Human Phenotype Ontology (HPO) Web App

The following guide provides the steps for an out-of-the-box setup for the Human Phenotype Ontology (HPO) Web application with minimum requirements for a local development environment.

This guide uses the H2 database which is a grails out-of-the-box in-memory or file-base database for quick setup of small-low-volume projects.

Requirements For Running

Java 1.8

Git (Latest)

Requirements For Development

AngularCLI (7.*)
Node (11+)
Node Package Manager (6.4.1+)

Setup

Clone the repo:

JAX Bitbucket (Internal)

  git clone https://bitbucket.jax.org/scm/hpo/hpo-web.git

JAX Github

  git clone https://github.com/TheJacksonLaboratory/hpo-web.git

Change directory to hpo-web
```
  cd hpo-web
```

Initialize the H2 DB and load the HPO ontology data. Run the following command in the command window inside the hpo-web directory. This step will take approximate 3+ minutes to complete

  ./gradlew runCommand -Pargs="load-hpo-db"
  
  E.g. when complete the output in the command window should look like this:
  ...
  finished refreshing database duration: 0:03:49.391 time: Thu Jan 11 11:28:56 EST 2018
   
  BUILD SUCCESSFUL
  
  Note:
  If you desire to re-initialize the application and the database, execute the command again.
  
  ./gradlew runCommand -Pargs="load-hpo-db" ..to initialize and reload the ontology data

Build the application with a gradle task.

  ./gradlew build -Dgrails.env="test" -DchromeHeadless=true -Dwdm.chromeDriverVersion=2.35
  
  E.g.
  ...
  :processTestResources
  :testClasses
  :test
  :check
  :build
   
  BUILD SUCCESSFUL
   
  Total time: 1 mins 29.306 secs

War creation with a gradle task.

./gradlew clean war -DwarName="hpo-web-someversion.war"
 
Will output a war to ./build/libs/

Usage

Run the hpo-web application. This step will launch the application in the local web container and make it available through the web browser
```
  ./gradlew bootRun
  * if you are looking to use the grails console provide argument `-Dgrails.console=true`
```
To open the application site launch the browser and go to
```
  http://<host>:8080/app/index.html
```
If client (Angular App) hot reload is desired open a new shell and execute
```
  ./gradlew buildClientWatch
```

Optionally to open the client (Angular app) via Cli

Change directory to hpo-web/src/main/client
```
cd hpo-web/src/main/client  
```

Execute

ng serve --open (will open application in the browser using port 4200)

Unit Testing

To execute the client (Angular app) unit tests, run
```
./gradlew clientTest
```
To execute backend and client unit tests, run
```
./gradlew test
```

Functional Testing

To execute functional testing with chrome browser, run
```
./gradlew integrationTest
```
To execute functional testing with chrome headless browser, run
```
./gradlew integrationTest -DchromeHeadless
```

Other

To see possible gradle tasks, execute:
```
./gradlew tasks
```
To delete the previous build, execute:
```
./gradlew clean
```
To build with chrome headless for functional tests, execute:
```
./gradlew clean build -DchromeHeadless=true
```
If you would like to use a local instance of mysql please read conf/application.groovy

belkassaby/hpo-web