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GEXF dynamic node attributes

Postby rshepherd » 25 Jul 2013 00:25

Hi. I'm using GEXF to import a network with dynamic nodes and dynamic node attributes, which looks like:

Code: Select all
<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
   <graph mode="dynamic" defaultedgetype="directed" timeformat="date">
      <attributes class="node" mode="dynamic">
         <attribute id="1" title="attr1" type="float" >
            <default>0.0</default>
         </attribute>
         <attribute id="2" title="attr2" type="float" >
            <default>0.0</default>
         </attribute>
      </attributes>
      <nodes>
         <node id="1" label="node1">
            <spells>
               <spell start="2012-02-09" end="2012-02-16" />
            </spells>
            <attvalues>
               <attvalue for="1" value="55.0" start="2012-02-09" end="2012-02-16" />
               <attvalue for="2" value="45.0" start="2012-02-09" end="2012-02-16" />
            </attvalues>
         </node>
         <node id="2" label="node22">
            <spells>
               <spell start="2012-02-20" end="2012-02-27" />
               <spell start="2012-04-19" end="2012-04-26" />
            </spells>
            <attvalues>
               <attvalue for="1" value="34.0" start="2012-02-20" end="2012-02-27" />
               <attvalue for="2" value="30.0" start="2012-02-20" end="2012-02-27" />
               <attvalue for="1" value="19.0" start="2012-04-19" end="2012-04-26" />
               <attvalue for="2" value="19.0" start="2012-04-19" end="2012-04-26" />
            </attvalues>
         </node>
      </nodes>
      ...
   </graph>
</gexf>


Gephi fails to load file and does not give me any details. Gephi seems to be processing the file indefinitely, and will throw the "java.lang.IllegalStateException: A task is still executing" if I attempt another operation.

I switched to static node attributes as a temporary fix, and found I could not exceed 25 static node attributes without Gephi failing to load. I attempted to load the network with only 2 dynamic node attributes, but experienced the same problem.

Is this a memory limitation problem? I followed the instructions for enabling 64-bit (here: https://gephi.org/users/install/) and have 32 gb memory available on the machine. The network size is on the order of hundreds of nodes, and the GEXF representation of the fully-hydrated dynamic network w/ dynamic attributes is 1.8mb.

Thanks for any input.

-Russ
rshepherd
 
Posts: 1
Joined: 24 Jul 2013 23:49
Location: Taiwan

Re: GEXF dynamic node attributes

Postby admin » 25 Jul 2013 07:54

Hi,

Problems usually happen when the parser faces interval problems, like inconsistent time boundaries between attributes and nodes, or between edges and non-existent nodes.

The other issue is whe not enough memory is available, but it doesn't seem to be your case and it doesn't raise such Exception.

Try to load the nodes only in static and dynamic mode. Does it work?
If yes, try to load part of the edges and grow /shrink until you isolate the error.
Otherwise, load a subset of the nodes and grow/shrink as well until you find the problem.
User avatar
admin
Gephi Community Manager
 
Posts: 960
Joined: 09 Dec 2009 15:41
Location: Paris, France

Re: GEXF dynamic node attributes

Postby Kugler » 02 Oct 2013 09:45

Same issue, no luck yet. I'm using pygexf, and I've got no idea what I'm doing wrong. I load my gexf file, and nothing happens. If I try to load something else, this error pops up:

Code: Select all
java.lang.IllegalStateException: A task is still executing
   at org.gephi.utils.longtask.api.LongTaskExecutor.execute(LongTaskExecutor.java:130)
[catch] at org.gephi.desktop.importer.DesktopImportControllerUI.importFile(DesktopImportControllerUI.java:171)
   at org.gephi.desktop.project.ProjectControllerUIImpl.openFile(ProjectControllerUIImpl.java:476)
   at org.gephi.branding.desktop.actions.OpenFile.actionPerformed(OpenFile.java:70)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.AbstractButton.doClick(Unknown Source)
   at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
   at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at org.netbeans.core.TimableEventQueue.dispatchEvent(TimableEventQueue.java:158)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)


Well, this is it... I'll give you part of my file as well, in case I'm doing something wrong there. For the record: It's working if I create the file without time stamps on attributes. No problem with nodes!

Code: Select all
      <node id="Si Liu" label="Si Liu" start="985" end="2068">
        <attvalues>
          <attvalue for="17" value="data_set_121" start="985" end="2067"/>
          <attvalue for="86" value="data_set_755" start="1122" end="2067"/>
          <attvalue for="184" value="data_set_1597" start="1597" end="2067"/>
          <attvalue for="80" value="data_set_698" start="1597" end="2067"/>
          <attvalue for="196" value="data_set_1646" start="1646" end="2067"/>
          <attvalue for="166" value="data_set_1447" start="1646" end="2067"/>
          <attvalue for="213" value="data_set_1781" start="1781" end="2067"/>
        </attvalues>
      </node>
      <node id="Rajkumar Buyya" label="Rajkumar Buyya" start="1013" end="2068">
        <attvalues>
          <attvalue for="104" value="data_set_1012" start="1013" end="2067"/>
          <attvalue for="21" value="data_set_137" start="1278" end="2067"/>
          <attvalue for="214" value="data_set_1785" start="1785" end="2067"/>
        </attvalues>
      </node>
Kugler
 
Posts: 2
Joined: 02 Oct 2013 09:39

Re: GEXF dynamic node attributes

Postby Kugler » 07 Oct 2013 12:19

Nothing? I'll upload my whole gexf file, could you please try and get it running, and if you do, could you tell me how? Thank you.
Attachments
dynamic_graph.gexf
(643.91 KiB) Downloaded 48 times
Kugler
 
Posts: 2
Joined: 02 Oct 2013 09:39

Re: GEXF dynamic node attributes

Postby bornakke » 17 Mar 2014 22:54

It appear like i'm hitting the same wall as Kugler did last years. I have now spent 6 hours trying to make dynamic attributes load in gephi, but without any luck :( Gephi fails to open the gexf file and doesn't give me any details to follow in the log other than the 'java.lang.IllegalStateException: A task is still executing'. I have cut down my gexf file to the bear minimum, but without get closer to identify the error:

Code: Select all
<?xml version="1.0" encoding="UTF-8"?>
      <gexf xmlns="http://www.gexf.net/1.2draft"
         xmlns:xsi="http://wwww.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://www.gexf.net/1.2draft
         http://www.gexf.net/1.2draft/gexf.xds"
         xmlns:viz="http://www.gexf.net/1.2draft/viz"
         version="1.2">
         <meta>
            <creator>Social Fabric</creator>
            <description>Location - Run id:17032014_c6569ef83a89d5f4b13123816e628d</description>
         </meta>
         <graph defaultedgetype="directed" mode="dynamic" timeformat="datetime">
         <attributes class="node" mode="dynamic">
            <attribute id="a-4073d41bb178273881fbc975e1af6118" title="lat" type="double"/>
            <attribute id="a-8b8a2268b5d3a89f348d5990b846c29b" title="lng" type="double"/>
         </attributes>
            
<nodes>
   <node id="6effe6abaf397c2c736ec6081a6d9c" label="1">
   <attvalues>
      <attvalue for="a-4073d41bb178273881fbc975e1af6118" value="55.7721805" start="2014-03-09T00:00:00" end="2014-03-09T00:00:00"/>"\n"<attvalue for="a-4073d41bb178273881fbc975e1af6118" value="55.7721805" start="2014-03-09T00:00:02" end="2014-03-09T00:00:02"/>"\n"<attvalue for="a-4073d41bb178273881fbc975e1af6118" value="55.7721805" start="2014-03-09T00:02:07" end="2014-03-09T00:02:07"/>"\n"<attvalue for="a-8b8a2268b5d3a89f348d5990b846c29b" value="12.4753833" start="2014-03-09T00:00:00" end="2014-03-09T00:00:00"/>"\n"<attvalue for="a-8b8a2268b5d3a89f348d5990b846c29b" value="12.4753833" start="2014-03-09T00:00:02" end="2014-03-09T00:00:02"/>"\n"</attvalues></node>
   <node id="a024c3e26f1a512f79cd8f64545a7e" label="2">
   <attvalues>
      <attvalue for="a-4073d41bb178273881fbc975e1af6118" value="55.8393541" start="2014-03-09T00:00:00" end="2014-03-09T00:00:00"/>"\n"<attvalue for="a-4073d41bb178273881fbc975e1af6118" value="55.8393541" start="2014-03-09T00:01:01" end="2014-03-09T00:01:01"/>"\n"<attvalue for="a-8b8a2268b5d3a89f348d5990b846c29b" value="12.2807123" start="2014-03-09T00:00:00" end="2014-03-09T00:00:00"/>"\n"<attvalue for="a-8b8a2268b5d3a89f348d5990b846c29b" value="12.2807123" start="2014-03-09T00:01:01" end="2014-03-09T00:01:01"/>"\n"</attvalues></node>
</nodes>
<edges>
</edges>
</graph>
</gexf>


Any suggestions anyone?? @Kugler did you by chance find a solution??

Best regards
Tobias
bornakke
 
Posts: 3
Joined: 21 Jun 2013 12:00
Location: Denmark


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