Gephi - The Open Graph Visualization Platform

Null Pointer exception when saving .gephi file

Reported by John Titus on 2010-12-12
22
This bug affects 4 people
Affects Status Importance Assigned to Milestone
Gephi
Fix Committed
Undecided
Unassigned

Bug Description

I have a graph of about 2k nodes and 3k edges, partitioned into about a dozen groups. I want to separate the groups, so I filter by partition, group them, move the group, expand, stop the filter, and try and save...and I get an error:

The project file couldn't be opened. Make sure it has a .gephi extension.

NullPointerException - null

This has happened repeatedly. I'm running Windows 7.

John Titus (john-titus) wrote :

Hi,

Could you share the .gephi file also?

Thanks

John Titus (john-titus) wrote :

The initial graph is generated from the .gexf - here is its as a .gephi. I generated it by opening the gexf file in gephi, and then saving it immediately as a .gephi.

Also - I ran into the same bug when I took the same steps in Ubuntu 10.04.

I don't have the issue.

do you use Gephi 0.7beta?
Did you updated it?

If not it may the reason. Go to "Help > Check for Updates".

Yes and yes. I'm getting the bug in two different OS's, but on the same
laptop. Could you send me the .gephi after you've partitioned by
location/grouped/moved? I'd like to see if I could a) open the file, and
then b) try moving another partition, and seeing if I can save it.

Thanks for your help.

On Sun, Dec 12, 2010 at 12:26 PM, Sébastien Heymann <
<email address hidden>> wrote:

> I don't have the issue.
>
> do you use Gephi 0.7beta?
> Did you updated it?
>
> If not it may the reason. Go to "Help > Check for Updates".
>
> --
> You received this bug notification because you are a direct subscriber
> of the bug.
> https://bugs.launchpad.net/bugs/689286
>
> Title:
> Null Pointer exception when saving .gephi file
>
> Status in Gephi - Network exploration and manipulation:
> New
>
> Bug description:
> I have a graph of about 2k nodes and 3k edges, partitioned into about a
> dozen groups. I want to separate the groups, so I filter by partition, group
> them, move the group, expand, stop the filter, and try and save...and I get
> an error:
>
> The project file couldn't be opened. Make sure it has a .gephi extension.
>
> NullPointerException - null
>
> This has happened repeatedly. I'm running Windows 7.
>
> To unsubscribe from this bug, go to:
> https://bugs.launchpad.net/gephi/+bug/689286/+subscribe
>

John Titus (john-titus) wrote :

By the way, looks like the file IS actually saving, but is incomplete. When
I try and open the file, I get this error:

The project file couldn't be opened. Please check that the file has a
.gephi extension.

SAXParseException - Premature end of file.

On Sun, Dec 12, 2010 at 1:34 PM, John Titus <email address hidden> wrote:

> Yes and yes. I'm getting the bug in two different OS's, but on the same
> laptop. Could you send me the .gephi after you've partitioned by
> location/grouped/moved? I'd like to see if I could a) open the file, and
> then b) try moving another partition, and seeing if I can save it.
>
> Thanks for your help.
>
>
> On Sun, Dec 12, 2010 at 12:26 PM, Sébastien Heymann <
> <email address hidden>> wrote:
>
>> I don't have the issue.
>>
>> do you use Gephi 0.7beta?
>> Did you updated it?
>>
>> If not it may the reason. Go to "Help > Check for Updates".
>>
>> --
>> You received this bug notification because you are a direct subscriber
>> of the bug.
>> https://bugs.launchpad.net/bugs/689286
>>
>> Title:
>> Null Pointer exception when saving .gephi file
>>
>> Status in Gephi - Network exploration and manipulation:
>> New
>>
>> Bug description:
>> I have a graph of about 2k nodes and 3k edges, partitioned into about a
>> dozen groups. I want to separate the groups, so I filter by partition, group
>> them, move the group, expand, stop the filter, and try and save...and I get
>> an error:
>>
>> The project file couldn't be opened. Make sure it has a .gephi extension.
>>
>> NullPointerException - null
>>
>> This has happened repeatedly. I'm running Windows 7.
>>
>> To unsubscribe from this bug, go to:
>> https://bugs.launchpad.net/gephi/+bug/689286/+subscribe
>>
>
>

Hmm I have some difficulties to follow what you did, because there is no need to filter to group nodes.

Could you send the .gephi file that Gephi fails to load? I'll see when it failed to write the file.

Changed in gephi:
milestone: none → 0.7beta
tags: added: project
John Titus (john-titus) wrote :

Right, I'm filtering so that I can manually change the layout of the graph.
I want the partitions to be separate a bit, based on their location, which
does not occur naturally based on their edges.

Here is one of the .gephi files that failed to load:

On Sun, Dec 12, 2010 at 4:04 PM, Sébastien Heymann <
<email address hidden>> wrote:

> Hmm I have some difficulties to follow what you did, because there is no
> need to filter to group nodes.
>
> Could you send the .gephi file that Gephi fails to load? I'll see when
> it failed to write the file.
>
> ** Changed in: gephi
> Milestone: None => 0.7beta
>
> ** Tags added: project
>
> --
> You received this bug notification because you are a direct subscriber
> of the bug.
> https://bugs.launchpad.net/bugs/689286
>
> Title:
> Null Pointer exception when saving .gephi file
>
> Status in Gephi - Network exploration and manipulation:
> New
>
> Bug description:
> I have a graph of about 2k nodes and 3k edges, partitioned into about a
> dozen groups. I want to separate the groups, so I filter by partition, group
> them, move the group, expand, stop the filter, and try and save...and I get
> an error:
>
> The project file couldn't be opened. Make sure it has a .gephi extension.
>
> NullPointerException - null
>
> This has happened repeatedly. I'm running Windows 7.
>
> To unsubscribe from this bug, go to:
> https://bugs.launchpad.net/gephi/+bug/689286/+subscribe
>

John Titus (john-titus) wrote :

Perhaps there's another way to accomplish what I want to do. The nodes in my graph have an attribute called location. I'd like the graph to separate the nodes by location, but that doesn't occur naturally with any of the layout algorithms. So, I want to manually group the nodes of each location, and move them around on the graph. To do that, I filter by partition, of say, New York, run a force atlas layout on them, group them, move them to another spot on the graph, then expand them, then turn off the filter.

I tried to upload the .gephi file that fails to load, then I saw that it is 0 bytes - just an empty file with a name.

John Titus (john-titus) wrote :

Just got another Null pointer exception. I was attempting to copy a partitioned graph to a new workspace, hoping it would lead to an eventual work around. I got this error, and was able to pull up the stack trace:

A java.lang.NullPointerException exception has occurred.
However, the system should continue working without further problems.
Click Show Details for the stack trace.

java.lang.NullPointerException
 at org.gephi.graph.dhns.graph.HierarchicalGraphImpl$1.evaluate(HierarchicalGraphImpl.java:55)
 at org.gephi.graph.dhns.graph.HierarchicalGraphImpl$1.evaluate(HierarchicalGraphImpl.java:52)
 at org.gephi.graph.dhns.edge.iterators.EdgeIterator.hasNext(EdgeIterator.java:72)
 at org.gephi.graph.dhns.graph.iterators.EdgeIteratorImpl.hasNext(EdgeIteratorImpl.java:44)
 at org.gephi.visualization.bridge.DHNSDataBridge.updateEdges(DHNSDataBridge.java:198)
 at org.gephi.visualization.bridge.DHNSDataBridge.updateWorld(DHNSDataBridge.java:135)
 at org.gephi.visualization.opengl.compatibility.CompatibilityEngine.updateWorld(CompatibilityEngine.java:181)
 at org.gephi.visualization.opengl.compatibility.CompatibilityScheduler.updateWorld(CompatibilityScheduler.java:285)
[catch] at org.gephi.visualization.scheduler.SimpleFPSAnimator.run(SimpleFPSAnimator.java:58)

Hi,

The .gephi i/o has been re-written last month. Please could you update your Gephi instance and see if the problem remains?

Thanks.

Changed in gephi:
status: New → Incomplete
Chris Diehl (cpdiehl) wrote :

FYI I've run across the same error in the last few days. I'm running 0.8 beta under Mac OSX v. 10.6.8.

Atheg (hoganaj) wrote :

I can't export to SVG, PNG, or PDF---I always receive this message.

ouss (oussjarrouse) wrote :

I also have the problem.
The gephi file opens fine. When i try to "save as" it with a different name, it shows the message:

"The project file couldn't be opened. Please check that the file has a
.gephi extension.

NullPointerException - null"

The file will be created but will have 0 Bytes.

Product Version: Gephi 0.8.1 beta 20120406-unknown-revn
Java: 1.6.0_24; OpenJDK 64-Bit Server VM 20.0-b12
System: Linux version 3.2.0-24-generic running on amd64; UTF-8; en_US (gephi)
User directory: /home/ouss/.gephi/0.8.1/dev
Cache directory: /home/ouss/.gephi/0.8.1/dev/var/cache

ouss (oussjarrouse) wrote :

So i have some good news...

1- I could open the project from a saved file, but once the project is loaded to Gephi, it was not possible to save it anymore
2- The problem didn't face all projects i've saved before
1&2 ==> 3- The problem is related to the specific project file
4- Not all project files are affected
5- Some Ok project files get affected
4&5 ==> 6- An operation or more corrupt the project and makes it unable to save
7- I have no 3rd party plugins ==> 8- It must be a core operation in Gephi
9- I looked around and eventually did the following
    - Clicked on Preview
    - Clicked the refresh button
    - Waited until refresh operation concluded
    - Clicked Save
and it worked
6&8&9 ==> 10- If Preview was once used for a gephi project, the preview must be refreshed before saving otherwise the project file is corrupt.
10 ==> 11- Gephi people please check that :-)

ouss, can you share the .gephi file so that we can reproduce the bug? thanks

Eduardo Ramos (eduramiba) wrote :

Hi ouss,
Thanks for the report.
I think this preview serialization problem is now fixed (changes here https://github.com/gephi/gephi/commit/4ae16e7faaae2e5e461bc645852ffcc185dd65f0) and will be available in the update center soon or now if you build from source code.

By the way, if you want to report any future problems do it at https://github.com/gephi/gephi please

Eduardo

Changed in gephi:
status: Incomplete → Fix Committed
ouss (oussjarrouse) wrote :

Hello Sébastian and Eduardo,
Thanks for the quick reply. About the .gephi file Sébastian, i think it is not nessesary anymore since Eduardo is aware of the bug.
Eduardo, I will be using https://github.com/gephi/gephi from now on to report problems. Thanks again guys

Andrew Berardy (ajb0614) wrote :

I had the same problem where there is a NullPointerException - null indicating the file did not have a valid gephi extension. Updating Gephi fixed it for me, for now. I had to manually check for updates to do so though.

Andrew Berardy (ajb0614) wrote :

Actually, I just encountered the same error after updating and thinking the problem was fixed. I have Gephi completely up to date, but it still gives me the nullpointerexception error.

Eduardo Ramos (eduramiba) wrote :

Hi Andrew,
Can you share your gephi log file after the exception happens?
Check this instructions to locate it http://wiki.gephi.org/index.php/HowTo_report_a_bug

Andrew Berardy (ajb0614) wrote :

Not sure which of three files to include, and I don't see a way to include three files in one post, so here's post 1 of 3

Andrew Berardy (ajb0614) wrote :

Second post

Andrew Berardy (ajb0614) wrote :

final attachment

Eduardo Ramos (eduramiba) wrote :

Ok, it is this same bug.
I forgot to say that this bugfix is not in the update center yet, but will be soon.

Meanwhile you can try to load the .gephi file with Preview perspective open, it could fix the problem.

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