SemanticWebImport - Query not working due to multiple errors
gabrielsaul opened this issue · 0 comments
gabrielsaul commented
Expected Behavior
Execution of a catch-all query should return all triples and visualise the entire graph in the Graph pane.
I cannot provide the expected behaviour in the form of logs/screenshots as I have yet to achieve expected behaviour with SemanticWebImport in Gephi.
Current Behavior
Log upon startup (nothing changed or executed):
Nov 13, 2023 10:02:10 PM org.gephi.ui.upgrader.Upgrader upgrade
-- INFO: Current Version is gephi
--
Nov 13, 2023 10:02:12 PM org.netbeans.core.ui.warmup.DiagnosticTask run
-- INFO: Diagnostic information -- Input arguments: -- -Dsun.java2d.metal=true -- -Dsun.java2d.noddraw=true -- -Dsun.awt.noerasebackground=true -- -Dapple.awt.graphics.UseQuartz=true -- -Dnetbeans.indexing.noFileRefresh=true -- -Dnetbeans.winsys.hideEmptyDocArea=true -- -Dplugin.manager.check.interval=EVERY_DAY -- -Dapple.awt.application.appearance=system -- --add-opens=java.base/java.net=ALL-UNNAMED -- --add-exports=java.desktop/sun.awt=ALL-UNNAMED -- --add-opens=java.desktop/javax.swing=ALL-UNNAMED -- --add-opens=java.base/java.nio=ALL-UNNAMED -- --add-exports=java.desktop/sun.awt=ALL-UNNAMED -- -Dnetbeans.user.dir=C:\Program Files\Gephi-0.10.1\bin -- -Djdk.home=jre-x64\jdk-11.0.17+8-jre -- -Dnetbeans.home=C:\Program Files\Gephi-0.10.1\platform -- -Dnetbeans.user=C:\Users\Owner\AppData\Roaming\gephi\0.10 -- -Dnetbeans.default_userdir_root=C:\Users\Owner\AppData\Roaming\gephi -- -XX:+HeapDumpOnOutOfMemoryError -- -XX:HeapDumpPath=C:\Users\Owner\AppData\Roaming\gephi\0.10\var\log\heapdump.hprof -- -Dsun.awt.keepWorkingSetOnMinimize=true -- -Djava.security.manager=allow -- -Dnetbeans.dirs=C:\Program Files\Gephi-0.10.1\extra;C:\Program Files\Gephi-0.10.1\gephi;C:\Program Files\Gephi-0.10.1\platform -- exit -- Compiler: HotSpot 64-Bit Tiered Compilers -- Heap memory usage: initial 128.0MB maximum 2020.0MB -- Non heap memory usage: initial 7.3MB maximum -1b -- Garbage collector: G1 Young Generation (Collections=6 Total time spent=0s) -- Garbage collector: G1 Old Generation (Collections=0 Total time spent=0s) -- Classes: loaded=9861 total loaded=9861 unloaded 0 --
--
Nov 13, 2023 10:02:12 PM org.netbeans.core.ui.warmup.DiagnosticTask logEnv
-- INFO: Total memory 8,468,533,248
--
Nov 13, 2023 10:02:12 PM org.netbeans.core.ui.warmup.DiagnosticTask logEnv
-- INFO: Total physical memory 8,468,533,248
--
Nov 13, 2023 10:02:12 PM org.gephi.visualization.swing.GLAbstractListener reshape
-- INFO: GL_VENDOR: Intel
--
Nov 13, 2023 10:02:12 PM org.gephi.visualization.swing.GLAbstractListener reshape
-- INFO: GL_RENDERER: Intel(R) UHD Graphics 620
--
Nov 13, 2023 10:02:12 PM org.gephi.visualization.swing.GLAbstractListener reshape
-- INFO: GL_VERSION: 4.5.0 - Build 23.20.16.4958
--
Nov 13, 2023 10:02:12 PM org.gephi.visualization.swing.GLAbstractListener reshape
-- INFO: GL_SURFACE_SCALE: 1.5
--
Nov 13, 2023 10:02:13 PM org.openide.filesystems.Ordering getOrder
-- WARNING: Not all children in Menu/View/ marked with the position attribute: [org-netbeans-core-windows-actions-ToggleFullScreenAction.instance\position], but some are: [ToggleFullScreenAction.shadow]
--
Nov 13, 2023 10:02:13 PM org.openide.filesystems.Ordering getOrder
-- WARNING: Not all children in Menu/Window/ marked with the position attribute: [fr-inria-edelweiss-SemanticWebImportMainWindowTopComponent.shadow], but some are: [org-gephi-desktop-clustering-ContextTopComponent.shadow, org-gephi-desktop-datalab-DataTableTopComponent.shadow, org-gephi-desktop-filters-FiltersTopComponent.shadow, org-gephi-visualization-component-GraphTopComponent.shadow, org-gephi-desktop-layout-LayoutTopComponent.shadow, org-netbeans-core-io-ui-IOWindowAction.shadow, org-gephi-desktop-preview-PreviewTopComponent.shadow, org-gephi-desktop-preview-PreviewSettingsTopComponent.shadow, org-gephi-desktop-appearance-AppearanceTopComponent.shadow, org-gephi-desktop-welcome-WelcomeAction.shadow, org-gephi-desktop-statistics-StatisticsTopComponent.shadow, org-gephi-desktop-timeline-TimelineWindowAction.shadow, Separator4_1.instance, Separator3.instance, ConfigureWindow, org-netbeans-core-windows-actions-ResetWindowsAction.shadow, Separator4.instance, CloseWindowAction.shadow, GroupsMenuAction.shadow]
--
Nov 13, 2023 10:02:22 PM fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent setConfigurationAction
-- INFO: Loading configuration "Humans"
--
Nov 13, 2023 10:02:22 PM fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent setConfigurationAction
-- INFO: Selecting the driver "fr.inria.edelweiss.sparql.corese.CoreseDriver"
--
Nov 13, 2023 10:02:40 PM org.netbeans.core.ui.warmup.MenuWarmUpTask$NbWindowsAdapter run
-- INFO: External Changes Refresh on focus gain disabled
--
First, I set the "Humans" example in the configuration pane, and execute the following default query:
construct{
?x ?r ?y
} where {
?x ?r ?y
}
Here is the log output for the attempt:
Nov 13, 2023 10:06:13 PM fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent startCreateGraphs
-- INFO: Entering startCreateGraphs
--
Nov 13, 2023 10:06:13 PM fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent startCreateGraphs
-- INFO: Starting the RDF importer for Gephi
--
Nov 13, 2023 10:06:13 PM fr.inria.edelweiss.semantic.importer.SemanticWebImportParser populateRDFGraph
-- INFO: resetWorkspace = false
--
Nov 13, 2023 10:06:13 PM fr.inria.edelweiss.semantic.importer.SemanticWebImportParser populateRDFGraph
-- INFO: postProcessing = true
--
Nov 13, 2023 10:06:13 PM org.netbeans.core.startup.TopLogging$AWTHandler uncaughtException
-- SEVERE: null
-- java.lang.NoSuchMethodError: 'void org.gephi.project.api.ProjectController.newProject()'
-- at fr.inria.edelweiss.sparql.GephiUtils.createProjectIfEmpty(GephiUtils.java:56)
-- at fr.inria.edelweiss.semantic.importer.SemanticWebImportParser.populateRDFGraph(SemanticWebImportParser.java:95)
-- at fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent.startCreateGraphs(SemanticWebImportMainWindowTopComponent.java:732)
-- at fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent.startCreateGraphsAction(SemanticWebImportMainWindowTopComponent.java:712)
-- at fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent.access$1400(SemanticWebImportMainWindowTopComponent.java:58)
-- at fr.inria.edelweiss.semantic.SemanticWebImportMainWindowTopComponent$15.actionPerformed(SemanticWebImportMainWindowTopComponent.java:631)
-- at java.desktop/javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
-- at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
-- at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
-- at java.desktop/javax.swing.DefaultButtonModel.setPressed(Unknown Source)
-- at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
-- at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
-- at java.desktop/java.awt.Component.processMouseEvent(Unknown Source)
-- at java.desktop/javax.swing.JComponent.processMouseEvent(Unknown Source)
-- at java.desktop/java.awt.Component.processEvent(Unknown Source)
-- at java.desktop/java.awt.Container.processEvent(Unknown Source)
-- at java.desktop/java.awt.Component.dispatchEventImpl(Unknown Source)
-- at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)
-- at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)
-- at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
-- at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
-- at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
-- at java.desktop/java.awt.Container.dispatchEventImpl(Unknown Source)
-- at java.desktop/java.awt.Window.dispatchEventImpl(Unknown Source)
-- at java.desktop/java.awt.Component.dispatchEvent(Unknown Source)
-- at java.desktop/java.awt.EventQueue.dispatchEventImpl(Unknown Source)
-- at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
-- at java.desktop/java.awt.EventQueue$4.run(Unknown Source)
-- at java.base/java.security.AccessController.doPrivileged(Native Method)
-- at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
-- at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
-- at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
-- at java.desktop/java.awt.EventQueue$5.run(Unknown Source)
-- at java.base/java.security.AccessController.doPrivileged(Native Method)
-- at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
-- at java.desktop/java.awt.EventQueue.dispatchEvent(Unknown Source)
-- at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:136)
-- at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
-- at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
-- at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
-- at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
-- at java.desktop/java.awt.EventDispatchThread.pumpEvents(Unknown Source)
-- at java.desktop/java.awt.EventDispatchThread.run(Unknown Source)
--
--
No visualisation occurred in the Graph pane.
Possible Solution
I manually updated the ICU4J jar file locally (as suggested in #2420 ) but this hasn't solved any issues. Looking at the full log, I realise there are more issues present.
Steps to Reproduce
- Start a new project in Gephi.
- Go to the Configuration tab in SemanticWebImport and set the "Humans" example
- Run the default query
- View the log
Context
I am trying to visualise my RDF graphs and run queries on them. I have tried to get SemanticWebImport working over the past couple of days.
Your Environment
- Version used: Gephi 0.10.1
- Operating System: Windows 11
- SemanticWebImport version 1.0.0 (downloaded and installed manually)