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cytoscape / cyREST

Core App: REST API module for Cytoscape
https://github.com/cytoscape/cyREST/wiki
MIT License
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Attempt to save session with non-absolute path raises NullPointer Exception on Linux #57

Closed krassowski closed 6 years ago

krassowski commented 6 years ago

Here is the generated (though not working for me) curl:

curl -X POST --header 'Content-Type: application/json' --header 'Accept: application/json' -d '{file: "test.cys"}' 'http://localhost:1234/v1/commands/session/save as'

And here is a response I got using Swagger UI: 

{
  "data": {},
  "errors": [
    {
      "status": 500,
      "type": "urn:cytoscape:ci:cyrest-core:v1:handle-json-command:errors:2",
      "message": "java.lang.NullPointerException",
      "link": "file:/home/krassowski/CytoscapeConfiguration/3/framework-cytoscape.log"
    }
  ]
}

It would be nice if there was a hint about using absolute paths.

And here is the backtrace:

qtp1448347804-117 - /v1/commands/session/save%20as ERROR [TaskMonitor.org.cytoscape.command.internal.CommandExecutorTask] - Error executing task: null
java.lang.NullPointerException
    at org.cytoscape.task.internal.session.CySessionWriter.canWrite(CySessionWriter.java:220)
    at org.cytoscape.task.internal.session.CySessionWriter.run(CySessionWriter.java:94)
    at org.cytoscape.task.internal.session.SaveSessionAsTask.run(SaveSessionAsTask.java:77)
    at org.cytoscape.command.internal.TFExecutor.execute(TFExecutor.java:91)
    at org.cytoscape.command.internal.CommandExecutorImpl.executeCommand(CommandExecutorImpl.java:175)
    at org.cytoscape.command.internal.CommandExecutorTask.run(CommandExecutorTask.java:54)
    at org.cytoscape.work.internal.sync.SyncTaskManager.execute(SyncTaskManager.java:92)
    at org.cytoscape.rest.internal.commands.resources.CommandResource.executeCommand(CommandResource.java:357)
    at org.cytoscape.rest.internal.commands.resources.CommandResource.handleJSONCommand(CommandResource.java:261)
    at sun.reflect.GeneratedMethodAccessor43.invoke(Unknown Source)
    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$1.run(AbstractJavaResourceMethodDispatcher.java:144)
    at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
    at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
    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:748)
dotasek commented 6 years ago

You are correct. The Swagger documentation for that endpoint is in the Swagger core, so I've created an issue you can track there: http://code.cytoscape.org/redmine/issues/4121

The inability to execute via curl is likely due to #55