Hi,
i just started using KNIME in combination with FlexX Docking software from Biosolveit. Testing the FlexX installation worked fine but everytime I try to execute the FlexX Node I get a NullPointerException. Maybe somebody can help me with this problem ( find Debug output below ). It looks like a problem occuring not in the FlexX part itself.
Philipp
DEBUG NodeContainerEditPart OpenBabel 0:0:1 (EXECUTED)
DEBUG NodeContainerEditPart SDF Reader 0:0:2 (EXECUTED)
DEBUG ExecuteAllAction Starting execution of all nodes
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: MARKEDFOREXEC
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: QUEUED
DEBUG KnimeResourceNavigator state changed to EXECUTING
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG NodeContainer Workflow Manager 0 has new state: EXECUTING
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforePreExecution
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: PREEXECUTE
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforeExecution
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: EXECUTING
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG LocalNodeExecutionJob Compute FlexX Docking 0:0:3 Start execute
DEBUG Compute FlexX Docking reset
DEBUG Compute FlexX Docking clean output ports.
ERROR Compute FlexX Docking Execute failed: ("NullPointerException"): null
DEBUG Compute FlexX Docking Execute failed: ("NullPointerException"): null
java.lang.NullPointerException
at biosolveit.toolkit.Toolkit.readMoleculeToBufferedDataTable(Unknown Source)
at biosolveit.flexx.docking.FlexXNodeModel.execute(Unknown Source)
at org.knime.core.node.NodeModel.execute(NodeModel.java:582)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:438)
at org.knime.core.node.Node.execute(Node.java:704)
at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:785)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:143)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:238)
DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doBeforePostExecution
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: POSTEXECUTE
DEBUG NodeContainer KNIME_project 0:0 has new state: EXECUTING
DEBUG WorkflowManager Compute FlexX Docking 0:0:3 doAfterExecute - failure
DEBUG Compute FlexX Docking reset
DEBUG Compute FlexX Docking clean output ports.
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: IDLE
DEBUG Compute FlexX Docking Configure succeeded. (Compute FlexX Docking)
DEBUG NodeContainer Compute FlexX Docking 0:0:3 has new state: CONFIGURED
DEBUG KnimeResourceNavigator state changed to CONFIGURED
DEBUG NodeContainer KNIME_project 0:0 has new state: CONFIGURED
DEBUG NodeContainer KNIME_project 0:0 has new state: CONFIGURED
DEBUG NodeContainer Workflow Manager 0 has new state: IDLE
DEBUG NodeContainerEditPart SDF Reader 0:0:2 (EXECUTED)
DEBUG NodeContainerEditPart Compute FlexX Docking 0:0:3 (CONFIGURED)
DEBUG WorkflowRootEditPart WorkflowRoot: command stack changed
DEBUG NodeContainerEditPart ExtraInfo changed, updating bounds and visuals...