dictifies model on retreival

Author: thejmazz

fba-api.js

@@ -10,13 +10,13 @@ var App = global.App = require('./lib/App');
 // ==== DB Connection ====
 connection = App.Lib('connection')
 connection.mongodb(); //wat
-mysqlConn = new Object();
-connection.mysql(function(connection) {
-	mysqlConn = connection;
-});
+// mysqlConn = new Object();
+// connection.mysql(function(connection) {
+// 	mysqlConn = connection;
+// });
 
 // above hasn't finished yet which is this is still {}. #callbacks #yolo
-console.log(mysqlConn)
+// console.log(mysqlConn)
 
 // ==== Apply global middleware ====
 App.MW('global-middleware').apply(app);

lib/router.js

@@ -1,11 +1,11 @@
 var fs   = require('fs');
 var path = require('path');
 
-var routerLogger = App.Lib('init-routers-logger'); 
+var routerLogger = App.Lib('init-routers-logger');
 
 var routesDir = path.resolve('routes');
 var validRouterFile = 'index.js'
-var ignoredInvalidRouters = ['.swp'];
+var ignoredInvalidRouters = ['.swp', '.DS_Store'];
 
 function pathmaker (rPath) {
     // remove everything up to and including '/route'
@@ -16,7 +16,13 @@ function pathmaker (rPath) {
     for (var i = 0; i < rPathArray.length - 1; i++) {
         i > 0 ? rPath += '/' + rPathArray[i] : rPath += rPathArray[i];
     }
-    return rPath; 
+
+    // replace all '$'s with ':'s
+    while(rPath.indexOf('$') !== -1) {
+        rPath = rPath.replace('$', ':');
+    }
+
+    return rPath;
 }
 
 
@@ -29,19 +35,19 @@ function findRouters (rPath, app) {
             findRouters(fullPath, app);
         } else {
             var fileName = fullPath.split('/')[fullPath.split('/').length - 1];
-            
+
             var currentPath = pathmaker(fullPath);
 
-            if (fileName === validRouterFile) { 
+            if (fileName === validRouterFile) {
                 var currentRouter = require(fullPath);
                 currentRouter.stack.forEach(function(router){
-                    routerLogger(router, currentPath); 
+                    routerLogger(router, currentPath);
                 });
                 console.log(currentRouter.stack[0].name)
                 app.use(currentPath, currentRouter);
             } else {
                 if (ignoredInvalidRouters.indexOf(path.extname(fileName)) === -1) {
-                    console.log('Error'.red + ': encountered invalid router file → '+ currentPath.red + '/'.red + fileName.red);        
+                    console.log('Error'.red + ': encountered invalid router file → '+ currentPath.red + '/'.red + fileName.red);
                 }
             }
         }

models/metabolicmodel.js

@@ -36,4 +36,20 @@ var MetabolicModelSchema = new mongoose.Schema({
   	id: String
 });
 
+MetabolicModelSchema.methods.dictifyReactionMetabolites = function dictifyReactionMetabolites(cb) {
+	var model = JSON.parse(JSON.stringify(this));
+
+	model.reactions.forEach(function(reaction) {
+		metabolitesDict = new Object();
+
+		reaction.metabolites.forEach(function(metabolite) {
+			metabolitesDict[metabolite.id] = metabolite.stoichiometric_coefficient;
+		});
+
+		reaction.metabolites = metabolitesDict;
+	});
+
+	cb(model);
+}
+
 module.exports = mongoose.model('metabolicmodel', MetabolicModelSchema);

routes/model/retrieve/index.js

@@ -2,7 +2,7 @@ var router = require('express').Router();
 
 var MetabolicModel = App.Model('metabolicmodel');
 
-function find(req, res, next) {
+function findAll(req, res, next) {
 	MetabolicModel.find(function(err, models) {
 		var ids = new Array();
 		models.forEach(function(model) {
@@ -13,6 +13,23 @@ function find(req, res, next) {
 	})
 }
 
-router.get('/', find)
+router.get('/', findAll);
+
+router.get('/:id', function(req,res, next) {
+	MetabolicModel.findOne({id: req.params.id}, function(err, model) {
+		if (err) {
+			res.status(500).send('500 Internal Server Error\n');
+			return;
+		}
+
+		if (!model) {
+			res.status(403).send('204 no content. That model does not exist.\n');
+		} else {
+			model.dictifyReactionMetabolites(function(model) {
+				res.send(model);
+			});
+		}
+	});
+});
 
 module.exports = router;