After a REST call with a null Current Network, further calls to MCODE fail

[dotasek]

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)

[chanchal99999]

The request called two times and the response gets wrong.

[chanchal99999]

Are there any solutions?

[chanchal99999]

Got solution >
Please ensure implemented security is correct.

[chanchal99999]

Now it's working fine