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A collection of services which comprise the XChemLab deployment

License: Apache License 2.0

Dockerfile 1.06% Shell 0.10% Rust 77.39% Open Policy Agent 1.29% Smarty 3.64% JavaScript 14.86% TypeScript 1.63% HTML 0.04%

xchemlab's Introduction

XChemLab

This repository contains a collection of services which comprise the XChemLab deployment.

Running

To run any of the services, simply execute cargo run -r <SERVICE_NAME>.

Note, deployments of the following ancillary services are required:

An Open Policy Agent instance serving the polcies in /policies is for authentication & authorization.
A PostgreSQL instance to provide a database backend for various services.
A RabbitMQ instance to communicate between services and analysis workers (e.g. chimp_chomp).

Developing

A devcontainer docker-compose configuration is provided in .devcontainer to aid development. If developing in VSCode this can be activated with the Dev Containers extension (ms-vscode-remote.remote-containers).

Test Data

A helper script, collect_test_data.sh, is included. This can be used to collect copies of all recent SoakDB databases into the test_data directory.

xchemlab's People

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ndevenish iamvigneshwars tizayi stan-dot

xchemlab's Issues

[`chimp_controller`] Create a shim between `targeting` & `chimp_chomp`

We need a small service which shims between the targeting service and chimp_chomp. It should subscribe to the image creation endpoint of the targeting service, generate jobs for chimp_chomp on the AMQP, parse their results and publish predictions back to targeting

Set up frontend monorepo

We need to set up the monorepo config for the frontend packages. Technologies to follow those used in the web-ui-components library

Move backend source to backend directory

Would be good to move all the backend source files a new backend/ directory prior to starting work on the frontend

Remove `graphql_types`

Shared API type libraries are known to encourage distributed monoliths, we should avoid falling into this trap

integrate Apollo Client

[`rock_imager_watcher`] Create a service to watch for images from the Rock Imager

We need a service to watch for new images from the Rock Imager and publish them to the targeting service.

add {.js, .ts, .jsx, .tsx, .css} to prettier format script

Set up dependabot for frontend dependencies

We should add the necessary entries to the dependabot configuration to allow automatic updating of frontend dependencies

[`targeting`] `GetObject` pre-signed url is incompatible with ONTAP S3 API

The GetObject pre-signed URL generated by the download_url property of the images query is incompatible with NetApp's ONTAP S3 API. A SigV4A pre-signed URL must be used for compatibility. aws-sdk-s3 compatibility is currently a work in progress and tracked here with a candidate implementation here.