Dictionary Project

Purpose

PIC-SURE is an application that allows users to build and export a dataset of phenotypic and genomic data. Building that dataset involves building a query that sets a series of constraints on variables present in that PIC-SURE. Large PIC-SURE servers can have tens of thousands of variables, making the query building process complex. Users need a mechanism to find the variables they want to query on. Currently, different implementations of PIC-SURE have developed competing solutions to this problem. None of these solutions fully meet PIC-SURE's variable refinement needs, and all the current solutions are fraught with architectural shortcomings, necessitating the need for a full replacement. The Dictionary Project's goal is to create a unified process for enabling the filtration of variables and the creation of a query. It needs to work across our current projects, and, in anticipation of our push to productize PIC-SURE, it needs to be workable for new PIC-SURE installations.

Contribution

Requirements

• Java 21
• Maven

Setup

1. Copy the linting commit hook:
   cp code-formatting/pre-commit.sh .git/hooks/pre-commit
2. Do a clean build of the project:
   mvn clean install

Usage

Create Env File

cp env.example .env
vi .env

Start DB

docker compose up -d --build dictionary-db

Once up, do some sanity checks in the database:

docker exec -ti dictionary-db psql -U picsure dictionary

Start API

docker compose up -d --build