Relevant to the feature/cyrest branch
To replicate, load galFiltered.cys and click some blank space in the Network Control Panel to make the current network null.
Execute POST /mcode/v1/analyze with the default arguments.
After this returns an error, select the current network, and try the call again. On my machine, the call returns, but no result panel is generated, and the following stacktrace shows up in the console:
qtp1433913513-77 - /mcode/v1/analyze ERROR [ca.utoronto.tdccbr.mcode.internal.model.MCODEAlgorithm] - In MCODEAlgorithm.findClusters: nodeInfoHashMap or nodeScoreSortedMap was null.
qtp1433913513-77 - /mcode/v1/analyze ERROR [TaskMonitor.ca.utoronto.tdccbr.mcode.internal.task.MCODEAnalyzeTask] - Error executing task: Error while executing the MCODE analysis
java.lang.Exception: Error while executing the MCODE analysis
at ca.utoronto.tdccbr.mcode.internal.task.MCODEAnalyzeTask.run(MCODEAnalyzeTask.java:180)
at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:92)
at ca.utoronto.tdccbr.mcode.internal.rest.MCODERestResource.analyze(MCODERestResource.java:160)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$TypeOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:205)
at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:503)
at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:69)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:240)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:429)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:75)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:366)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:696)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:53)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at ca.utoronto.tdccbr.mcode.internal.util.MCODEUtil.sortClusters(MCODEUtil.java:770)
at ca.utoronto.tdccbr.mcode.internal.task.MCODEAnalyzeTask.run(MCODEAnalyzeTask.java:142)
Relevant to the feature/cyrest branch
To replicate, load galFiltered.cys and click some blank space in the Network Control Panel to make the current network null.
Execute POST /mcode/v1/analyze with the default arguments.
After this returns an error, select the current network, and try the call again. On my machine, the call returns, but no result panel is generated, and the following stacktrace shows up in the console: