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nodes4knime-cdk2's Issues

Can't render CDK cells

`Exception in thread "OutPortView-Updater-4" org.knime.core.node.util.InvocationTargetRuntimeException: Exception during execution in Event Dispatch Thread
at org.knime.core.node.util.ViewUtils.invokeAndWaitInEDT(ViewUtils.java:179)
at org.knime.core.node.workflow.OutPortView.updateInternal(OutPortView.java:265)
at org.knime.core.node.workflow.OutPortView$2.run(OutPortView.java:249)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)

Caused by: java.lang.IllegalAccessError: failed to access class org.openscience.cdk.layout.CorrectGeometricConfiguration from class org.openscience.cdk.layout.LayoutHelper (org.openscience.cdk.layout.CorrectGeometricConfiguration is in unnamed module of loader org.eclipse.osgi.internal.loader.EquinoxClassLoader @bcfbd54; org.openscience.cdk.layout.LayoutHelper is in unnamed module of loader org.eclipse.osgi.internal.loader.EquinoxClassLoader @73d30c7d)
at org.openscience.cdk.layout.LayoutHelper.adjustStereo(LayoutHelper.java:27)
at org.openscience.cdk.knime.type.CDKValueRenderer.setAtomContainer(CDKValueRenderer.java:154)
at org.openscience.cdk.knime.type.CDKValueRenderer.setValue(CDKValueRenderer.java:200)
at org.knime.core.data.renderer.AbstractPainterDataValueRenderer.getTableCellRendererComponent(AbstractPainterDataValueRenderer.java:200)
at org.knime.core.data.renderer.DefaultDataValueRendererFamily.getTableCellRendererComponent(DefaultDataValueRendererFamily.java:217)
at org.knime.core.data.renderer.SetOfRendererFamilies.getTableCellRendererComponent(SetOfRendererFamilies.java:138)
at java.desktop/javax.swing.JTable.prepareRenderer(JTable.java:5738)
at org.knime.core.node.tableview.TableContentView.prepareRenderer(TableContentView.java:299)
at org.knime.core.node.tableview.TableContentView.fitCellSizeToRenderer(TableContentView.java:1020)
at org.knime.core.node.tableview.TableContentView.tableChanged(TableContentView.java:1041)
at java.desktop/javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:297)
at java.desktop/javax.swing.table.AbstractTableModel.fireTableStructureChanged(AbstractTableModel.java:217)
at org.knime.core.node.tableview.TableContentModel.setDataTableIntern(TableContentModel.java:430)
at org.knime.core.node.tableview.TableContentModel.lambda$0(TableContentModel.java:317)
at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:367)
at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:221)
at org.knime.core.node.util.ViewUtils.invokeAndWaitInEDT(ViewUtils.java:136)
at org.knime.core.node.tableview.TableContentModel.setDataTable(TableContentModel.java:317)
at org.knime.core.node.tableview.TableContentView.setDataTable(TableContentView.java:322)
at org.knime.core.node.tableview.TableView.setDataTable(TableView.java:483)
at org.knime.core.node.workflow.BufferedDataTableView.updateDataTable(BufferedDataTableView.java:106)
at org.knime.core.node.workflow.BufferedDataTableView.(BufferedDataTableView.java:92)
at org.knime.core.node.BufferedDataTable.getViews(BufferedDataTable.java:1138)
at org.knime.core.node.workflow.OutPortView$3.runWithContext(OutPortView.java:285)
at org.knime.core.node.workflow.OutPortView$3.run(OutPortView.java:270)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:303)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)`

Assess test issues

Test workflows

  • ChemSpider

  • Converter

  • HydrogenManipulation

  • Depiction

  • Depiction No Highlight

  • Element Filter

  • Line Notation

  • Lipinski

  • Signature

  • Symmetry

  • Three D

  • Fingerprints

  • Whim

  • Connectivity

  • Molecular Properties

  • Smarts Query

  • Substructure Search

  • XlogP

Nodes without test flows:

  • OPSIN
  • Sugar Remover
  • Mass Calculator
  • Sum formula
  • 2D coordinates
  • Fingerprint Similarity
  • 3D D-Moments
  • 3D D-Similarity
  • 3D RMSD

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