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Semantic Web plugin for Cytoscape 3.0

Home Page: http://vsdlc3.blogspot.com

Java 75.09% JavaScript 24.91%

semscape's People

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andrawaag pferns abargnesi snikproject

semscape's Issues

In an effort to mitigate the log4shell vulnerability in the Cytoscape ecosystem, we have scanned all the apps in the Cytoscape App Store. Your SemScape app is 1 of 5 remaining apps that reference either log4j or pax logging dependencies.

Please update your package and upload a new version of your app to the App Store as soon as possible.
https://apps.cytoscape.org/apps/semscape

Incompatible with Cytoscape 3.2.1

When attempting to load SemScape with Cytoscape 3.2.1 on a Microsoft Windows 7 64-bit system with Oracle Java Version 7 Update 65 the following error message is generated:

Cytoscape 3.2.1> java.lang.VerifyError: (class: org/apache/xerces/impl/dv/xs/AbstractDateTimeDV, method: signature: ()V) Bad type in putfield/putstatic
at org.apache.xerces.impl.dv.xs.XSSimpleTypeDecl.(Unknown Source)
at org.apache.xerces.impl.dv.xs.SchemaDVFactoryImpl.createBuiltInTypes(Unknown Source)
at org.apache.xerces.impl.dv.xs.SchemaDVFactoryImpl.(Unknown Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at org.apache.xerces.impl.dv.ObjectFactory.newInstance(Unknown Source)
at org.apache.xerces.impl.dv.SchemaDVFactory.getInstance(Unknown Source)
at org.apache.xerces.impl.dv.SchemaDVFactory.getInstance(Unknown Source)
at com.hp.hpl.jena.datatypes.xsd.XSDDatatype.(XSDDatatype.java:230)
at com.hp.hpl.jena.datatypes.xsd.XSDDatatype.(XSDDatatype.java:242)
at com.hp.hpl.jena.datatypes.xsd.impl.XSDFloat.(XSDFloat.java:49)
at com.hp.hpl.jena.datatypes.xsd.XSDDatatype.(XSDDatatype.java:63)
at com.hp.hpl.jena.sparql.expr.nodevalue.XSDFuncOp.(XSDFuncOp.java:766)
at com.hp.hpl.jena.query.ARQ.setNormalMode(ARQ.java:381)
at com.hp.hpl.jena.query.ARQ.defaultSettings(ARQ.java:463)
at com.hp.hpl.jena.query.ARQ.init(ARQ.java:438)
at com.hp.hpl.jena.query.ARQ.(ARQ.java:458)
at org.apache.jena.riot.RIOT.(RIOT.java:38)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at com.hp.hpl.jena.rdf.model.impl.IO_Ctl.callByRefection(IO_Ctl.java:54)
at com.hp.hpl.jena.rdf.model.impl.IO_Ctl.init(IO_Ctl.java:36)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.(ModelCom.java:65)
at com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:140)
at org.cytoscape.vsdl3c.internal.SPARQLEndpointConfig.(SPARQLEndpointConfig.java:50)
at org.cytoscape.vsdl3c.internal.CyActivator.start(CyActivator.java:75)
at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:645)
at org.apache.felix.framework.Felix.activateBundle(Felix.java:2146)
at org.apache.felix.framework.Felix.startBundle(Felix.java:2064)
at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)
at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundle(DirectoryWatcher.java:1245)
at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundles(DirectoryWatcher.java:1217)
at org.apache.felix.fileinstall.internal.DirectoryWatcher.doProcess(DirectoryWatcher.java:509)
at org.apache.felix.fileinstall.internal.DirectoryWatcher.process(DirectoryWatcher.java:358)
at org.apache.felix.fileinstall.internal.DirectoryWatcher.run(DirectoryWatcher.java:310)

This error message is only visible if Cytoscape is run from a Command Prompt. From the graphical user interface, SemScape will be reported as having been loaded however the menu items will be missing from the Apps menu and the tabs will be missing from the Control Panel.

Trying to fork & fix, problem with karaf

Noticing that SemScape does not work with the new Cytoscapes, I forked it to https://github.com/IMISE/SemScape (commit snikproject@da4baf4), updated the dependencies and adapted the code in case the APIs changed. While the single modules compile fine now, as soon as I do mvn compile in the parent module, I get a karaf error, see below. How can I get it to compile from parent without errors?

SemScape$ mvn compile
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Visualizing Semantic Data Landscapes 3.0 Parent POM
[INFO] SemScape: Visualizing Semantic Data Landscapes App (vsdl3c-app)
[INFO] Visualizing Semantic Data Landscapes Feature (vsdl3c-feature)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Visualizing Semantic Data Landscapes 3.0 Parent POM 1.0.6
[INFO] ------------------------------------------------------------------------
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building SemScape: Visualizing Semantic Data Landscapes App (vsdl3c-app) 1.0.6
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ vsdl3c-app ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 6 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.6.0:compile (default-compile) @ vsdl3c-app ---
[INFO] Nothing to compile - all classes are up to date
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Visualizing Semantic Data Landscapes Feature (vsdl3c-feature) 1.0.6
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ vsdl3c-feature ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /localstorage/projekte/java/SemScape/feature/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ vsdl3c-feature ---
[INFO] No sources to compile
[INFO] 
[INFO] --- karaf-maven-plugin:3.0.8:features-generate-descriptor (generate) @ vsdl3c-feature ---
[INFO] Generating feature descriptor file /localstorage/projekte/java/SemScape/feature/target/features.xml
[WARNING] Error while opening artifact
java.io.FileNotFoundException: /localstorage/projekte/java/SemScape/app/target/classes (Ist ein Verzeichnis)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.apache.karaf.tooling.features.GenerateDescriptorMojo.getManifest(GenerateDescriptorMojo.java:460)
	at org.apache.karaf.tooling.features.GenerateDescriptorMojo.writeFeatures(GenerateDescriptorMojo.java:369)
	at org.apache.karaf.tooling.features.GenerateDescriptorMojo.execute(GenerateDescriptorMojo.java:274)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	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 org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[WARNING] Manifest not present in the first entry of the zip - apache-jena-libs-3.1.1.pom
[WARNING] Manifest not present in the first entry of the zip - servlet-api-2.3.jar
[INFO] ...done!
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Visualizing Semantic Data Landscapes 3.0 Parent POM  SUCCESS [  0.001 s]
[INFO] SemScape: Visualizing Semantic Data Landscapes App (vsdl3c-app) SUCCESS [  3.986 s]
[INFO] Visualizing Semantic Data Landscapes Feature (vsdl3c-feature) SUCCESS [  1.863 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 8.366 s
[INFO] Finished at: 2016-12-12T17:23:53+01:00
[INFO] Final Memory: 18M/171M
[INFO] ------------------------------------------------------------------------

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sgtp / semscape Goto Github PK

semscape's People

Contributors

Stargazers

Watchers

Forkers

semscape's Issues

Missing LICENSE file

Log4Shell Vulnerability

Incompatible with Cytoscape 3.2.1

Trying to fork & fix, problem with karaf

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent