PR-OWL2.0 Plugin: How to see MTheory after saving & reopening the UBF file

Suvarna
2013-05-25
2014-08-12
  • Suvarna
    Suvarna
    2013-05-25

    Hi,

    When I create a new MEBN, add some MFrags and nodes, and save with UnBbayes, I can reopen with "UnBbayes" option and see the MTheory and MFrags visually (green, yellow and grey nodes).
    However if I follow the same steps; create a new MEBN, add some Mfrags and nodes and save it with "UnBBayes with PROWL2.0" option, and then reopen with "UnBbayes with PR-OWL2.0" then I cannot visually see the MTheory and MFrags. When I try to find them in ontology in owl2entities tab, I can find the Frags & variables I created earlier.

    I have followed steps given by Shau in https://sourceforge.net/p/unbbayes/discussion/1116682/thread/6839647a/#db27.
    I also read the contents of .ubf files in both cases with a text editor and found that file saved with "UnBBayes with Pr-OWL 2.0" does not store the rendering information for nodes. Any ideas what I may be doing wrong?

    TIA

    Suvarna

     
  • Hi Suvarna,

    I am not sure I was able to follow your problem. Could you send the files you saved? Also, could you explain which MFrags and nodes you created step by step so that I can try to replicate them here?

    Best,
    Rommel

     
  • Suvarna
    Suvarna
    2013-05-25

    Thanks for you reply.

    PFA files. I have first created a simple HelloWorld MEBN. Then while saving the file with .ubf extension, UnBBayes asks me which IO component to use. If I choose "UnBBayes File" and save the file, then if I close-and-reopen the same file, I can see MTheory, MFrags and nodes. But if I choose "UnBBayes File with PROWL 2.0" and save the file, then if I close-and-reopen the same file, I can not see MTheory, MFrags and nodes.

    I also noticed that I am getting a stack trace while reopening the file saved with "UnBBayes with PROWL 2.0" option. It may be the cause of the problem. I am also attaching the stack trace for you reference.

    Thanks & Best Regards
    Suvarna

     
    Attachments
    • Suvarna
      Suvarna
      2013-05-26

      Hi Rommel,

      The problem is gone after I re-installed the PR-OWL2.0 plugin afresh. I still don't know what has caused it. But I guess I made a mistake earlier while installing. I got confused with the instruction in https://sourceforge.net/p/unbbayes/discussion/156015/thread/cb2e0887/
      that tells to extract the two plugin zips "inside UnBBayes Core plugin folder". Since I was not sure whether it meant unbbayes-4.11.4\plugins or unbbayes-4.11.4\plugins\unbbayes.core, so I extracted in both. I think we need it only in the plugins folder.

      I hope this helps someone some day :)

      Thanks
      Suvarna

       
      Last edit: Suvarna 2013-05-26
  • Glad to hear you again were able to solve the problem for yourself! :-)

    I will try to make that post more clear!

    Cheers,
    Rommel

     
  • GiannisCh
    GiannisCh
    2013-10-14

    Hi Rommel,

    I am currently facing the same problem with that described by Suvarna.
    However, I cannot solve this, even if I install the latest plugins.
    Can you make more clear the correct procedure to avoid this problem?

    Thank you very much,

    Best regards

    Giannis

     
  • Hi Giannis,

    Have you installed the plugins inside the unbbayes-4.11.4\plugins folder?

    Cheers,
    Rommel

     
  • GiannisCh
    GiannisCh
    2013-10-14

    Hi Rommel,

    Yes, I have installed them. The plugins in the 'plugins' folder are the following:

    unbbayes.core
    unbbayes.gui.mebn.ontology.protege-1.1.1
    unbbayes.io.DneIO
    unbbayes.io.mebn.UbfIO
    unbbayes.io.mebn.UbfIO2
    unbbayes.io.NetIO
    unbbayes.io.XMLBIFIO
    unbbayes.prs.mebn-1.13.1
    unbbayes.prs.msbn-1.1.0

    Is that OK?

    Thanks for your immediate reply

    Giannis

     
  • unbbayes.prs.mebn-1.13.1 or unbbayes.prs.mebn-1.13.10?

     
  • And, which core version do you have? Check the plugin.xml file inside the unbbayes.core folder.

     
  • GiannisCh
    GiannisCh
    2013-10-14

    Yes, it is 1.13.10 (and not 1.13.1 as I mistakenly wrote)
    The unbbayes core version is 4.11.4

    Giannis

     
  • I do not see any problem then. What is happening? Can you describe the problem in detail?

     
  • GiannisCh
    GiannisCh
    2013-10-14

    The problem seems exactly as that described in the firt post of this thread.
    In more details, I follow the procedure proposed in the tutorial "PR-OWL_2_Tutorial_Patient_Diagnosis.pdf". When I create a very basic MTheory, with the three empty MFrags (PatientMF,RegionMF, RegionVisitedMF), and then save it in a .ubf file with the option "Unbbayes file with PR-OWL2.0", and load it again with the very same option, the MFrages disappear.
    So, I though this thread could help me. I tried re-installing the plugins but the problem remains.

    I hope my description of the problem is clear.

    Giannis

     
  • Stephan
    Stephan
    2014-03-06

    Hey,
    I have the same problem with this Tutorial. I can save a File, but I won't open if I'm trying. I followed the steps in the Tutorial to save/load the file, but it don't work. My error-messages are different.

    First I made an Ontology with Protege like explained in the Tutorial. Then I opened it with UnBBayes (which works). Next step I made, was to save, which also worked. The problem is to open the file. I got 3 different error-messages:

    1) When I want to open the .owl file: Error to load file (and then the path of the file)
    2) When I'm trying to open the .ubf file : Error to load file (and then the path of the file and the message that the .owl File contains invalid pr-owl format)
    3) The other Error message I had, was that some Axioms are wrong, but I can't generate that error any more. Maybe I made an error during the save/load process.

    So, I really don't know what I'm doing wrong. I have the UnBBayes Version 4.17.8 and all Plugins in the actuall version. I hope someone can/might help me with this problem. I would like to use UnBBayes in my Bachelor-Thesis.

    Thanks and regards

    Stephan

     
    Last edit: Stephan 2014-03-07
    • Hi Stephan,

      Can you send me the files? Have you saved the files using the new version before loading them?

      Cheers,
      Rommel

       
  • Stephan
    Stephan
    2014-03-07

    Hi Rommel,

    here are the files:

    The PatientDiagnosis.owl is the file i made with Protege and which i can load without problems in UnBBayes.

    The PatientDiagnosis_i.owl is the finished Tutorial.

    And the PatientDiagnosis_i.ubf is the ubf file for this project.

    I've only worked with the latest version of UnBBayes 4.17.8.

    Thank you very much for your time and help,
    Stephan

     
    Last edit: Stephan 2014-03-07
  • paulo elias
    paulo elias
    2014-03-29

    Hi!

    I had this same issue in my mac... I couldn't properly read the ubf files I saved. The MFrags I created were simply not there... After opening the ubf file and creating a new MFrag, UnbBayes names it 'MFrag4' (if I had saved the ubf with 3 MFrags in it). So I presume that the MFrags were in the 'model' but not in the 'view'.

    After spending some time installing UnBBayes and the PR-OWL2 plugins in a Windows and in a Linux machine, and trying to fix this problem, back in the mac I discovered what was causing the problem!

    I had 2 versions of the same plugin in the plugins folder:
    unbbayes.gui.mebn.ontology.protege-1.1.3
    unbbayes.gui.mebn.ontology.protege-1.1.1

    When I deleted the oldest one, the problem has finally been solved. I can now save and read the ubf file with the MTheory and MFrags correctly appearing.

    One thing I noted after deleting the version 1.1.1 plugin was that the popup menu that asks how to open a ubf file stopped showing the option 'open as PR-OWL 1 with OWL2' (or something similar, hehe).

    Best,

    Paulo

     
  • Hi Stephan,

    Were you able to make it work with the tip Paulo gave above?

    Cheers,
    Rommel

     
  • Pat
    Pat
    2014-06-26

    Hello,
    I'm new to this field. I'm having similar problems following the UnBayes PR-OWL 2.0 Tutorial. I have acquired the latest Protege SW and have the ontologies PatientDiagnosis.owl and PatientDiagnosis_i.owl. However, when I try to open the ontology per Haberlin's tutorial, I receive this error message - "Error to load net file: There was an error reading the file ...". I have attach screenshots of the cmd window and my plugin file structures

     
    Attachments
    • cardialfly
      cardialfly
      2014-06-27

      Hi.

      From your stack trace (i.e. the messages in your console), it looks like UnBBayes was not able to load the PR-OWL 2 plug-in.

      Usually, when you open owl files in UnBBayes (assuming the plug-ins of PR-OWL 2 were correctly set up), a dialog asking you to choose whether to open it as a "UnBBayes file" or "UnBBayes file with PR-OWL 2" should pop-up. You need to choose "UnBBayes file with PR-OWL 2" in order to trigger PR-OWL 2 features. If a dialog did not even pop-up, then PR-OWL 2 plug-in was not properly set up.

      I can imagine 5 situations that this can happen:

      1 - you are not using compatible versions of the plug-ins and core. This is not likely to be your case, since from your attachments I see you've downloaded the newest versions of core and plug-ins.

      By the way, a potential solution to this is to re-download the newest core (UnBBayes) and plug-ins (unbbayes.prs.mebn and PR-OWL2).

      2 - The plug-ins were not placed in the correct folder. This can be your case, since I can deduct from your screen captures that you've placed the PR-OWL 2 plug-in (composed with 2 folders) in a folder called "unbbayes.gui.mebn.ontology.protege-1.1.3-ALPHA".
      Perhaps you used "extract to unbbayes.gui.mebn.ontology.protege-1.1.3-ALPHA" or "extract to ./" instead of "extract to here" when you executed your zip extractor, so it automatically created an additional folder level.

      Solution: move the content of "unbbayes.gui.mebn.ontology.protege-1.1.3-ALPHA" out. Your "plugin" folder should contain at least the following folders in order to make PR-OWL 2 to work:

      unbbayes.prs.mebn-1.13.11
      unbbayes.core
      unbbayes.gui.mebn.ontology.protege-1.1.3
      unbbayes.io.mebn.UbfIO
      unbbayes.io.mebn.UbfIO2
      unbbayes.io.NetIO

      3 - You've placed/installed UnBBayes in a protected folder, with no full read/write permissions.

      Solution: grant read/write permissions of UnBBayes' folder to your user profile. In Windows, this can be done by right-clicking the folder, and then go to property > security.
      Another simple way is to install UnBBayes in a folder which is not protected by default. For example, create a new folder "C:\UnBBayes" and install everything there.

      4 - When protege is loaded from UnBBayes, it may ask you to update protege and/or its components (and to automatically download updates if you choose to update). Please, do not update them, because it will break compatibility between protege and UnBBayes.

      Solution: re-download (re-install) UnBBayes and plug-ins if you accidentally web-updated protege from UnBBayes.

      5 - The Protege installed in your computer and the one loaded by UnBBayes are not the same instances, but they share the same registry. Changes in the registry made from your protege (the one you installed) may influence/break the protege loaded from UnBBayes, so you may need to reset preferences.

      Solution: see http://protegewiki.stanford.edu/wiki/ClearingP4Preferences

      Hope this helps.
      Best regards.

       
  • Pat
    Pat
    2014-08-12

    Thanks for the above help. Item 2 fixed the problem. Sorry for the delay. I was pulled off onto another project and now back using UnBBayes and MEBN. Like Paulo, when I return to a saved ubf file I do not see the MFrags either. I do not have the earlier protege plugin. Thanks for any tips

    Pat