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Graphviz

Julian Vincent-2
I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
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Re: Graphviz

Rafael Gonçalves
Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

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


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Re: Graphviz

Julian Vincent-3
Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

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

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Re: Graphviz

Rafael Gonçalves
If Graphviz is correctly installed then Dot should be in your system. You can verify that by opening a Terminal window and typing:

dot -? (this should bring up dot's usage information)

If the ‘dot’ command is not found then Graphviz isn’t installed properly. Did you customize the Graphviz installation in any way? By default Dot will be located at /usr/local/bin/dot. Did you try just putting this path into the Protege-OWLViz preferences as the Dot application path? If that particular path doesn’t work, then open Terminal and run:

sudo find / -name dot

If dot is installed, this will tell you where. Once the correct path for the Dot application is entered, the OWLViz plugin will work after restarting Protege. 

Rafael

On Dec 16, 2014, at 12:49, Julian Vincent <[hidden email]> wrote:

Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Graphviz

Julian Vincent-3
I didn’t do anything funny installing Graphviz - I know enough to leave well alone!  There’s nothing at usr/local/bin/dot, and I get nothing if I use Dot in the search.  On a Mac running OS X 9 the path has Graphviz-2.38 as the third item, which is what I was expecting.  I pick up a few other dot files using your sudo command, but nothing relevant.  My suspicion is that the Mac OS - the latest one (Yosemite) - isn’t loading Graphviz properly (other people have found problems with Yosemite, and the first patch came out within a few weeks of launch!).

Who do I complain to?  Graphviz for not keeping up to date, or Apple for trying to rig the market??!

Thanks for your help.

Julian


On 16 Dec 2014, at 21:15, Rafael Goncalves <[hidden email]> wrote:

If Graphviz is correctly installed then Dot should be in your system. You can verify that by opening a Terminal window and typing:

dot -? (this should bring up dot's usage information)

If the ‘dot’ command is not found then Graphviz isn’t installed properly. Did you customize the Graphviz installation in any way? By default Dot will be located at /usr/local/bin/dot. Did you try just putting this path into the Protege-OWLViz preferences as the Dot application path? If that particular path doesn’t work, then open Terminal and run:

sudo find / -name dot

If dot is installed, this will tell you where. Once the correct path for the Dot application is entered, the OWLViz plugin will work after restarting Protege. 

Rafael

On Dec 16, 2014, at 12:49, Julian Vincent <[hidden email]> wrote:

Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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

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Re: Graphviz

Rafael Gonçalves
Strange. It seems Graphviz isn’t fully installed.

On Dec 16, 2014, at 13:37, Julian Vincent <[hidden email]> wrote:

I didn’t do anything funny installing Graphviz - I know enough to leave well alone!  There’s nothing at usr/local/bin/dot, and I get nothing if I use Dot in the search.  

There must be some output from doing dot -? in the Terminal: Either you’ll get the dot application usage or a “command not found” type error. I'm assuming the latter (?)

On a Mac running OS X 9 the path has Graphviz-2.38 as the third item, which is what I was expecting.  I pick up a few other dot files using your sudo command, but nothing relevant.  My suspicion is that the Mac OS - the latest one (Yosemite) - isn’t loading Graphviz properly (other people have found problems with Yosemite, and the first patch came out within a few weeks of launch!).

Which path? The path variable? Or the Dot path? Exactly what OS X version are you using? I’m running OS X 10.10.1, and Graphviz 2.36 installed fine; as expected it put the dot application in the right place (/usr/local/bin/).

Who do I complain to?  Graphviz for not keeping up to date, or Apple for trying to rig the market??!

Well Graphviz has no mention of Yosemite anywhere, or a Yosemite-compatible distribution. The mountain lion release (2.36) works though. I'd recommend (re-)installing Graphviz 2.36, and during the installation in the “Installation Type” click “Customize” and make sure that “Command line tools and libraries” is selected.

Rafael

On 16 Dec 2014, at 21:15, Rafael Goncalves <[hidden email]> wrote:

If Graphviz is correctly installed then Dot should be in your system. You can verify that by opening a Terminal window and typing:

dot -? (this should bring up dot's usage information)

If the ‘dot’ command is not found then Graphviz isn’t installed properly. Did you customize the Graphviz installation in any way? By default Dot will be located at /usr/local/bin/dot. Did you try just putting this path into the Protege-OWLViz preferences as the Dot application path? If that particular path doesn’t work, then open Terminal and run:

sudo find / -name dot

If dot is installed, this will tell you where. Once the correct path for the Dot application is entered, the OWLViz plugin will work after restarting Protege. 

Rafael

On Dec 16, 2014, at 12:49, Julian Vincent <[hidden email]> wrote:

Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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

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Re: Graphviz

Julian Vincent-2
Stranger still
It now works, although the path defined in Preferences doesn’t mention Graphviz (which it always has in previous incarnations).
I deleted Graphviz from the Applications folder, then reinstalled from the package I had downloaded yesterday.  I checked for ‘Installation Type’ and both types were already ticked, so no change needed there.  And when I went into Protege, OWLViz was up-and-running.  Large as life and twice as natural.  What changed??  I’m just grateful.

Many thanks
Julian


On 16 Dec 2014, at 23:32, Rafael Goncalves <[hidden email]> wrote:

Strange. It seems Graphviz isn’t fully installed.

On Dec 16, 2014, at 13:37, Julian Vincent <[hidden email]> wrote:

I didn’t do anything funny installing Graphviz - I know enough to leave well alone!  There’s nothing at usr/local/bin/dot, and I get nothing if I use Dot in the search.  

There must be some output from doing dot -? in the Terminal: Either you’ll get the dot application usage or a “command not found” type error. I'm assuming the latter (?)

On a Mac running OS X 9 the path has Graphviz-2.38 as the third item, which is what I was expecting.  I pick up a few other dot files using your sudo command, but nothing relevant.  My suspicion is that the Mac OS - the latest one (Yosemite) - isn’t loading Graphviz properly (other people have found problems with Yosemite, and the first patch came out within a few weeks of launch!).

Which path? The path variable? Or the Dot path? Exactly what OS X version are you using? I’m running OS X 10.10.1, and Graphviz 2.36 installed fine; as expected it put the dot application in the right place (/usr/local/bin/).

Who do I complain to?  Graphviz for not keeping up to date, or Apple for trying to rig the market??!

Well Graphviz has no mention of Yosemite anywhere, or a Yosemite-compatible distribution. The mountain lion release (2.36) works though. I'd recommend (re-)installing Graphviz 2.36, and during the installation in the “Installation Type” click “Customize” and make sure that “Command line tools and libraries” is selected.

Rafael

On 16 Dec 2014, at 21:15, Rafael Goncalves <[hidden email]> wrote:

If Graphviz is correctly installed then Dot should be in your system. You can verify that by opening a Terminal window and typing:

dot -? (this should bring up dot's usage information)

If the ‘dot’ command is not found then Graphviz isn’t installed properly. Did you customize the Graphviz installation in any way? By default Dot will be located at /usr/local/bin/dot. Did you try just putting this path into the Protege-OWLViz preferences as the Dot application path? If that particular path doesn’t work, then open Terminal and run:

sudo find / -name dot

If dot is installed, this will tell you where. Once the correct path for the Dot application is entered, the OWLViz plugin will work after restarting Protege. 

Rafael

On Dec 16, 2014, at 12:49, Julian Vincent <[hidden email]> wrote:

Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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

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Re: Graphviz

Rafael Gonçalves
Odd that previous paths were pointing specifically at Graphviz; that should only happen if the dot application is within Graphviz's folder. 

Anyway, it seems Graphviz is now properly installed, Protege knows where dot is, and consequently OWLViz is working, problem solved.

Cheers,
Rafael

On Dec 17, 2014, at 02:28, Julian Vincent <[hidden email]> wrote:

Stranger still
It now works, although the path defined in Preferences doesn’t mention Graphviz (which it always has in previous incarnations).
I deleted Graphviz from the Applications folder, then reinstalled from the package I had downloaded yesterday.  I checked for ‘Installation Type’ and both types were already ticked, so no change needed there.  And when I went into Protege, OWLViz was up-and-running.  Large as life and twice as natural.  What changed??  I’m just grateful.

Many thanks
Julian


On 16 Dec 2014, at 23:32, Rafael Goncalves <[hidden email]> wrote:

Strange. It seems Graphviz isn’t fully installed.

On Dec 16, 2014, at 13:37, Julian Vincent <[hidden email]> wrote:

I didn’t do anything funny installing Graphviz - I know enough to leave well alone!  There’s nothing at usr/local/bin/dot, and I get nothing if I use Dot in the search.  

There must be some output from doing dot -? in the Terminal: Either you’ll get the dot application usage or a “command not found” type error. I'm assuming the latter (?)

On a Mac running OS X 9 the path has Graphviz-2.38 as the third item, which is what I was expecting.  I pick up a few other dot files using your sudo command, but nothing relevant.  My suspicion is that the Mac OS - the latest one (Yosemite) - isn’t loading Graphviz properly (other people have found problems with Yosemite, and the first patch came out within a few weeks of launch!).

Which path? The path variable? Or the Dot path? Exactly what OS X version are you using? I’m running OS X 10.10.1, and Graphviz 2.36 installed fine; as expected it put the dot application in the right place (/usr/local/bin/).

Who do I complain to?  Graphviz for not keeping up to date, or Apple for trying to rig the market??!

Well Graphviz has no mention of Yosemite anywhere, or a Yosemite-compatible distribution. The mountain lion release (2.36) works though. I'd recommend (re-)installing Graphviz 2.36, and during the installation in the “Installation Type” click “Customize” and make sure that “Command line tools and libraries” is selected.

Rafael

On 16 Dec 2014, at 21:15, Rafael Goncalves <[hidden email]> wrote:

If Graphviz is correctly installed then Dot should be in your system. You can verify that by opening a Terminal window and typing:

dot -? (this should bring up dot's usage information)

If the ‘dot’ command is not found then Graphviz isn’t installed properly. Did you customize the Graphviz installation in any way? By default Dot will be located at /usr/local/bin/dot. Did you try just putting this path into the Protege-OWLViz preferences as the Dot application path? If that particular path doesn’t work, then open Terminal and run:

sudo find / -name dot

If dot is installed, this will tell you where. Once the correct path for the Dot application is entered, the OWLViz plugin will work after restarting Protege. 

Rafael

On Dec 16, 2014, at 12:49, Julian Vincent <[hidden email]> wrote:

Yes, thanks.  I got all that before.  I’ve tried Graphviz-2.36 and -2.38, but I can’t find it anywhere other than in the Applications.  I’ve opened up the hidden files and followed through from usr/local/ . . . and get a folder for graphviz, but no dot files or anything else looking promising.  So it looks as if it isn’t installing itself.  Ideas?

Julian


On 16 Dec 2014, at 17:41, Rafael Goncalves <[hidden email]> wrote:

Hi Julian,

Do you mean the OWLViz plugin? OWLViz doesn’t work out of the box because it relies on Graphviz, which should be installed separately. Then the Dot application path needs to be inserted in the Protege preferences (under the OWLViz tab). By default the Graphviz OS X installer will place the Dot application in /usr/local/bin/dot, so give that a try. For more information see: http://protegewiki.stanford.edu/wiki/OWLViz

Hope this helps.

Rafael

On Dec 16, 2014, at 02:50, Julian Vincent <[hidden email]> wrote:

I can’t sort out how to access Graphviz from P5 using the latest MacOS Yosemite.  Ideas?
B.t.w. this is the ‘usual’ problem when I’m starting Protege in a new computer or OS.  Is there an easier or (for the non-programmer) more obvious way of getting Graphviz to work?  Why can’t it just slot in like the other plugins do?

Julian Vincent
_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
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