simple graph seems correctly recorded, but does not show when loaded

[Fred March]

I created a small test graph, and the XML file seems fine (for all I know). On loading the graph, I only get a root node labeled "1", and a very quick status bar message that seems to mention more nodes, but disappears too fast to read. The error message on a terminal is

QGtkStyle cannot be used together with the GTK_Qt engine.

I assume this has to do with a conflict between KDE rendering tools and native Gnome tools. I am using a Gnome desktop, with occasional KDE apps, but this happens both when launched both from a KDE app like Dolphin, and straight from the Gnome menu or any (Gnome or not) terminal. I could not find any configuration files that would allow me to try and tweak the rendering choices.

The XML file is (sorry for the length)
<?xml version="1.0" encoding="UTF-8"?>
 <!-- Created by SocNetV-->
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance " xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
  <key id="d0" for="node" attr.name="label" attr.type="string">
    <default></default>
  </key>
  <key id="d1" for="node" attr.name="x_coordinate" attr.type="double">
    <default>0.0</default>
  </key>
  <key id="d2" for="node" attr.name="y_coordinate" attr.type="double">
    <default>0.0</default>
  </key>
  <key id="d3" for="node" attr.name="size" attr.type="double">
    <default>4</default>
  </key>
  <key id="d4" for="node" attr.name="color" attr.type="string">
    <default>gold</default>
  </key>
  <key id="d5" for="node" attr.name="shape" attr.type="string">
    <default>circle</default>
  </key>
  <key id="d6" for="edge" attr.name="weight" attr.type="double">
    <default>1.0</default>
  </key>
  <key id="d7" for="edge" attr.name="color" attr.type="string">
    <default>grey</default>
  </key>
  <graph id="G" edgedefault="directed">
    <node id="1">
      <data key="d0">Math 142</data>
      <data key="d1">0.56486</data>
      <data key="d2">0.278169</data>
      <data key="d3">9</data>
      <data key="d5">circle</data>
    </node>
    <node id="2">
      <data key="d0">Exponentials & Logs</data>
      <data key="d1">0.220033</data>
      <data key="d2">0.272887</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="3">
      <data key="d0">right-triangle trig</data>
      <data key="d1">0.34647</data>
      <data key="d2">0.0299296</data>
      <data key="d4">azure</data>
      <data key="d5">triangle</data>
    </node>
    <node id="4">
      <data key="d0">Trig</data>
      <data key="d1">0.563218</data>
      <data key="d2">0.149648</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="5">
      <data key="d0">Linear Sys/Matrices</data>
      <data key="d1">0.745484</data>
      <data key="d2">0.169014</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="6">
      <data key="d0">Linear sys/sub & elim</data>
      <data key="d1">0.596059</data>
      <data key="d2">0.0193662</data>
      <data key="d4">azure</data>
      <data key="d5">triangle</data>
    </node>
    <edge id="e1" directed="true" source="1" target="2"/>
    <edge id="e2" directed="true" source="1" target="4"/>
    <edge id="e3" directed="true" source="1" target="5"/>
    <edge id="e4" directed="true" source="3" target="4"/>
    <edge id="e5" directed="true" source="6" target="5"/>
  </graph>
</graphml>
Again, none of the nodes (except a root node, with no label), nor edges comes up when this file is loaded.

[Dimitris Kalamaras (dimitris-kalamaras)]

You're using version 0.70? If so, this bug might be fixed in development trunk. Please, download and check:

svn co http://socnetv.svn.sourceforge.net/svnroot/socnetv/trunk

Meanwhile, I will be examining your data file and get back with some answers shortly.

[Dimitris Kalamaras (dimitris-kalamaras)]

OK, this bug has been triaged.
Seems that the error lies in the label lines (key="d0"):

 <data key="d0">Exponentials & Logs</data>

Probably its the "&" character that breaks the parser.

[Dimitris Kalamaras (dimitris-kalamaras)]

Fred, seems that this problem of yours is not a bug after all.
It's the GraphML spec. :)
I mean GraphML is actually XML, and in any XML document ampersands are treated as special characters [usually denoting the start of variables]. To resolve this, you need to use &amp; instead of plain &.

To be honest, we need to implement a "eliminate strange characters like ampersand" check in SocNetV when the user enters some label data, or else people will think is broken.

You see, ambersand (&) is not the only character that XML (and by definition GraphML) treats as special. The same is true for these characters as well:
 & &amp;
< &lt;
> &gt;
" &quot;
 ' &apos;

[Dimitris Kalamaras (dimitris-kalamaras)]

To recap:

 SocNetV 0.70 does not tolerate &. Instead use &amp;

This file will work alright for you:

<?xml version="1.0" encoding="UTF-8"?>
 <!-- Created by SocNetV-->
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance " xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
  <key id="d0" for="node" attr.name="label" attr.type="string">
    <default></default>
  </key>
  <key id="d1" for="node" attr.name="x_coordinate" attr.type="double">
    <default>0.0</default>
  </key>
  <key id="d2" for="node" attr.name="y_coordinate" attr.type="double">
    <default>0.0</default>
  </key>
  <key id="d3" for="node" attr.name="size" attr.type="double">
    <default>4</default>
  </key>
  <key id="d4" for="node" attr.name="color" attr.type="string">
    <default>gold</default>
  </key>
  <key id="d5" for="node" attr.name="shape" attr.type="string">
    <default>circle</default>
  </key>
  <key id="d6" for="edge" attr.name="weight" attr.type="double">
    <default>1.0</default>
  </key>
  <key id="d7" for="edge" attr.name="color" attr.type="string">
    <default>grey</default>
  </key>
  <graph id="G" edgedefault="directed">
    <node id="1">
      <data key="d0">Math 142</data>
      <data key="d1">0.56486</data>
      <data key="d2">0.278169</data>
      <data key="d3">9</data>
      <data key="d5">circle</data>
    </node>
    <node id="2">
      <data key="d0">Exponentials &amp; Logs</data>
      <data key="d1">0.220033</data>
      <data key="d2">0.272887</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="3">
      <data key="d0">right-triangle trig</data>
      <data key="d1">0.34647</data>
      <data key="d2">0.0299296</data>
      <data key="d4">azure</data>
      <data key="d5">triangle</data>
    </node>
    <node id="4">
      <data key="d0">Trig</data>
      <data key="d1">0.563218</data>
      <data key="d2">0.149648</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="5">
      <data key="d0">Linear Sys/Matrices</data>
      <data key="d1">0.745484</data>
      <data key="d2">0.169014</data>
      <data key="d3">6</data>
      <data key="d5">circle</data>
    </node>
    <node id="6">
      <data key="d0">Linear sys/sub &amp; elim</data>
      <data key="d1">0.596059</data>
      <data key="d2">0.0193662</data>
      <data key="d4">azure</data>
      <data key="d5">triangle</data>
    </node>
    <edge id="e1" directed="true" source="1" target="2"/>
    <edge id="e2" directed="true" source="1" target="4"/>
    <edge id="e3" directed="true" source="1" target="5"/>
    <edge id="e4" directed="true" source="3" target="4"/>
    <edge id="e5" directed="true" source="6" target="5"/>
  </graph>
</graphml>

[Dimitris Kalamaras (dimitris-kalamaras)]

Fred, my comment #3 was a little bit wrong in recognizing the value of your bug report.

True, this bug is due to XML specs, but still the bug is in SocNetV:

We really needed an "eliminate strange characters like ampersand" check in SocNetV when saving network data in GraphML.

The patch has been committed to trunk:

http://socnetv.svn.sourceforge.net/viewvc/socnetv?view=rev&revision=417

This fixes all cases mentioned above, not only & -> &amp;

Please, use the trunk version to see if it's ok with you.

Thanks again for your nice bug report.

Cheers

[Fred March (fredsea)]

On Sat, 2009-08-29 at 17:15 +0000, Dimitris Kalamaras wrote:

> Fred, my comment #3 was a little bit wrong in recognizing the value of
> your bug report.
>
> True, this bug is due to XML specs, but still the bug is in SocNetV:
>
> We really needed an "eliminate strange characters like ampersand"
> check
> in SocNetV when saving network data in GraphML.
>
> The patch has been committed to trunk:
>
> http://socnetv.svn.sourceforge.net/viewvc/socnetv?view=rev&revision=417
>
> This fixes all cases mentioned above, not only & -> &amp;
>
> Please, use the trunk version to see if it's ok with you.
>
> Thanks again for your nice bug report.

Well, Dimitris, I apologize for a) answering personally, b) quite some
time after your kind mail, but...

I guess, something's still not right. Getting the latest version from
the trunk was a breeze, and so was installing it, but it still won't
work. More precisely:

      * My old file still won't get correctly parsed (I get two nodes,
        no link, the nodes labeled "1" and "2"...)
      * Trying to create a new chart I can't get the parser to a) show
        the label, b) obey the directive to show the number in the node,
        and not on its side.

Sorry to bug you with this. I will file a formal bug report after I do a
little more experimenting. I am so eager to use this program, as I am no
hacker at all, but would love to have such a convenient
"organizer" (don't ask :)).

Thank you for your wonderful work!
--
Fred March <email address hidden>

[Dimitris Kalamaras (dimitris-kalamaras)]

Fred, as I said in my previous comments, you cannot have the character "&" inside a label in a graphml file. That's why SocNetV prematurely stops parsing your file. This is due to the XML limitations. So, please, use "&amp;" instead - test with the network in #4 to see that it works - just replace "&" with "&amp;" in your file...

To make it clearer, the patch I mention in comment #5 fixes the (previously) erroneous behavior of SocNetV when saving networks: now the development version of SocNetV converts any "&" in node labels to "&amp;" when you save a network in GraphML format.

As for your second point, please open a new bug report and elaborate on this. BTW, numbers do appear inside nodes, although I have to admit the implementation sucks. :)