diff options
| -rw-r--r-- | wqflask/wqflask/markdown_routes.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/markdown.css | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/environment.html | 134 |
3 files changed, 162 insertions, 0 deletions
diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py index 59a465e7..183f4caa 100644 --- a/wqflask/wqflask/markdown_routes.py +++ b/wqflask/wqflask/markdown_routes.py @@ -7,6 +7,8 @@ import markdown import os import sys +from bs4 import BeautifulSoup + from flask import Blueprint from flask import render_template @@ -68,10 +70,21 @@ def references(): @environments_blueprint.route("/") def environments(): + md_file = get_file_from_python_search_path("wqflask/DEPENDENCIES.md") + svg_file = get_file_from_python_search_path( + "wqflask/dependency-graph.html") + svg_data = None + if svg_file: + with open(svg_file, 'r') as f: + svg_data = "".join( + BeautifulSoup(f.read(), + 'lxml').body.script.contents) + if md_file is not None: return ( render_template("environment.html", + svg_data=svg_data, rendered_markdown=render_markdown( md_file, is_remote_file=False)), @@ -80,6 +93,7 @@ def environments(): # Fallback: Fetch file from server return (render_template( "environment.html", + svg_data=None, rendered_markdown=render_markdown( "general/environments/environments.md")), 200) diff --git a/wqflask/wqflask/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css index 0c0309fb..38d664e2 100644 --- a/wqflask/wqflask/static/new/css/markdown.css +++ b/wqflask/wqflask/static/new/css/markdown.css @@ -57,6 +57,20 @@ word-spacing: 0.2em; } +.graph-legend h1 { + text-align: center; +} + +.graph-legend, +#guix-graph { + width: 90%; + margin: 10px auto; +} + +#guix-graph { + border: solid 2px black; +} + #markdown table { width: 100%; } diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html index cd30e768..5fe01dad 100644 --- a/wqflask/wqflask/templates/environment.html +++ b/wqflask/wqflask/templates/environment.html @@ -13,4 +13,138 @@ <div class="cls-table-style">{{ rendered_markdown|safe }} </div> </div> +{% if svg_data %} + +<div class="graph-legend"> + <h1>Chord dependency Graph of Genenetwork2</h1> + Graph generated from <a href="http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics/src/branch/master/gn/packages/genenetwork.scm">genenetwork.scm</a>. You can zoom in and out within the bounding box. +</div> + +<div id="guix-graph"></div> +{% endif %} + +{% endblock %} + +{% block js %} + +{% if svg_data %} +<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> +<script type="text/javascript"> + {{ svg_data|safe }} + // based on http://bl.ocks.org/mbostock/1046712 under GPLv3 + // Adapted from: https://elephly.net/graph.html + var outerRadius = (nodeArray.length * 10) / 2, + innerRadius = outerRadius - 100, + width = outerRadius * 2, + height = outerRadius * 2, + colors = d3.scale.category20c(), + matrix = []; + + function neighborsOf (node) { + return links.filter(function (e) { + return e.source === node; + }).map(function (e) { + return e.target; + }); + } + + function zoomed () { + zoomer.attr("transform", + "translate(" + d3.event.translate + ")" + + "scale(" + d3.event.scale + ")"); + } + + function fade (opacity, root) { + return function (g, i) { + root.selectAll("g path.chord") + .filter(function (d) { + return d.source.index != i && d.target.index != i; + }) + .transition() + .style("opacity", opacity); + }; + } + + // Now that we have all nodes in an object we can replace each reference + // with the actual node object. + links.forEach(function (link) { + link.target = nodes[link.target]; + link.source = nodes[link.source]; + }); + + // Construct a square matrix for package dependencies + nodeArray.forEach(function (d, index, arr) { + var source = index, + row = matrix[source]; + if (!row) { + row = matrix[source] = []; + for (var i = -1; ++i < arr.length;) row[i] = 0; + } + neighborsOf(d).forEach(function (d) { row[d.index]++; }); + }); + + // chord layout + var chord = d3.layout.chord() + .padding(0.01) + .sortSubgroups(d3.descending) + .sortChords(d3.descending) + .matrix(matrix); + + var arc = d3.svg.arc() + .innerRadius(innerRadius) + .outerRadius(innerRadius + 20); + + var zoom = d3.behavior.zoom() + .scaleExtent([0.1, 10]) + .on("zoom", zoomed); + + var svg = d3.select("#guix-graph").append("svg") + .attr("width", "100%") + .attr("height", "100%") + .attr('viewBox','0 0 '+Math.min(width,height)+' '+Math.min(width,height)) + .attr('preserveAspectRatio','xMinYMin') + .call(zoom); + + var zoomer = svg.append("g"); + + var container = zoomer.append("g") + .attr("transform", "translate(" + outerRadius + "," + outerRadius + ")"); + + // Group for arcs and labels + var g = container.selectAll(".group") + .data(chord.groups) + .enter().append("g") + .attr("class", "group") + .on("mouseout", fade(1, container)) + .on("mouseover", fade(0.1, container)); + + // Draw one segment per package + g.append("path") + .style("fill", function (d) { return colors(d.index); }) + .style("stroke", function (d) { return colors(d.index); }) + .attr("d", arc); + + // Add circular labels + g.append("text") + .each(function (d) { d.angle = (d.startAngle + d.endAngle) / 2; }) + .attr("dy", ".35em") + .attr("transform", function (d) { + return "rotate(" + (d.angle * 180 / Math.PI - 90) + ")" + + "translate(" + (innerRadius + 26) + ")" + + (d.angle > Math.PI ? "rotate(180)" : ""); + }) + .style("text-anchor", function (d) { return d.angle > Math.PI ? "end" : null; }) + .text(function (d) { return nodeArray[d.index].label; }); + + // Draw chords from source to target; color by source. + container.selectAll(".chord") + .data(chord.chords) + .enter().append("path") + .attr("class", "chord") + .style("stroke", function (d) { return d3.rgb(colors(d.source.index)).darker(); }) + .style("fill", function (d) { return colors(d.source.index); }) + .attr("d", d3.svg.chord().radius(innerRadius)); +</script> +{% endif %} + {% endblock %} |