gephi-toolkit
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gephi
NullPointerException in demo PartitionGraph
I'm trying to do the same as in the demo PartitionGraph, but I get a NullpointerException when doing Function func2 = appearanceModel.getNodeFunction(..), because appearanceModel has no function with PartitionElementColorTransformer.class. When I do the same importing any of the samples datasets, lesmiserables.gexf or Java.gexf, it works fine.. Trying to limit where the problem is, I've found a strange behavior in partitioning. I've changed the code to import the graph via ImportController and a GEXF file containing a small graph. I've created this two GEXF files .When I import the file from the right, it works fine, but sometimes it gives different results. However, when I import the one of the left, it doesn't work the most of times (sometimes partitioning works). Here is a capture made when debugging showing the problem. I'm not sure if it's a bug problem or I'm doing something wrong. Here is my code:
AppearanceController appearanceController = Lookup.getDefault().lookup(AppearanceController.class);
AppearanceModel appearanceModel = appearanceController.getModel();
//Init a project - and therefore a workspace
ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);
pc.newProject();
Workspace workspace = pc.getCurrentWorkspace();
GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
DirectedGraph directedGraph = graphModel.getDirectedGraph();
//Get controllers and models
ImportController importController = Lookup.getDefault().lookup(ImportController.class);
//Import file
Container container;
try {
File file = new File("C:\\projects\\gephi_demo\\sample.gexf");
container = importController.importFile(file);
container.getLoader().setEdgeDefault(EdgeDirectionDefault.DIRECTED); //Force DIRECTED
container.getLoader().setAllowAutoNode(false); //Don't create missing nodes
} catch (Exception ex) {
ex.printStackTrace();
return null;
}
//Append imported data to GraphAPI
importController.process(container, new DefaultProcessor(), workspace);
//Run modularity algorithm - community detection
Modularity modularity = new Modularity();
modularity.execute(graphModel);
//Partition with 'modularity_class', just created by Modularity algorithm
Column modColumn = graphModel.getNodeTable().getColumn(Modularity.MODULARITY_CLASS);
Function func2 = appearanceModel.getNodeFunction(directedGraph, modColumn, PartitionElementColorTransformer.class);
Partition partition2 = ((PartitionFunction) func2).getPartition();
System.out.println(partition2.size() + " partitions found");
Palette palette2 = PaletteManager.getInstance().randomPalette(partition2.size());
partition2.setColors(palette2.getColors());
appearanceController.transform(func2);
And here is the exception:
java.lang.NullPointerException: null at org.alxhierro.backend.gephidemo.services.SNAService.getCommunities(SNAService.java:119) ~[classes/:na] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_72] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_72] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_72] at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_72] at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:832) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:743) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:961) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:895) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:967) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:858) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at javax.servlet.http.HttpServlet.service(HttpServlet.java:622) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:843) ~[spring-webmvc-4.2.6.RELEASE.jar:4.2.6.RELEASE] at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) ~[tomcat-embed-websocket-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:87) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-4.2.6.RELEASE.jar:4.2.6.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212) ~[tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:522) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1095) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:672) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1502) [tomcat-embed-core-8.0.33.jar:8.0.33] at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1458) [tomcat-embed-core-8.0.33.jar:8.0.33] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_72] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_72] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-8.0.33.jar:8.0.33] at java.lang.Thread.run(Thread.java:745) [na:1.8.0_72]
