updating pom.xml file to avoid maven errors

[lauren...@gmail.com]

Hi Everyone!

I am in the process of updating my cytoscape app. However, I am running into an error with when I run Maven install.

mainly, i have issues with the ekstazi plugin, resulting in errors such as:

[ERROR] Failed to execute goal org.ekstazi:ekstazi-maven-plugin:5.3.0:select (ekstazi) on project OCSANA: excludesFile must be set when forking JVM for each test class -> [Help 1]

I remember previously having similar issues, and think this might have to do with the JVM the app was built under, vs what is on my laptop. I am most interested in a permanent solution to this, meaning updating the pom.xml so that it stays current with Cytoscape standards, and does not cause this compilation issue that I don't know how to fix. I am the second developer on this app, so I unfortunately, all this architecture was built before I jumped on the project.

i am linking here the repository for the app, as it may be easiest for someone to just poke around in the code. Additionally, a link directly to the pom.xml file. Any and all help is appreciated! thank you!

https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode/tree/master/OCSANA_Plus

https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode/blob/master/OCSANA_Plus/pom.xml

[David Otasek]

Hello,

Our last major update of Cytoscape's Maven plugins and libraries changed a few things throughout. I've included some of the information that we used to update our internal apps to bring them up to date below. Hopefully this helps at least get plugins and Java dependencies up to date for you.

You can also see all of our current default properties here: https://github.com/cytoscape/cytoscape-parent/blob/develop/pom.xml

Maven plugins and OSGi artifacts must also be specific minimum versions to work in Java 11. I've included a sample of these common below. Note that our maven plugins reference these version parameters later in the POM (see here in the JSON Core App POM)

<properties>

  ...

  <cytoscape.api.version>3.8.0-SNAPSHOT</cytoscape.api.version>

  <!-- Maven Plugin Settings -->

  <junit.version>4.12</junit.version>

  <maven-compiler-plugin.version>3.8.0</maven-compiler-plugin.version>

  <maven-surefire-plugin.version>3.0.0-M3</maven-surefire-plugin.version>

  <maven-bundle-plugin.version>4.1.0</maven-bundle-plugin.version>

  <osgi.api.version>6.0.0</osgi.api.version>

</properties>

Finally, JavaX must be included as several dependencies in Java 11. The relevant elements are below.

<dependency>

  <groupId>javax.xml.bind</groupId>

  <artifactId>jaxb-api</artifactId>

  <version>2.3.0</version>

</dependency>

<dependency>

  <groupId>com.sun.xml.bind</groupId>

  <artifactId>jaxb-core</artifactId>

  <version>2.3.0</version>

</dependency>

<dependency>

  <groupId>com.sun.xml.bind</groupId>

  <artifactId>jaxb-impl</artifactId>

  <version>2.3.0</version>

</dependency>

[lauren...@gmail.com]

thank you! this worked perfectly

[pritam saha]

Hi ,

I am trying to install create sample network cytoscape-app from the example repository. But I am running into an error with when I run Maven install.

[Error] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.0:compile (default-compile) on project sample-create-network: Compilation failure

The repository link : https://github.com/cytoscape/cytoscape-app-samples

Please help me to understand these issues and I am new to cytoscape and I need to know some fixed solution which can work later also when these type of error comes.

Thanks

[Scooter Morris]

I'm not having a problem building that particular sample.  Which version of java do you have installed?  Make sure you have the full JDK and not just the JRE.

-- scooter