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HELP cannot open .gephi file

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HELP cannot open .gephi file

Postby ticoalu » 18 Jul 2013 18:55

When I open my project file today I was faced with error message"
"The project file couldn't be opened. Please check the file has .gephi extension.
IllegamArgumenetException - [255,255,25] "

I try to open the file from within gephi (click open file > open > select_file ) but still get the same error message.
I try to open the same file in gephi in different computer (fresh gephi install), and I get the same error message.
I try to open the same file in freshly installed gephi in another computer with older version of java, I still get the same error.

Is there anyway to recover my file? Any help is greatly appreciated.
ticoalu
 
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Re: HELP cannot open .gephi file

Postby felwert » 19 Jul 2013 19:11

I also get these errors quite regularly. In my latest case, the message read “IlleagalArgumentException - true”. It looks like gephi files with multiple workspaces are more prone to these errors, but I am not 100% sure this is the case.

Anyway, it makes working with gephi a bit like Russian Roulette. After saving the result of your work, you might or might not be able to open it again. :/

Is there any way to fix these files? Would it help to provide a file for inspection?

I am running Gephi 0.8.2 beta on Ubuntu, but it looks like this does not depend on the operating system (https://forum.gephi.org/viewtopic.php?f=4&t=2837 describes the issue on Win8).
felwert
 
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Re: HELP cannot open .gephi file

Postby ticoalu » 19 Jul 2013 20:08

My file also have multiple workspace. It actually affect almost all of my .gephi file.
I'll try not to have multiple workspace for now, but any way to recover my work would be appreciated.
ticoalu
 
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Re: HELP cannot open .gephi file

Postby seinecle » 21 Jul 2013 11:32

Hi,
No good news here, just a message to confirm that there are many reports of .gephi files to be unstable. The short term solution is to always save files in gexf. The long term solution is that Gephi core devs are aware of this issue, and are currently working hard at getting Gephi to version 1.0, which will be stable - not a beta version.

Best,
Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
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seinecle
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Re: HELP cannot open .gephi file

Postby ticoalu » 22 Jul 2013 04:36

is there a difference between .gephi and .gexf?
ticoalu
 
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Re: HELP cannot open .gephi file

Postby felwert » 22 Jul 2013 10:08

Just as a side note, it might be of help for some people: I just noticed that opening the .gephi files works fine with Java 6, but not with Java 7 (both OpenJDK on Ubuntu). Does this work for others as well?
felwert
 
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Re: HELP cannot open .gephi file

Postby seinecle » 22 Jul 2013 15:28

Hi,

The difference between .gephi and .gexf:

.gephi files are files that save a working session of Gephi: the network itself, but also parameters related to the Gephi software when you were working on it. For example, you can have a .gephi file saving the 2 working spaces that you have currently open in Gephi. Opening the .gephi files will restore the 2 workspaces.
Gephi files can only be opened with Gephi.

.gexf files are much more modest in purpose: they just save the network in the current workspace you are working in: the nodes, edges, and their attributes. Gexf files are an interesting way to save a network because they preserve many more aspects of the network than other network formats. For example the colors and the positions (x, y, z coordinates) of the nodes will be preserved. Also, if you were working on a dynamic network (a network evolving through time), gexf will also preserve the time-dependent aspects of the network. No other network format does that.

gexf files can be opened with any text editor (right click on a gexf file and select: "open with notepad" or the equivalent). gexf is not read by any other net viz software that I am aware of, still this becomes a more and more popular file format, with many apps generating gexf files for their viz.
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
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seinecle
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Re: HELP cannot open .gephi file

Postby ticoalu » 22 Jul 2013 15:35

Seinecle,

Thank you very much for your input. I will definitely start saving a backup of my work in .gexf format. Do you know if there is a way to convert my old faulty .gephi file or extract the network information within to another format (salvaging the file)?

Thanks.
ticoalu
 
Posts: 13
Joined: 18 Jul 2013 18:46

Re: HELP cannot open .gephi file

Postby seinecle » 22 Jul 2013 15:41

No, I am afraid not.

If I was in the same situation, I would:
- run Gephi from the source
- open the faulty gephi file
- read the details of the error message.
- see from this msg if anything easy can be changed in the Gephi code source to allow the import to proceed, even imperfectly.

But that's a time consuming operation, and I am not sure a solution could be found. You can pm me with your gephi file, I'd try to see if I can get anything in a short amount of time?

Best,

Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
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seinecle
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Re: HELP cannot open .gephi file

Postby stenoboard » 15 Jan 2014 14:31

In Windows 7, after removing Java 7 and installing Java SE 6 Update 24 opening the .gephi files works fine. Thanks.
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