Hi Akram, I get a similar error often on the first time I run the configuration after a “rebuild” … I just press run again and then it runs just fine with the expected results. It never happens on consecutive launches on the same build ( tested many many times), at least that is the case for me.
There is obviously a problem there that we should look into but since I am running on a tight schedule and there is no impact otherwise, I have not looked further into it … Kind Regards, Eugenia Monogyiou From: Akram <as...@yahoo.com> Sent: 15 February 2021 21:58 To: dev@ctakes.apache.org; Monogyiou, Eugenia <eugenia.monogy...@nttdata.com> Subject: Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL] Thanks Eugenia I can see PiperRunnerGui now but it gives this error when executed !! Exception in thread "main" java.lang.IndexOutOfBoundsException: Invalid index at javax.swing.DefaultRowSorter.convertRowIndexToModel(DefaultRowSorter.java:514) at sun.swing.FilePane$SortableListModel.getElementAt(FilePane.java:670) at javax.swing.plaf.basic.BasicListUI.updateLayoutState(BasicListUI.java:1360) at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311) at javax.swing.plaf.basic.BasicListUI.getCellBounds(BasicListUI.java:952) at javax.swing.JList.getCellBounds(JList.java:1637) at javax.swing.JList.ensureIndexIsVisible(JList.java:1149) at sun.swing.FilePane.ensureIndexIsVisible(FilePane.java:1708) at sun.swing.FilePane.doDirectoryChanged(FilePane.java:1631) at sun.swing.FilePane.propertyChange(FilePane.java:1681) at java.beans.PropertyChangeSupport.fire(PropertyChangeSupport.java:335) at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:327) at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:263) at java.awt.Component.firePropertyChange(Component.java:8434) at javax.swing.JFileChooser.setCurrentDirectory(JFileChooser.java:598) at org.apache.ctakes.gui.pipeline.PiperRunnerPanel.<init>(PiperRunnerPanel.java:100) at org.apache.ctakes.gui.pipeline.PiperRunnerGui.createMainPanel(PiperRunnerGui.java:40) at org.apache.ctakes.gui.pipeline.PiperRunnerGui.main(PiperRunnerGui.java:53) Process finished with exit code 1 Any idea how to resolve that? On Monday, 15 February 2021, 06:50:09 am GMT-8, Monogyiou, Eugenia <eugenia.monogy...@nttdata.com<mailto:eugenia.monogy...@nttdata.com>> wrote: Hi Akram, If you update from the trunk you must be able to locate this : \ctakes-gui\src\main\java\org\apache\ctakes\gui\pipeline\PiperRunnerGui.java I have done a fresh update last night so I am pretty sure it is there ... Kind Regards, Eugenia Monogyiou | NTT Data UK Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com<mailto:eugenia.monogy...@nttdata.com> -----Original Message----- From: Akram <as...@yahoo.com.INVALID<mailto:as...@yahoo.com.INVALID>> Sent: 14 February 2021 22:14 To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL] Hi Finan Thanks for the support you provide. The solution you gave me before does not work anymore. I cannot find RunPiperGui class anywhere in cTAKES now!. has this chaged? is there anyway I can run cTAKES GUI? Thanks On Monday, 23 December 2019, 06:27:36 am GMT-8, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Akram, I think that the problem is your classpath. When you run a main(..) class in intellij, it uses the classpath of the module in which that class lies. For the PIperRunnerGui it uses the classpath of ctakes-gui. ctakes-gui does not have any dependency upon modules such as ctakes-chunker. Running PiperRunnerGui.main(..) in ctakes-gui module has no ctakes-chunker classes or files in the classpath. Getting used to running with maven can take a little while. Intellij does have some things that can help. Instead of running just by main(..) methods, use specific run configurations. https://www.jetbrains.com/help/idea/creating-and-editing-run-debug-configurations.html 1. In the top toolbar, select Run > Edit Configurations ... This should launch a Run/Debug Configurations dialog. 2. Above the left panel, click the + button This should pop up a list of Configuration types. 3. Select Application This should populate the right panel with options. 4. The important items: Main class : RunPiperGui VM Options: -Xmx3g Use classpath of Module: ctakes-examples Sean From: Akram <as...@yahoo.com<mailto:as...@yahoo.com>> Sent: Sunday, December 22, 2019 7:54 PM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org>; Finan, Sean Subject: Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL] | * External Email - Caution * | I have checked the file ChunkerSubPipe.piper for sure exists in ctakes-chunker-res\target\classes\org\apache\ctakes\chunker\pipeline and in \ctakes-chunker-res\src\main\resources\org\apache\ctakes\chunker\pipeline loading DefaultTokenizerPipelineshows no errors, the problem only with ChunkerSubPipe.piper I tried to install cTAKES on 2 different computers and got same issue on both. it only happens when I run from PiperRunnerGui (same as the image attached) No problems if I use Profilers On Monday, 23 December 2019, 4:54:05 am AEDT, Finan, Sean <sean.fi...@childrens.harvard.edu<mailto:sean.fi...@childrens.harvard.edu>> wrote: Hi Akram, I am not sure why you are seeing that error message. That method will search the classpath for "ChunkerSubPipe.piper", which includes the ctakes-chunker-res*.jar in the lib/ directory of a binary installation or the ctakes-chunker-res/src/main/resources/ directory tree in a source sandbox. It should also traverse the resources/ directory tree in both installation types. As long as the file exists in there and the classpath is set it should find it. Can you check your installation and see if that file is missing for some reason? The path is something like org.apache.ctakes.chunker.pipeline. Sean From: Akram <as...@yahoo.com.INVALID<mailto:as...@yahoo.com.INVALID>> Sent: Sunday, December 22, 2019 3:50 AM To: dev@ctakes.apache.org<mailto:dev@ctakes.apache.org> Subject: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL] | * External Email - Caution * | I followed Sean's instructions to run "runPiperGUI" from Profiles using "DefaultFastPipeline_Test.piper" file works perfectly. I tried to debug the process ( I will do some changes later ) I run "PiperRunnerGUI" using "DefaultFastPipeline_Test.piper" file but I get this error ! "No piper file found for ChunkerSubPipe" Then this error "Piper File not found: ChunkerSubPipe" Then this error "Could not load Piper File J:\cTAKES\ctakes-clinical-res\src\main\resources\org\apache\ctakes\clinical\pipeline\DefaultFastPipeline_Test.piper" I tried to debug. and limited the problem in Line 319 in PiperFileReader.java stream = FileLocator.getStreamQuiet( packageName.replace( '.', '/' ) + "/pipeline/" + filePath ); Then stopped at getStreamQuietfunction and could not know why it does not find the ChunkerSubPipe.piper! Can someone help me identifying what is the cause of this problem? Appreciate your help. Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding. Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
