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Development Environment Setup

This step-by-step guide explains how to set up your development environment, using either Eclipse or IntelliJ for the backend and web UI and Android Studio for the mobile app. Please follow it strictly to make sure that development will run as smoothly as possible and your code adheres to our guidelines.

Please note that these instructions are optimized for Windows and Linux systems. If you're developing on a Mac and, we would be glad to get your feedback about how this guide can be extended with OS-specific instructions through our GitHub Discussions.

Step 1: Check Out the SORMAS Repository

  • Download and install the latest Git version for your operating system
  • Optional: Install a Git client such as TortoiseGit or GitHub Desktop if you don't want to handle version control from the command-line or within your IDE
  • Optional: Clone the SORMAS-Project repository with git clone https://github.com/sormas-foundation/SORMAS-Project.git; if you want to use Git from within your IDE, you can also clone the repository in Step 4
  • Open Git Bash and execute the following command to ensure that rebase is used when pulling the development branch rather than merge: git config --global branch.development.rebase true

Step 2: Install Java

Download and install the Java 11 JDK (not JRE) for your operating system, which is also needed for the Server Setup. We suggest using Zulu OpenJDK. If you're running Linux, please refer to the official documentation on how to install Zulu OpenJDK on your system.

Note: To work with the Android app JDK 17 is needed for the gradle build. The needed JDK is part of Android Studio, thus there is no need to manually install it.

The SORMAS CI is using JDK 17 to build all modules. The only known difference though are slight differences in the Java time API that affect unit tests, so again there is no need to setup two JDKs on your local system.

Step 3: Install Maven

The scripts in sormas-base/dev expect mvn as command-line tool. Download and install Maven for your operating system, see binaries.

Step 4: Install a Local SORMAS Server

Please follow the Server Installation Instructions to set up a local SORMAS instance that you will use to test your code. Alternatively, you can also use Maven Cargo, or a Docker installation (not recommended at this time).

Step 5: Install and Configure Your IDE

IntelliJ

  • Download and install the latest IntelliJ IDEA Ultimate; (newer than version of 2020-04-15 to enable debugging, see https://youtrack.jetbrains.com/issue/IDEA-216528)
  • Set the project SDK to the installed JDK
  • Optional: Clone the SORMAS-Project repository if you haven't done so already
  • Open the project in IntelliJ. Make sure the project is recognized by IntelliJ as a maven project; if not, right-click the pom.xml file in sormas-base and select Add as maven project.
  • Make sure that under File -> Project Structure -> Modules all modules EXCEPT sormas-app are recognized; if not, add the missing modules with the + button
  • Navigate to File -> Settings -> Plugins and make sure that Glassfish integration is enabled
  • Make a copy of sormas-base/dev.env.example, rename it to dev.env and set GLASSFISH_DOMAIN_ROOT to the location of the SORMAS domain inside your Payara installation
  • Run mvn install on the sormas-base project (e.g. by opening the Maven view and executing sormas-base -> Lifecycle -> install).
    Alternatively, execute the dev/build.sh script. You can create a run configuration and use the Git bash executable as interpreter to directly run it from the IDE.
  • Execute dev/deploy-serverlibs.sh script
  • Add a Payara server to IntelliJ:
    • Open Run -> Edit Configurations, add a new configuration and choose the Glassfish server template
    • Click on Configure next to Application server and create a new server configuration by selecting your Payara installation directory
    • Check the After launch checkbox and specify the browser that you want SORMAS to open in once the server has been deployed
    • Enter http://localhost:6080/sormas-ui into the URL field
    • Make sure that the correct JRE is specified (your Java 11 JDK)
    • Enter the path to the SORMAS domain and the credentials that you've specified when setting up the server
    • Open the Deployment tab and add the artifacts sormas-ear, sormas-rest and sormas-ui (make sure to respect this order as there are dependencies between artifacts at startup)
    • Open the Logs tab and add a new log file pointing to the logs/server.log file in your SORMAS domain
    • Open the Startup/Connection tab and make sure that Pass environment variables is NOT checked; ignore warnings about the debug configuration not being correct
    • Open the config/domain.xml file in your domain directory and make sure that the java-config node contains the following code: <java-config classpath-suffix="" debug-enabled="true" debug-options="-agentlib:jdwp=transport=dt_socket,address=6009,server=n,suspend=y" ...
  • Set the default working directory for run configurations by navigating to Run -> Edit Configurations -> Templates -> Application and setting Working directory to $MODULE_WORKING_DIR$
  • Optional: Setup database access from Intellij: Open View -> Tool View -> Database, click on + icon and select DataSource -> PostgreSQL and configure the database (set user and password and download the missing driver files if needed)

Known issues

  • The first time you build the project in IntelliJ, you have to switch the java compiler to "Eclipse" to workarround a dependency resolution problem in sormas-api.

Eclipse

  • Download and install the latest Eclipse IDE for Enterprise Java and Web Developers
  • Set the default JRE of Eclipse to the installed JDK: Assigning the default JRE for the workbench
  • Optional: Clone the SORMAS-Project repository if you haven't done so already via File -> Import -> Git -> Projects from Git and cancel the process when you're asked to create a new project from the cloned repository
  • Import the projects from the SORMAS-Project repository into your workspace via File -> Import -> Maven -> Existing Maven Projects
  • Install the Payara Tools plugin
  • Install the Vaadin Plugin for Eclipse; the commercial UI designer is not needed
  • Add a Payara server to Eclipse and enter the credentials you specified when setting up the local SORMAS server
  • Make a copy of sormas-base/dev.env.example, rename it to dev.env and set GLASSFISH_DOMAIN_ROOT to the location of the SORMAS domain inside your Payara installation
  • Either run mvn install on the sormas-base project or execute the dev/build.sh script (for example with Git Bash)
  • Execute dev/deploy-serverlibs.sh script
  • Highlight all Eclipse projects and choose Maven -> Update Project from the right-click menu; perform the update for all projects
  • Start the Glassfish server and deploy sormas-ear, sormas-rest and sormas-ui by dragging the respective projects onto it, or use the Add and Remove... function by right-clicking on the server (make sure to respect this order as there are depdendencies between artifacts at startup)
  • Open your browser and type in http://localhost:6080/sormas-ui to test whether the server and IDE have been set up correctly

Android Studio

Please note: You only need to install Android Studio if you're developing code for the Android app. This is likely the case when you're adding new fields or entities to the system, or if you specifically want to work on the mobile app.

  • Download and install the latest Android Studio version
    • Please make sure to run the installer with admin rights if you're using Windows
    • Ensure that the Android SDK installation path does not contain whitespaces; you can also change this later via Tools -> SDK Manager -> Android SDK Location
  • Open Android Studio and import the sormas-app module from the SORMAS-Project repository
  • Make a copy of keystore.properties.example and rename it to keystore.properties
  • Make sure to use the JDK version 11 (File -> Project Structure -> SDK Location -> JDK Location)
  • Build the Android Studio project by executing the Gradle build (this may be done automatically)
  • Add an emulator and set the SDK version to the minSdkVersion or targetSdkVersion from build.gradle; we suggest to test your code on both, but minSdkVersion should be preferred to ensure compatibility to the minimum supported SDK
  • Click on Run 'app' to install and run the app on your emulator; enter http://10.0.2.2:6080/sormas-rest as the server URL when you start the newly installed app for the first time

Important: Whenever you do or pull changes in the sormas-api project that you want to use in the mobile app or that are referenced there already, you need to execute the dev/build.sh script to notify the sormas-app project of the changes.

Step 6: Configure Code Formatting and Import Settings

In order to ensure a consistent code style and prevent so-called edit wars, we have set up custom configuration files for automatic code formatting and import ordering. Please make sure to adhere to the following steps for your IDE(s) before you start developing.

IntelliJ and Android Studio Settings

  • Install the Eclipse Code Formatter for IntelliJ/Android Studio plugin
  • Open the plugin settings via File -> Settings -> Other Settings -> Eclipse Code Formatter and select Use the Eclipse Code Formatter
  • Under Eclipse formatter config, choose Eclipse workspace/project folder or config file and select sormas-base/java-formatter-profile.xml
  • Check Optimize Imports
  • Under Import order, choose From file and select sormas-base/java-importorder-profile.importorder
  • Make sure that Do not format other file types by IntelliJ formatter is selected
  • Go to Editor -> Code Style -> Java -> Imports and set Class count to use import with '*' and Names count to use static import with '*' to 99
  • Navigate to Editor -> General -> Auto Import and disable Optimize imports on the fly

Optional, but strongly recommended:

  • Install the Save Actions plugin that automatically applies code formatting and import reordering whenever you save a file - otherwise you will manually have to do so (by default with Ctrl+Alt+L)
  • Open the plugin settings via File -> Settings -> Other Settings -> Save Actions and make sure that the first three checkboxes under General and the first two checkboxes under Formatting Actions are selected

Eclipse Settings

  • Open Window -> Preferences
  • Navigate to Java -> Code Style -> Formatter, import sormas-base/java-formatter-profile.xml and apply the changes
  • Navigate to Java -> Code Style -> Organize Imports and import sormas-base/java-importorder-profile.importorder
  • On the same screen, set Number of imports needed for .* and Number of static imports needed for .* to 99
  • On the same screen, make sure that Do not create import for types starting with a lowercase letter is checked and apply the changes
  • Navigate to Java -> Editor -> Save Actions and make sure that the following options are selected: Perform the selected actions on save, Format source code, Format all lines and Organize imports

Issues which can appear during installation process of the project

  1. If debug mode does not work: To replace opt\payara5\glassfish\modules\launcher.jar with sormas-base/setup/launcher.jar

  2. For Windows: Please check your java_version. In case if you have the multiple java_versions installed on the system, it will always show to you the first version installed. I had the java 8 instead of 11. In order to fix it, go to environment variables, and move the 11 version up. And rerun the script. Seems that the console is reading those variables at the starting point, and the values of it can be updated only after console/script restart.

  3. For Windows: Pay attention to the postgres SQL files rights permissions after unziping the downloaded ZIP archive. Files physically were present but next script error has been generated: psql:setup.sql:7: ERROR: could not open extension control file "C:/Program Files/PostgreSQL/10/share/extension/temporal_tables.control": No such file or directory -I checked the file rights, and under windows they has AV attribute, however, all others has only A attribute. When I was trying to open them with Notepad++ it was saying that such file does not exist. Do you want to create it? If yes will be pressed - another message saying that the file exists, appeared. Very strange scenario...

  4. All the postgres commands (of added users, etc.) which were added at first startup of the application - will raise errors in case if such entity exists. Just ignore those errors at repeated installation of .\server-setup.sh

  5. Check always the port number 6048 which can be occupied by an old instance of payara. -> For every installation, kill all Java/javaw processes and check the availability of 6048 port number. -> Delete files with generated domain folders and payara. In order to have a clean installation of each next ./server-setup.sh run.

  6. For the sormas-base/dev scripts Maven needs to be installed as command-line tool or defined in sormas-base/dev.env as MVN_BIN which Maven to be used.

  7. For eclipse formatted plugin, there is an issue for Idea: https://plugins.jetbrains.com/plugin/6546-eclipse-code-formatter - cannot save settings Path to custom eclipse folder is not valid - it works only when settings were saved from down to up. And not vice versa.

If something is still not working: -> Stop the payara domain, run dev/deploy-serverlibs.sh to update libs -> clean up (delete all from domains/sormas/autodeploy, domains/sormas/applications, domains/sormas/generated, and domains/sormas/osgi-cache) try to build again by executing mvn clean install -DskipTests on the sormas-base module -> start the domain and deploy again

Avoid redeployment problems

Problem: Due to currently a not mitigated problem, it is only possible to deploy the sormas-ear.ear (contains sormas-backend) once without problems. If you undeploy it and deploy sormas-ear.ear again, the other artifacts sormas-uiand sormas-rest cannot successfully call the backend.

Workaround: Undeploy sormas-ear and all other sormas artifacts, restart the Payara domain, deploy sormas-ear again (the same or changed version).

Symptom: This exception occurs when sormas-ui or sormas-rest calls the sormas-backend.

Caused by: java.lang.IllegalArgumentException: Can not set java.util.Properties field de.symeda.sormas.backend.common.ConfigFacadeEjb.props to de.symeda.sormas.backend.common.ConfigFacadeEjb
    at java.base/jdk.internal.reflect.UnsafeFieldAccessorImpl.throwSetIllegalArgumentException(UnsafeFieldAccessorImpl.java:167)
    at java.base/jdk.internal.reflect.UnsafeFieldAccessorImpl.throwSetIllegalArgumentException(UnsafeFieldAccessorImpl.java:171)
    at java.base/jdk.internal.reflect.UnsafeFieldAccessorImpl.ensureObj(UnsafeFieldAccessorImpl.java:58)
    at java.base/jdk.internal.reflect.UnsafeObjectFieldAccessorImpl.set(UnsafeObjectFieldAccessorImpl.java:75)
    at java.base/java.lang.reflect.Field.set(Field.java:780)
   at com.sun.enterprise.container.common.impl.util.InjectionManagerImpl._inject(InjectionManagerImpl.java:594)

Additional info:

  • You can undeploy and deploy all other modules without restarting the Payara domain, as long as nothing changes on sormas-ear (implicates sormas-api and sormas-backend).
  • The problem occurs no matter if you deploy directly from your IDE or as packaged ears/wars into the autodeploy directory.
  • Related ticket: #2511