Data

The gene data (~36.5M records, ~5GB) can be downloaded from here: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

Place the downloaded tsv file in the root folder of this project into a folder called ./dataloader/data and name it 'gene_info.tsv'.

Purpose

This repository will hold the projects for the different exercises in the module "Medical Software Development".

System landscape

Projects

• dataanalyzer
  • a python script which will load the tsv file and extract its data into a pandas dataframe to perform basic analyzing and row counting
  • note: these python packages are required to run the script:

    jupyterlab
    pandas
    matplotlib
    

• dataloader
  • a java project for loading the data into a MySQL database. Due to the high volume of data, the script can run for several minutes.
  • works with Apache Ant

    ant clean && ant dist
    

• geneservice (:9090)
  • REST API Webservice created with Java SpringBoot
  • connects to the MySql gene database running on port 3306
  • <java.version>17</java.version>
  • Uses Maven as build tool

    mvn clean && mvn package
    

  • creates logs with logback under the folder "logs" with a RollingFileAppender (one log file per day)
  • uses Swagger-UI to describe the various endpoints (http://localhost:9090/swagger-ui/index.html)
• genewebapp (:8080)
  • JSF web application
  • connects to the API
  • <java.version>17</java.version>
  • Uses Maven as build tool

    mvn clean && mvn tomcat7:redeploy
    

    
  • Addtitional features: Pagination, API status message, custom styling with Bootstrap 5, additional table column "taxId"
• genereactapp (:3000)
  • additional gene client application
  • connects to the API
  • responsive design for mobile devices
  • highlight: pagination through infinite scroll feature
  • React uses NPM as package and build tool

    npm install
    npm run start