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ensembl-elastic-rest-final

This application has two main tasks.

  1. Add JSON objects into Elastic-Search server by querying MySQL database for latest tracks.
  2. Provide rest end points to search tracks loaded from MySQL database.

Tracks can be searched by following parameters.

  1. Unique keyword
  2. Species
  3. Type
  4. Release
  5. Division

You can get the deployed application here. And the working rest end point with provided data. When you are searching, Unique keyword (text) is a mandetory parameter.

https://ensembl-elastic-rest.herokuapp.com/api/elastic-test/master/track/search_advanced?text=Genes&species=homo_sapiens&type=gene&release=89&division=ensembl

Main technologies used in the project.

  1. Spring Boot
  2. JPA
  3. Maven
  4. Elastic-Search
  5. MySQL

How to clone repository and install dependencies

You need to clone the applicaton from github. To do so, please use the following command.

git clone https://github.com/chanakaDe/ensembl-elastic-rest-final.git

Now you have the latest update of this application. Next part is installing all the dependencies.

Since this is a maven applicatoion, there are many ways to install all the dependencies. It should be quite straightforward to run your application from an IDE with some maven support (Eclipse, IntellIJ , NetBeans). These IDEs will take care about creating the correct classpath and also all the dependencies. This application is created using IntelliJ IDEA Community Version.

If you want to do it manually, please run the following command at the root folder structure of the project.

mvn clean install

This will compile your project and create the jar you defined in the pom.xml file. It runs the maven phases clean and every phase up to install (compile, test, etc).

This is a maven application and there are plenty of ways to run a maven application. Since this is a Spring Boot application, it doesn't need a seperate to run. If you need more information, please check https://projects.spring.io/spring-boot/ and "Features" section.

How to configure application with database locations and elastic-search locations

This application contains one elastic search instance and also one mysql database instance. These two instances are configure in the project's application.properties file.

The project location : /src/main/resources/application.properties

Github location : https://github.com/chanakaDe/ensembl-elastic-rest-final/blob/master/src/main/resources/application.properties

To change Elastic-Search instance , you need to change following properties.

elasticsearch.clustername = ensembl-cluster
elasticsearch.host = 138.197.117.104
elasticsearch.port = 9300

To change MySQL database instance, you need to change following properties.

spring.datasource.url=jdbc:mysql://138.197.117.104:3306/ensembl_new
spring.datasource.username=root
spring.datasource.password=*******

How to deploy application into Heroku

Since this is a Spring Boot application, it has it's own embeded server. so it's really easy to deploy into Heroku. Following instructions show how to deploy current application into Heroku uisng a free account.

cd ensembl-elastic-rest-final
heroku login
git init
git add .
git commit -m "first commit"
heroku create
git push heroku master

Now your application is up and running. Since this is a REST API, there is no any front end parts to check. Here's how you can check your application is working or not.

When you use the command heroku create , you can get a random generated application name, eg : nameless-lake-8055. So you can use this name to check your application as follows :

https://nameless-lake-8055.herokuapp.com/api/elastic-test/master/track/search_advanced?text=Genes&species=homo_sapiens&type=gene&release=89&division=ensembl

All you have to do is replace nameless-lake-8055 with your application name and opne this link in your browser. If you can get a JSON output with Track information, your application is up and running.

For more information, please visit official heroku spring boot deployment documentation :

https://devcenter.heroku.com/articles/deploying-spring-boot-apps-to-heroku

How to import data from new MySQL Track DB to Elastic-Search Instance

When we are using the rest api, we need to have data stored in Elastic Search server. So this data import part is also a component of this application. When you run the application, it's also auto starting and importing data from new MySQL Track DB to Elastic Search server.

So you don't need to build or re run the application again and again. When you run the Old database to New database convert application (https://github.com/chanakaDe/ensembl-db-convert) , you might add new records to New MySQL Track Db. Then all you have to do is go to Heroku Admin Panel (Or any other admin panel you have hosted the application) and restart the application. It's so easy. Then automatically all the data is importing to Elastic Search Server.

Where to find data importing method ?

You can get the automatically running code from followng URL :

https://github.com/chanakaDe/ensembl-elastic-rest-final/blob/master/src/main/java/com/chanaka/Application.java#L37