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Creating a docker container

This document explains how to create a package that is capable of running docker containers on the Datagrok instance.

Overview

Datagrok enables users to incorporate a custom Docker container into their package and leverage it throughout the package's lifecycle. Users have the flexibility to use a custom image or an image from Docker Hub. When a custom image is used, Datagrok takes care of building and running it automatically.

Once a user publishes a package that includes a Docker image, Datagrok adds the image to the build queue and builds it. Additionally, Datagrok creates a Docker container instance that can be accessed via HTTP(s) using the Datagrok JS-API. Users can monitor the status of both images and containers in the Manage -> Docker view, which is useful for checking status or troubleshooting.

This system is cloud-agnostic and works with local instances using Docker Compose or AWS. The only requirement is that the grok-spawner container must be running in the same environment. Users can access the container via HTTP, but only one EXPOSE $PORT is allowed in the image.

1. Create a dockerfile

Before we start, get familiar with docker docs, which are related to the process of application containerizing.

Now, let's create a folder dockerfiles. You should put there a Dockerfile with the commands that are needed to build a docker image and run the container. Follow all the best practices for writing dockerfiles in order to make them simple, small and efficient.

Example of such Dockerfile is located in PepSeA package.

2. Implement the function to get a response

Add code that is responsible for making a request to the container:

async function requestAlignedObjects(id: string, body: PepseaBodyUnit[], method: string,
gapOpen: number | null, gapExtend: number | null): Promise<PepseaRepsonse> {
const params = {
method: 'POST',
headers: {'Accept': 'application/json', 'Content-Type': 'application/json'},
body: JSON.stringify(body),
};
const path = `/align?method=${method}&gap_open=${gapOpen}&gap_extend=${gapExtend}`;
const response = await grok.dapi.docker.dockerContainers.request(id, path, params);
return JSON.parse(response ?? '{}');
}

To make a request grok.dapi.dockerfiles.request is used. You should specify the id in order to make the request to the right container, path and params of the request. To get id do:

const dockerfileId = (await grok.dapi.docker.dockerContainers.filter('pepsea').first()).id;

That's it!

3. Build and publish

Run webpack and publish your package to one of the Datagrok instances:

webpack
grok publish dev

The return code should be 0 to indicate a successful deployment.

4. Test

Now go to Datagrok and open Manage -> Dockerfiles. You should see the created container in the list. In order to run it, right click on the container and choose the Run option. Here is how it looks:

docker-container