Automatic graph layout with JointJS and Dagre

xholonWorkbook.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Sun Dec 08 2013 13:53:45 GMT-0500 (EST)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: Automatic graph layout with JointJS and Dagre
Description: 
Url: http://www.primordion.com/Xholon/gwt/
InternalName: gist 7890549
Keywords: 

My Notes
--------

December 10, 2013

A google search for "automatic graph layout" found David Durman's blog post on "Automatic graph layout with JointJS and Dagre".
  http://www.daviddurman.com/automatic-graph-layout-with-jointjs-and-dagre.html

He includes an on-page demo that uses both JointJS and Dagre to layout a graph specified with a JSON-like format,
render it to SVG, and display it on the page. His default data is only a few nodes. It looks promising,
so I've tried it with my larger Countries of Europe data (see gist https://gist.github.com/kenwebb/7851572).

To run this workbook as a Xholon app, use this URL:
  http://www.primordion.com/Xholon/gwt/Xholon.html?app=7890549&src=gist&gui=clsc

My first step is to write a simple script for the Xholon app, that can be pasted into the Chameleon node, once the app has loaded.
The script consists of everything from the opening <Chameleonbehavior to the closing </Chameleonbehavior>, inclusive.
Copy these lines to the "clipboard" tab in the Xholon app, right-click on the Chameleon node in the Xholon app, and select "Paste Last Child".

<Chameleonbehavior implName="org.primordion.script.Behavior_gwtjs">
var c;
var beh = {
  postConfigure: function() {
    c = this.cnode.parent();
    var node = c.xpath("Countries/*");
    c.println("{");
    while (node) {
      c.print("  '" + node.xhc().name() + "': [");
      var ports = node.ports();
      for (var i = 0; i != ports.length; i++) {
        if (i == ports.length) {break;}
        var remote = ports[i].obj().reffedNode.xhc().name();
        if (i > 0) {
          c.print(", ");
        }
        c.print("'" + remote + "'");
      }
      c.print("]");
      node = node.next();
      if (node) {
        c.print(",");
      }
      c.print("\n");
    }
    c.println("}");
  }
}
</Chameleonbehavior>

It generates this data structure in the "out" tab:

{
  'Albania': ['Kosovo', 'Serbia', 'Macedonia', 'Greece'],
  'Andorra': ['France', 'Spain'],
  'Armenia': ['Georgia', 'Azerbaijan', 'Turkey'],
  'Austria': ['Germany', 'Czech_Republic', 'Slovakia', 'Hungary', 'Slovenia', 'Italy', 'Switzerland'],
  'Azerbaijan': ['Georgia', 'Russia', 'Armenia'],
  'Belarus': ['Russia', 'Ukraine', 'Poland', 'Lithuania', 'Latvia'],
  'Belgium': ['Netherlands', 'Germany', 'Luxemburg', 'France'],
  'Bosnia': ['Croatia', 'Serbia'],
  'Bulgaria': ['Romania', 'Serbia', 'Turkey', 'Greece', 'Macedonia'],
  'Croatia': ['Slovenia', 'Hungary', 'Serbia', 'Bosnia'],
  'Cyprus': ['Turkey'],
  'Czech_Republic': ['Germany', 'Poland', 'Slovakia', 'Austria'],
  'Denmark': ['Sweden', 'Germany'],
  'Estonia': ['Russia', 'Latvia'],
  'Finland': ['Norway', 'Sweden', 'Russia'],
  'France': ['Belgium', 'Luxemburg', 'Germany', 'Switzerland', 'Italy', 'Spain', 'Andorra', 'United_Kingdom'],
  'Georgia': ['Russia', 'Azerbaijan', 'Armenia', 'Turkey'],
  'Germany': ['Denmark', 'Poland', 'Czech_Republic', 'Austria', 'Switzerland', 'France', 'Luxemburg', 'Belgium', 'Netherlands'],
  'Greece': ['Albania', 'Macedonia', 'Bulgaria', 'Turkey'],
  'Hungary': ['Austria', 'Slovakia', 'Ukraine', 'Romania', 'Serbia', 'Croatia', 'Slovenia'],
  'Iceland': ['United_Kingdom'],
  'Ireland': ['United_Kingdom'],
  'Italy': ['France', 'Switzerland', 'Austria', 'Slovenia', 'Malta'],
  'Kosovo': ['Serbia', 'Albania'],
  'Latvia': ['Estonia', 'Russia', 'Lithuania'],
  'Lithuania': ['Latvia', 'Belarus', 'Poland'],
  'Luxemburg': ['Belgium', 'Germany', 'France'],
  'Macedonia': ['Serbia', 'Bulgaria', 'Greece', 'Albania'],
  'Malta': ['Italy'],
  'Moldava': ['Ukraine', 'Romania'],
  'Netherlands': ['Germany', 'Belgium'],
  'Norway': ['Russia', 'Finland', 'Sweden'],
  'Poland': ['Lithuania', 'Belarus', 'Ukraine', 'Slovakia', 'Czech_Republic', 'Germany'],
  'Portugal': ['Spain'],
  'Romania': ['Hungary', 'Ukraine', 'Moldava', 'Bulgaria', 'Serbia'],
  'Russia': ['Norway', 'Finland', 'Estonia', 'Latvia', 'Belarus', 'Ukraine', 'Georgia', 'Azerbaijan'],
  'Serbia': ['Hungary', 'Romania', 'Bulgaria', 'Macedonia', 'Albania', 'Kosovo', 'Bosnia', 'Croatia'],
  'Slovakia': ['Czech_Republic', 'Poland', 'Ukraine', 'Hungary', 'Austria'],
  'Slovenia': ['Italy', 'Austria', 'Hungary', 'Croatia'],
  'Spain': ['France', 'Andorra', 'Portugal'],
  'Sweden': ['Norway', 'Finland', 'Denmark'],
  'Switzerland': ['Germany', 'Austria', 'Italy', 'France'],
  'Turkey': ['Bulgaria', 'Greece', 'Cyprus', 'Georgia', 'Armenia'],
  'Ukraine': ['Belarus', 'Russia', 'Moldava', 'Romania', 'Hungary', 'Slovakia', 'Poland'],
  'United_Kingdom': ['Ireland', 'Iceland', 'France']
}

When I paste this into the input area on David's page, his code generates and displays an SVG image.
The SVG text is about 330K in size, so I'm only including a portion of it here.
The nodes are nicely laid out, and the edges between nodes all correctly have an arrow head at each end.
But the lines cross the nodes, rather than going around them.
I don't know if this is an issue with Dagre or JointJS or David's demo code.

Note that the resulting SVG is intended to work interactively with one or more of the libraries used on David's page,
and includes a number of normally invisible shapes. These appear on my Xholon page as large black circles and arrow heads.

I don't have time to explore this further at the moment, but it looks promising.

The following are my original notes from the earlier workbook.
December 7, 2013

I'm doing a simple model showing which European countries are next to each other. Mostly, I want to explore the simplest way to do this with Xholon GWT, and my new version of the Xholon Workbook editor. I think I can generate it all from a simple text list of lists. I'll list all the countries in alphabetical order, and then put the names of all the adjacent countries after the name. At runtime, Xholon will generate the normal Xholon structure.

At runtime, if I hover above a D3 (http://d3js.org/) node, all the adjacent countries will be highlighted.

Here's my list of European countries, in alphabetical order:
  Albania
  Andorra
  Armenia
  Austria
  Azerbaijan
  Belarus
  Belgium
  Bosnia
  Bulgaria
  Croatia
  Cyprus
  Czech_Republic
  Denmark
  Estonia
  Finland
  France
  Georgia
  Germany
  Greece
  Hungary
  Iceland
  Ireland
  Italy
  Kosovo
  Latvia
  Lithuania
  Luxemburg
  Macedonia
  Malta
  Moldava
  Netherlands
  Norway
  Poland
  Portugal
  Romania
  Russia
  Serbia
  Slovakia
  Slovenia
  Spain
  Sweden
  Switzerland
  Turkey
  Ukraine
  United_Kingdom

I've only implemented ports for France so far, which works. With the D3 gui, the countries that the ports reference are highlighted. What is a universal way to show the names of the countries, and not just their first letter?

December 8

I've done about as much as I can from memory. It's time to check the atlas for final details.

My composite structure hierarchy is an adjacency list
  http://en.wikipedia.org/wiki/Adjacency_list

Another standard way to express adjacency is through an adjacency matrix
  http://en.wikipedia.org/wiki/Adjacency_matrix

The adjacency list is probably the simplest way for people to specify the structure.

It might be good to have a built-in Xholon class that can read an adjacency list, and produce a complets set of Xholon trees and graphs from this - an inheritance hierarchy tree, a composite structure hierarchy tree, and a port graph. It's toString() method would print out a nicely formatted comma-separated? list. Possibly it should also be able to generate an adjacency matrix.

I can generate a good graph by right-clicking on the Countries node, and selecting Export > Graphviz. I then need to save the output (starting with "digraph") to a file (Countries.gv), and run the following (Linux) command to generate an SVG file:
  dot -Tsvg -O Countries.gv
Because it's a directed graph (digraph), the diagram includes lines and arrows for each direction, so there's redundancy in this case. With countries it's always true that if country A is adjacent to country B, then country B is adjacent to country A.

I've pasted the generated SVG content back into the SVG editor of this workbook. The SVG image appears when the Xholon GWT runs this Xholon Workbook.

]]></Notes>

<_-.XholonClass>
  <CountrySystem/>
  <Countries/>

</_-.XholonClass>

<xholonClassDetails>
  
</xholonClassDetails>

<CountrySystem>
  <Attribute_String>
Albania,Kosovo,Serbia,Macedonia,Greece
Andorra,France,Spain
Armenia,Georgia,Azerbaijan,Turkey
Austria,Germany,Czech_Republic,Slovakia,Hungary,Slovenia,Italy,Switzerland
Azerbaijan,Georgia,Russia,Armenia
Belarus,Russia,Ukraine,Poland,Lithuania,Latvia
Belgium,Netherlands,Germany,Luxemburg,France
Bosnia,Croatia,Serbia
Bulgaria,Romania,Serbia,Turkey,Greece,Macedonia
Croatia,Slovenia,Hungary,Serbia,Bosnia
Cyprus,Turkey
Czech_Republic,Germany,Poland,Slovakia,Austria
Denmark,Sweden,Germany
Estonia,Russia,Latvia
Finland,Norway,Sweden,Russia
France,Belgium,Luxemburg,Germany,Switzerland,Italy,Spain,Andorra,United_Kingdom
Georgia,Russia,Azerbaijan,Armenia,Turkey
Germany,Denmark,Poland,Czech_Republic,Austria,Switzerland,France,Luxemburg,Belgium,Netherlands
Greece,Albania,Macedonia,Bulgaria,Turkey
Hungary,Austria,Slovakia,Ukraine,Romania,Serbia,Croatia,Slovenia
Iceland,United_Kingdom
Ireland,United_Kingdom
Italy,France,Switzerland,Austria,Slovenia,Malta
Kosovo,Serbia,Albania
Latvia,Estonia,Russia,Lithuania
Lithuania,Latvia,Belarus,Poland
Luxemburg,Belgium,Germany,France
Macedonia,Serbia,Bulgaria,Greece,Albania
Malta,Italy
Moldava,Ukraine,Romania
Netherlands,Germany,Belgium
Norway,Russia,Finland,Sweden
Poland,Lithuania,Belarus,Ukraine,Slovakia,Czech_Republic,Germany
Portugal,Spain
Romania,Hungary,Ukraine,Moldava,Bulgaria,Serbia
Russia,Norway,Finland,Estonia,Latvia,Belarus,Ukraine,Georgia,Azerbaijan
Serbia,Hungary,Romania,Bulgaria,Macedonia,Albania,Kosovo,Bosnia,Croatia
Slovakia,Czech_Republic,Poland,Ukraine,Hungary,Austria
Slovenia,Italy,Austria,Hungary,Croatia
Spain,France,Andorra,Portugal
Sweden,Norway,Finland,Denmark
Switzerland,Germany,Austria,Italy,France
Turkey,Bulgaria,Greece,Cyprus,Georgia,Armenia
Ukraine,Belarus,Russia,Moldava,Romania,Hungary,Slovakia,Poland
United_Kingdom,Ireland,Iceland,France
  </Attribute_String>
</CountrySystem>

<CountrySystembehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
var cs, app;
var beh = {

postConfigure: function() {
  cs = this.cnode.parent();
  app = $wnd.xh.app();
  $wnd.xh.param("MaxPorts", "10");
  var text = cs.first().text();
  
  // get xhRoot
  var xhRoot = cs.parent();

  // get xhcRoot
  var xhcRoot = cs.xhc().parent();
  
  // get XholonHelperService
  var service = $wnd.xh.service("XholonHelperService");
  
  // ih
  var ihStr = this.makeIhStr(text);
  service.call(-2013, ihStr, xhcRoot); // ISignal.ACTION_PASTE_LASTCHILD_FROMSTRING = -2013
  
  // cd
  var cdStr = this.makeCdStr(text);
  service.call(-2013, cdStr, xhcRoot);
  
  // csh
  var cshStr = this.makeCshStr(text);
  service.call(-2013, cshStr, xhRoot);
},

// Make an Inheritance Hierarchy XML string
makeIhStr: function(text) {
  var classXml = "<_-.XholonClass><Country>\n";
  var arr = text.split("\n");
  for (var i = 0; i < arr.length; i++) {
    var country = arr[i];
    if (country) {
      var items = country.split(",");
      classXml += "  <" + items[0] + "/>\n";
    }
  }
  classXml += "</Country></_-.XholonClass>\n";
  return classXml;
},

// Make an Class Details XML string
makeCdStr: function(text) {
  var classXml = "<xholonClassDetails>\n";
  var arr = text.split("\n");
  for (var i = 0; i < arr.length; i++) {
    var country = arr[i];
    if (country) {
      var items = country.split(",");
      classXml += "  <" + items[0] + ">\n";
      for (var j = 1; j < items.length; j++) {
        classXml += '    <port name="port" index="' + (j-1) + '" connector="../' + items[j] + '"/>\n';
      }
      classXml += "  </" + items[0] + ">\n";
    }
  }
  classXml += "</xholonClassDetails>\n";
  return classXml;
},

// Make an Composite Structure Hierarchy XML string
makeCshStr: function(text) {
  var xml = "<Countries>\n";
  var arr = text.split("\n");
  for (var i = 0; i < arr.length; i++) {
    var country = arr[i];
    if (country) {
      var items = country.split(",");
      xml += "  <" + items[0] + "/>\n";
    }
  }
  xml += "</Countries>\n";
  return xml;
}
  
}
]]></CountrySystembehavior>

<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
<svg xmlns="http://www.w3.org/2000/svg" xlink="http://www.w3.org/1999/xlink" version="1.1" id="v_5" width="2000" height="2000">
<g id="v_6" class="viewport" transform="translate(20,20) "><g id="j_234" class="element basic Rect" model-id="Belgium" fill="white" stroke="none" transform="translate(273.6,16)"><g class="rotatable" id="v_4226" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4229" transform="scale(1.0000093901122118,1)"><rect id="v_4227" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4228" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(23.60000228881836,11) ">Belgium</text></g></g><g id="j_235" class="element basic Rect" model-id="Denmark" fill="white" stroke="none" transform="translate(41.60000000000002,202)"><g class="rotatable" id="v_4231" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4234" transform="scale(1.0000093901122118,1)"><rect id="v_4232" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4233" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(23.60000228881836,11) ">Denmark</text></g></g><g id="j_236" class="element basic Rect" model-id="Finland" fill="white" stroke="none" transform="translate(41.60000000000002,388)"><g class="rotatable" id="v_4236" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4239" transform="scale(1.0000093901122118,1)"><rect id="v_4237" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4238" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(24.10000228881836,11) ">Finland</text></g></g><g id="j_237" class="element basic Rect" model-id="France" fill="white" stroke="none" transform="translate(367.40000000000003,264)"><g class="rotatable" id="v_4241" transform="rotate(0,36.8,16)"><g class="scalable" id="v_4244" transform="scale(0.9999787708311219,1)"><rect id="v_4242" fill="white" stroke="#555" width="73.6" height="32" rx="5" ry="5"/></g><text id="v_4243" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(21.799999237060547,11) ">France</text></g></g><g id="j_238" class="element basic Rect" model-id="Germany" fill="white" stroke="none" transform="translate(273.6,140)"><g class="rotatable" id="v_4246" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4249" transform="scale(1.0000093901122118,1)"><rect id="v_4247" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4248" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(24.10000228881836,11) ">Germany</text></g></g><g id="j_239" class="element basic Rect" model-id="Iceland" fill="white" stroke="none" transform="translate(579.4000000000001,388)"><g class="rotatable" id="v_4251" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4254" transform="scale(1.0000093901122118,1)"><rect id="v_4252" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4253" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(24.10000228881836,11) ">Iceland</text></g></g><g id="j_240" class="element basic Rect" model-id="Ireland" fill="white" stroke="none" transform="translate(432.6000000000001,388)"><g class="rotatable" id="v_4256" transform="rotate(0,41.6,16)"><g class="scalable" id="v_4259" transform="scale(1.0000093901122118,1)"><rect id="v_4257" fill="white" stroke="#555" width="83.2" height="32" rx="5" ry="5"/></g><text id="v_4258" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(24.10000228881836,11) ">Ireland</text></g></g><g id="j_241" class="element basic Rect" model-id="Luxemburg" fill="white" stroke="none" transform="translate(321.00000000000006,326)"><g class="rotatable" id="v_4261" transform="rotate(0,51.199999999999996,16)"><g class="scalable" id="v_4264" transform="scale(1.0000152590218967,1)"><rect id="v_4262" fill="white" stroke="#555" width="102.39999999999999" height="32" rx="5" ry="5"/></g><text id="v_4263" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(28.700000762939453,11) ">Luxemburg</text></g></g><g id="j_242" class="element basic Rect" model-id="Netherlands" fill="white" stroke="none" transform="translate(319,78)"><g class="rotatable" id="v_4266" transform="rotate(0,60.8,16)"><g class="scalable" id="v_4269" transform="scale(0.9999871506585287,1)"><rect id="v_4267" fill="white" stroke="#555" width="121.6" height="32" rx="5" ry="5"/></g><text id="v_4268" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(32.79999923706055,11) ">Netherlands</text></g></g><g id="j_243" class="element basic Rect" model-id="Norway" fill="white" stroke="none" transform="translate(75.00000000000006,326)"><g class="rotatable" id="v_4271" transform="rotate(0,36.8,16)"><g class="scalable" id="v_4274" transform="scale(0.9999787708311219,1)"><rect id="v_4272" fill="white" stroke="#555" width="73.6" height="32" rx="5" ry="5"/></g><text id="v_4273" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(21.799999237060547,11) ">Norway</text></g></g><g id="j_244" class="element basic Rect" model-id="Sweden" fill="white" stroke="none" transform="translate(41.60000000000002,264)"><g class="rotatable" id="v_4276" transform="rotate(0,36.8,16)"><g class="scalable" id="v_4279" transform="scale(0.9999787708311219,1)"><rect id="v_4277" fill="white" stroke="#555" width="73.6" height="32" rx="5" ry="5"/></g><text id="v_4278" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(21.799999237060547,11) ">Sweden</text></g></g><g id="j_245" class="element basic Rect" model-id="Switzerland" fill="white" stroke="none" transform="translate(348.80000000000007,202)"><g class="rotatable" id="v_4281" transform="rotate(0,60.8,16)"><g class="scalable" id="v_4284" transform="scale(0.9999871506585287,1)"><rect id="v_4282" fill="white" stroke="#555" width="121.6" height="32" rx="5" ry="5"/></g><text id="v_4283" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(33.29999923706055,11) ">Switzerland</text></g></g><g id="j_246" class="element basic Rect" model-id="United_Kingdom" fill="white" stroke="none" transform="translate(560.8000000000001,326)"><g class="rotatable" id="v_4286" transform="rotate(0,75.2,16)"><g class="scalable" id="v_4289" transform="scale(1.0000103890706977,1)"><rect id="v_4287" fill="white" stroke="#555" width="150.4" height="32" rx="5" ry="5"/></g><text id="v_4288" font-size="8" fill="black" font-family="monospace" dominant-baseline="hanging" transform="translate(39.69999694824219,11) ">United_Kingdom</text></g></g><g id="j_247" class="link" model-id="84295de7-f778-44d8-b4c7-060929bdf82c"><path class="connection" 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