weso / protegeshex Goto Github PK

Protege plugin for Shape Expressions

Home Page: http://www.weso.es/protegeShEx/

Java 65.57% HTML 16.77% CSS 3.47% JavaScript 14.20%

shex protege-plugin shape-expressions protege

protegeshex's Introduction

protegeShEx - Protégé plugin for ShEx

This plugin adds ShEx features to the Protégé editor in order to allow the users to validate their ontologies using ShEx. To do that, this plugin incorporate YASHE editor, offering a better experience to the users.

Use the plugin

Get a copy of the example code:

 git clone https://github.com/weso/protegeShEx.git

Change into the protegeShEX directory.
Type mvn clean package. On build completion, the "target" directory will contain a protege.plugin.examples-${version}.jar file.
Copy the JAR file from the target directory to the "plugins" subdirectory of your Protege distribution.

As YASHE is built in JavaScript we use the JavaFX library in order to re-use YASHE code. This library doesn´t work at all with protege at the moment (more info) and while we look for another more elegant solution we need to do the following steps:

Change into Protege/conf directory
Open in a text editor the config.xml file

Add the following line in the frameworkProperties:

<property name="org.osgi.framework.system.packages.extra" 
value="javax.xml.parsers,org.xml.sax,org.xml.sax.ext,org.xml.sax.helpers,javafx.collections,javafx.embed.swing,javafx.geometry,javafx.scene,javafx.scene.text,javafx.scene.layout,javafx.scene.paint,javafx.scene.web,javafx.application,javafx.beans.property,javafx.beans.value"/>

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protegeshex's Issues

Problem compiling the plugin

Hi, first of all, thanks for sharing this plugin, I think it is very useful for integrating shapes in protege ontology editor.
I am trying to follow the instructions from the readme file but, when I try to generate the jar, I get the following error from maven (it seems that it cant find javafx stuff):

[INFO] Scanning for projects...
[INFO] 
[INFO] ------------< edu.stanford.protege:protege.plugin.examples >------------
[INFO] Building Protege Plugin Examples 2.0.0-SNAPSHOT
[INFO] -------------------------------[ bundle ]-------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ protege.plugin.examples ---
[INFO] Deleting /home/fabad/Proyectos_java/protegeShEx/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ protege.plugin.examples ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ protege.plugin.examples ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/fabad/Proyectos_java/protegeShEx/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[17,26] package javafx.application does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[18,26] package javafx.embed.swing does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[19,20] package javafx.scene does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[20,27] package javafx.scene.layout does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[21,24] package javafx.scene.web does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[22,24] package javafx.scene.web does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[28,24] cannot find symbol
  symbol:   class WebView
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[29,24] cannot find symbol
  symbol:   class JFXPanel
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[31,24] cannot find symbol
  symbol:   class WebEngine
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[60,29] cannot find symbol
  symbol:   class JFXPanel
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[66,17] cannot find symbol
  symbol:   class Scene
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[36,31] cannot find symbol
  symbol:   class JFXPanel
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[52,17] cannot find symbol
  symbol:   variable Platform
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[62,17] cannot find symbol
  symbol:   class Scene
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[68,17] cannot find symbol
  symbol:   class StackPane
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[68,39] cannot find symbol
  symbol:   class StackPane
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[70,17] cannot find symbol
  symbol:   class Scene
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[70,35] cannot find symbol
  symbol:   class Scene
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[71,31] cannot find symbol
  symbol:   class WebView
  location: class edu.stanford.bmir.protege.examples.view.YASHE
[INFO] 19 errors 
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.678 s
[INFO] Finished at: 2022-04-27T15:43:14+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.3:compile (default-compile) on project protege.plugin.examples: Compilation failure: Compilation failure: 
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[17,26] package javafx.application does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[18,26] package javafx.embed.swing does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[19,20] package javafx.scene does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[20,27] package javafx.scene.layout does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[21,24] package javafx.scene.web does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[22,24] package javafx.scene.web does not exist
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[28,24] cannot find symbol
[ERROR]   symbol:   class WebView
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[29,24] cannot find symbol
[ERROR]   symbol:   class JFXPanel
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[31,24] cannot find symbol
[ERROR]   symbol:   class WebEngine
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[60,29] cannot find symbol
[ERROR]   symbol:   class JFXPanel
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[66,17] cannot find symbol
[ERROR]   symbol:   class Scene
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[36,31] cannot find symbol
[ERROR]   symbol:   class JFXPanel
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[52,17] cannot find symbol
[ERROR]   symbol:   variable Platform
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[62,17] cannot find symbol
[ERROR]   symbol:   class Scene
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[68,17] cannot find symbol
[ERROR]   symbol:   class StackPane
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[68,39] cannot find symbol
[ERROR]   symbol:   class StackPane
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[70,17] cannot find symbol
[ERROR]   symbol:   class Scene
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[70,35] cannot find symbol
[ERROR]   symbol:   class Scene
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[71,31] cannot find symbol
[ERROR]   symbol:   class WebView
[ERROR]   location: class edu.stanford.bmir.protege.examples.view.YASHE
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

I am using maven with java version 1.8.0_312 (openjdk).
I have tried to replace the javafx dependence by the following ones in the pom file:

		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-controls</artifactId>
			<version>11</version>
		</dependency>
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-web</artifactId>
			<version>11</version>
		</dependency>
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-fxml</artifactId>
			<version>11</version>
		</dependency>
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-swing</artifactId>
			<version>11</version>
		</dependency>

But the, I get the following maven error (seems to be that I have to use java 11):

[INFO] Scanning for projects...
[INFO] 
[INFO] ------------< edu.stanford.protege:protege.plugin.examples >------------
[INFO] Building Protege Plugin Examples 2.0.0-SNAPSHOT
[INFO] -------------------------------[ bundle ]-------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ protege.plugin.examples ---
[INFO] Deleting /home/fabad/Proyectos_java/protegeShEx/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ protege.plugin.examples ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ protege.plugin.examples ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/fabad/Proyectos_java/protegeShEx/target/classes
[INFO] -------------------------------------------------------------
[ERROR] COMPILATION ERROR : 
[INFO] -------------------------------------------------------------
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[17,26] cannot access javafx.application.Platform
  bad class file: /home/fabad/.m2/repository/org/openjfx/javafx-graphics/11/javafx-graphics-11-linux.jar(javafx/application/Platform.class)
    class file has wrong version 54.0, should be 52.0
    Please remove or make sure it appears in the correct subdirectory of the classpath.
[INFO] 1 error
[INFO] -------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  1.539 s
[INFO] Finished at: 2022-04-27T15:54:04+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.3:compile (default-compile) on project protege.plugin.examples: Compilation failure
[ERROR] /home/fabad/Proyectos_java/protegeShEx/src/main/java/edu/stanford/bmir/protege/examples/view/YASHE.java:[17,26] cannot access javafx.application.Platform
[ERROR]   bad class file: /home/fabad/.m2/repository/org/openjfx/javafx-graphics/11/javafx-graphics-11-linux.jar(javafx/application/Platform.class)
[ERROR]     class file has wrong version 54.0, should be 52.0
[ERROR]     Please remove or make sure it appears in the correct subdirectory of the classpath.
[ERROR] 
[ERROR] -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

After this, I changed to oracle java 11, but then I get the following error:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[INFO] Scanning for projects...
[INFO] 
[INFO] ------------< edu.stanford.protege:protege.plugin.examples >------------
[INFO] Building Protege Plugin Examples 2.0.0-SNAPSHOT
[INFO] -------------------------------[ bundle ]-------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ protege.plugin.examples ---
[INFO] Deleting /home/fabad/Proyectos_java/protegeShEx/target
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ protege.plugin.examples ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ protege.plugin.examples ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/fabad/Proyectos_java/protegeShEx/target/classes
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:resources (default-resources) @ protege.plugin.examples ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:compile (default-compile) @ protege.plugin.examples ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 4 source files to /home/fabad/Proyectos_java/protegeShEx/target/classes
[INFO] 
[INFO] --- maven-resources-plugin:3.2.0:testResources (default-testResources) @ protege.plugin.examples ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Using 'UTF-8' encoding to copy filtered properties files.
[INFO] skip non existing resourceDirectory /home/fabad/Proyectos_java/protegeShEx/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.3:testCompile (default-testCompile) @ protege.plugin.examples ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M6:test (default-test) @ protege.plugin.examples ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-bundle-plugin:3.0.0:bundle (default-bundle) @ protege.plugin.examples ---
[WARNING] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Bundle-Activator org.protege.editor.owl.ProtegeOWL is being imported into the bundle rather than being contained inside it. This is usually a bundle packaging error
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/index.html
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/src/main.js
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/css/style.css
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yashe.bundled.min.js
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yate.bundled.min.js
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yasme.bundled.min.js
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yashe.min.css
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yate.min.css
[ERROR] Bundle edu.stanford.protege:protege.plugin.examples:bundle:2.0.0-SNAPSHOT : Input file does not exist: /src/main/java/edu/stanford/bmir/protege/examples/view/lib/yasme.min.css
[ERROR] Error(s) found in bundle configuration
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  3.136 s
[INFO] Finished at: 2022-04-27T16:02:37+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.felix:maven-bundle-plugin:3.0.0:bundle (default-bundle) on project protege.plugin.examples: Error(s) found in bundle configuration -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

I dont know what to do at this point. I have checked that I have the files that maven tells that do not exist. Any clue about this? Additionally I would suggest to provide the resulting jar as a release so that users do not have to compile by themselves.

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