sspdemo-taskscript task script, which is v5.0.0 of the task script.

Create a protocol.yml File

Create a protocol.yml file in your code editor by using the following code snippet:

protocolSchema: "v3"
name: "Push - v3 protocol"
description: "Protocol that pushes data to 3rd party application."

config:
  kaggle_username:
    label: "Kaggle Username."
    description: "Kaggle Username to use for pushing data."
    type: "string"
    required: true
  kaggle_api_key:
    label: "Kaggle API Key."
    description: "Kaggle API Key to use for pushing data."
    type: "secret"
    required: true

steps:
  - id: push-step
    task:
      namespace: private-training-sspdemo
      slug: sspdemo-taskscript
      version: v5.0.0
      function: push-data
    input:
      input_file_pointer: $( workflow.inputFile )
      kaggle_username: $( config.kaggle_username )
      kaggle_api_key: $( config.kaggle_api_key )

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NOTE

When using a new task script version, you must use the new version number when weโ€™re calling that task script in the protocol step. This example protocol.yml file refers to v5.0.0.

Deploy the Protocol

To the deploy the protocol, run the following command from your command line (for example, bash):

ts-sdk put protocol private-{TDP ORG} v3-push v1.0.0 {protocol-folder} -c {auth-folder}/auth.json

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NOTE

Make sure to replace {TDP ORG} with your organization slug, {protocol-folder} with the local folder that contains your protocol code, and {auth-folder} with the local folder that contains your authentication information.

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NOTE

To redeploy the same version of your code, you must include the -f flag in your deployment command. This flag forces the code to overwrite the file. The following are example protocol deployment command examples:

  • ts-sdk put protocol private-xyz hello-world v1.0.0 ./protocol -f -c auth.json
  • ts-sdk put task-script private-xyz hello-world v1.0.0 ./task-script -f -c auth.json

For more details about the available arguments, run the following command:

ts-sdk put --help

Create a Pipeline That Uses the Deployed Protocol

To use your new protocol on the TDP, create a new pipeline that uses the protocol that you deployed. Then, upload a file that matches the pipelineโ€™s trigger conditions.

For the configuration elements in the UI configuration of your pipeline, you can use your shared setting (kaggle_username) and shared secret (kaggle_api_key).