Re: [Cytoscape-discuss] Hierarchy of the type CyActivator is inconsistent

[Jason Montojo]

Hi Victor,

That error happens when one of the super classes/interfaces can't be resolved through the classpath.  It's likely that your classpath is incomplete.  What error are you getting from Maven or your IDE?

Thanks,

Jason

On Wed, May 22, 2013 at 1:08 PM, victor <victor...@gmail.com> wrote:

Right now I'm going slowly through the bundled app tutorial. I've already pulled all the sample code from the git repository. However I can't export them properly because Java (or Maven) doesn't recognize some of the jars being used.

For example it says that the hierarchy of type CyActivator is inconsistent even though AbstractCyActivator has already been referenced via: 

import org.cytoscape.service.util.AbstractCyActivator;

Can anybody give me some insight on his?

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[victor]

Hey Jason, 

The bolded is exactly what eclipse is telling me: The hierarchy of the type CyActivator is inconsistent

& this is the offending line: 

public class CyActivator extends AbstractCyActivator {

I don't have any trouble accessing any super classes/interfaces except for this one.

[Jason Montojo]

Hi Victor,

Do you have m2Eclipse installed?  Can you verify that service-api-X.jar shows up under the "Maven Dependencies" node in your project?

Thanks,

Jason

[victor]

Hi Jason, 

I'm not sure what you mean by "Maven Dependencies" node, but I clicked on the pom.xml file in the code directory & then I clicked on the dependencies tab & it showed this:

swing-application-api : ${cytoscape.api.version}

work-api : ${cytoscape.api.version}

service-api : ${cytoscape.api.version}

org.osgi.core : ${osgi.api.version}

junit : [test]

mockito-all : [test]

pax-loggin-api : [test]

service-api : [test]

Does that look okay?

[Jason Montojo]

Hi Victor,

It looks fine.  I've attached a screenshot of what you should be looking for.  The Maven Dependencies node in your project shows you what Eclipse/Maven is able to resolve for your classpath.  If the service-api JAR doesn't show up there, you've got a configuration error somewhere.  Do you have any "Missing artifact" errors in your project?

Thanks,

Jason

[victor]

Hi John, 

My setup looks very different from yours. Maybe I haven't set Maven up correctly. 

All the Maven stuff is enclosed in the cytoscape-app-developer folder uptop and essentially all I've been doing is cherry picking which jars I need from there (i.e. cytoscape-swing-app-api-3.1.0-SNAPSHOT.jar )

[victor]

Hey Jason, 

I was able to resolve the issue. I hadn't converted the project to maven. that's what was causing all the problems. thanks for all the help.