______   _                                  _                 _______     ___     ___  _         _
(_____ \ | |                                (_)               (_______)   / __)   / __)(_)       (_)   _
 _____) )| |__   _____  ____    ___   ____   _   ____   ___    _______  _| |__  _| |__  _  ____   _  _| |_  _   _
|  ____/ |  _ \ | ___ ||  _ \  / _ \ |    \ | | / ___) /___)  |  ___  |(_   __)(_   __)| ||  _ \ | |(_   _)| | | |
| |      | | | || ____|| | | || |_| || | | || |( (___ |___ |  | |   | |  | |     | |   | || | | || |  | |_ | |_| |
|_|      |_| |_||_____)|_| |_| \___/ |_|_|_||_| \____)(___/   |_|   |_|  |_|     |_|   |_||_| |_||_|   \__) \__  |
                                                                                                           (____/

Introduction

Phenmomic-Affinity is a Java8 SpringBoot Application powered by Luwak and Lucene to identify affinities in biomedical text.

Following are key components for this service:

Engine

• Generate lucene reverse indices based on curated queries for different ontologies
• Provide an interface for a text string to be passed through index and return:
  • String Ids of queries -> Directly mapped to ontology ID
  • Offsets of lucene hits
• Currently there is not processing is performed on the input text.
• Queries and text are case independent

Index handling

• Mondo: Ontology is parsed by index generator and as Json is created.

Interfaces Restful APIs.

APIs A few notable points:

• There is only one controller (AnnotationController)

Setup

1. The build tool is gradle to keep dependencies clean and build process simple.
2. To run the application locally ./gradlew bootRun can be used.
3. Application uses port 9020 (All phenomics microservices are following 90*0 pattern)

Deployment

1. DevOps code contains script to build docker image, tag it and publish it to ECR.
2. DevOps requires AWS CLI and credentials in environment variables.

Install in Intellij

This project uses Lombok and you need to install the following to get it to work:

• Lombok plugin
• Enable Annotation processing by going to: Preferences -> Build, execution, deployment, compiler, Annotation Processors Creating a profile for the project and enabling it

https://www.jetbrains.com/help/idea/2016.1/configuring-annotation-processing.html

Rebuild and then you should be good to go.