dependencies cytoscape 3 app

[Jose Villaveces]

Hi All,

I'm working on a new cytoscape 3 app and recently, I added a new dependecy (lucene) to my pom file. However when I test the app jar in Cytoscape, the app fails to load. I had a look into the jar and apparently the dependencies are not exported, from that I conclude that I'm missing something while building the jar. How should I use external dependencies in a cytoscape app? Also, is there a way to debug an app from Eclipse?

Thanks in advance,

José

[Ruth]

Hi Jose,

I was able to set up eclipse debugging using this tutorial:

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Remote_Execution_for_Debugging

Are you making a bundle or a simple app? Are you using the maven-bundle-plugin to create your jar?

Ruth

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[Jose Villaveces]

Hi Ruth,

Thanks for your answer, I'm trying the tutorial you suggested. 

Are you making a bundle or a simple app? 

I'm making a bundle 

Are you using the maven-bundle-plugin to create your jar?

Yes

[Ruth]

Hi Jose,

If it is bundle app I don’t think the dependencies are exported into the jar.  (not sure though).  In my bundle app all my dependencies are listed in the Manifest file of the jar under “Import-Package”.  Is lucene listed in the Import-Package of your Manifest?

[Jose Villaveces]

Yes, the dependencies are listed in the manifest as follows:

Bundle-Version: 0.0.1.SNAPSHOT

Created-By: Apache Maven Bundle Plugin

Import-Package: javax.swing,org.apache.lucene.analysis,org.apache.lucene

 .analysis.standard,org.apache.lucene.document,org.apache.lucene.index,o

 rg.apache.lucene.queryparser.classic,org.apache.lucene.search,org.apach

 e.lucene.store,org.apache.lucene.util,org.cytoscape.application;version

 ="[3.0,4)",org.cytoscape.application.swing;version="[3.0,4)",org.cytosc

 ape.service.util;version="[3.0,4)",org.cytoscape.view.model;version="[3

 .0,4)",org.osgi.framework;version="[1.5,2)"

Tool: Bnd-1.50.0

Since I extracted the jar contents, I can tell that the dependencies are not packed. However I don't know if that is just the default behavior and dependencies should be exported in the jar by modifying the pom.xml 

[Ruth]

Hi Jose,

When you say the app fails to load in cytoscape is there an error in the cytoscape console or do you just fail to see your app in the apps menu?

[Jose Villaveces]

Hi Ruth,

I can see no error reported in the console, and the app is not reachable from the apps menu.

[Ruth]

Hi Jose,

I had the same issue.  My Cyactivator class was never being called.  I was missing Bundle-Activator in my Manifest file which specified my CyActivator class.

(to the maven-bundle-plugin in my pom file I was missing: <Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>)

[Jose Villaveces]

Hi Ruth,

My CyActivator is referenced in the pom file, it is being called and works just fine. The problem comes when I use Lucene or jdom in my CyActivator class, as soon as I do that then the app is fails the console shows no error but the app is not reachable anymore from the apps menu. Thats why I think it  has something to do with the dependencies.

[James Grammatikos]

I actually just struggled with this problem for the last few days and I found the answer here https://groups.google.com/forum/?fromgroups=#!searchin/cytoscape-discuss/maven/cytoscape-discuss/nu4XaM1iK8c/1U1dU1pPC0UJ . Essentially, I just added these two lines to my build instructions

<Embed-Dependency>commons-math;groupId=org.apache.commons;inline=true</Embed-Dependency>

<Import-Package>*;resolution:=optional</Import-Package>

replacing the id's with the correct ones and everything worked fine for me.

[Jose Villaveces]

Hey James,

Thanks for the advice, my app is now running!