Menu

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

Suvarna
2013-05-25
2021-07-15
1 2 > >> (Page 1 of 2)
  • 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

     
  • Rommel Novaes Carvalho

    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

     
    • 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
  • Rommel Novaes Carvalho

    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

     
  • Rommel Novaes Carvalho

    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

     
  • Rommel Novaes Carvalho

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

     
  • Rommel Novaes Carvalho

    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

     
  • Rommel Novaes Carvalho

    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
    • Rommel Novaes Carvalho

      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

     
  • Rommel Novaes Carvalho

    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

     
    • Shou Matsumoto

      Shou Matsumoto - 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

     
  • Stefan Lüders

    Stefan Lüders - 2019-01-24

    For future readers: When trying cardialfly's solution above, pay attention to your java version. It seems PR-OWL 2 only works on Java 8, even if it's one of the newer Plugins. I could get PR-OWL 2 release 1.2.7 to work with UnBBayes-4.22 and MEBN Plugin version 1.18.14 using Java 8.

     

    Last edit: Stefan Lüders 2019-01-24
  • Qian Wang

    Qian Wang - 2021-05-24

    Hello,
    I'm new to this field. I'm having some problems about the plug-ins of PR-OWL 2.
    After I put the plug-ins in the correct folder(because when I open owl files in UnBBayes,a dialog asking you to choose whether to open it as a "UnBBayes file" or "UnBBayes file with PR-OWL 2" will pop-up), I want to see the example VehicleIdentification of the plug-ins of PR-OWL 2 in the folder.
    One of the problem is to open the file. When I chose to open it as "UnBBayes file with PR-OWL 2", I got 2 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)

    And if I open the example VehicleIdentification of the folder of the plug-ins of MEBN as "UnBBayes file with PR-OWL 2", I succeeded. But there isn't Property2Node tab and OWL2Entities tab on the right of MTheory tab.
    I have the UnBBayes Version 4.22.18 and the only unbbayes.gui.mebn.ontology.protege-1.2.7.

     
    • Shou Matsumoto

      Shou Matsumoto - 2021-05-24

      One of the problem is to open the file. When I chose to open it as "UnBBayes file with PR-OWL 2", I got 2 different error-messages:

      I suspect your instance of UnBBayes was unable to load the PR-OWL 2 schema from the internet. This may happen in some network environments due to TLS/SSL encryption. Please try the following procedure to load the PR-OWL 2 schema from a local file instead:

      1. You may need to manually delete the catalog-v001.xml file (automatically created in the same folder where the ontologies are stored) to clear any cache.
      2. Temporarily disconnect your computer from the internet.
      3. Follow the normal process to open an ontology in UnBBayes.
      4. Eventually, it should show a pop-up with a message like "The system couldn't locate the ontology. Would you like to attempt to resolve the missing import?"
      5. Choose "Yes" and then choose the file called "pr-owl2.owl" located at "UNBBAYES_DIRECTORY/plugins/unbbayes.gui.mebn.ontology.protege-1.2.7/resources/pr-owl/pr-owl2.owl".

      Also, please run UnBBayes in debug-mode and in console (command line) so that we can debug your console output. Please take a look on this wiki page for instructions on how to run UnBBayes (debug-mode) in console and how to save the console outputs to a log file. You can then send a message to this forum/thread with the resulting log file attached.

      And if I open the example VehicleIdentification of the folder of the plug-ins of MEBN as "UnBBayes file with PR-OWL 2", I succeeded. But there isn't Property2Node tab and OWL2Entities tab on the right of MTheory tab.

      I'm afraid the VehicleIdentification ontology in the MEBN plug-in folder is written in PR-OWL version 1 (in contrast to the VehicleIdentification ontology in the PR-OWL 2 folder, which is written in PR-OWL version 2).

      Ontologies in PR-OWL 1 are extensions to the OWL version 1 and they do not have the appropriate meta-information to reuse the concepts of OWL2 direct semantics (i.e., the information in the OWL2Entities tab won't be applicable) nor to connect OWL properties to MEBN nodes (i.e., there is nothing to show in the Property2Node tab). That's why these tabs are not enabled when you open an ontology written in PR-OWL 1.

      Best.

       

      Last edit: Shou Matsumoto 2021-05-24
      • Qian Wang

        Qian Wang - 2021-05-26

        I first followed the five steps you gave me. In the fourth step, there is no pop-up with a message like "The system couldn't locate the ontology. Would you like to attempt to resolve the missing import?" as you mentioned, but the same pop-up as before. Then I followed the tutorial and started UnBBayes in debug mode. Here is my log.txt, and the pr-owl2.owl file path is null. How should I set it?
        Also, my Unbbayes home page only has five menu options (" File ", "View", "Window", "Plugins", and "Help"). Compared to the tutorial video, there seem to be two menu options missing. Is this normal?

         
1 2 > >> (Page 1 of 2)

Log in to post a comment.