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Force-layout of Cable2Graph

Update: This prototype has turned into a bigger project: http://is.gd/CableWeaver


Here's a small gallery of Cable2Graph cable reference culsters (the graphs are named after countries, but they don't "represent" the entire body of cables related to them. It's just a handy naming convention). Each node (circle) represents a cable. Each link (line) represents reference between 2 cables.

Instructions

  • Hover over a node to see details of the cable it represents.
  • Click on a node to open the related cable in a new tab.
  • Shift+click on the node to toggle between manual placement and auto placement modes (see below). Default is auto placement.
  • When you drag a node, all nodes in auto placement mode rearrange themselves as if the links were "rubber bands".
  • When you release a node that is in auto placement mode, it snaps into place according to the "rubber bands" attached to it. This is why it is usually best to switch a node to manual placement before dragging it.

Reaching a readable layout (where all arrows are visible and distinguishable) can take up to 20 minutes depending on the graph (Syria and Jordan are the most complex, Iran is easy). Here's a screenshot gallery of all graphs after tidying them up a bit.

Legend

  • Node's fill color represents sending Embassy.
  • Border is dashed if cable is missing, otherwise the color represents classification (UNCLASSIFIED, CONFIDENTIAL, and SECRET).
  • Border is darker when node is in manual placement mode.
  • Border width represents node's HITS authority (how "strongly" it is involved in [in]direct reference).
  • Link arrowhead points to the referenced (i.e. earlier) cable.
  • Link width represents [betweenness centrality](The color represents the embassy send://en.wikipedia.org/wiki/Betweenness_centrality) of the reference (in how many shortest-paths between pairs of cables it appears).

Under the hood

  • This is a proof of concept: trying to use d3 force-layout to render WikiLeaks Cable2Graph clusters. Hopefully, this will become a public web service with a server-side component generating the graphs on demand.
  • If you fork this, bear in mind that the json file contains additional information you may wish to visualize (e.g. pagerank).
  • If you want to try this with your own nbh/splitgrraph graphml files, you can convert them with g2json - a minimalistic fork of g2svg (included in this gist).
#!/usr/bin/env python
#
# GPLv3 2011-2012 by anonymous
#
import igraph, math, csv, time, json
from sys import argv, exit, stderr
from os import listdir, path, environ, closerange
from optparse import OptionParser
from datetime import datetime
from hashlib import sha1
from struct import unpack
def str2hsl(s):
h = unpack('!I',sha1(s).digest()[:4])[0]
hsl = []
for mod in [360,50,50]:
hsl.append(h%mod)
h/=mod
return "hsl({0},{1}%,{2}%)".format(hsl[0],hsl[1]+50,hsl[2]+50)
environ['TZ'] = 'UTC'
time.tzset()
parser = OptionParser()
parser.add_option("-g", "--gml", dest="gmlfile",
help="Single source graph in gml format FILE", metavar="FILE")
parser.add_option("-i", "--include", dest="gmllist",
help="Load all .gml graphs listed in FILE", metavar="FILE")
parser.add_option("-d", "--dest", dest="destdir",
default=".",
help="Destination DIR. Default: current dir",
metavar="DIR")
parser.add_option("-r", "--reverb", dest="reverb",
help="Load sentences from a ReVerb result tsv FILE (e.g. mycables.reverb)",
metavar="FILE")
parser.add_option("-s", "--subjects", dest="subjects",
default="data/subjects.list",
help="Load map of label -> subject. Default: subjects.list", metavar="FILE")
parser.add_option("-u", "--uri", dest="uri",
default="data/wikileaks.org.map",
help="Load map of label -> uri from FILE. Default: wikileaks.org.map", metavar="FILE")
(options, args) = parser.parse_args()
graph_files = set()
if options.gmlfile:
graph_files.add(options.gmlfile.strip())
if options.gmllist:
gfh = open(options.gmllist)
for gf in gfh.readlines():
graph_files.add(gf.strip())
gfh.close()
if len(graph_files) < 1:
print "No source .gml files"
exit(1)
def format_timestamp(ts, tsformat = '%Y-%m-%d'):
d = datetime.fromtimestamp(float(ts))
return d.strftime(tsformat)
if options.reverb:
reverb_csv = csv.reader(
open(options.reverb),
delimiter='\t',
quotechar = None,
lineterminator = '\n')
reverb_map = {}
for row in reverb_csv:
type, reverb_cable_id, num, argument1, relation, argument2, score = row
# TODO have a custom threshold as cmd line parameter
if float(score) > 0.7:
if reverb_map.has_key(reverb_cable_id):
reverb_map[reverb_cable_id].append({
'a1': argument1,
'rel': relation,
'a2': argument2,
'score': score
})
else:
reverb_map[reverb_cable_id] = [{
'a1': argument1,
'rel': relation,
'a2': argument2,
'score': score
}]
# load optional uri map
if options.uri:
cmap = {}
f = open(options.uri)
for l in f.readlines():
k,v = l.strip().split()
cmap[k.strip()] = v.strip()
f.close()
# load optional subject map
if options.subjects:
smap = {}
f = open(options.subjects)
for l in f.readlines():
k,v = l.split(' ',1)
smap[k.strip()] = v.strip()
f.close()
for gml in graph_files:
destfile = "{0}/{1}.json".format(options.destdir, path.basename(gml).rsplit('.',1)[0])
if path.exists(destfile):
print "%s exists. skipping" % destfile
continue
# load graph from file
g = igraph.load(gml)
# apply sentences to graph
if options.reverb:
sentence = []
for l in g.vs.get_attribute_values('label'):
if l in reverb_map.keys():
sentence.append(reverb_map[l])
else:
sentence.append('')
g.vs['sentence'] = sentence
# apply uris to graph
if options.uri:
uri = []
for l in g.vs.get_attribute_values('label'):
if l in cmap:
uri.append(cmap[l])
else:
uri.append('')
g.vs['uri'] = uri
# apply subjects to graph
if options.subjects:
subjects = []
for l in g.vs.get_attribute_values('label'):
if l in smap:
subjects.append(smap[l])
else:
subjects.append('')
g.vs['subjects'] = subjects
labels = g.vs['label']
places = list(set(g.vs['place'])) # remove duplicates, for color index
edges = []
vertices = []
for eidx, edge in enumerate(g.es):
vidxs = edge.tuple
# Fix bogus directionality in graphml:
# 1) If there are timestaps, the later cable refers to the earlier cable
# 2) Missing cables should be reference and not referrer
# (regardless of the date we've guessed for them)
zero_refs_one = False
if 'timestamp' in g.vs.attribute_names() and g.vs['timestamp'][vidxs[0]]>g.vs['timestamp'][vidxs[1]]:
zero_refs_one = True
if 'missing' in g.vs.attribute_names():
if g.vs['missing'][vidxs[0]]:
zero_refs_one = False
elif g.vs['missing'][vidxs[1]]:
zero_refs_one = True
if zero_refs_one:
stderr.write('flipped {0}<->{1}\n'.format(g.vs['label'][vidxs[0]],g.vs['label'][vidxs[1]]))
edge['source'] = vidxs[0]
edge['target'] = vidxs[1]
else:
edge['source'] = vidxs[1]
edge['target'] = vidxs[0]
for vidx,v in enumerate(g.vs):
# Add stuff I fine easier to do in Python than in JS :)
if 'place' in v.attribute_names():
# [hopefully] gives each place a unique color (if you don't have your own scale)
v['color'] = str2hsl(v['place'])
# This is a unique-per-place index, if you want to use a preset color scale
v['colorindex'] = places.index(v['place'])
if 'timestamp' in v.attribute_names():
# Nicely formatted date
v['date'] = v['timestamp'] and format_timestamp(v['timestamp']) or None
if 'missing' in v.attribute_names() and v['missing']:
v['nodeclass'] = 'MISSING'
elif 'classification' in v.attribute_names():
v['nodeclass'] = v['classification'].replace('//','-').replace(' ','-').upper()
try:
dfh = open(destfile,'w')
except IOError:
# TODO tmp fix for too many open files
closerange(100,255)
dfh = open(destfile,'w')
json.dump(
{'nodes': map(lambda x: x.attributes(),g.vs),'links': map(lambda x: x.attributes(),g.es)},
dfh,indent=1)
dfh.close()
print "%s -> %s" % (gml, destfile)
<!DOCTYPE html>
<meta charset="utf-8">
<style>
.menu, .menu li { display: inline; padding:0 4px }
.menu a { text-decoration: none }
.menu a hover { text-decoration: underline }
.menu a.active { color: black; font-weight: bold }
.node {
stroke: #000;
stroke-width: 1.5px;
stroke-opacity: .6;
}
.node.MISSING { stroke:#black; stroke-dasharray:2,2 }
.node.SECRET-NOFORN { stroke: #7f0000; }
.node.SECRET { stroke: #7f0000; }
.node.CONFIDENTIAL-NOFORN { stroke: #00007f; }
.node.CONFIDENTIAL { stroke: #00007f; }
.node.UNCLASSIFIED { stroke: #007f00; }
.node.UNCLASSIFIED-FOR-OFFICIAL-USE-ONLY { stroke: #007f00; }
.node.active {
stroke-opacity: 1;
}
.link {
stroke: #000;
stroke-opacity: .6;
}
</style>
<body>
<div id="header">
Example <a target="_blank" href="http://wlwardiary.github.com/cable2graph/">Cable2Graph</a>
clusters (please see instructions):
</div>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script>
// Helper so that a link doesn't cover the nodes
// returns a line between x1,x2 and y1,y2 that is
// begins r1 "later" and ends r2 "earlier"
// is there a fancy d3 way to do this?!?
function shorten(x1,y1,x2,y2,r1,r2) {
if (x1==y1 && x2==y2)
return {x1:x1,x2:x2,y1:y1,y2:y2};
a = Math.atan(Math.abs(y2-y1)/Math.abs(x2-x1)); // atan can swallow Infinity
return {
x1:x1+(x2>x1?1:-1)*r1*Math.cos(a),
y1:y1+(y2>y1?1:-1)*r1*Math.sin(a),
x2:x2+(x2>x1?-1:1)*r2*Math.cos(a),
y2:y2+(y2>y1?-1:1)*r2*Math.sin(a)
}
}
var menu = [
{name:"Iran",file:"iran.json"},
{name:"Ireland",file:"ireland.json"},
{name:"Jordan",file:"jordan.json"},
{name:"Palestine",file:"palestine.json"},
{name:"Spain",file:"spain.json"},
{name:"Syria",file:"syria.json"}
]
d3.select("#header")
.append("ul").attr("class","menu")
.selectAll("li")
.data(menu)
.enter().append("li")
.append("a").attr("href", "#")
.attr("id", function(d) { return d.name; })
.attr("class", "menu-item")
.text(function(d) { return d.name })
.on("click", function(d) { populate(d.name,d.file); return false; })
var width = 960,
height = 480;
var node_color = d3.scale.category20().domain(d3.range(0,1000));
var force = d3.layout.force()
.charge(-100)
.linkDistance(30)
.size([width, height]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
svg.append("svg:defs")
.append("svg:marker")
.attr("id","arrow-head").attr("viewBox", "0 0 10 10")
.attr("refX", 1).attr("refY", 5)
.attr("markerWidth", 4).attr("markerHeight", 3)
.attr("markerUnit", "strokeWidth").attr("orient", "auto")
.append("svg:polyline")
.style("fill","#000")
.attr("points", "0,0 5,5 0,10 1,5");
function populate(name,file) {
force.stop();
svg.selectAll("line.link").remove();
svg.selectAll("circle.node").remove();
d3.selectAll("a.menu-item").classed("active",false);
d3.select("#"+name).classed("active",true);
d3.json(file, function(error, graph) {
force
.nodes(graph.nodes)
.links(graph.links)
.start();
var link = svg.selectAll("line.link").data(graph.links)
.enter().append("line")
.attr("marker-end","url(#arrow-head)")
.attr("class", "link");
var node = svg.selectAll("circle.node").data(graph.nodes)
.enter().append("circle")
.attr("id", function(d) { return "c"+d.label })
.attr("class", function(d) {return "node "+d.nodeclass; })
.attr("r", 8)
// hash-generated unique colors - less readable (close colors are possible)
//.style("fill", function(d) { return d.color; })
// more readable color scale, but cycles thru 20 colors (duplicates if >20)
.style("fill", function(d) { return node_color(d.colorindex); })
.on("contextmenu",function(d) {
console.log(d);
return false;
})
.on("click",function(d) {
if (d3.event.shiftKey) {
d3.select(this).classed("active",d.fixed = !d.fixed)
} else {
if (d.uri) {
window.open(d.uri);
} else {
alert('Missing cable');
}
}
})
.call(force.drag);
var link_stroke = d3.scale.linear()
.domain([
d3.min(graph.links,function(d) { return d.betweenness || 0 }),
d3.max(graph.links,function(d) { return d.betweenness || 0 })
])
.range([2,6]);
link.property("stroke_width", function(d) { return link_stroke(d.betweenness || 0); });
link.style("stroke-width", function(d) { return this.stroke_width+"px"; });
var node_stroke = d3.scale.linear()
.domain([
d3.min(graph.nodes,function(d) { return d.authority || 0 }),
d3.max(graph.nodes,function(d) { return d.authority || 0 })
])
.range([2,6]);
node.style("stroke-width", function(d) { return node_stroke(d.authority || 0)+"px"; });
node.append("title")
.text(function(d) {
return d.label + (d.date?" ("+d.date+(d.classification?", "+d.classification:"")+")":"") + (d.subjects?":\n"+d.subjects:"");
});
force.on("tick", function() {
link.property("shorty", function(d) {
return shorten(d.source.x,d.source.y,d.target.x,d.target.y,
parseFloat(d3.select('#c'+d.source.label).attr("r"))+3,
parseFloat(d3.select("#c"+d.target.label).attr("r"))+3+this.stroke_width
);
})
.attr("x1", function(d) { return this.shorty.x1 })
.attr("y1", function(d) { return this.shorty.y1 })
.attr("x2", function(d) { return this.shorty.x2 })
.attr("y2", function(d) { return this.shorty.y2 })
// The https://gist.github.com/1129492 trick to avoid out-of-the-box nodes
node.attr("cx", function(d) { return d.x = Math.max(12, Math.min(width - 12, d.x)); })
.attr("cy", function(d) { return d.y = Math.max(12, Math.min(height - 12, d.y)); });
});
});
}
populate("Palestine","palestine.json")
</script>
{ "nodes": [ { "degree": 1.0, "classification": "UNCLASSIFIED", "missing": 0.0, "color": "hsl(32,87%,91%)", "timestamp": 1259130000.0, "id": "n230647", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09ALGIERS1048.html", "authority": 4.34555e-16, "label": "09ALGIERS1048", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "ALGIERS", "date": "2009-11-25", "colorindex": 0, "subjects": "ALGERIA ON IAEA - IRAN NEXT STEPS", "nodeclass": "UNCLASSIFIED" }, { "degree": 1.0, "classification": "UNCLASSIFIED//FOR OFFICIAL USE ONLY", "missing": 0.0, "color": "hsl(80,91%,58%)", "timestamp": 1259860000.0, "id": "n231762", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/12/09ANKARA1719.html", "authority": 5.57221e-17, "label": "09ANKARA1719", "caption": "", "betweenness": 0.0, "pagerank": 2.10783e-06, "place": "ANKARA", "date": "2009-12-03", "colorindex": 56, "subjects": "TURKEY ON ISRAEL'S SETTLEMENT MORATORIUM", "nodeclass": "UNCLASSIFIED-FOR-OFFICIAL-USE-ONLY" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(28,87%,95%)", "timestamp": 1259170000.0, "id": "n234472", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09ATHENS1655.html", "authority": 4.34555e-16, "label": "09ATHENS1655", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "ATHENS", "date": "2009-11-25", "colorindex": 35, "subjects": "AMBASSADOR AND DROUTSAS DISCUSS MACEDONIA, IRAN, TURKEY, MORE", "nodeclass": "CONFIDENTIAL" }, { "degree": 2.0, "classification": "UNCLASSIFIED//FOR OFFICIAL USE ONLY", "missing": 0.0, "color": "hsl(43,99%,77%)", "timestamp": 1259940000.0, "id": "n239816", "constraint": 0.5, "uri": "https://wikileaks.org/cable/2009/12/09BERLIN1544.html", "authority": 5.51288e-17, "label": "09BERLIN1544", "caption": "", "betweenness": 1.99914e-05, "pagerank": 4.13974e-06, "place": "BERLIN", "date": "2009-12-04", "colorindex": 15, "subjects": "GERMANY TRACKS U.S. MESSAGE ON ISRAEL'S SETTLEMENT MORATORIUM", "nodeclass": "UNCLASSIFIED-FOR-OFFICIAL-USE-ONLY" }, { "degree": 4.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(219,90%,56%)", "timestamp": 1259080000.0, "id": "n240332", "constraint": 0.25, "uri": "https://wikileaks.org/cable/2009/11/09BERN505.html", "authority": 4.37585e-16, "label": "09BERN505", "caption": "", "betweenness": 0.000119845, "pagerank": 6.05623e-06, "place": "BERN", "date": "2009-11-24", "colorindex": 28, "subjects": "IAEA BOG: SWISS VIEWS REGARDING IRAN, SYRIA, AND THE ANGARSK RESERVE CONCEPT", "nodeclass": "CONFIDENTIAL" }, { "degree": 1.0, "classification": "UNCLASSIFIED", "missing": 0.0, "color": "hsl(88,87%,99%)", "timestamp": 1259180000.0, "id": "n241042", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09BOGOTA3439.html", "authority": 4.34555e-16, "label": "09BOGOTA3439", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "BOGOTA", "date": "2009-11-25", "colorindex": 53, "subjects": "DEMARCHE DELIVERED: U.S. POSTURE ON IRAN NUCLEAR PROGRAM", "nodeclass": "UNCLASSIFIED" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(98,94%,53%)", "timestamp": 1259320000.0, "id": "n241351", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09BRASILIA1371.html", "authority": 4.34555e-16, "label": "09BRASILIA1371", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "BRASILIA", "date": "2009-11-27", "colorindex": 75, "subjects": "BRAZIL ON IRAN AT IAEA: NOT SUPPORTIVE OF P5+1 TABLING RESOLUTION AT THIS TIME", "nodeclass": "CONFIDENTIAL" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(281,70%,65%)", "timestamp": 1259300000.0, "id": "n242288", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09BRUSSELS1596.html", "authority": 4.34555e-16, "label": "09BRUSSELS1596", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "BRUSSELS", "date": "2009-11-27", "colorindex": 21, "subjects": "BELGIUM: U.S. POSTURE ON IRAN'S NUCLEAR PROGRAM AND NEXT STEPS", "nodeclass": "CONFIDENTIAL" }, { "degree": 4.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(149,52%,67%)", "timestamp": 1259670000.0, "id": "n243170", "constraint": 0.25, "uri": "https://wikileaks.org/cable/2009/12/09BUDAPEST855.html", "authority": 4.35142e-16, "label": "09BUDAPEST855", "caption": "", "betweenness": 0.00136565, "pagerank": 6.30497e-06, "place": "BUDAPEST", "date": "2009-12-01", "colorindex": 27, "subjects": "DAS QUANRUD'S VISIT TO BUDAPEST", "nodeclass": "CONFIDENTIAL" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(147,75%,74%)", "timestamp": 1259140000.0, "id": "n244512", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09CANBERRA1043.html", "authority": 4.34555e-16, "label": "09CANBERRA1043", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "CANBERRA", "date": "2009-11-25", "colorindex": 30, "subjects": "AUSTRALIA AGREES WITH U.S. POSTURE ON IRAN'S NUCLEAR PROGRAM", "nodeclass": "CONFIDENTIAL" }, { "degree": 3.0, "classification": "UNCLASSIFIED//FOR OFFICIAL USE ONLY", "missing": 0.0, "color": "hsl(138,90%,96%)", "timestamp": 1259070000.0, "id": "n246957", "constraint": 0.333333, "uri": "https://wikileaks.org/cable/2009/11/09COPENHAGEN532.html", "authority": 4.3756e-16, "label": "09COPENHAGEN532", "caption": "", "betweenness": 9.98541e-05, "pagerank": 4.4259e-06, "place": "COPENHAGEN", "date": "2009-11-24", "colorindex": 60, "subjects": "DENMARK: MESSAGES DELIVERED FOR IAEA MEETING", "nodeclass": "UNCLASSIFIED-FOR-OFFICIAL-USE-ONLY" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(161,93%,93%)", "timestamp": 1259080000.0, "id": "n247657", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09DARESSALAAM814.html", "authority": 4.34555e-16, "label": "09DARESSALAAM814", "caption": "", "betweenness": 0.0, "pagerank": 1.93937e-06, "place": "DARESSALAAM", "date": "2009-11-24", "colorindex": 51, "subjects": "IRAN/IAEA: TANZANIA AGREES WITH U.S. POSITION", "nodeclass": "CONFIDENTIAL" }, { "degree": 2.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(73,91%,79%)", "timestamp": 1259590000.0, "id": "n248995", "constraint": 0.5, "uri": "https://wikileaks.org/cable/2009/11/09DUBLIN511.html", "authority": 4.3613e-16, "label": "09DUBLIN511", "caption": "", "betweenness": 2.47262e-05, "pagerank": 3.25006e-06, "place": "DUBLIN", "date": "2009-11-30", "colorindex": 69, "subjects": "IRELAND ON IRAN'S NUCLEAR PROGRAM, IAEA'S SYRIA REPORT", "nodeclass": "CONFIDENTIAL" }, { "degree": 1.0, "classification": "CONFIDENTIAL", "missing": 0.0, "color": "hsl(248,77%,69%)", "timestamp": 1259100000.0, "id": "n250716", "constraint": 1.0, "uri": "https://wikileaks.org/cable/2009/11/09GUATEMALA985.html", "authority": 4.34555e-16, "label": "09GUATEMALA985", 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