maldisoft/maldisoft-engine.py

import os
from flask import Flask, session, redirect, url_for, escape, request, render_template
from werkzeug import secure_filename

from maldisql import *
from readsample import *
from dataanalysis import *

app = Flask(__name__)
app.config["UPLOAD_FOLDER"] = "data"

def CheckINT(eid):
	ceid = None
	try:
		ceid = int(eid)
	except:
		return ceid

	return ceid

def alert(msg, mtype="danger"):
	mhash = {"type": mtype, "msg": msg}

	return mhash

###############################################################################
#
# 	@app.route /
#
###############################################################################

@app.route('/', methods=['GET', 'POST'])
def index():
	if  not 'uid' in session:
		return redirect(url_for("login"))

	msql = maldisql()

	msg = []
	if "msg" in session:
		msg = session["msg"][:]
		session.pop("msg", None)

	if request.method == 'POST':
		if "deid" in request.form:
			eid = CheckINT(request.form["deid"])
			if eid and msql.CheckEIDOwner(eid, session["uid"]):
				if msql.DeleteExperiment(eid):
					msg.append(alert("Experiment delete successful!", "success"))
			else:
				msg.append(alert("Wrong experiment or permissions!"))

	experiments = msql.GetExperiments(session["uid"])
	col_experiments = msql.GetCollaborations(session["uid"])

	msql.close()
	return render_template("index.html", email=escape(session['email']), 
		experiments=experiments, col_experiments=col_experiments, msg=msg)

###############################################################################
#
# 	@app.route /experiment
#
###############################################################################

@app.route('/experiment', methods=['GET', 'POST'])
def experiment():
	if  not 'uid' in session:
		return redirect(url_for("login"))

	# Initialize EID
	msg = []
	eid = None
	if "eid" in session:
		eid = session["eid"]

	msql = maldisql()
	if request.method == 'POST':

		# Create a new Experiment Fast Creation
		if 'expname' in request.form and 'inpeaks' in request.form and not 'eid' in request.form:
			result = msql.CreateExperiment(escape(request.form["expname"]), "Description here", session["uid"])
			print eid
			eid = CheckINT(result)
			print eid
			if eid:
				session["eid"] = eid
			else:
				session["msg"] = [alert(result)]
				return redirect(url_for("index"))

			for peak in request.form["inpeaks"].split(","):
				try:
					peak = float(peak.strip())
					msql.AddExperimentPeak(eid, peak)
				except:
					msg.append(alert("Peak format error it MUST be a decimal \
						value or a list of decimal values separated by commas"))

		# If EID is in the request.  
		# anymore.
		if "eid" in request.form:
			eid = CheckINT(request.form["eid"])
			if eid and msql.CheckEIDOwner(eid, session["uid"]):
				session["eid"] = eid
			else:
				session["msg"] = [alert("You have not permission to view that experiment")]
				return redirect("index")


	if not eid:
		msql.close()
		return redirect(url_for("index"))

	experiment = msql.GetExperiment(eid)
	samples = msql.GetSamples(eid)
	exp_peaks = msql.GetExperimentPeaks(eid)

	da = dataanalysis()

	abundances = []

	for sample in samples:
		sample["peaks"] = msql.GetPeaks(sample["sid"])
		if sample["peaks"]:
			sample["rel_ints"] =  da.computePeaksRelativeIntensity(sample["peaks"])
			if sample["rel_ints"]:
				abundances.append(sample["rel_ints"])

	msql.close()

	averages = None
	stdDevs = None
	sems = None
	if len(abundances) > 1:
		averages = da.relativeAbundanceAverage(abundances)
		stdDevs = da.relativeAbundanceStdDeviation(abundances, averages)
		sems = da.relativeAbundanceSDM(stdDevs, len(abundances))
	else:
		msg.append(alert("Wait for it!  To get Averages, Standard Dev, and SEMs you \
			need to have more than one sample file.", "success"))

	return render_template("experiment.html", email=escape(session['email']), 
		experiment=experiment, exp_peaks=exp_peaks, samples=samples, averages=averages,
		stdDevs=stdDevs, sems=sems, eid=eid, msg=msg)


###############################################################################
#
# 	@app.route /editExperiment
#
###############################################################################

@app.route('/editExperiment', methods=['GET', 'POST'])
def editExperiment():

	if not request.method == 'POST':
		return redirect(url_for("index"))

	msg = []
	
	experiment = None
	exp_peaks = None
	name = None
	description = None
	eid = None

	msql = maldisql()
	if "eid" in session:
		eid = session["eid"]


	if eid  and "name" in request.form and "description" in request.form:
		# Save information in database and redirect to experiment with eid
		result = msql.UpdateExperiment(escape(request.form["name"]), escape(request.form["description"]), eid)
			
		if not result:
			#msql.close()
			msg.append(alert("Update successful", "success"))
			#return redirect(url_for("experiment"), code=307)
		else:
			msg.append(alert("Experiment Info Update failed!"))


	if eid and "inpeaks" in request.form:
		for peak in request.form["inpeaks"].split(","):
			try:
				peak = float(peak.strip())
				msql.AddExperimentPeak(eid, peak)
			except:
				msg.append(alert("Bad peak format!"))

	if eid and "collaborators" in request.form:
		result = msql.AddExperimentCollaborator(eid, escape(request.form["collaborators"]))
		if type(result) in [int, long]:
			msg.append(alert("Collaborator added successfuly!", "success"))
		else:
			msg.append(alert(result))

	if eid and "remove_peak" in request.form:
		# Remove one peak but first check if it belongs to uid
		exp_peaks = msql.GetExperimentPeaks(eid)
		peak = CheckINT(request.form["remove_peak"])
		for epeak in exp_peaks:
			if peak == epeak["ep_id"]:	
				if msql.RemovePeak(peak):
					msg.append(alert("Peak deleted successfuly!", "success"))
				else:
					msg.append(alert("Couldn't delete peak!"))
				break


	if eid and "remove_col" in request.form:
		collaborators = msql.GetExperimentCollaborators(eid)
		colid = CheckINT(request.form["remove_col"])
		for col in collaborators:
			if colid == col["ueid"]:	
				if msql.RemoveExperimentCollaborator(colid):
					msg.append(alert("Collaborator removed successfuly!", "success"))
				else:
					msg.append(alert("Couldn't remove collaborator!"))
				break

	if eid:
		experiment = msql.GetExperiment(eid)
		exp_peaks = msql.GetExperimentPeaks(eid)
		collaborators = msql.GetExperimentCollaborators(eid)
		name = experiment["name"]
		description = experiment["description"]
		samples = msql.GetSamples(eid)
		if len(samples):
			samples=True
	msql.close()

	return render_template("editexperiment.html", email=escape(session['email']), 
		name=name, description=description, exp_peaks=exp_peaks, collaborators=collaborators,
		samples=samples, msg=msg)




###############################################################################
#
# 	@app.route /login
#
###############################################################################

@app.route('/login', methods=['GET', 'POST'])
def login():

	msg = []
	if request.method == 'POST':
		
		if "email" in request.form and "passwd" in request.form:
			msql = maldisql()
			uid = msql.Login(escape(request.form["email"]), escape(request.form["passwd"]))	
			msql.close()		
			if uid:
				session["uid"] = uid
				session["email"] = escape(request.form["email"])
				return redirect(url_for('index'))
			else:
				msg.append(alert("Bad username or password."))
    
	return render_template("login.html", msg=msg)


###############################################################################
#
# 	@app.route /upload
#
###############################################################################

@app.route('/upload', methods=['GET', 'POST'])
def upload_file():

	if  not 'uid' in session:
 		return redirect(url_for("login"))

	if "eid" in request.form and CheckINT(request.form["eid"]) == session["eid"]:
		eid = session["eid"]

		if 'file' in request.files:
			msql = maldisql()
			f = request.files['file']
			try:
				import uuid
				uuid = str(uuid.uuid1())
				filename = secure_filename(f.filename)
				f.save("%s/%s" % (app.config["UPLOAD_FOLDER"], uuid))
				msql = maldisql()
				sid = msql.AddSample(eid, uuid, filename)
			except:
				msql.close()
				error = "Unexpected problem saving file"
				return error

			peaks = msql.GetExperimentPeaks(eid)
			# List of floats
			try:
				samples = readsample("%s/%s" % (app.config["UPLOAD_FOLDER"], uuid), ["peak", "intensity"])

			except:
				return "Couldn't read the file!"

			try:
				mda = dataanalysis()
				peaks_childs = mda.getPeaksFromFile(samples, [float(x["peak"]) for x in peaks])

				for peak in peaks_childs.keys(): 
					pid = msql.AddPeak(sid, peak)
					for child in peaks_childs[peak].keys():
						msql.AddIntensity(pid, peaks_childs[peak][child]["peak"], 
							peaks_childs[peak][child]["intensity"])
			except:
				return "Error processing the file"

			# CHECK BECAUSE IF SECOND PART FAILS THERE WILL BE A FILENAME INSERTED
			# ANYWAYS. CHECK AND REMOVE.


	else:
		return "Error"
	return "OK"


###############################################################################
#
# 	@app.route /profile
#
###############################################################################

@app.route('/profile', methods=['GET', 'POST'])
def profile():

	if not "uid" in session:
		return redirect(url_for("login"))

	msql = maldisql()
	msg = []
	pmsg = []
	if request.method == 'POST':
		#if request.form["name"] and request.form["last"] and request.form["email"]:
		if "name" in request.form and "last" in request.form and "email" in request.form:
			# Update data to db 
			error = msql.UpdateUser(session["uid"], escape(request.form["email"]), escape(request.form["name"]), escape(request.form["last"]))
			if not error:
				msg.append(alert("Successful profile update", "success"))	
			else:
				msg.append(alert(error))

		elif "pwd" in request.form and "pwd2" in request.form:
			# Update password
			if request.form["pwd"] == request.form["pwd2"]:
				perror = msql.UpdatePassword(escape(request.form["pwd"]), escape(session["uid"]))
				if not perror:
					pmsg.append(alert("Password change successful", "success"))
				else:
					pmsg.append(alert(perror))
			else:
				pmsg.append(alert("Passwords don't match"))
	
	# Get Profile
	uinfo = msql.GetUser(session["uid"])

	return render_template("profile.html", name=uinfo["name"], last=uinfo["last"], email=uinfo["email"], msg=msg, pmsg=pmsg)

###############################################################################
#
# 	@app.route /logout
#
###############################################################################

@app.route('/logout')
def logout():
	if  not 'uid' in session:
		return redirect(url_for("login"))
	# remove the username from the session if it's there
	session.pop('uid', None)
	session.pop('email', None)
	if "eid" in session:
		session.pop('eid', None)
	return redirect(url_for('login'))

# set the secret key.  keep this really secret:
app.secret_key = 'A0Zr98j/3yX R~XHH!jmN]LWX/,?RT'

if __name__ == '__main__':
	app.run(host="0.0.0.0", port=8080, threaded=True, debug=True)