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monarch-initiative / loinc2hpo

Java library to map LOINC-encoded test results to Human Phenotype Ontology
http://loinc2hpo.readthedocs.io/en/latest/
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Running v1.1.6 on Ubuntu for the first time fails #101

Closed ShahimEssaid closed 4 years ago

ShahimEssaid commented 5 years ago

/usr/lib/jvm/java-8-oracle/bin/java -jar Loinc2HpoGui-jar-with-dependencies.jar ..... java.io.FileNotFoundException: /home/shahim/.loinc2hpo/loinc2hpo.settings (No such file or directory)

This is on Ubuntu 19.04 with version v1.1.6 built locally. I've never ran the GUI before on this machine. the .loinc2hpo was created but a new settings file isn't being created.

kingmanzhang commented 5 years ago

Hi Shahim, I have not tested it on Linux. I will try it and get back to you.

kingmanzhang commented 5 years ago

At the same time, I suggest you try the compiled version: https://github.com/monarch-initiative/loinc2hpo/releases/tag/v1.1.6

kingmanzhang commented 5 years ago

Could you post the entire stack trace? Thanks!

ShahimEssaid commented 5 years ago

The compiled version you linked to above ran without a similar error.

May 15, 2019 8:21:18 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version 8.0.201
May 15, 2019 8:21:18 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version 8.0.201
May 15, 2019 8:21:19 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version 8.0.201
[JavaFX-Launcher] TRACE (Loinc2HpoAnnotationsTabController.java:70) - Calling initialize
May 15, 2019 8:21:19 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 9 by JavaFX runtime of version 8.0.201
java.io.FileNotFoundException: /home/shahim/.loinc2hpo/loinc2hpo.settings (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.(FileInputStream.java:138)
    at java.io.FileInputStream.(FileInputStream.java:93)
    at java.io.FileReader.(FileReader.java:58)
    at org.monarchinitiative.loinc2hpo.model.Settings.loadSettings(Settings.java:50)
    at org.monarchinitiative.loinc2hpo.controller.MainController.initialize(MainController.java:132)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71)
    at sun.reflect.GeneratedMethodAccessor2.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2566)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2441)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3214)
    at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3175)
    at javafx.fxml.FXMLLoader.load(FXMLLoader.java:3165)
    at org.monarchinitiative.loinc2hpo.gui.Main.init(Main.java:54)
    at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:841)
    at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$412(LauncherImpl.java:182)
    at java.lang.Thread.run(Thread.java:748)
2019-05-15 20:21:19,618 pool-2-thread-1 DEBUG Stopping LoggerContext[name=33909752, org.apache.logging.log4j.core.LoggerContext@23f7375a]
2019-05-15 20:21:19,618 pool-2-thread-1 DEBUG Stopping LoggerContext[name=33909752, org.apache.logging.log4j.core.LoggerContext@23f7375a]...
kingmanzhang commented 5 years ago

Hi Shahim, this is really puzzling to me. Sorry, I don't have a clue why it could not create this file on your machine. Again, I have to go home and test whether I can reproduce the error message. At the present, I think one solution is to create the file yourself :

touch /home/shahim/.loinc2hpo/loinc2hpo.settings

Then start the compile app. I hope this would at least let you start it.

kingmanzhang commented 4 years ago

Close this for now. Will also release a docker image in a few month.