hello.template

from flask import Flask, render_template, redirect, url_for, abort, request, jsonify, send_from_directory
import glob
import os
import sys
import subprocess
import atexit

from flask_wtf import FlaskForm
from flask_wtf.csrf import CSRFProtect
from wtforms import StringField, SubmitField
import context_processors as cp

from bokeh.embed import server_document

import nameProcessing as np


# Configure flask stuff
app = Flask(__name__)
app.config['SECRET_KEY']='la'
app.url_map.strict_slashes = False
csrf = CSRFProtect(app)
cp.setup(app)


# Start bokeh servers
bokeh_process1 = subprocess.Popen(
    ['bokeh', 'serve', '--allow-websocket-origin={{dnprefix}}', 'lolliplotServer.py'], stdout=subprocess.PIPE)
bokeh_process2 = subprocess.Popen(
    ['bokeh', 'serve', '--allow-websocket-origin={{dnprefix}}', '--port=5007', 'lolliplotServerDetail.py'], stdout=subprocess.PIPE)

@atexit.register
def kill_server():
    bokeh_process1.kill()
    bokeh_process2.kill()


# Functions/classes needed for index page
@app.route('/autocomplete', methods=['GET'])
def autocomplete():
    search = request.args.get('q').upper()
    filelist = glob.glob(os.path.expanduser('~/data/*.ssw11.hhr'))
    orflist = []
    for f in filelist:
        name = os.path.basename(f).split('.')[0].upper()
        if np.is_systematic_name(name): # Accept only ORF's in the standard list
            orflist.append( np.display_name(name) )
    filteredlist = [orf for orf in sorted(orflist) if search in orf]
    return jsonify(matching_results=filteredlist)

class IndexForm(FlaskForm):
    filename = StringField('autocomplete')
    display = SubmitField(label='Display plot')
    download = SubmitField(label='Download file')


# Index page
@app.route('/', methods=['POST','GET'])
def index():
    form = IndexForm()
    if form.validate_on_submit():
        filename = form.filename.data
        name = filename.split('/')[-1]
        if form.display.data:
            url = url_for( 'load_name',filename=(np.single_name(name)) )
            return redirect(url)
        else:
            return send_from_directory(os.path.expanduser('~/data'),np.systematic_name(name)+'.0.ssw11.hhr',as_attachment=True)
    return render_template('index.html',form=form)


# Custom error handlers
@app.errorhandler(406)
def wrong_case_url(e):
    url = ''
    input_list = e.description.split(' ')
    if len(input_list)==1:
        url = url_for('load_name', filename=input_list[0].upper())
    elif len(input_list)==2:
        url = url_for('load_detail', filename=input_list[0].upper(), db=input_list[1].lower())
    return redirect(url)

@app.errorhandler(410)
def syst_name_in_url(e):
    url = ''
    input_list = e.description.split(' ')
    if len(input_list)==1:
        url = url_for( 'load_name', filename=np.standard_name(input_list[0].upper()) )
    elif len(input_list)==2:
        url = url_for('load_detail', filename=np.standard_name(input_list[0].upper()), db=input_list[1].lower())
    return redirect(url)


# Summary page
@app.route('/<filename>', methods=['POST','GET'])
def load_name(filename):
    if filename!=filename.upper():
        abort(406, filename)
    if np.is_systematic_name(filename) and not np.is_hypothetical_protein(filename) :
        abort(410, filename)

    if np.is_unknown_protein(filename): # Accept only ORF's in the standard list
        return render_template(
            'error.html',
            msg=filename+" is not a valid ORF. Please choose a different one.")

    filepath = os.path.join(os.path.expanduser('~/data'),np.systematic_name(filename)+'.0.ssw11.hhr')
    prob = request.args.get('prob', default=0.5, type=float)
    ov_min = request.args.get('ovm', default=10, type=int)
    ov_min_r = request.args.get('ovm1', default=0.1, type=float)
    if os.path.isfile(filepath):
        bokeh_script = server_document(
            url='http://{{dnprefix}}:5006/lolliplotServer',
            arguments=dict(filename=filepath, prob=prob, ov_min=ov_min, ov_min_r=ov_min_r))

        return render_template(
               'plot.html',
               plot_script=bokeh_script,
               name=filename,
               prob=prob,
               ov_min=ov_min,
               ov_min_r=ov_min_r)
    else:
        return render_template(
            'error.html',
            msg="Data for "+filename+" does not exist. Please choose a different ORF.")


# Detail page
@app.route('/<filename>/<db>', methods=['POST','GET'])
def load_detail(filename, db):
    if filename!=filename.upper() or db!=db.lower():
        abort(406, filename+" "+db)
    if np.is_systematic_name(filename) and not np.is_hypothetical_protein(filename) :
        abort(410, filename+" "+db)

    if np.is_unknown_protein(filename): # Accept only ORF's in the standard list
        return render_template(
            'error.html',
            msg=filename+" is not a valid ORF. Please choose a different one.")

    filepath = os.path.join(os.path.expanduser('~/data'),np.systematic_name(filename)+'.0.ssw11.hhr')
    if db in ['pdb', 'pfam', 'yeast']:

        if os.path.isfile(filepath):
           bokeh_script = server_document(
               url='http://{{dnprefix}}:5007/lolliplotServerDetail', arguments=dict(filename=filepath, db=db))
           return render_template(
                  'detail.html',
                  plot_script=bokeh_script,
                  name=filename,
                  db=db )
        else:
           return render_template(
                  'error.html',
       	          msg="Data for "+filename+" does not exist. Please choose a different ORF.")

    else:
        return render_template(
       	       'error.html',
               msg="Data for database "+db+" does not exist. Please choose between pdb, pfam or yeast.")