Updating directed graph

<!DOCTYPE html>
<svg width="960" height="700"></svg>
<script src="https://d3js.org/d3.v4.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.4/lodash.min.js"></script>
<style>
  .link {
    fill: none;
  }
</style>
<script>
var svg = d3.select("svg"),
    width = +svg.attr("width"),
    height = +svg.attr("height"),
    color = ['blue', 'red'];
  
var defs = svg.append('svg:defs');
    defs.append('svg:marker')
      .attr('id', 'end-arrow')
      .attr('viewBox', '0 -5 10 10')
      .attr('refX', 16)
    	.attr('refY', -1)
      .attr('markerWidth', 6)
      .attr('markerHeight', 6)
      .attr('orient', 'auto')
      .append('svg:path')
      .attr('d', 'M0,-5L10,0L0,5')
    	.attr('fill', '#666');

var nodes = [],
    links = [],
    i = 1;

const getLink = (link) => {
  const {source: s, target: t} = link;
  var source = nodes.find(n => n.id === s);
  var target = nodes.find(n => n.id === t);
  return { source, target };
}

d3.json('000.json', (err, data) => {
  nodes = _.cloneDeep(data.nodes);
  updateNodes(nodes);

var simulation = d3.forceSimulation(nodes)
    .force("charge", d3.forceManyBody().strength(-100))
    .force("link", d3.forceLink(links).distance(50))
    .force("x", d3.forceX())
    .force("y", d3.forceY())
    .alphaTarget(1)
    .on("tick", ticked);

var g = svg.append("g").attr("transform", "translate(" + width / 2 + "," + height / 2 + ")"),
    link = g.append("g").attr("stroke", "#000").attr("stroke-width", 1.5).selectAll("path"),
    node = g.append("g").attr("stroke", "#fff").attr("stroke-width", 1.5).selectAll(".node");

restart();

const pad = num => `00${i}`.slice(-3);
  
d3.timeout(function() {
  links = (data.links.map(getLink))
  restart();
}, 1000);

d3.interval(() => {
  d3.json(`${pad(i)}.json`, (err, data) => {
    i++;
    console.log(data.nodes[2]);
    newNodes = _.cloneDeep(data.nodes);
    updateNodes(newNodes);
    console.log(nodes[2])
    newLinks = _.cloneDeep(data.links);
    links = data.links.map(getLink);
    restart()
  })
}, 1000, 2000);
  
function restart() {

// Apply the general update pattern to the nodes.
  node = node.data(nodes, (d) => d.id);
  
  node
    .attr("fill", d => color[d.weight])
  
  node.exit().transition()
    .duration(300)
  	.attr("opacity", 0)
    .remove()
  
  node = node.enter()
    .append("circle")
    .attr("fill", (d) => color[d.value])
    .attr("r", 6)
    .merge(node);
  
  node.append('title').text(d => d.id)

// Apply the general update pattern to the links.
  link = link.data(links, (d, i) => {
    return `${d.source.id}-${d.target.id}`;
  });
  
  link.exit()
  		.attr("marker-end", "none")
  		.transition()
  		.duration(200)
  		.attr("stroke", "red")
  	  .attr("stroke-opacity", 0)
      .attrTween("x1", (d) => () => d.source.x)
      .attrTween("x2", (d) => () => d.target.x)
      .attrTween("y1", (d) => () => d.source.y)
      .attrTween("y2", (d) => () => d.target.y)
    .remove();
  
  link = link.enter().append("svg:path")
  	.attr("marker-end", "url(#end-arrow)")
    .call((link) => link
          .attr("stroke", "green")
          .attr("stroke-opacity", 0)
          .transition()
          .duration(300)
          .attr("stroke-opacity", 0.6)
  				.attr("stroke", "#333333")
          .attr("fill", "none")
     	  	.attr("marker-end", "url(#end-arrow)"))
    .merge(link);

// Update and restart the simulation.
  simulation.nodes(nodes);
  simulation.force("link").links(links);
  simulation.alpha(1).restart();
}

function ticked() {
  node
    	.transition()
  		.duration(2)
    	.attr("cx", (d) => d.x)
      .attr("cy", (d) => d.y)

link.attr("d", function(d) {
        var dx = d.target.x - d.source.x,
            dy = d.target.y - d.source.y,
            dr = Math.sqrt(dx * dx + dy * dy)*1.5;
        return "M" + 
            d.source.x + "," + 
            d.source.y + "A" + 
            dr + "," + dr + " 0 0,1 " + 
            d.target.x + "," + 
            d.target.y;
    });
}
})

</script>

https://d3js.org/d3.v4.js

https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.4/lodash.min.js