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Root Error Fixing in D3

<html>
  <head>
    <title>Clustering, betweenness centrality and eigenvector centrality</title>
    <meta charset="utf-8" />
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
    <script src="/emeeks/9915de8989e2a5c34652/7d22d8e4f05e944ced10408ae64579beff3c0858/jsnetworkx.js" type="text/javascript"></script>
    <script src="https://cdn.jsdelivr.net/gh/eligrey/canvas-toblob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toblob.js"></script>
    <script src="https://cdn.jsdelivr.net/gh/eligrey/filesaver.js/e9d941381475b5df8b7d7691013401e171014e89/filesaver.min.js"></script>
    <script src="https://d3js.org/d3.v3.min.js"></script>

var color_map = {
        "O": "rgb(255, 165, 0)", 
        "P": "rgb(255, 192, 203)", 
        "B": "rgb(0, 0, 255)", 
        "W": "rgb(255, 255, 255)", 
        "G": "rgb(0, 128, 0)", 
        "R": "rgb(255, 0, 0)", 
        "M": "rgb(255,0,255)", 
        "C": "rgb(0,255,255)"
      }

var canvas_width = 940,
          canvas_height = 480, 
          svg_rule_width = 1.00 * canvas_width,           
          svg_rule_height = canvas_height - 30.23;
      
      d3.select('#saveButton').on('click', function(){
        var svgString = getSVGString(d3.select("svg.rule").node());
        svgString2Image( svgString, 10*svg_rule_width, 10*svg_rule_height, 'png', save ); // passes Blob and filesize String to the callback

function save( dataBlob, filesize ){
          saveAs( dataBlob, 'D3 PNG.png' ); // FileSaver.js function
        }
      });

d3.select("div#canvas")
        .style("width", canvas_width + 'px')
        .style("height", canvas_height + 'px')
        .select("svg.rule")
        .style("width", svg_rule_width + 'px')
        .style("height", svg_rule_height + 'px');

function encode_rule(rule) {
        rule = rule.replace("==", "_eq_");
        rule = rule.replace("!=", "_neq_");
        rule = rule.replace(">", "_g_");
        rule = rule.replace(">=", "_ge_");
        rule = rule.replace("<", "_l_");
        rule = rule.replace("<=", "_le_");

vov = rule.split("_");

return {
          'rule': rule, 
          'variable': vov[0], 
          'operator': vov[1], 
          'value': vov[2]
        };
      }

function random_int(min, max) {
        return Math.floor(Math.random() * (max - min + 1)) + min;
      }

d3.json(rule_graph_file, function(error, graph) {
        if (error) throw error;

graph.nodes.forEach(function(n) {
          r = encode_rule(n.id);
          n.rule = r.rule;
          n.variable = r.variable;
          n.operator = r.operator;
          n.value = r.value;
        });

var nodeHash = graph.nodes.reduce(function(map, n) {
          map[n.id] = n;
          return map;
        }, {});

graph.links.forEach(function(e, i) {
          e.id = i;
          e.source = nodeHash[e.source];
          e.target = nodeHash[e.target];
          e.weight = 5;
        });

create_rule_network(graph.nodes, graph.links);
      });

function create_rule_network(nodes, edges) {
        var rule_force = d3.layout.force()
        .nodes(nodes)
        .links(edges)
        .size([svg_rule_width, svg_rule_height])
        .charge(-300)
        .chargeDistance(100)
        .gravity(0.05)
        .on("tick", update_rule_network)
        .on('end', function() { 
          console.log('Layout finished. Start processing data...'); 
          process_data_error(data_error_file, nodes, edges);
        });

var rule_drag = rule_force.drag();

var svg = d3.select("svg.rule"), 
            g = svg.append("g");

svg.append("svg:defs").selectAll("marker")
          .data(["end"])
          .enter().append("svg:marker")
          .attr("id", String)
          .attr("viewBox", "0 -5 10 10")
          .attr("refX", 15)
          .attr("refY", -1.5)
          .attr("markerWidth", 6)
          .attr("markerHeight", 6)
          .attr("orient", "auto")
          .append("svg:path")
          .attr("d", "M0,-5L10,0L0,5")
          .attr("class", "arrow");

g.append("g").attr("class", "edges")
          .selectAll("g.edge")
          .data(edges, function (d) {return d.id})
          .enter()
          .append("g")
          .attr("class", "edge")
          .append("line")
          .attr("marker-end", "url(#end)");

var g_nodes = g.append("g").attr("class", "nodes")
        .selectAll("g.node")
        .data(nodes)
        .enter()
        .append("g")
        .attr("class", function (d) {return "node " + d.rule})
        .attr("variable", function (d) {return d.variable})
        .attr("operator", function (d) {return d.operator})
        .attr("value", function (d) {return d.value})
        .call(rule_drag);

g_nodes.append("circle")
          .attr("r", 6);

g_nodes.append("text")
          .style("text-anchor", "middle")
          .attr("y", 3)
          .style("stroke-width", "1px")
          .style("stroke-opacity", 0.75)
          .style("stroke", "white")
          .style("font-size", "8px")
          .text(function (d) {return d.id})
          .style("pointer-events", "none");

g_nodes.append("text")
          .style("text-anchor", "middle")
          .attr("y", 3)
          .style("font-size", "8px")
          .text(function (d) {return d.id})
          .style("pointer-events", "none");

rule_force.start(); 
      }

function update_rule_network(e) {
        d3.select("svg.rule").selectAll("line")
          .attr("x1", function (d) {return d.source.x})
          .attr("y1", function (d) {return d.source.y})
          .attr("x2", function (d) {return d.target.x})
          .attr("y2", function (d) {return d.target.y});

d3.select("svg.rule").selectAll("g.node")
          .attr("transform", function (d) {
          return "translate(" + d.x + "," + d.y + ")";
        });
      }

function process_data_error(data_error_file, nodes, edges) {        
        d3.csv(data_error_file, function(error, data_error) {
          process_record_wrapper(data_error, 0);
        });
      }

function process_record_wrapper(data_error, i) {
        if (i >= data_error.length) return;
        if (i > 10) return;

console.log("+++++ PROCESSING RECORD #" + (i+1) + " +++++");

process_record(data_error[i], function() {
          process_record_wrapper(data_error, i+1);
        });
      }

function process_record(data, finish_callback) {
        var nodes_el = d3.selectAll(".node")
        .each(function(d) {
          d.input = data[d.variable];
          if (d.input == null || d.input == "") d.input = "NULL";
        });

start_evaluation(Number.MAX_SAFE_INTEGER, finish_callback);
      }

function start_evaluation(previous_error, finish_callback) {
        var current_error = previous_error, 
            init_color_it = 0;

d3.selectAll(".node")
          .selectAll("circle")
          .each(function(d) {
          if (d.id.startsWith("G") && d.id.endsWith("-in")) {
            d.color = "P";
          } else if(d.id.startsWith("G") && d.id.endsWith("-out")) {
            d.color = "B";
          } else if(d.id.startsWith("C")) {
            d.color = "W";
          } else {
            d.color = "O";
          }

init_color_it += 1;
        })
          .transition()
          .duration(200)
          .style("fill", function(d) {
          return color_map[d.color]
        })
          .delay(100)
          .each("end", function(d) {
          init_color_it -= 1;

if (init_color_it == 0) {
            validate_input(this, d, function() {
              console.log("   => Set valid rule(s) to " + color_map["G"]);

calculate_centrality(function(error_rules) {
                current_error = error_rules.length;
                console.log("   => Set error rule(s): " + error_rules.join(", ") + 
                            " to " + color_map["M"]);

}, function(max_centrality_nodes) {
                console.log("   => Max centrality rule(s): " + max_centrality_nodes.join(", "));

make_revision(max_centrality_nodes, function(selected_node) {
                  console.log("   => Selected rule: " + selected_node);

}, function(variable, old_val, new_val) {
                  console.log("   => Value of variable " + variable + 
                              " is revised from " + old_val + 
                              " to " + new_val);

}, function() {
                  if (current_error < previous_error) {
                    start_evaluation(current_error, finish_callback);
                  } else {
                    console.log("FINISH");
                    finish_callback();
                  }
                });
              });
            });
          }
        });
      }

function validate_input(el, d, callback) {
        var val_inp_iter = 0;

d3.selectAll(".node")
          .selectAll("circle")
          .filter(function(d) {
          if (d.id.startsWith("R")) return true;
          else return false;
        })
          .each(function(d) {
          d.valid = false;
        }).each(function(d) {
          var str_value = d.input, 
              val = Number(str_value), 
              rule_val = Number(d.value);

if (d.value == "NULL" && str_value == "NULL") d.valid = true;
          if (d.operator == "eq") {
            if (d.value.indexOf("-") !== -1) {
              var min_max = d.value.split("-");
              try {
                var min = Number(min_max[0]),
                    max = Number(min_max[1]);
                if (val >= min && val <= max) d.valid = true;
              } catch (err) {}
            } 
            else if (d.value == str_value) d.valid = true;
          } 
          if (val != NaN && rule_val != NaN) {
            if (d.operator == "g") {
              if (val > rule_val) d.valid = true;
            } else if (d.operator == "ge") {
              if (val >= rule_val) d.valid = true;
            } else if (d.operator == "l") {
              if (val < rule_val) d.valid = true;
            } else if (d.operator == "le") {
              if (val <= rule_val) d.valid = true;
            }
          }
        }).filter(function(d) {
          if (d.valid) return true;
          else false;
        })
          .each(function(d) {
          d.color = "G";
          val_inp_iter += 1;
        }).transition()
          .duration(500)
          .style("fill", function(d) {
          return color_map[d.color]
        }).delay(200)
          .each("end", function(d) {
          // Greenify the related group too
          d3.selectAll("." + d.group + "-in,." + d.group + "-out")
            .selectAll("circle")
            .each(function(d) {
            d.valid = true;
            d.color = "G";
          })
            .transition()
            .duration(500)
            .style("fill", function(d) {
            return color_map[d.color];
          })
            .delay(200)
            .each("end", function(d) {});

val_inp_iter -= 1;
          if (val_inp_iter == 0) {
            callback();
          }
        });
      }

function calculate_centrality(err_callback, cent_callback) {
        var hyper_edges = {}, 
            error_rules = [],
            rule_error_iter = 0;

var err_nodes = d3.selectAll(".node")
        .selectAll("circle")
        .filter(function(d) {
          if (d.id.startsWith("C")) return true;
          return false
        }).each(function(d) {
          var source_variables = [], 
              target_variables = [], 
              is_target_error = false;

in_edges = d3.selectAll(".edge")
            .filter(function(e) {
            if (e.target.id == d.id) return true;
            else return false;
          }).each(function(f) {
            // console.log(d.variable, f.source.id, f.source.color)

if (f.source.color == "G") {

if (f.source.rule.startsWith("G")) {
                d3.selectAll(".edge")
                  .filter(function(e) {
                  if (e.target.id == f.source.id) return true;
                  return false;
                })
                  .each(function(g) {
                  source_variables.push(g.source.variable);
                });
              } else {
                source_variables.push(f.source.variable);
              }
            }
          });

out_edges = d3.selectAll(".edge")
            .filter(function(e) {
            if (e.source.id == d.id) return true;
            else return false;
          }).each(function(d) {
            if (d.target.rule.startsWith("G")) {
              d3.selectAll(".edge")
                .filter(function(e) {
                if (e.source.id == d.target.id) return true;
                return false;
              })
                .each(function(d) {
                target_variables.push(d.target.variable);
              });
            } else {
              target_variables.push(d.target.variable);
            }

if (d.target.color == "G") is_target_error = true;
          });

// console.log(d.rule, source_variables, target_variables)

d.source_variables = source_variables;
          d.target_variables = target_variables;

if (source_variables.length != 0 && !is_target_error) {
            d.error = true;
            d.color = "M";
          }

else d.error = false;
        })
        .each(function(d) {          
          var hyper_edge = [];
          if (d.error) {
            d.source_variables.forEach(function(sv) {
              d.target_variables.forEach(function(tv) {
                if(! hyper_edge.includes(sv)) {
                  hyper_edge.push(sv);
                }
                if(! hyper_edge.includes(tv)) {
                  hyper_edge.push(tv);
                }
              });
            });

// console.log("Hyperedges : ", d.rule, hyper_edge);

d.hyper_edge = hyper_edge;
            hyper_edges[d.rule] = hyper_edge;
            error_rules.push(d.id);;
          }
        })
        .filter(function(d) {
          return d.error;
        })
        .each(function(d) {
          rule_error_iter += 1;
        })
        .transition()
        .duration(1000)
        .attr("r", 12)
        .style("fill", function(d) {
          return color_map[d.color];
        })
        .delay(200)
        .each("end", function(d) {
          d3.select(this)
            .transition()
            .duration(1000)
            .attr("r", 6);

rule_error_iter -= 1;
          if (rule_error_iter == 0) {
            err_callback(error_rules);

var max = -1, 
                selected_nodes = [];
            max_centrality_nodes.forEach(function(n) {
              var count = 0;
              Object.keys(c_hyper_edges).forEach(function(k) {
                var he = c_hyper_edges[k];
                if (he.includes(n)) {
                  count += 1;
                }
              });

// console.log(n, count)
              if (count > max) {
                selected_nodes = [];
                selected_nodes.push(n);
                max = count;
              } else if (count == max) {
                selected_nodes.push(n);
              }
            });
            max_centrality_nodes = selected_nodes;

cent_callback(max_centrality_nodes)
          }
        });
      }

function make_revision(max_centrality_nodes, cdt_callback, change_callback, finish_callback) {
        var revision_iter = 0, 
            candidate = 0;

var sel_cdt_idx = random_int(0, candidate-1)

candidate_nodes.filter(function(d) {
          if (d.candidate == sel_cdt_idx) {
            d.color = "R";
            cdt_callback(d.id)
            return true;
          }
          return false;
        })
          .each(function() {
          revision_iter += 1;
        })
          .transition()
          .duration(1000)
          .attr("r", 12)
          .style("fill", function(d) {
          return color_map[d.color];
        })
          .delay(200)        
          .each("end", function(d) {
          d3.select(this)
            .transition()
            .duration(1000)
            .attr("r", 6)
            .delay(200)
            .each("end", function(e) {
            var val = d.value;
            if (val.indexOf("-") !== -1) {
              val = val.split("-")[0];
              val = Number(val);
            } else {
              val = Number(val);
            }
            if (d.operator == "g") {
              val += val;
            } else if (d.operator == "l") {
              val -= val;
            }

change_callback(d.variable, d.input, val);
            d.input = val;

// revision_iter -= 1;
            // if (revision_iter == 0) {
            finish_callback();
            // }
          });
        });
      }

function getSVGString( svgNode ) {
        svgNode.setAttribute('xlink', 'https://www.w3.org/1999/xlink');
        var cssStyleText = getCSSStyles( svgNode );
        appendCSS( cssStyleText, svgNode );

var serializer = new XMLSerializer();
        var svgString = serializer.serializeToString(svgNode);
        svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
        svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix

return svgString;

function getCSSStyles( parentElement ) {
          var selectorTextArr = [];

// Add Parent element Id and Classes to the list
          selectorTextArr.push( '#'+parentElement.id );
          for (var c = 0; c < parentElement.classList.length; c++)
            if ( !contains('.'+parentElement.classList[c], selectorTextArr) )
              selectorTextArr.push( '.'+parentElement.classList[c] );

// Add Children element Ids and Classes to the list
          var nodes = parentElement.getElementsByTagName("*");
          for (var i = 0; i < nodes.length; i++) {
            var id = nodes[i].id;
            if ( !contains('#'+id, selectorTextArr) )
              selectorTextArr.push( '#'+id );

var classes = nodes[i].classList;
            for (var c = 0; c < classes.length; c++)
              if ( !contains('.'+classes[c], selectorTextArr) )
                selectorTextArr.push( '.'+classes[c] );
          }

// Extract CSS Rules
          var extractedCSSText = "";
          for (var i = 0; i < document.styleSheets.length; i++) {
            var s = document.styleSheets[i];

try {
              if(!s.cssRules) continue;
            } catch( e ) {
              if(e.name !== 'SecurityError') throw e; // for Firefox
              continue;
            }

var cssRules = s.cssRules;
            for (var r = 0; r < cssRules.length; r++) {
              if ( contains( cssRules[r].selectorText, selectorTextArr ) )
                extractedCSSText += cssRules[r].cssText;
            }
          }

return extractedCSSText;

function contains(str,arr) {
            return arr.indexOf( str ) === -1 ? false : true;
          }

}

function appendCSS( cssText, element ) {
          var styleElement = document.createElement("style");
          styleElement.setAttribute("type","text/css"); 
          styleElement.innerHTML = cssText;
          var refNode = element.hasChildNodes() ? element.children[0] : null;
          element.insertBefore( styleElement, refNode );
        }
      }

function svgString2Image( svgString, width, height, format, callback ) {
        var format = format ? format : 'png';

var imgsrc = 'data:image/svg+xml;base64,'+ btoa( unescape( encodeURIComponent( svgString ) ) ); // Convert SVG string to data URL

var canvas = document.createElement("canvas");
        var context = canvas.getContext("2d");

canvas.width = width;
        canvas.height = height;

var image = new Image();
        image.onload = function() {
          context.clearRect ( 0, 0, width, height );
          context.drawImage(image, 0, 0, width, height);

canvas.toBlob( function(blob) {
            var filesize = Math.round( blob.length/1024 ) + ' KB';
            if ( callback ) callback( blob, filesize );
          });

};

image.src = imgsrc;
      }
    </script>
  </footer>
</html>

Updated missing url https://bl.ocks.org/emeeks/raw/9915de8989e2a5c34652/7d22d8e4f05e944ced10408ae64579beff3c0858/jsnetworkx.js to /emeeks/9915de8989e2a5c34652/7d22d8e4f05e944ced10408ae64579beff3c0858/jsnetworkx.js

Updated missing url https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js to https://cdn.jsdelivr.net/gh/eligrey/canvas-toblob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toblob.js

Updated missing url https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js to https://cdn.jsdelivr.net/gh/eligrey/filesaver.js/e9d941381475b5df8b7d7691013401e171014e89/filesaver.min.js

https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js

https://bl.ocks.org/emeeks/raw/9915de8989e2a5c34652/7d22d8e4f05e944ced10408ae64579beff3c0858/jsnetworkx.js

https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js

https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js

https://d3js.org/d3.v3.min.js