loading data from .txt file

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2009-02-20
2014-08-15
  • Kathrin Grundner-Culemann

    Hello everyone.

    When trying to load my data from a .txt into the Multipe Array Viewer, the Connecting to Host window opens, but instead of the Loading Data window I get the following error message in the cmd window:

    MultiExperimentViewer - version 4.3 - Windows XP
    Java Runtime Environment version: 1.6.0_11
    Java Runtime Environment vendor: Sun Microsystems Inc.
    Java Virtual Machine name: Java HotSpot(TM) Client VM
    Java Virtual Machine version: 11.0-b16
    Java Virtual Machine vendor: Sun Microsystems Inc.
    Java 3D Runtime Environment: Java 3D Core Runtime Environment
    Java 3D Runtime Environment vendor: Sun Microsystems, Inc.
    Java 3D Runtime Environment version:1.2
    Operating System name: Windows XP
    Operating System version: 5.1
    Operating System architecture: x86
    Could not download default properties from tm4.org.
    Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
            at java.lang.String.concat(Unknown Source)
            at ftp.FtpBean.getRespond(Unknown Source)
            at ftp.FtpBean.ftpConnect(Unknown Source)
            at ftp.FtpBean.ftpConnect(Unknown Source)
            at org.tigr.microarray.mev.resources.FTPFileDownloader.connect(FTPFileDo wnloader.java:75)
            at rg.tigr.microarray.mev.resources.FileResourceManager.getUpdatesIfAvailable(FileResourceManager.java:230)
            at org.tigr.microarray.mev.resources.FileResourceManager.getSupportFiles(FileResourceManager.java:173)
            at org.tigr.microarray.mev.resources.FileResourceManager.getSupportFile(FileResourceManager.java:106)
            at org.tigr.microarray.mev.MultipleArrayViewer$FrameworkImpl.getSupportFile(MultipleArrayViewer.java:6024)
            at org.tigr.microarray.mev.MultipleArrayViewer.getSupportFile(MultipleArrayViewer.java:6058)
            at rg.tigr.microarray.mev.file.SuperExpressionFileLoader.initializeAnnotationInfo(SuperExpressionFileLoader.java:154)
            at org.tigr.microarray.mev.file.SuperExpressionFileLoader.<init>(SuperExpressionFileLoader.java:140)
            at org.tigr.microarray.mev.MultipleArrayViewer.loadData(MultipleArrayViewer.java:3920)
            at org.tigr.microarray.mev.MultipleArrayViewer.access$3100(MultipleArrayViewer.java:219)
            at org.tigr.microarray.mev.MultipleArrayViewer$EventListener.actionPerformed(MultipleArrayViewer.java:5112)
            at org.tigr.microarray.mev.action.ActionManager.forwardAction(ActionManager.java:68)
            at org.tigr.microarray.mev.action.DefaultAction.actionPerformed(DefaultAction.java:60)
            at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
            at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
            at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
            at javax.swing.AbstractButton.doClick(Unknown Source)
            at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
            at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(UnknownSource)
            at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
            at java.awt.Component.processMouseEvent(Unknown Source)
            at javax.swing.JComponent.processMouseEvent(Unknown Source)
            at java.awt.Component.processEvent(Unknown Source)
            at java.awt.Container.processEvent(Unknown Source)
            at java.awt.Component.dispatchEventImpl(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
            at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
            at java.awt.Container.dispatchEventImpl(Unknown Source)
            at java.awt.Component.dispatchEvent(Unknown Source)
            at java.awt.EventQueue.dispatchEvent(Unknown Source)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
            at java.awt.EventDispatchThread.run(Unknown Source)

    However, opening a saved analysis (saved on another computer where MeV works fine) works.
    The MeV folder is in a directory without spaces, I have Java 1.6.0_11 and my system is Windows XP Professional, Version 2002 Service Pack3.

    I would greatly appreciate your help and suggestions.
    Thanks a lot

    Kathrin

     
    • Eleanor Howe

      Eleanor Howe - 2009-02-20

      Hi Kathrin,

      When MeV starts up, it tries to download a few files from the web to update its list of available annotations. It seems to be failing while doing this and I'm not sure why. Has MeV ever been able to load data properly on this computer? Is this a new installation of MeV?

      From what you have told me about your system, I don't see anything that should cause a problem. How is the internet connection there? Could it have flaked out mid-download?

      Eleanor

       
    • Kathrin Grundner-Culemann

      Hi Eleanor,
      thank you for your answer.

      I installed MeV newly on the computer returning the error message.

      At another computer in our lab, I'll get everything in the cmd window up to and including the "Could not download default properties from tm4.org. " line. And there MeV functions well.

      I compared all the internet settings and Java settings (in the control panel) of the two computers and matched everything to the functioning system. The error message was returned still.

      Do you have any suggestions what I might have overlooked or where else I should adjust settings?

      Thanks so much,
      Kathrin

       
      • Eleanor Howe

        Eleanor Howe - 2009-02-20

        Hi Kathrin,

        So you downloaded MeV very recently on the computer that's having the trouble (computer #1), right? And the computer where MeV works fine (computer #2) had MeV installed a while ago? That helps a lot, actually. MeV was updated on Feb 5, so you're probably working with two different versions. Ok, in the short term, you should be able to use the older version of MeV on computer #1 and avoid these errors. Then I can see if I can track down what happened when we updated MeV.

        One thing is interesting - that error, "Could not download default properties from tm4.org", means that MeV can't contact our ftp server to look for an updated properties file. This won't affect MeV's ability to do it's job, but it tells me that MeV can't get online. Now, MeV is supposed to be able to do everything it needs to without getting online, but this bug we've found is obviously related to the lack of internet access. Can you try unblocking the internet access? That may solve the problem with Computer #1's copy of MeV as well.

        If you'd prefer not to do that, you can download the previous version of MeV (v4.2.02) here:
        http://downloads.sourceforge.net/mev-tm4/MeV_4_3_01_win.zip

        And if this doesn't work, we'll know there's something very strange about computer #1. :)

        Sound good?
        Eleanor

         
    • Kathrin Grundner-Culemann

      Hi Eleanor,

      It seems I can't (or don't know how to) unblock the internet access on computer#2. I turned off the windows firewall and java is configured with the correct proxy settings of my network. Maybe I can't get through the institut's firewall? Any other settings I would need to configure?

      Also, I'm sorry to say, but computer 1 and 2 both have the same MeV version (v4.03.02).  I only installed the program this week on both computers.

      So it seems computer#1 is strange :). Computer #1 is much newer and has ServicePack3 installed while Computer #2 has only ServicePack 2 installed. Could that influence anything?

      Thanks for your help and efforts
      Kathrin

       
    • Eleanor Howe

      Eleanor Howe - 2009-02-20

      Hi Kathrin,

      Ok, so I guess it's not a versioning problem, then. I'm guessing it's the proxy. We don't have a proxy, so I wasn't able to test MeV with that sort of internet setup. I bet that's part of the problem.

      I'm not sure what would cause the difference between the two computers' behavior, unless it is the operating system difference. I could see SP3 doing some sort of updates to the proxy handling.

      Wow. You've found a good one here. Ouch.

      Ok, this may take me a while to test out and try to get fixed. So in the meantime, let's see if we can get you a workaround. Will MeV function at all after you see the error you reported? Or does it stop working completely?

      Eleanor

       
    • Kathrin Grundner-Culemann

      Hello Eleanor,

      first of all, thanks for all your help.

      On computer#2 all MeV functions I need work fine, even if it gives this  "Could not download default properties from tm4.org. " error in the cmd window. So I'm fine working on this computer at the moment.

      However, in the long run, it would be great if it also worked on computer #1. I'd be very glad for any suggestions.

      Thanks again,
      Kathrin

       
    • Eleanor Howe

      Eleanor Howe - 2009-02-23

      Hi Kathrin,

      Well, in the short term you could try out this build I made of MeV on computer #1. It's got a small tweak that should allow it to get past that error message you saw. Can you try it out and let me know how it works?

      ftp://occams.dfci.harvard.edu/pub/bio/devel/MeV_4_3_r1572_win.zip

      I'm working on some better fixes. Wish me luck.

      Eleanor

       
    • Kathrin Grundner-Culemann

      Hi Eleanor,

      Well, the Expression file loader window opens now, I can open a .txt file and the colums are displayed correctly, but when I click load, it doesn't load. Here is the cmd error:

      java.lang.ArrayIndexOutOfBoundsException: 0
              at org.tigr.microarray.mev.file.StanfordFileLoader.loadStanfordExpressio
      nFile(StanfordFileLoader.java:253)
              at org.tigr.microarray.mev.file.StanfordFileLoader.loadExpressionFiles(S
      tanfordFileLoader.java:122)
              at org.tigr.microarray.mev.file.SuperExpressionFileLoader$Loader.run(Sup
      erExpressionFileLoader.java:746)
              at java.lang.Thread.run(Unknown Source)

      Any clues?
      Good luck and thanks for trying.

      Kathrin

       
    • Eleanor Howe

      Eleanor Howe - 2009-02-23

      Hi Kathrin,

      Thanks for being patient with us here.

      This one seems to be a different bug entirely. Do you have any gene annotation in your input text file? If not, can you try adding a column of annotation (could be anything, like a list of numbers) and trying to load it? Be sure to click on the upper-leftmost expression value in the table there - that's how MeV knows what columns and rows of data are annotation and which should be loaded as numbers. MeV should color-code the cells for you so you know what it's planning to do.

      Eleanor

       
    • Kathrin Grundner-Culemann

      Hi Eleanor,
      I'm sorry to get back to you so late, I wasn't in the lab the last days.
      Thanks for all your help.
      Computer 1 can load my .txt file and the analyses runs through smoothly. The fix works wonderfully. What was it actually?
      My .txt are annotated with an id, I must have misclicked before loading the last time I tried.
      Sorry for the confusion.
      Thanks again for all your efforts.
      Kathrin

       
    • Eleanor Howe

      Eleanor Howe - 2009-02-26

      Hi Kathrin,

      The bug I fixed was one where MeV wasn't failing gracefully when it wasn't able to contact the FTP server. Now that I know it works, I can commit it to our repository. :) Thanks for being my tester. Good luck with MeV!

      Eleanor

       
  • Shankara Pattabhiraman

    Hi, i use mev inubuntu 12.04 and have the same problem, do you have a fix for the connection issue? Thanx a lot

     
  • Craig Gedye

    Craig Gedye - 2014-07-09

    Hi, I have used MeV intermittently in Mac OSX for some time, but for some reason 4.4 stopped working, so I loaded 4.8.1, then back to 4.4.1, then 4.7.1. Old analysis files will load, but when I attempt to load data from a txt file it freezes before I can even select the file. Alt-Cmd-Esc to kill the program. Java updated. Very strange. Any help please?

     
  • hlwright

    hlwright - 2014-08-15

    I am having the same problem with MeV 4.8.1 in Mac OSX. Have used for some time but now it seems to freeze when I open the app. I cannot open any files.

    Any advice please?

     

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