d3.json: “Uncaught TypeError: Cannot read property 'children' of undefined”

I am trying out d3 as a tool for representing biological data.

I am trying to open the following example in my chrome browser so that I can understand how it works. Unfortunately I get the following error "Uncaught TypeError: Cannot read property 'children' of undefined ".

http://bl.ocks.org/4063550

If you click the link, the source code for both the .html file and the .json file are displayed below the output of the visualization. Clearly the visualization is working on the above page. I'm not sure what I could be doing wrong.

I have copied both the index.html file and the flare.json file to a directory on a web server. If I tried to load it from a local file I got another error: XMLHttpRequest cannot load file:///C:/Users/(..omitted..)/flare.json. Cross origin requests are only supported for HTTP.

The flare.json file indeed can be loaded from the webserver (I can see its text content). It contains the tree data I am trying to graph.

Clearly the flare.json file begins as follows:

{ "name": "flare", "children": [ ...

Unfortunately d3.json is having trouble parsing this information...

If it helps, here is the .html file I am trying to open in Chrome:

<!DOCTYPE html>

<html>
<head>
    <title>heirarchical graph</title>


<meta charset="utf-8">
<style>

.node circle {
  fill: #fff;
  stroke: steelblue;
  stroke-width: 1.5px;
}

.node {
  font: 10px sans-serif;
}

.link {
  fill: none;
  stroke: #ccc;
  stroke-width: 1.5px;
}

</style>
    <script type="text/javascript"
            src="https://raw.github.com/mbostock/d3/master/d3.v2.min.js">
    </script>

    </head>
    <body>
    <script>

var diameter = 960;

var tree = d3.layout.tree()
    .size([360, diameter / 2 - 120])
    .separation(function(a, b) { return (a.parent == b.parent ? 1 : 2) / a.depth; });

var diagonal = d3.svg.diagonal.radial()
    .projection(function(d) { return [d.y, d.x / 180 * Math.PI]; });

var svg = d3.select("body").append("svg")
    .attr("width", diameter)
    .attr("height", diameter - 150)
  .append("g")
    .attr("transform", "translate(" + diameter / 2 + "," + diameter / 2 + ")");

d3.json("flare.json", function(error, root) {
  var nodes = tree.nodes(root),
      links = tree.links(nodes);

  var link = svg.selectAll(".link")
      .data(links)
    .enter().append("path")
      .attr("class", "link")
      .attr("d", diagonal);

  var node = svg.selectAll(".node")
      .data(nodes)
    .enter().append("g")
      .attr("class", "node")
      .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")"; })

  node.append("circle")
      .attr("r", 4.5);

  node.append("text")
      .attr("dy", ".31em")
      .attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
      .attr("transform", function(d) { return d.x < 180 ? "translate(8)" : "rotate(180)translate(-8)"; })
      .text(function(d) { return d.name; });
});

d3.select(self.frameElement).style("height", diameter - 150 + "px");

</script>
</body>

</html>

And, here is the flare.json file:

{
 "name": "flare",
 "children": [
  {
   "name": "analytics",
   "children": [
    {
     "name": "cluster",
     "children": [
      {"name": "AgglomerativeCluster", "size": 3938},
      {"name": "CommunityStructure", "size": 3812},
      {"name": "HierarchicalCluster", "size": 6714},
      {"name": "MergeEdge", "size": 743}
     ]
    },
    {
     "name": "graph",
     "children": [
      {"name": "BetweennessCentrality", "size": 3534},
      {"name": "LinkDistance", "size": 5731},
      {"name": "MaxFlowMinCut", "size": 7840},
      {"name": "ShortestPaths", "size": 5914},
      {"name": "SpanningTree", "size": 3416}
     ]
    },
    {
     "name": "optimization",
     "children": [
      {"name": "AspectRatioBanker", "size": 7074}
     ]
    }
   ]
  },
  {
   "name": "animate",
   "children": [
    {"name": "Easing", "size": 17010},
    {"name": "FunctionSequence", "size": 5842},
    {
     "name": "interpolate",
     "children": [
      {"name": "ArrayInterpolator", "size": 1983},
      {"name": "ColorInterpolator", "size": 2047},
      {"name": "DateInterpolator", "size": 1375},
      {"name": "Interpolator", "size": 8746},
      {"name": "MatrixInterpolator", "size": 2202},
      {"name": "NumberInterpolator", "size": 1382},
      {"name": "ObjectInterpolator", "size": 1629},
      {"name": "PointInterpolator", "size": 1675},
      {"name": "RectangleInterpolator", "size": 2042}
     ]
    },
    {"name": "ISchedulable", "size": 1041},
    {"name": "Parallel", "size": 5176},
    {"name": "Pause", "size": 449},
    {"name": "Scheduler", "size": 5593},
    {"name": "Sequence", "size": 5534},
    {"name": "Transition", "size": 9201},
    {"name": "Transitioner", "size": 19975},
    {"name": "TransitionEvent", "size": 1116},
    {"name": "Tween", "size": 6006}
   ]
  },
  {
   "name": "data",
   "children": [
    {
     "name": "converters",
     "children": [
      {"name": "Converters", "size": 721},
      {"name": "DelimitedTextConverter", "size": 4294},
      {"name": "GraphMLConverter", "size": 9800},
      {"name": "IDataConverter", "size": 1314},
      {"name": "JSONConverter", "size": 2220}
     ]
    },
    {"name": "DataField", "size": 1759},
    {"name": "DataSchema", "size": 2165},
    {"name": "DataSet", "size": 586},
    {"name": "DataSource", "size": 3331},
    {"name": "DataTable", "size": 772},
    {"name": "DataUtil", "size": 3322}
   ]
  },
  {
   "name": "display",
   "children": [
    {"name": "DirtySprite", "size": 8833},
    {"name": "LineSprite", "size": 1732},
    {"name": "RectSprite", "size": 3623},
    {"name": "TextSprite", "size": 10066}
   ]
  },
  {
   "name": "flex",
   "children": [
    {"name": "FlareVis", "size": 4116}
   ]
  },
  {
   "name": "physics",
   "children": [
    {"name": "DragForce", "size": 1082},
    {"name": "GravityForce", "size": 1336},
    {"name": "IForce", "size": 319},
    {"name": "NBodyForce", "size": 10498},
    {"name": "Particle", "size": 2822},
    {"name": "Simulation", "size": 9983},
    {"name": "Spring", "size": 2213},
    {"name": "SpringForce", "size": 1681}
   ]
  },
  {
   "name": "query",
   "children": [
    {"name": "AggregateExpression", "size": 1616},
    {"name": "And", "size": 1027},
    {"name": "Arithmetic", "size": 3891},
    {"name": "Average", "size": 891},
    {"name": "BinaryExpression", "size": 2893},
    {"name": "Comparison", "size": 5103},
    {"name": "CompositeExpression", "size": 3677},
    {"name": "Count", "size": 781},
    {"name": "DateUtil", "size": 4141},
    {"name": "Distinct", "size": 933},
    {"name": "Expression", "size": 5130},
    {"name": "ExpressionIterator", "size": 3617},
    {"name": "Fn", "size": 3240},
    {"name": "If", "size": 2732},
    {"name": "IsA", "size": 2039},
    {"name": "Literal", "size": 1214},
    {"name": "Match", "size": 3748},
    {"name": "Maximum", "size": 843},
    {
     "name": "methods",
     "children": [
      {"name": "add", "size": 593},
      {"name": "and", "size": 330},
      {"name": "average", "size": 287},
      {"name": "count", "size": 277},
      {"name": "distinct", "size": 292},
      {"name": "div", "size": 595},
      {"name": "eq", "size": 594},
      {"name": "fn", "size": 460},
      {"name": "gt", "size": 603},
      {"name": "gte", "size": 625},
      {"name": "iff", "size": 748},
      {"name": "isa", "size": 461},
      {"name": "lt", "size": 597},
      {"name": "lte", "size": 619},
      {"name": "max", "size": 283},
      {"name": "min", "size": 283},
      {"name": "mod", "size": 591},
      {"name": "mul", "size": 603},
      {"name": "neq", "size": 599},
      {"name": "not", "size": 386},
      {"name": "or", "size": 323},
      {"name": "orderby", "size": 307},
      {"name": "range", "size": 772},
      {"name": "select", "size": 296},
      {"name": "stddev", "size": 363},
      {"name": "sub", "size": 600},
      {"name": "sum", "size": 280},
      {"name": "update", "size": 307},
      {"name": "variance", "size": 335},
      {"name": "where", "size": 299},
      {"name": "xor", "size": 354},
      {"name": "_", "size": 264}
     ]
    },
    {"name": "Minimum", "size": 843},
    {"name": "Not", "size": 1554},
    {"name": "Or", "size": 970},
    {"name": "Query", "size": 13896},
    {"name": "Range", "size": 1594},
    {"name": "StringUtil", "size": 4130},
    {"name": "Sum", "size": 791},
    {"name": "Variable", "size": 1124},
    {"name": "Variance", "size": 1876},
    {"name": "Xor", "size": 1101}
   ]
  },
  {
   "name": "scale",
   "children": [
    {"name": "IScaleMap", "size": 2105},
    {"name": "LinearScale", "size": 1316},
    {"name": "LogScale", "size": 3151},
    {"name": "OrdinalScale", "size": 3770},
    {"name": "QuantileScale", "size": 2435},
    {"name": "QuantitativeScale", "size": 4839},
    {"name": "RootScale", "size": 1756},
    {"name": "Scale", "size": 4268},
    {"name": "ScaleType", "size": 1821},
    {"name": "TimeScale", "size": 5833}
   ]
  },
  {
   "name": "util",
   "children": [
    {"name": "Arrays", "size": 8258},
    {"name": "Colors", "size": 10001},
    {"name": "Dates", "size": 8217},
    {"name": "Displays", "size": 12555},
    {"name": "Filter", "size": 2324},
    {"name": "Geometry", "size": 10993},
    {
     "name": "heap",
     "children": [
      {"name": "FibonacciHeap", "size": 9354},
      {"name": "HeapNode", "size": 1233}
     ]
    },
    {"name": "IEvaluable", "size": 335},
    {"name": "IPredicate", "size": 383},
    {"name": "IValueProxy", "size": 874},
    {
     "name": "math",
     "children": [
      {"name": "DenseMatrix", "size": 3165},
      {"name": "IMatrix", "size": 2815},
      {"name": "SparseMatrix", "size": 3366}
     ]
    },
    {"name": "Maths", "size": 17705},
    {"name": "Orientation", "size": 1486},
    {
     "name": "palette",
     "children": [
      {"name": "ColorPalette", "size": 6367},
      {"name": "Palette", "size": 1229},
      {"name": "ShapePalette", "size": 2059},
      {"name": "SizePalette", "size": 2291}
     ]
    },
    {"name": "Property", "size": 5559},
    {"name": "Shapes", "size": 19118},
    {"name": "Sort", "size": 6887},
    {"name": "Stats", "size": 6557},
    {"name": "Strings", "size": 22026}
   ]
  },
  {
   "name": "vis",
   "children": [
    {
     "name": "axis",
     "children": [
      {"name": "Axes", "size": 1302},
      {"name": "Axis", "size": 24593},
      {"name": "AxisGridLine", "size": 652},
      {"name": "AxisLabel", "size": 636},
      {"name": "CartesianAxes", "size": 6703}
     ]
    },
    {
     "name": "controls",
     "children": [
      {"name": "AnchorControl", "size": 2138},
      {"name": "ClickControl", "size": 3824},
      {"name": "Control", "size": 1353},
      {"name": "ControlList", "size": 4665},
      {"name": "DragControl", "size": 2649},
      {"name": "ExpandControl", "size": 2832},
      {"name": "HoverControl", "size": 4896},
      {"name": "IControl", "size": 763},
      {"name": "PanZoomControl", "size": 5222},
      {"name": "SelectionControl", "size": 7862},
      {"name": "TooltipControl", "size": 8435}
     ]
    },
    {
     "name": "data",
     "children": [
      {"name": "Data", "size": 20544},
      {"name": "DataList", "size": 19788},
      {"name": "DataSprite", "size": 10349},
      {"name": "EdgeSprite", "size": 3301},
      {"name": "NodeSprite", "size": 19382},
      {
       "name": "render",
       "children": [
        {"name": "ArrowType", "size": 698},
        {"name": "EdgeRenderer", "size": 5569},
        {"name": "IRenderer", "size": 353},
        {"name": "ShapeRenderer", "size": 2247}
       ]
      },
      {"name": "ScaleBinding", "size": 11275},
      {"name": "Tree", "size": 7147},
      {"name": "TreeBuilder", "size": 9930}
     ]
    },
    {
     "name": "events",
     "children": [
      {"name": "DataEvent", "size": 2313},
      {"name": "SelectionEvent", "size": 1880},
      {"name": "TooltipEvent", "size": 1701},
      {"name": "VisualizationEvent", "size": 1117}
     ]
    },
    {
     "name": "legend",
     "children": [
      {"name": "Legend", "size": 20859},
      {"name": "LegendItem", "size": 4614},
      {"name": "LegendRange", "size": 10530}
     ]
    },
    {
     "name": "operator",
     "children": [
      {
       "name": "distortion",
       "children": [
        {"name": "BifocalDistortion", "size": 4461},
        {"name": "Distortion", "size": 6314},
        {"name": "FisheyeDistortion", "size": 3444}
       ]
      },
      {
       "name": "encoder",
       "children": [
        {"name": "ColorEncoder", "size": 3179},
        {"name": "Encoder", "size": 4060},
        {"name": "PropertyEncoder", "size": 4138},
        {"name": "ShapeEncoder", "size": 1690},
        {"name": "SizeEncoder", "size": 1830}
       ]
      },
      {
       "name": "filter",
       "children": [
        {"name": "FisheyeTreeFilter", "size": 5219},
        {"name": "GraphDistanceFilter", "size": 3165},
        {"name": "VisibilityFilter", "size": 3509}
       ]
      },
      {"name": "IOperator", "size": 1286},
      {
       "name": "label",
       "children": [
        {"name": "Labeler", "size": 9956},
        {"name": "RadialLabeler", "size": 3899},
        {"name": "StackedAreaLabeler", "size": 3202}
       ]
      },
      {
       "name": "layout",
       "children": [
        {"name": "AxisLayout", "size": 6725},
        {"name": "BundledEdgeRouter", "size": 3727},
        {"name": "CircleLayout", "size": 9317},
        {"name": "CirclePackingLayout", "size": 12003},
        {"name": "DendrogramLayout", "size": 4853},
        {"name": "ForceDirectedLayout", "size": 8411},
        {"name": "IcicleTreeLayout", "size": 4864},
        {"name": "IndentedTreeLayout", "size": 3174},
        {"name": "Layout", "size": 7881},
        {"name": "NodeLinkTreeLayout", "size": 12870},
        {"name": "PieLayout", "size": 2728},
        {"name": "RadialTreeLayout", "size": 12348},
        {"name": "RandomLayout", "size": 870},
        {"name": "StackedAreaLayout", "size": 9121},
        {"name": "TreeMapLayout", "size": 9191}
       ]
      },
      {"name": "Operator", "size": 2490},
      {"name": "OperatorList", "size": 5248},
      {"name": "OperatorSequence", "size": 4190},
      {"name": "OperatorSwitch", "size": 2581},
      {"name": "SortOperator", "size": 2023}
     ]
    },
    {"name": "Visualization", "size": 16540}
   ]
  }
 ]
}

Answers:

Answer

The code is from d3.v3 but it's pointing to d3.v2, which does not use the error call in the d3.json function.

Answer

In order to get it to work I had to replace the line

d3.json("flare.json", function(error, root) {

with

d3.json("flare.json", function(root) {

I used my intuition here and I still do not understand how it worked on the example website and not mine, or what the true significance of my change in the code is. If you know how to answer this in a more in-depth fashion, please contribute and I will accept your answer.

Answer

It's because the returned json object is received by the first parameter of the function. It might because of the versions of d3.

Answer

Had the same exact error. The solution is pretty simple: You are not providing a JSON object array. You said your JSON begun as follows:

{ "name": "flare", "children": [ ...

Please change so change is begins as follows:

[{ "name": "flare", "children": [ ...}]

That way D3 will be able to locate the "first child"

Answer
<script>
        function liveProject() {
           var  a=200;
           this. x=600;
           this. y=300;
           this. z= function () {
               return this.x+this.y;
           }
        }
        var lp=new liveProject();
        document.write(lp.z());
    </script>

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