Developer Setup

Install and Update Ubuntu Desktop (cur ver 20.04)

  1. Boot to a live version of Ubuntu Desktop on a cd or a usb key

  2. Install Ubuntu on the target hard drive

  3. Update ubuntu once it is finished installing

  4. sudo apt update

  5. sudo apt upgrade

  6. sudo apt full-upgrade

  7. sudo apt autoremove

Install Java (cur ver21)

Detailed instructions found here

  1. sudo apt install default-jdk

  2. java -version

  3. javac -version

Install Docker

Detailed instructions found here

  1. curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

  2. sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"

  3. sudo apt-get update

  4. apt-cache policy docker-ce

  5. sudo apt-get install -y docker-ce

  6. sudo systemctl status docker

Setup Docker (Optional)

Detailed instructions found here. This will enable you to call docker without calling sudo.

  1. sudo usermod -aG docker ${USER}

  2. su - ${USER}

  3. id -nG

Install Docker-Compose

Detailed instructions found here

  1. sudo curl -L https://github.com/docker/compose/releases/download/1.21.2/docker-compose-`uname -s`-`uname -m` -o /usr/local/bin/docker-compose

  2. sudo chmod +x /usr/local/bin/docker-compose

  3. docker-compose --version

Install Chrome

  1. Download Chrome

  2. Run Chrome installer

  3. Make chrome your default browser

Download OpenELIS-Global-2

  1. Fork the repo at https://github.com/I-TECH-UW/OpenELIS-Global-2

  2. cd /path/to/eclipse/workspace

  3. git clone [git@github.com](mailto:git@github.com):{Your_Github_Account}/OpenELIS-Global-2.git --recurse-submodules

Test If OpenELIS-Global-2 Deploys

  1. Open terminal to the OpenELIS-Global-2 directory

  2. docker-compose up -d

  3. Access the application at https://localhost:8443/OpenELIS-Global

  4. Might need to dismiss a security warning

Setting Developer Enviroment with Docker Compose (Dev Setup in Docker)

  1. Build the War file

      mvn clean install -DskipTests

  2. Start the containers to mount the locally compiled artifacts

    docker-compose -f dev.docker-compose.yml up -d

    Note : For Reflecting Local changes in the Running Containers ;

The Instaces can be accesed at

Instance

URL

credentials (user : password)

Legacy UI

https://localhost/api/OpenELIS-Global/ 

 admin: adminADMIN!

New React UI

https://localhost/

admin: adminADMIN!

Setting Developer Enviroment With Tomcat and Eclipse (Native Dev Setup )

Install Maven

Detailed instructions here

  1. sudo apt install maven

  2. mvn -version

Install Eclipse

  1. Navigate to Eclipse download website (https://www.eclipse.org/downloads/ )

  2. Download the installer

  3. Run the installer, choosing the Java ee version of eclipse

Optionally Install Eclipse Plugins

  1. Jaspersoft Reports

  2. eGit

Install Lombok in Eclipse

Instructions are here https://projectlombok.org/setup/eclipse

Setup Project in Eclipse

  1. File > Import > Projects from Folder or Archive

  2. ensure OpenELIS-Global-2 is selected (and dataexport-core and dataexport-api which are under eclipse)

  3. ensure detect and configure project natures is selected

  4. finish

  5. right click OpenELIS-Global-2 project > properties > Java Build Path > Projects > classpath > add

  6. add dataexport-core and dataexport-api

Setup Tomcat Server

  1. Download tomcat as tar.gz (cur ver 9)

  2. Extract into to your eclipse workspace directory (or wherever you want, but remember the location)

  3. Select servers tab in eclipse

  4. Right click in the servers tab, and select new > server

  5. Find tomcat 9 in the list, click it, and select next

  6. Select your tomcat installation directory (wherever you extracted it in step 2)

  7. Click next

  8. Add Open-Elis-Global-2 to the server and click finish

Configure Tomcat server

  1. Double click on the tomcat 9.0 server in the servers tab

  2. Click ‘Open launch configuration’

  3. Navigate to the Arguments tab

  4. Add the following 3 arguments to the VM arguments section, substituting whatever your local arguments are for your database

  5. -Ddatasource.password=clinlims -Ddatasource.username=clinlims -Ddatasource.url=jdbc:postgresql://localhost:15432/clinlims?currentSchema=clinlims

  6. click OK to finish

  7. optionally, extend the server timeout to 200 seconds

Configure Tomcat to Support ssl

  1. Expand the Servers folder in the projects tab

  2. Expand the server that runs OE

  3. Copy the contents of OpenELIS-Global-2/dev/tomcat/oe_server.xml into Tomcat v9.0 Server at localhost-config/server.xml

  4. Edit Tomcat v9.0 Server at localhost-config/server.xml, substituting your paths

  5. replace <Server port="-1" shutdown="SHUTDOWN"> with <Server port="8005" shutdown="SHUTDOWN">

  6. replace keystoreFile=”/run/secrets/keystore” with keystoreFile=”/path/to/openelis_global_2/dev/https/oe_selfsigned.keystore”

  7. replace truststoreFile="/run/secrets/truststore" with truststoreFile="/path/to/openelis_global_2/dev/https/oe_selfsigned.truststore"

  8. save

Point to your dev common.properties

  1. sudo mkdir /run/secrets

  2. sudo ln -s /path/to/project/dev/eclipse_common.properties /run/secrets/common.properties

  3. this is the file that will allow you to configure OE while running in eclipse. Ensure values filled out work for your dev environment. do not commit changes made for your deve environement.

create directory for logs

  1. sudo mkdir /var/lib/openelis-global/logs/

  2. sudo chmod 777 /var/lib/openelis-global/logs/

Run Everything but OE in docker

  1. Comment out the oe.openelisci.org service in docker-compose.yml

  2. docker-compose up -d

  3. if oe is already running in docker, kill the container

Start Tomcat in Eclipse

  1. Make sure your project builds (project clean will normally trigger this)

  2. Click start server in normal, or debug mode