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POET

Details
GitHub TheJacksonLaboratory/POET
Language Java
Description A curation application for HPO and MAxO

Documentation

POET

A Full-Stack annotation application to generate data for disease and associated ontologies.

Setup

Java 11

Intellij

  • Import project as gradle project
  • Ensure the gradle runtime is the wrapper (usually defaults)

Requirements for development - Node - Npm - Java 11 - Mysql or Mariadb

Running

Setup the database

First, open the database console.

sudo mysql -u root

Then create the database poet, a user (e.g. poetdev), and grant poetdev the privileges for the poet database. 

> create database poet;
> create user 'poetdev'@localhost identified by 'password1';
> grant all privileges on poet.* to 'poetdev'@localhost;
> flush privileges;

Replace password1 with a better choice.

Configure datasources under, replace username and password with the credentials from the previous step: - /src/main/resources/application-*.yml

Initalize Data (~30min)

./gradlew bootRun --args="--initializePoet=true"

Run the app

Open in two terminals

Run Server

./gradle bootRun

Run Client src/main/poet

cd src/main/poet; npm run start

Navigate to http://localhost:4200/, endpoints will be served at http://localhost:8080/api/v1/

Unit & Functional Testing Before Deployment

./gradlew test_release

Building For Deployment

Test Environment Internal Only

./gradlew bootWar -Dspring.profiles.active=stage

Production Environment Deployment ./gradlew bootWar -Dspring.profiles.active=production

Contributors

Michael iimpulse Gargano