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monarch-initiative / fenominal

Phenomenal text mining for disease and phenotype concepts
https://monarch-initiative.github.io/fenominal/
GNU General Public License v3.0
9 stars 1 forks source link

HpoTextMining error on Mac #21

Closed pnrobinson closed 2 years ago

pnrobinson commented 3 years ago

Only on macintosh, I get an except when trying to call the HpoTextMining widget in FenominalMainControl line 172,

 HpoTextMining hpoTextMining = HpoTextMining.builder()
                    .withTermMiner(this.fenominalMiner)
                    .withOntology(this.fenominalMiner.getHpo())
                    .withExecutorService(executor)
                    .withPhenotypeTerms(new HashSet<>()) // maybe you want to display some terms from the beginning
                    .build();

an exception is thrown Caused by: java.lang.NullPointerException: Cannot invoke "java.lang.ClassLoader.loadClass(String)" because the return value of "javafx.fxml.FXMLLoader.getClassLoader()" is null

This is strange because if I run similar code from the HpoTextMining (demo) app, there is no problem. I have checked that the arguments to the builder are initialized.

any ideas? (use develop branch to see error in dialog). To reproduce the error, start the GUI, click get started and choose one of the options ON A MAC. 

javafx.fxml.LoadException: 
file:/Users/robinp/.m2/repository/org/monarchinitiative/hpotextmining/hpotextmining-gui/0.2.8/hpotextmining-gui-0.2.8.jar!/org/monarchinitiative/hpotextmining/gui/controller/Main.fxml

    at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2707)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2685)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2548)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:2517)
    at org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.<init>(HpoTextMining.java:141)
    at org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining$HpoTextMiningBuilder.build(HpoTextMining.java:306)
    at org.monarchinitiative.fenominal.gui.FenominalMainController.parseButtonPressed(FenominalMainController.java:177)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:567)
    at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:76)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:567)
    at com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:273)
    at com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:83)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1857)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1729)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8889)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:208)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3856)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1851)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2584)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127)
Caused by: java.lang.NullPointerException: Cannot invoke "java.lang.ClassLoader.loadClass(String)" because the return value of "javafx.fxml.FXMLLoader.getClassLoader()" is null
    at javafx.fxml.FXMLLoader.loadTypeForPackage(FXMLLoader.java:3017)
    at javafx.fxml.FXMLLoader.loadType(FXMLLoader.java:3006)
    at javafx.fxml.FXMLLoader.importClass(FXMLLoader.java:2947)
    at javafx.fxml.FXMLLoader.processImport(FXMLLoader.java:2793)
    at javafx.fxml.FXMLLoader.processProcessingInstruction(FXMLLoader.java:2758)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2624)
    ... 61 more
julesjacobsen commented 3 years ago

Sure, I'll look into it but you'll need to send me one of these first as I'm only using Linux on Intel... ;)

I'd suggest you check that version of Java you're running - e.g. is it 8 or 11+ and is the Java FX library included in that Mac version? For instance try running against Temurin JDK 17.

pnrobinson commented 2 years ago

this was related to getClass() apparently not being equivalent to Classname.class Fixed now