app.js

/**
 * Module dependencies.
 */
var express = require('express'), routes = require('./routes'), http = require('http'), path = require('path'), fs = require('fs'), autoComplete = require('./aquaria/autocomplete');
var get_matching_structures = require('./aquaria/matching_structures');
var secondary_clustering = require('./aquaria/secondary_clustering');
var metainfo = require('./aquaria/metainfo');
var viewer_format = require('./aquaria/generate_viewer_format');
var viewer = require('./aquaria/viewer');
var snapshot = require('./aquaria/snapshot');
var config = require('./common/config');
var shoe = require('shoe');
var dnode = require('dnode');
//var expiry = require('static-expiry');


var JAR_EXPIRY = 1000 * 60 * 60 * 24 * 7;

//var dark_domains = require ('./aquaria/dark_domains');
//var queryConstraints = require('./aquaria/queryDistanceConstraints');
//var new_sql = require('./aquaria/sql_example');
var app = express();


// http://www.hacksparrow.com/express-js-logging-access-and-errors.html
var access_logfile = fs.createWriteStream('log/access.log', {flags: 'a'});

app.configure(function(){
	app.set('port', process.env.PORT || config.get('port'));
	app.set('views', __dirname + '/views');
	// Switched to EJS engine - see http://stackoverflow.com/questions/4600952/
	// Info on EJS ('Embedded JavaScript templates') - https://github.com/visionmedia/ejs
	app.set('view engine', 'ejs');
	app.use(express.favicon(__dirname + '/public/images/favicon.ico'));
	app.use(express.logger('dev'));
	app.use(express.bodyParser());
	app.use(express.methodOverride());
	app.use(express.cookieParser('your secret here'));
	app.use(express.session());
//	app.use(expiry(app, { dir: path.join(__dirname, 'public') }));
//	app.use(expiry(app, { dir: path.join(__dirname, 'public') }));
	app.use(app.router);
	app.use(express.static(path.join(__dirname, 'public'), { maxAge: 3600000 }));
  app.use('/jar', express.static(path.join(__dirname, 'jar'), { maxAge: JAR_EXPIRY}));
    app.use(express.logger({stream: access_logfile }));
    app.set('views', __dirname + '/views');
});

//app.configure('development', function(){
app.configure('production', function(){
  app.use(express.errorHandler());
});

var server = http.createServer(app);
server.listen(app.get('port'), function(){
	console.log("Express server listening on port " + app.get('port'));
});



var sock = shoe(function (stream) {
    var d = dnode({
        transform : function (s, cb) {
            var res = s.replace(/[aeiou]{2,}/, 'oo').toUpperCase();
            cb(res);
        },
    		queryOrganism : autoComplete.queryOrganism,
    		queryProtein : autoComplete.queryProtein,
    		queryProteinWildOrganism: autoComplete.queryProteinWildOrganism,
		    queryPDB : autoComplete.queryPDB,
		    loadSnapshot : snapshot.loadSnapshot,
		    getJNLP : snapshot.getJNLP,
		    get_matching_structures : matching_structures.get_matching_structures,
		    getAccessionForPDB: matching_structures.getAccessionForPDBCallback,
		    get_secondary_clusters : secondary_clustering.get_secondary_clusters,
        queryPDBTitle : secondary_clustering.queryPDBTitle,
		    get_3D_alignment : viewer_format.get_3D_alignment,
		    getPubMedForPDB : metainfo.getPubMedForPDB,
		    getOrganismInfo : metainfo.getOrganismInfo,
		    getProteinSynonyms : metainfo.getProteinSynonyms,
		    getOrganismSynonyms : metainfo.getOrganismSynonyms,
		    getOrganismName : metainfo.getOrganismName,
		    getChainInfo : metainfo.getChainInfo,
		    getOrganismId : metainfo.getOrganismId,
		    createAppJNLP : viewer.createJNLP,
		    createToolkitAppJNLP : viewer.createToolkitJNLP,
		    get_sequence : matching_structures.get_sequence
    });
    d.pipe(stream).pipe(d);
});
sock.install(server, '/dnode');

//var everyone = require("now").initialize(server);

//everyone.now.getDarkDomains = dark_domains.getDarkDomains;


//everyone.now.queryConstraints = queryConstraints.queryConstraints;
//everyone.now.sql_query = new_sql.function_name;

// Disable layout - http://stackoverflow.com/questions/4600952/
app.set('view options', {
	layout: false
});

app.get('/launch', routes.launchPage);
app.get('/googlehostedservice.html', routes.googleHostedService);

//app.get('/jar/:jarname', routes.jar);
//app.get('/jar/:{jarname}?version-id=:{version}', routes.jar);
//app.post('/jnlp/app/:filename.jnlp', routes.jnlpApp);
app.get('/jnlp/:versionString/:filename.jnlp', routes.jnlp);

app.get('/:id/cluster:clusterId.:format', routes.matchingStructuresExt);
//app.get('/:id/cluster:clusterId.json', routes.matchingStructuresJSON);
//app.get('/:id/cluster:clusterId.txt', routes.matchingStructuresTXT);
//app.get('/:id/cluster:clusterId.csv', routes.matchingStructuresCSV);

app.get('/:id/:pdbid?/:chainid?.:format', routes.matchingStructuresExt);
//app.get('/:id/:pdbid.:ext', routes.matchingStructuresExt);
//app.get('/:id/:pdbid/:chainid.tsv', routes.matchingStructuresTSV);
//app.get('/:id/:pdbid/:chainid.csv', routes.matchingStructuresCSV);
//app.get('/:id/:pdbid/:chainid.txt', routes.matchingStructuresTXT);

//app.get('/:id.:format', routes.matchingStructuresExt);
//app.get('/:id.csv', routes.matchingStructuresCSV);
//app.get('/:id.txt', routes.matchingStructuresTXT);
//app.get('/:id/:pdbid', routes.home_page);
app.get('/:id/:pdbid?/:chainid?', routes.home_page);
//app.get('/leap/:id/:pdbid', routes.home_page);
//app.get('/leap/:id/:pdbid/:chainid', routes.home_page);
app.get('/', routes.home_page);
//app.get('/:id.json', routes.matchingStructuresJSON);
//app.get('/json/:id', routes.matchingStructuresJSON);
//app.get('/pdb/:id', routes.pdb);
//app.get('/:id.pdb:ext?', routes.pdb);
//app.get('/:id', routes.home_page);
//app.get('/leap/:id', routes.home_page);
//app.get('/interactions/:id', routes.interactions);
//app.get('/sean/:id', routes.sean);