OWLVIZ Display problems

[sidkgp]

OwlViz is displaying the entire hierarchy at (0,0). Not sure how to move this to center.

[matthewhorridge]

Do you have GraphViz installed on your system? You need this, and you need to set the path to the "DOT" application in the OWLViz preferences. This is set on the OWLViz tab on the preference dialog. On my system the path is "/usr/local/bin/dot".

[iisai1821]

I had the same problem; I thought I had GraphViz installed already and was wrong. Downloading the zip file and pointing the preferences setting to dot.exe fixed it. Thanks!

[macedoj]

For Ubuntu users getting this error nowadays (2020):

1. Run:

$ sudo apt install graphviz

2. Then restart Protégé;
3. Done!

Source: https://graphviz.org/download/

[mgraauw]

Had the same problem with Windows, could not get Owlviz to work with Graphviz 2.44.1 (current stable), installed from Anaconda (Graphviz 2.38), that did work.

[drdavide]

Same problem, thank you @mgraauw, anaconda pkgs works in Windows 10

[MartinKoelbl]

I had the same trouble in win10. Adjust inside of Protege in menu File/Preferences/OWLViz the path to dot.exe
I had to name the path and the program name C:...\Graphviz\bin\dot.exe

[hpl002]

Find the realpath to the dotfile.

For those installing via homebrew on osx:

For some reason the dotfile was not symlinked into /usr/local/bin

Test by trying to get the realpath via which graphviz. If found then just use this, if not then get the realpath yourself or create the symbolic link.

For a quick hack i ended up with: /usr/local/Cellar/graphviz/2.46.1/bin/dot

[HjoshM]

I have the real path to the dot app, but still cannot see the graph. What am I missing?

[MarkOcean]

@HjoshM
Install it https://graphviz.org/download/
Restart Protege.

Path: C:\Program Files\Graphviz\bin\dot.exe

[ikramlalmi]

I tried these commands to help me locate the DOT file path on my mac. It was not: "/usr/local/bin/dot" on my system.

dot -V

dot - graphviz version 2.49.2 (20211016.1639)

which dot

/opt/homebrew/bin/dot

I had installed Graphviz, but I was still running into trouble finding the right path. I am using Protege, and I had to modify the path for OwlViz since it was displaying the entire hierarchy at (0,0). I copied the path that I got by running the which dot command to the OWLViz tab on the preference dialog, and restarted protege and it worked perfectly! Good luck!

[SergeMIT]

Probably User rights linked issue.
I has the same issue on Windows due to GraphViz being installed under C:\Program Files (x86)\Graphviz
=> For windows, the xxx\Graphviz\bin\dot.exe must be placed under a folder with "normal rights access" and the file no be "read only" => I moved the dot.exe file under C:\Users\Serge\OneDrive\Documents\XXXX, adapted protege preferences (File/Preferences/OwlViz => Path to dot file: C:\Users\Serge\OneDrive\Documents\XXXX\dot.exe
Then after a relaunch, the issue was solved. Good luck!

[Sophal24]

I tried these commands to help me locate the DOT file path on my mac. It was not: "/usr/local/bin/dot" on my system.

dot -V

dot - graphviz version 2.49.2 (20211016.1639)

which dot

/opt/homebrew/bin/dot

I had installed Graphviz, but I was still running into trouble finding the right path. I am using Protege, and I had to modify the path for OwlViz since it was displaying the entire hierarchy at (0,0). I copied the path that I got by running the which dot command to the OWLViz tab on the preference dialog, and restarted protege and it worked perfectly! Good luck!

(mac m1) This works for me. Check path of dot and change it in Protégé OWLViz, Path to DOT.

[Misbah-khan786]

@HjoshM Install it https://graphviz.org/download/ Restart Protege.

Path: C:\Program Files\Graphviz\bin\dot.exe

I have installed the Graphicviz installed it in the same directory and set the same directory in the file--> owlviz /path to dot (C:\Program Files\Graphviz\bin\dot.exe) but the issue is still there

[MarkOcean]

I have installed the Graphicviz installed it in the same directory and set the same directory in the file--> owlviz /path to dot (C:\Program Files\Graphviz\bin\dot.exe) but the issue is still there

I would try restarting the computer and/or reinstalling Protege itself. I don't remember if I did it myself, but I think so. I hope it helps you.

[garciadiazjaime]

In os x I used brew

brew install graphviz

and then adjust the dot path:

 which dot
/opt/homebrew/bin/dot

[taxles]

Thank you @garciadiazjaime for the instructions.
They worked for me on macOS 15.0.1 (Sequoia).

[rbenami-cell]

I running into the problem that I cannot move any objects on the OWLViz and all the association indicate is-a and not the specified association. I'm running on Macpro recent OS

[NathanHughes]

I am also having this problem, I was pointed to the dot.exe file and it wasn't working, but I have tried

Reinstalling to C:\Graphviz
Installing via Anaconda
Rebooting
Reinstalling

The only error that consistently comes up is

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.jgoodies.common.internal.RenderingUtils (file:/C:/Protege-5.6.4/bundles/protege-editor-core.jar) to method sun.swing.SwingUtilities2.drawStringUnderlineCharAt(javax.swing.JComponent,java.awt.Graphics,java.lang.String,int,int,int)
WARNING: Please consider reporting this to the maintainers of com.jgoodies.common.internal.RenderingUtils
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

But I'm not sure if it's related

[NathanHughes]

Additional Steps I have now tried

Installing 32 bit version
Running Protege as admin

The app errors if I point the preferences to the wrong place but does nothing if it is pointed correctly to dot.exe, but the result is the same; all the circles at 0,0

I am using the latest stable builds of protege and graphviz

[AndreaCostagliola]

Same problem. I downloaded Protégé Desktop(https://protege.stanford.edu/software.php#desktop-protege) and Graphviz Installer (https://graphviz.org/download/#windows) for Windows 10. Then I add the path to dot.exe from File->Preferences and find the right path which in my case is C:\Program Files\Graphviz\bin\dot.exe . However, this did not work and I have the same problem. Any suggestion?

[kegoosse]

I had the same issue. Downloaded everything and set the path correctly... Didn't work. Tried it out with an older version of GraphViz: 7.0.2, then it worked

[AndreaCostagliola]

@kegoosse It worked. Thank you very much

[NathanHughes]

@kegoosse this also worked for me thanks

[sophiedxf]

Had the same problem with Windows, could not get Owlviz to work with Graphviz 2.44.1 (current stable), installed from Anaconda (Graphviz 2.38), that did work.

Thank you so much. This worked for me!

[HoWilgh]

had the same problem with protege installed via flatpak on Ubuntu 22.04.
Protege did not rise any error or warning but all classes in my ontology stick in OWLViz a position 0/0. Graphviz was installed locally with apt but obviously could not be accessed.
I tried to use Flatseal to overcome this by explicitly giving access to the /usr/local/bin folder and others, without access.
Finally I downloaded the current version from https://github.com/protegeproject/protege-distribution/releases Protege-5.6.5-linux.tar.gz unpacked it, ran 'protege' and everything works as it should.

[Foadsf]

yeah, I had to also install an older version of Graphviz from here. I tried version 7.0.2 and it worked. It would be great if we could test other versions and see which one(s) work. And then do some diffing to see what has changed after that.

P.S. the OntoGraf plugin seems OK. I wonder why not using that one to begin with?

[fatinnabilah97]

I use Graphviz 10.0.1 and it works. I also leave the Graphviz file properties to read only. Not sure if I will face some challenges later since its not an up to date version.

[brittd]

I verified that Graphviz 10.0.1 also installed and worked on my system. Then I upgraded to Graphviz 12.0.0 and it also worked. Finally, I upgraded to Graphviz 12.2.0 and it has the "display bug". I'm returning to Graphviz 12.0.0. Perhaps others can further diagnose the issue.