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monarch-initiative / HpoCaseAnnotator

Next-generation Biocuration App for annotating cases and PhenoPackets
https://hpocaseannotator.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
8 stars 0 forks source link

error of reading a file #73

Closed lingluodlut closed 4 years ago

lingluodlut commented 4 years ago

Error while reading the file. What should I do? Thanks

Error details: java.io.IOException: Unable to decode JSON file at org.monarchinitiative.hpo_case_annotator.gui.controllers.MainController.lambda$openMenuItemAction$6(MainController.java:228) at java.util.Optional.orElseThrow(Unknown Source) at org.monarchinitiative.hpo_case_annotator.gui.controllers.MainController.openMenuItemAction(MainController.java:228) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.reflect.misc.Trampoline.invoke(Unknown Source) at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at sun.reflect.misc.MethodUtil.invoke(Unknown Source) at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1771) at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1657) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49) at javafx.event.Event.fireEvent(Event.java:198) at javafx.scene.control.MenuItem.fire(MenuItem.java:462) at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1405) at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.lambda$createChildren$6(ContextMenuContent.java:1358) at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218) at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238) 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.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$MouseHandler.process(Scene.java:3757) at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485) at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762) at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:394) at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295) at java.security.AccessController.doPrivileged(Native Method) at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:432) at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:410) at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:431) at com.sun.glass.ui.View.handleMouseEvent(View.java:555) at com.sun.glass.ui.View.notifyMouse(View.java:937) at com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at com.sun.glass.ui.win.WinApplication.lambda$null$4(WinApplication.java:186) at java.lang.Thread.run(Unknown Source)

pnrobinson commented 4 years ago

hmm, possibly there is a version mixup. I will check this

lingluodlut commented 4 years ago

hmm, possibly there is a version mixup. I will check this

Thanks.

pnrobinson commented 4 years ago

Sorry for my mixup. This tool does not ingest phenopackets in exports them. If you are looking for Java code that imports phenopackets and turns them into a Java data structure, consult the LIRICAL code base: https://github.com/TheJacksonLaboratory/LIRICAL this test class should get you started: https://github.com/TheJacksonLaboratory/LIRICAL/blob/master/src/test/java/org/monarchinitiative/lirical/io/PhenopacketImporterTest.java