route to optimize model

Author: thejmazz

python-scripts/optimize.py

@@ -0,0 +1,32 @@
+import sys
+import json
+# COnstraint Based Reconstruction and Analysis
+import cobra
+
+# Get command line arguments
+# Full file path including extension. e.g. /path/to/iJO1366.json
+model_file = sys.argv[1]
+# Just name: 'iJO1366' will save to 'iJO1366_solution.json'
+out_file   = sys.argv[2]
+
+# Load JSON model
+model = cobra.io.load_json_model(model_file)
+
+# Optimize for biomass
+model.optimize()
+
+# Create a dictionary out of Solution object
+solution = {}
+solution['f'] = model.solution.f
+solution['status'] = model.solution.status
+solution['x_dict'] = model.solution.x_dict
+# solution['x'] = model.solution.x
+solution['y_dict'] = model.solution.y_dict
+# solution['y'] = model.solution.x
+
+# Write solution dictionary to json file
+# solution_filename = out_file.split('.json')[0] + '_solution.json'
+solution_filename = out_file + '_solution.json'
+with open(solution_filename, 'w') as outfile:
+    json.dump(solution, outfile)
+print 'Dumped ' + solution_filename

routes/model/optimize/index.js

@@ -0,0 +1,64 @@
+var router = require('express').Router();
+var fs = require('fs')
+var cp = require('child_process');
+
+MetabolicModel = App.Model('metabolicmodel');
+
+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');
+			return;
+		}
+
+		if (!model) {
+			res.status(204).send('204 no content. That model does not exist.\n');
+		} else {
+			model.dictifyReactionMetabolites(function(model) {
+				fileName = 'temp/' + req.params.id + '.json';
+
+				fs.writeFile(fileName, JSON.stringify(model), function(err) {
+					if (err) {
+						res.status(500).send('500 Internal Server Error');
+					} else {
+
+						var results = {
+					        output   : new String(),
+					        errorlog : new String(),
+					        exitcode : null
+					    };
+
+						args = [
+							'python-scripts/optimize.py',
+							fileName,
+							'temp/' + req.params.id
+						]
+
+						var optimizeScript = cp.spawn('python', args)
+
+						// get stdout
+						optimizeScript.stdout.on('data', function(stdout) {
+					        results.output += stdout.toString();
+					    });
+
+					    // get stderr
+					    optimizeScript.stderr.on('data', function(stderr) {
+					        results.errorlog += stderr.toString();
+					    });
+
+					    // script finished
+					    optimizeScript.on('close', function(code) {
+					        results.exitcode = code;
+
+					        // Respond on process close
+					        // otherwise, async problems!
+					        res.send(results);
+					    });
+					}
+				});
+			});
+		}
+	})
+})
+
+module.exports = router;

routes/model/retrieve/index.js

@@ -23,7 +23,7 @@ router.get('/:id', function(req,res, next) {
 		}
 
 		if (!model) {
-			res.status(403).send('204 no content. That model does not exist.\n');
+			res.status(204).send('204 no content. That model does not exist.\n');
 		} else {
 			model.dictifyReactionMetabolites(function(model) {
 				res.send(model);