Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 'res' not found"
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Entering edit mode
@matthew-thornton-5564
Last seen 4 weeks ago
USA, Los Angeles, USC

I recently updated to Cytoscape 3.10 and the latest RCy3. I am trying to import graphNEL network graphs from 'GOstats' into Cytoscape. Previously I was not having any problems. I'm sure that it is a formatting error. my graphNEL looks like this:

> str(y1$`1`)
Formal class 'graphNEL' [package "graph"] with 6 slots
  ..@ nodes     : chr [1:79] "GO:0015267" "GO:0022803" "GO:0015318" "GO:0022836" ...
  ..@ edgeL     :List of 79
  .. ..$ GO:0015267:List of 1
  .. .. ..$ edges: int 2
  .. ..$ GO:0022803:List of 1
  .. .. ..$ edges: int 5
  .. ..$ GO:0015318:List of 1
   Truncated
  .. ..$ GO:0005253:List of 1
  .. .. ..$ edges: int [1:2] 8 70
  ..@ edgeData  :Formal class 'attrData' [package "graph"] with 2 slots
  .. .. ..@ data    : Named list()
  .. .. ..@ defaults:List of 1
  .. .. .. ..$ weight: num 1
  ..@ nodeData  :Formal class 'attrData' [package "graph"] with 2 slots
  .. .. ..@ data    :List of 79
  .. .. .. ..$ GO:0015267:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:417] "100360100" "100361584" "100362565" "113995" ...
  .. .. .. .. ..$ pvalue   : num 7.71e-28
  .. .. .. .. ..$ oddsRatio: num 4.99
  .. .. .. .. ..$ expCount : num 22.8
  .. .. .. ..$ GO:0022803:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:417] "100360100" "100361584" "100362565" "113995" ...
  .. .. .. .. ..$ pvalue   : num 7.71e-28
  .. .. .. .. ..$ oddsRatio: num 4.99
  .. .. .. .. ..$ expCount : num 22.8
  .. .. .. ..$ GO:0015318:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:609] "100360100" "100361584" "100362565" "113918" ...
  .. .. .. .. ..$ pvalue   : num 4.25e-27
  .. .. .. .. ..$ oddsRatio: num 4.07
  .. .. .. .. ..$ expCount : num 33.2
truncated 
  .. .. .. ..$ GO:0015501:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:4] "25550" "29482" "29483" "84012"
  .. .. .. .. ..$ pvalue   : num 0.000621
  .. .. .. .. ..$ oddsRatio: num 52.2
  .. .. .. .. ..$ expCount : num 0.218
  .. .. .. ..$ GO:0005313:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:14] "116638" "25550" "266767" "291840" ...
  .. .. .. .. ..$ pvalue   : num 0.000632
  .. .. .. .. ..$ oddsRatio: num 9.69
  .. .. .. .. ..$ expCount : num 0.764
  .. .. .. ..$ GO:0005254:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:66] "100361584" "114516" "116638" "140674" ...
  .. .. .. .. ..$ pvalue   : num 0.000812
  .. .. .. .. ..$ oddsRatio: num 3.5
  .. .. .. .. ..$ expCount : num 3.6
  .. .. .. ..$ GO:0140161:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:9] "171163" "24777" "289459" "305309" ...
  .. .. .. .. ..$ pvalue   : num 0.000889
  .. .. .. .. ..$ oddsRatio: num 13.9
  .. .. .. .. ..$ expCount : num 0.491
  .. .. .. ..$ GO:0005253:List of 4
  .. .. .. .. ..$ geneIds  : chr [1:77] "100361584" "114516" "116638" "140674" ...
  .. .. .. .. ..$ pvalue   : num 0.000889
  .. .. .. .. ..$ oddsRatio: num 3.24
  .. .. .. .. ..$ expCount : num 4.2
  .. .. ..@ defaults:List of 5
  .. .. .. ..$ pvalue     : num 1
  .. .. .. ..$ geneIds    : num(0) 
  .. .. .. ..$ condGeneIds: num(0) 
  .. .. .. ..$ oddsRatio  : num 1
  .. .. .. ..$ expCount   : num(0) 
  ..@ renderInfo:Formal class 'renderInfo' [package "graph"] with 4 slots
  .. .. ..@ nodes: list()
  .. .. ..@ edges: list()
  .. .. ..@ graph: list()
  .. .. ..@ pars : list()
  ..@ graphData :List of 1
  .. ..$ edgemode: chr "directed"

Here is the error:

       > createNetworkFromGraph(y1$`1`, "male1v0_GOMF")
        Loading data...

        Error: Not Found
        In addition: Warning message:
        In .local(x, container, collapse, ..., .level = .level, .withNames = .withNames,  :
          non-fininte values in numeric vector may not be approriately represented in JSON
        Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"),  : 
          object 'res' not found

Is there some package that I need? What is 'res' and how do I specify it. I googled it and I didn't find anything.

When I start up Cytoscape I get no errors, when I try the import I get these errors:

        karaf.base: /usr/local/lib/cytoscape/Cytoscape_v3.10.2/framework
        JAVA_HOME: /usr/lib/jvm/jdk-17/
                     _                                    
           ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  
          / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 
         | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 
          \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 
               |___/                         |_|          

        Cytoscape 3.10.2

        Hit '<tab>' for a list of available commands
           and '[cmd] --help' for help on a specific command.
        Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

        karaf@Cytoscape 3.10.2()> Found 1 platforms                                                                                                              
        Got 1 platforms
        Got 1 devices
        Platform: NVIDIA CUDA
        Device: OpenCL 3.0 CUDA Quadro T2000 with Max-Q Design
        The cl_program [0x78AA00BB92A0] was built successfully
        BUILD LOG:
        ----


        -----
        Program built
        Top device after init = OpenCL 3.0 CUDA Quadro T2000 with Max-Q Design
        UserAgent = Cytoscape v3.10.2 Java 17.0.2 Linux 6.5.0-28-generic
        latestVersion = 3.10.2
        com.fasterxml.jackson.core.JsonParseException: Non-standard token 'Infinity': enable JsonParser.Feature.ALLOW_NON_NUMERIC_NUMBERS to allow
         at [Source: org.glassfish.jersey.message.internal.EntityInputStream@e3b340; line: 451, column: 24]
            at com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1586)
            at com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:521)
            at com.fasterxml.jackson.core.json.UTF8StreamJsonParser._handleUnexpectedValue(UTF8StreamJsonParser.java:2613)
            at com.fasterxml.jackson.core.json.UTF8StreamJsonParser.nextFieldName(UTF8StreamJsonParser.java:1069)
            at com.fasterxml.jackson.databind.deser.std.BaseNodeDeserializer.deserializeObject(JsonNodeDeserializer.java:219)
            at com.fasterxml.jackson.databind.deser.std.BaseNodeDeserializer.deserializeArray(JsonNodeDeserializer.java:270)
            at com.fasterxml.jackson.databind.deser.std.BaseNodeDeserializer.deserializeObject(JsonNodeDeserializer.java:227)
            at com.fasterxml.jackson.databind.deser.std.JsonNodeDeserializer.deserialize(JsonNodeDeserializer.java:69)
            at com.fasterxml.jackson.databind.deser.std.JsonNodeDeserializer.deserialize(JsonNodeDeserializer.java:15)
            at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:3807)
            at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:2867)
            at org.cytoscape.rest.internal.resource.TableResource.updateTable(TableResource.java:319)
            at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
            at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
            at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
            at java.base/java.lang.reflect.Method.invoke(Method.java:568)
            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$1.call(Errors.java:267)
            at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
            at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
            at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
            at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
            at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
            at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
            at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
            at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
            at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
            at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
            at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
            at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76)
            at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)
            at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1631)
            at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:292)
            at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
            at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
            at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
            at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:74)
            at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
            at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:600)
            at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
            at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
            at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
            at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
            at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1440)
            at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:294)
            at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
            at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
            at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
            at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
            at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1355)
            at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
            at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:90)
            at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
            at org.eclipse.jetty.server.Server.handle(Server.java:516)
            at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:487)
            at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:732)
            at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:479)
            at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
            at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
            at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
            at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
            at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
            at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
            at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
            at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
            at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:409)
            at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
            at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
            at java.base/java.lang.Thread.run(Thread.java:833
RCy3 • 481 views
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Entering edit mode

Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" failed to be returned. This could be caused by a failure at any number of steps. In order to better troubleshoot, it would be helpful to have a test case that I can run locally and debug...

Ah, I see you already posted on our GitHub issue tracker. Great. It will be easier to share attachments, etc. So, I'll continue to help there: https://github.com/cytoscape/RCy3/issues/223

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Entering edit mode
@matthew-thornton-5564
Last seen 4 weeks ago
USA, Los Angeles, USC

So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!

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