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h3abionet / genesis2

Implementation of the Genesis 2 tool
MIT License
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Genesis2JavaFX-2.2b-macArm64.jar new project error #28

Closed shaze closed 1 month ago

shaze commented 2 months ago

When I try create a new project using the "all-qc" data the following pop up appears.

"Index 2 out of bounds for length 2"

There are no errors on the command line. When I click on "OK" on the pop-up the following gets spilled

[As an aside, when I first ran this, I realised there were some individuals in the fam file who were not in the phone file -- I fixed that a the error still occurs. Genesis 1 handles this data OK.

A^[Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1858)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1726)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    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:8875)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:207)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3984)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1890)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2708)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:551)
    at com.sun.glass.ui.View.notifyMouse(View.java:937)
    at com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127)
    at com.sun.glass.ui.mac.MacApplication._enterNestedEventLoopImpl(Native Method)
    at com.sun.glass.ui.mac.MacApplication._enterNestedEventLoop(MacApplication.java:168)
    at com.sun.glass.ui.Application.enterNestedEventLoop(Application.java:515)
    at com.sun.glass.ui.EventLoop.enter(EventLoop.java:107)
    at com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(QuantumToolkit.java:650)
    at javafx.stage.Stage.showAndWait(Stage.java:469)
    at org.h3abionet.genesis.controller.MainController.newProject(MainController.java:192)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:72)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:270)
    at com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:84)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1853)
    at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1726)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8875)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:207)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:232)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:189)
    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$MouseHandler.process(Scene.java:3984)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1890)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2708)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:411)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:301)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:450)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:449)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:551)
    at com.sun.glass.ui.View.notifyMouse(View.java:937)
    at com.sun.glass.ui.mac.MacView.notifyMouse(MacView.java:127)
Caused by: java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at com.sun.javafx.reflect.Trampoline.invoke(MethodUtil.java:72)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at com.sun.javafx.reflect.MethodUtil.invoke(MethodUtil.java:270)
    at com.sun.javafx.fxml.MethodHelper.invoke(MethodHelper.java:84)
    at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1853)
    ... 107 more
Caused by: java.lang.NullPointerException: Cannot load from object array because the return value of "org.h3abionet.genesis.model.Subject.getPhenos()" is null
    at org.h3abionet.genesis.model.Project.createGroups(Project.java:158)
    at org.h3abionet.genesis.model.Project.<init>(Project.java:124)
    at org.h3abionet.genesis.controller.ProjectDetailsController.handlePcaEntryOK(ProjectDetailsController.java:143)
    ... 119 more
philip-mach commented 2 months ago

Thanks for picking this up. Where can I find this dataset?

I was planning on asking if anyone had additional data for testing, so this is well timed.

shaze commented 2 months ago

Slack

philip-mach commented 1 month ago

I added checks that both the .phe and .fam files must have the same number of columns (fields) on every row (line).

The first row that is incorrect triggers and error dialog and halts the file read(s).