gexf file import: infinite loop when duplicated nodes in hierarchy

Bug #731617 reported by Bernie Armour
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
Gephi
Confirmed
Low
Sébastien Heymann

Bug Description

Product Version: Gephi 0.7 beta
Java: 1.6.0_20; Java HotSpot(TM) Client VM 16.3-b01
System: Windows 7 version 6.1 running on x86; Cp1252; en_US (gephi07beta)

Import never completes. Graph never displays The bottom right-hand progress bar just keeps revolving. I don't think it is a bad graph. Here's the gexf file contents:

<?xml version="1.0" encoding="utf-8"?>
<gexf xmlns:viz="http://www.gexf.net/1.2draft/viz" 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" xmlns="http://www.gexf.net/1.2draft">
  <graph mode="static" defaultedgetype="undirected">
    <nodes>
      <node id="0" label="0">
        <nodes>
          <node id="0-0" label="0-0">
            <nodes>
              <node id="2" label="0-0-0" />
              <node id="11" label="0-0-1" />
              <node id="13" label="0-0-2" />
              <node id="15" label="0-0-3" />
              <node id="17" label="0-0-4" />
            </nodes>
          </node>
          <node id="0-1" label="0-1">
            <nodes>
              <node id="7" label="0-1-0" />
              <node id="8" label="0-1-1" />
              <node id="12" label="0-1-2" />
              <node id="14" label="0-1-3" />
              <node id="16" label="0-1-4" />
            </nodes>
          </node>
          <node id="0-2" label="0-2">
            <nodes>
              <node id="0" label="0-2-0" />
              <node id="6" label="0-2-1" />
              <node id="9" label="0-2-2" />
              <node id="10" label="0-2-3" />
            </nodes>
          </node>
          <node id="0-3" label="0-3">
            <nodes>
              <node id="1" label="0-3-0" />
              <node id="3" label="0-3-1" />
              <node id="4" label="0-3-2" />
              <node id="5" label="0-3-3" />
            </nodes>
          </node>
        </nodes>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="0" target="1" />
      <edge id="1" source="0" target="3" />
      <edge id="2" source="0" target="4" />
      <edge id="3" source="1" target="3" />
      <edge id="4" source="1" target="4" />
      <edge id="5" source="1" target="5" />
      <edge id="6" source="2" target="0" />
      <edge id="7" source="3" target="4" />
      <edge id="8" source="3" target="5" />
      <edge id="9" source="5" target="0" />
      <edge id="10" source="6" target="0" />
      <edge id="11" source="7" target="0" />
      <edge id="12" source="8" target="0" />
      <edge id="13" source="9" target="0" />
      <edge id="14" source="10" target="0" />
      <edge id="15" source="11" target="0" />
      <edge id="16" source="12" target="0" />
      <edge id="17" source="13" target="0" />
      <edge id="18" source="14" target="0" />
      <edge id="19" source="15" target="0" />
      <edge id="20" source="16" target="0" />
      <edge id="21" source="17" target="0" />
    </edges>
  </graph>
</gexf>

Tags: import gexf
Revision history for this message
Bernie Armour (barmour) wrote :

Follow-up: by "import" I actually mean File/Open...
I have found the main problem. It is with this graph itself. Top hierarchy node is labeled "0", however, there is also a leaf node labeled "0". This probably causes an endless loop somewhere.

Opening the following graph, I get the correct graph displayed.

<?xml version="1.0" encoding="utf-8"?>
<gexf xmlns:viz="http://www.gexf.net/1.2draft/viz" 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" xmlns="http://www.gexf.net/1.2draft">
  <graph mode="static" defaultedgetype="undirected">
    <nodes>
      <node id="R" label="R">
        <nodes>
          <node id="R-0" label="R-0">
            <nodes>
              <node id="2" label="R-0-0" />
              <node id="11" label="R-0-1" />
              <node id="13" label="R-0-2" />
              <node id="15" label="R-0-3" />
              <node id="17" label="R-0-4" />
            </nodes>
          </node>
          <node id="R-1" label="R-1">
            <nodes>
              <node id="7" label="R-1-0" />
              <node id="8" label="R-1-1" />
              <node id="12" label="R-1-2" />
              <node id="14" label="R-1-3" />
              <node id="16" label="R-1-4" />
            </nodes>
          </node>
          <node id="R-2" label="R-2">
            <nodes>
              <node id="0" label="R-2-0" />
              <node id="6" label="R-2-1" />
              <node id="9" label="R-2-2" />
              <node id="10" label="R-2-3" />
            </nodes>
          </node>
          <node id="R-3" label="R-3">
            <nodes>
              <node id="1" label="R-3-0" />
              <node id="3" label="R-3-1" />
              <node id="4" label="R-3-2" />
              <node id="5" label="R-3-3" />
            </nodes>
          </node>
        </nodes>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="0" target="1" />
      <edge id="1" source="0" target="3" />
      <edge id="2" source="0" target="4" />
      <edge id="3" source="1" target="3" />
      <edge id="4" source="1" target="4" />
      <edge id="5" source="1" target="5" />
      <edge id="6" source="2" target="0" />
      <edge id="7" source="3" target="4" />
      <edge id="8" source="3" target="5" />
      <edge id="9" source="5" target="0" />
      <edge id="10" source="6" target="0" />
      <edge id="11" source="7" target="0" />
      <edge id="12" source="8" target="0" />
      <edge id="13" source="9" target="0" />
      <edge id="14" source="10" target="0" />
      <edge id="15" source="11" target="0" />
      <edge id="16" source="12" target="0" />
      <edge id="17" source="13" target="0" />
      <edge id="18" source="14" target="0" />
      <edge id="19" source="15" target="0" />
      <edge id="20" source="16" target="0" />
      <edge id="21" source="17" target="0" />
    </edges>
  </graph>
</gexf>

Revision history for this message
Sébastien Heymann (sebastien.heymann) wrote :

We could improve the parser to detect such case.

summary: - gexf file import fails to complete
+ gexf file import: infinite loop when duplicate node in hierarchy
summary: - gexf file import: infinite loop when duplicate node in hierarchy
+ gexf file import: infinite loop when duplicated nodes in hierarchy
tags: added: gexf import
Changed in gephi:
milestone: none → 0.7beta
status: New → Confirmed
importance: Undecided → Low
assignee: nobody → Sébastien Heymann (sebastien.heymann)
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