new version

ReadMe.md

@@ -0,0 +1,27 @@
+#Online PhyloViZ
+
+This web application allows you to choose between two layout rendering engines (SVG and WebGl) and display 4 different MLST datasets using minimum spanning trees.
+
+Node.js is required.
+
+Launch the application
+======================
+
+`node app` and in your browser listen on port `3000`
+
+Choose a rendering engine
+=========================
+
+On the main page there is a choice between `SVG` and `WebGL`. You can also select one by typing `:3000/svg` or `:3000/webgl`
+
+Choose a dataset
+================
+
+Select between 4 datasets:
+
+* `:3000/webgl?data=sample` - a dataset with sample MLST data
+* `:3000/webgl?data=pyogenes` - a dataset with MLST data of `S.pyogenes` (647 nodes)
+* `:3000/webgl?data=saureus` - a dataset with MLST data of `S.aureus` (2960 nodes)
+* `:3000/webgl?data=spneumo` - a dataset with MLST data of `S.pneumoniae` (10261 nodes)
+
+* webgl can be changed by svg

app.js

@@ -0,0 +1,101 @@
+var express = require('express');
+var path = require('path');
+var favicon = require('serve-favicon');
+var logger = require('morgan');
+//var cookieParser = require('cookie-parser');
+var bodyParser = require('body-parser');
+// var busboy = require('connect-busboy');
+var restful = require('node-restful')
+var mongoose = require('mongoose');
+var fs = require('fs');
+
+var parseGoe = require('goeBURSTparser');
+
+var users = require('./routes/users');
+var upload = require('./routes/api/database/upload');
+var goeBURST = require('./routes/api/algorithms/goeBURST');
+var apiHome = require('./routes/api/index');
+var mongoSearch = require('./routes/api/database/mongo');
+var phylovizInput = require('./routes/api/utils/phyloviz_input');
+var phyloviztableData = require('./routes/api/utils/tableData');
+
+var routes = require('./routes/app/index');
+var main = require('./routes/app/main');
+
+var done = false;
+
+// var inputData = require('./routes/inputData');
+
+var app = express();
+
+// view engine setup
+app.set('views', path.join(__dirname, 'views'));
+app.set('view engine', 'jade');
+
+// uncomment after placing your favicon in /public
+//app.use(favicon(__dirname + '/public/favicon.ico'));
+app.use(logger('dev'));
+app.use(bodyParser.json());
+app.use(bodyParser.urlencoded({ extended: false }));
+
+//app.use(cookieParser());
+app.use(express.static(path.join(__dirname, 'public')));
+
+app.use('/', routes);
+app.use('/users', users);
+app.use('/main', main);
+app.use('/api', apiHome);
+app.use('/api/db/upload', upload);
+app.use('/api/algorithms/goeBURST', goeBURST);
+app.use('/api/utils/phylovizInput', phylovizInput);
+app.use('/api/utils/tableData', phyloviztableData);
+app.use('/api/db', mongoSearch);
+// app.use('/inputData',inputData);
+
+//load all files in models dir
+// fs.readdirSync(__dirname + '/models').forEach(function(filename){
+//   if(~filename.indexOf('.js')) require(__dirname + '/models/' + filename);
+// })
+
+mongoose.connect('mongodb://localhost/phyloviz');
+
+
+// catch 404 and forward to error handler
+app.use(function(req, res, next) {
+  var err = new Error('Not Found');
+  err.status = 404;
+  next(err);
+});
+
+
+// error handlers
+
+// development error handler
+// will print stacktrace
+if (app.get('env') === 'development') {
+  app.use(function(err, req, res, next) {
+    res.status(err.status || 500);
+    res.render('error', {
+      message: err.message,
+      error: err
+    });
+  });
+}
+
+// production error handler
+// no stacktraces leaked to user
+app.use(function(err, req, res, next) {
+  res.status(err.status || 500);
+  res.render('error', {
+    message: err.message,
+    error: {}
+  });
+});
+
+
+app.listen(3000, function(){
+  console.log('Server Running');
+});
+
+
+module.exports = app;

bin/www

@@ -0,0 +1,90 @@
+#!/usr/bin/env node
+
+/**
+ * Module dependencies.
+ */
+
+var app = require('../app');
+var debug = require('debug')('Force_Layout_ViZ:server');
+var http = require('http');
+
+/**
+ * Get port from environment and store in Express.
+ */
+
+var port = normalizePort(process.env.PORT || '3000');
+app.set('port', port);
+
+/**
+ * Create HTTP server.
+ */
+
+var server = http.createServer(app);
+
+/**
+ * Listen on provided port, on all network interfaces.
+ */
+
+server.listen(port);
+server.on('error', onError);
+server.on('listening', onListening);
+
+/**
+ * Normalize a port into a number, string, or false.
+ */
+
+function normalizePort(val) {
+  var port = parseInt(val, 10);
+
+  if (isNaN(port)) {
+    // named pipe
+    return val;
+  }
+
+  if (port >= 0) {
+    // port number
+    return port;
+  }
+
+  return false;
+}
+
+/**
+ * Event listener for HTTP server "error" event.
+ */
+
+function onError(error) {
+  if (error.syscall !== 'listen') {
+    throw error;
+  }
+
+  var bind = typeof port === 'string'
+    ? 'Pipe ' + port
+    : 'Port ' + port;
+
+  // handle specific listen errors with friendly messages
+  switch (error.code) {
+    case 'EACCES':
+      console.error(bind + ' requires elevated privileges');
+      process.exit(1);
+      break;
+    case 'EADDRINUSE':
+      console.error(bind + ' is already in use');
+      process.exit(1);
+      break;
+    default:
+      throw error;
+  }
+}
+
+/**
+ * Event listener for HTTP server "listening" event.
+ */
+
+function onListening() {
+  var addr = server.address();
+  var bind = typeof addr === 'string'
+    ? 'pipe ' + addr
+    : 'port ' + addr.port;
+  debug('Listening on ' + bind);
+}

data/Linkspneumo.txt

@@ -0,0 +1,150 @@
+ERR047925.fa -- 21.spades_contigs.fasta (level: 538)
+21.spades_contigs.fasta -- 15.spades_contigs.fasta (level: 31)
+12.spades_contigs.fasta -- 21.spades_contigs.fasta (level: 34)
+8.spades_contigs.fasta -- 15.spades_contigs.fasta (level: 66)
+ERR067851.fa -- 21.spades_contigs.fasta (level: 75)
+ERR048076.fa -- ERR067851.fa (level: 25)
+ERR067851.fa -- ERR048079.fa (level: 40)
+ERR048116.fa -- ERR048079.fa (level: 5)
+ERR273494.fa -- ERR048079.fa (level: 25)
+ERR049108.fa -- ERR273494.fa (level: 24)
+ERR064159.fa -- ERR048116.fa (level: 35)
+ERR048079.fa -- 39.spades_contigs.fasta (level: 68)
+12.spades_contigs.fasta -- CACI01000001-CACI01000025.fasta (level: 784)
+FQ312045.fa -- CACI01000001-CACI01000025.fasta (level: 67)
+NC_021006.fna -- FQ312045.fa (level: 3)
+NC_021006.fna -- ERR025288.fa (level: 221)
+46.spades_contigs.fasta -- ERR025288.fa (level: 191)
+46.spades_contigs.fasta -- ERR026235.fa (level: 31)
+46.spades_contigs.fasta -- ERR025281.fa (level: 37)
+ERR056793.fa -- ERR025288.fa (level: 204)
+ERR056793.fa -- ERR048063.fa (level: 31)
+ERR048063.fa -- ERR025290.fa (level: 171)
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+ERR025296.fa -- ERR025307.fa (level: 12)
+ERR025306.fa -- ERR025307.fa (level: 11)
+ERR025296.fa -- ERR025304.fa (level: 12)
+ERR025307.fa -- ERR025318.fa (level: 14)
+ERR025318.fa -- ERR025321.fa (level: 7)
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+ERR025285.fa -- ERR025289.fa (level: 8)
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+ERR026214.fa -- ERR026227.fa (level: 10)
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+ERR025301.fa -- ERR025302.fa (level: 4)
+ERR025302.fa -- ERR025308.fa (level: 16)
+ERR026214.fa -- ERR026228.fa (level: 16)
+ERR025295.fa -- ERR025296.fa (level: 16)
+ERR025318.fa -- ERR026232.fa (level: 17)
+ERR026232.fa -- ERR026233.fa (level: 13)
+ERR025316.fa -- ERR025318.fa (level: 17)
+ERR025309.fa -- ERR025318.fa (level: 17)
+ERR025296.fa -- ERR025323.fa (level: 17)
+ERR025318.fa -- ERR026231.fa (level: 18)
+ERR026232.fa -- ERR026245.fa (level: 18)
+ERR026239.fa -- ERR026245.fa (level: 16)
+ERR026242.fa -- ERR026245.fa (level: 17)
+ERR025296.fa -- ERR025310.fa (level: 19)
+ERR025283.fa -- ERR025310.fa (level: 7)
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+ERR025316.fa -- ERR026247.fa (level: 20)
+ERR026238.fa -- ERR026247.fa (level: 17)
+ERR025316.fa -- ERR026216.fa (level: 20)
+ERR025316.fa -- ERR026215.fa (level: 20)
+ERR025284.fa -- ERR025310.fa (level: 21)
+ERR025286.fa -- ERR025307.fa (level: 21)
+ERR025296.fa -- ERR025324.fa (level: 21)
+ERR025296.fa -- ERR026217.fa (level: 21)
+ERR025296.fa -- ERR025327.fa (level: 21)
+ERR025295.fa -- ERR025314.fa (level: 21)
+ERR025298.fa -- ERR025307.fa (level: 22)
+ERR025296.fa -- ERR026224.fa (level: 22)
+ERR026232.fa -- ERR026248.fa (level: 22)
+ERR026244.fa -- ERR026248.fa (level: 17)
+ERR025312.fa -- ERR026232.fa (level: 22)
+ERR026234.fa -- ERR026239.fa (level: 22)
+ERR026216.fa -- ERR026220.fa (level: 22)
+ERR025284.fa -- ERR026246.fa (level: 22)
+ERR025296.fa -- ERR025322.fa (level: 23)
+ERR026213.fa -- ERR026232.fa (level: 23)
+ERR025284.fa -- ERR026240.fa (level: 23)
+ERR025316.fa -- ERR026243.fa (level: 24)
+ERR025297.fa -- ERR025316.fa (level: 24)
+1.spades_contigs.fasta -- ERR025295.fa (level: 25)
+6.spades_contigs.fasta -- 1.spades_contigs.fasta (level: 6)
+1.spades_contigs.fasta -- 33.spades_contigs.fasta (level: 11)
+49.spades_contigs.fasta -- 1.spades_contigs.fasta (level: 13)
+6.spades_contigs.fasta -- 13.spades_contigs.fasta (level: 17)
+NC_021005.fna -- 1.spades_contigs.fasta (level: 24)
+NC_021005.fna -- NC_021026.fna (level: 2)
+NC_021005.fna -- FQ312044.fa (level: 4)
+FQ312041.fa -- FQ312044.fa (level: 2)
+FQ312044.fa -- CACH01000001-CACH01000022.fasta (level: 12)
+13.spades_contigs.fasta -- 10.spades_contigs.fasta (level: 24)
+44.spades_contigs.fasta -- 1.spades_contigs.fasta (level: 25)
+ERR025310.fa -- ERR026237.fa (level: 25)
+ERR025294.fa -- ERR025307.fa (level: 25)
+ERR025316.fa -- ERR026219.fa (level: 25)
+ERR025313.fa -- ERR025326.fa (level: 25)
+ERR026226.fa -- ERR026246.fa (level: 25)
+ERR025280.fa -- ERR026232.fa (level: 26)
+ERR026239.fa -- ERR026241.fa (level: 26)
+20.spades_contigs.fasta -- 1.spades_contigs.fasta (level: 27)
+31.spades_contigs.fasta -- 1.spades_contigs.fasta (level: 27)
+ERR025282.fa -- ERR025296.fa (level: 27)
+ERR025293.fa -- ERR026232.fa (level: 28)
+ERR026225.fa -- ERR026232.fa (level: 28)
+ERR025295.fa -- ERR026222.fa (level: 28)
+FQ312044.fa -- FQ312027.fasta (level: 29)
+NC_017592.fna -- FQ312027.fasta (level: 5)
+ERR026214.fa -- ERR026218.fa (level: 29)
+ERR026217.fa -- ERR067983.fa (level: 29)
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+ERR069832.fa -- ERR069701.fa (level: 34)
+FQ312043.fa -- FQ312044.fa (level: 35)
+NC_021028.fna -- FQ312043.fa (level: 4)
+ERR069748.fa -- ERR069689.fa (level: 36)
+ERR025287.fa -- ERR025296.fa (level: 39)
+ERR025316.fa -- ERR129212.fa (level: 39)
+ERR129180.fa -- ERR129212.fa (level: 41)
+ERR054282.fa -- ERR048063.fa (level: 448)
+NC_021006.fna -- ERR050070.fa (level: 732)
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+ERR054297.fa -- ERR049941.fa (level: 16)
+ERR047925.fa -- 37.spades_contigs.fasta (level: 808)
+16.spades_contigs.fasta -- 37.spades_contigs.fasta (level: 228)
+34.spades_contigs.fasta -- 16.spades_contigs.fasta (level: 21)
+4.spades_contigs.fasta -- 16.spades_contigs.fasta (level: 28)
+42.spades_contigs.fasta -- 16.spades_contigs.fasta (level: 55)
+18.spades_contigs.fasta -- 16.spades_contigs.fasta (level: 294)
+18.spades_contigs.fasta -- 9.spades_contigs.fasta (level: 62)
+18.spades_contigs.fasta -- 47.spades_contigs.fasta (level: 65)
+18.spades_contigs.fasta -- 25.spades_contigs.fasta (level: 75)
+18.spades_contigs.fasta -- 11.spades_contigs.fasta (level: 84)