DOT Error even after path to Graphviz correctly mapped (Protege 4.3)

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DOT Error even after path to Graphviz correctly mapped (Protege 4.3)

kettinger
Hello,

I am trying to visualize my ontology in Protégé 4.3 using Graphviz. I installed Graphviz, and set the path on the OWLViz tab of preferences to point at the Graphviz application on my machine (/Applications/Graphviz.app) - which I located using the “Browse” option. 

However, even after doing this I am getting the message anytime I navigate to the OWLViz tab: “A DOT error has occurred. This is probably because OWLViz could not find the DOT application. OWLViz requires that Graphviz is installed and the path to the DOT application is set properly (in options).”

On the online postings I have read on this topic, this message generally comes up when the path to Graphviz hasn’t been correctly specified, but I can’t figure out what I might be doing wrong, since I thought I had done that. Some other oddities that may help provide clues:

• When I go back into the OWLViz tab of Preferences, the Dot application path always changes to: /Applications/Graphviz.app/Contents/MacOS/dot (instead of the shorter version indicated above, which is what populates the field when I first use the Browse button to locate my Graphviz application).

• The visualizer seems to almost be working – I can see the edges of graphical circles with text in the center corresponding to my classes (which change when I select a different class). But these circles are right at the top left corner of the box displaying the model (so I can only see the edges of them) and are all stacked on top of one another. When I try to click them, or to select another class, the same DOT error message as above pops up repeatedly.

I am using Graphviz 2.36 (for Mountain Lion). I am running Mac OS X 10.9.2 (Mavericks – but I read documentation suggesting that the 2.36 version of Graphviz has been used successfully with Mavericks — so thinking this isn’t the issue, although it is possible). My machine is a 15-inch MacBook Pro from 2009 with a 2.66 GHz Intel Core 2 Duo processor.

Any advice would be greatly appreciated! Thanks so much.
Kaki

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Re: DOT Error even after path to Graphviz correctly mapped (Protege 4.3)

Jennifer Vendetti
Administrator
Hello Kaki,

You need to configure the preferences to point to the “dot” executable that is part of the Graphviz installation.  To determine the path to dot on your Mac, launch the Terminal application and type “which dot” at the prompt, e.g.:


In the Protege Preferences dialog, enter this path. e.g.:




I’m also on Mavericks and using v2.36 of Graphviz, and these steps work for me.

Jennifer



On Jul 16, 2014, at 1:39 PM, Ettinger, Kaki S. <[hidden email]> wrote:

Hello,

I am trying to visualize my ontology in Protégé 4.3 using Graphviz. I installed Graphviz, and set the path on the OWLViz tab of preferences to point at the Graphviz application on my machine (/Applications/Graphviz.app) - which I located using the “Browse” option. 

However, even after doing this I am getting the message anytime I navigate to the OWLViz tab: “A DOT error has occurred. This is probably because OWLViz could not find the DOT application. OWLViz requires that Graphviz is installed and the path to the DOT application is set properly (in options).”

On the online postings I have read on this topic, this message generally comes up when the path to Graphviz hasn’t been correctly specified, but I can’t figure out what I might be doing wrong, since I thought I had done that. Some other oddities that may help provide clues:

• When I go back into the OWLViz tab of Preferences, the Dot application path always changes to: /Applications/Graphviz.app/Contents/MacOS/dot (instead of the shorter version indicated above, which is what populates the field when I first use the Browse button to locate my Graphviz application).

• The visualizer seems to almost be working – I can see the edges of graphical circles with text in the center corresponding to my classes (which change when I select a different class). But these circles are right at the top left corner of the box displaying the model (so I can only see the edges of them) and are all stacked on top of one another. When I try to click them, or to select another class, the same DOT error message as above pops up repeatedly.

I am using Graphviz 2.36 (for Mountain Lion). I am running Mac OS X 10.9.2 (Mavericks – but I read documentation suggesting that the 2.36 version of Graphviz has been used successfully with Mavericks — so thinking this isn’t the issue, although it is possible). My machine is a 15-inch MacBook Pro from 2009 with a 2.66 GHz Intel Core 2 Duo processor.

Any advice would be greatly appreciated! Thanks so much.
Kaki
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https://mailman.stanford.edu/mailman/listinfo/protege-user


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https://mailman.stanford.edu/mailman/listinfo/protege-user

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