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markerminer.py
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markerminer.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import os.path as op
import shlex
import subprocess
from tempfile import mkdtemp
from multiprocessing import cpu_count
from flask import Flask, render_template, request, redirect, \
send_from_directory, url_for
from flask_appconfig import AppConfig
from flask_bootstrap import Bootstrap
from flask_wtf import Form
from flask_wtf.file import FileField, FileAllowed, FileRequired
from wtforms import StringField, IntegerField, FloatField, SelectField, \
FieldList, FormField, SubmitField, ValidationError, validators
from wtforms.widgets import FileInput as _FileInput
from wtforms.validators import Email, Optional
from sendmail import EmailClient
from helpers import regexp, mkdir_p, upload_files, build_job_cmd, \
get_result_url, SCRIPT_PATH, ALLOWED_EXTENSIONS, ORGANISMS
from filesystem import Folder, File
from action import View
class FileInput(_FileInput):
def __init__(self, multiple=False):
self.multiple = multiple
def __call__(self, field, **kwargs):
if self.multiple:
kwargs['multiple'] = 'multiple'
return super(FileInput, self).__call__(field, **kwargs)
class MultiFileField(FileField):
widget = FileInput(multiple=True)
class JobSubmitForm(Form):
fileupload = MultiFileField('Input FASTA file(s). <a href="download_sample_data">Download sample dataset</a>', \
validators=[
FileRequired(),
FileAllowed(ALLOWED_EXTENSIONS, 'Plain-text FASTA file(s) only!'),
regexp(u'(?=.*-)[a-zA-Z0-9-]+')
])
singleCopyReference = SelectField(u'Select single copy transcript reference', \
choices=list(ORGANISMS))
minTranscriptLen = IntegerField('Minimum transcript length')
minProteinCoverage = FloatField('Minimum percentage of protein length aligned', \
[validators.NumberRange(max=100)])
minTranscriptCoverage = FloatField('Minimum percentage of transcript length aligned', \
[validators.NumberRange(max=100)])
minSimilarity = FloatField('Minimum similarity percent with which sequences are aligned', \
[validators.NumberRange(max=100)])
cpus = IntegerField('Number of CPUs to use', [validators.NumberRange(min=1, max=cpu_count())])
email = StringField('Email address (to send notification)', \
validators=[
Optional(),
Email(message='Please provide a valid email address')
])
submit_button = SubmitField('Submit Job')
def create_app(configfile=None):
app = Flask(__name__)
AppConfig(app, configfile)
Bootstrap(app)
email_handler = EmailClient(email_from=app.config['EMAIL_DEFAULT_FROM'], \
from_name=app.config['EMAIL_FROM_NAME'], \
api_key=app.config['EMAIL_API_KEY'])
@app.route('/', methods=['GET', 'POST'])
def index():
form = JobSubmitForm(singleCopyReference="Athaliana", minTranscriptLen=900, \
minProteinCoverage=80, minTranscriptCoverage=70, minSimilarity=70, cpus=1)
if request.method == 'POST' and form.validate_on_submit(): # to get error messages to the browser
mkdir_p(app.config['UPLOADS_DIRECTORY'])
UPLOADS_DIRECTORY = mkdtemp(dir=app.config['UPLOADS_DIRECTORY'])
RESULTS_DIRECTORY = "{0}-output".format(UPLOADS_DIRECTORY)
upload_files(form, UPLOADS_DIRECTORY)
debug = app.config['DEBUG']
cmd = build_job_cmd(form, UPLOADS_DIRECTORY, RESULTS_DIRECTORY, debug=debug)
subprocess.Popen(shlex.split(cmd), env=os.environ)
job_id = op.basename(UPLOADS_DIRECTORY)
result_url = get_result_url(request, job_id)
email_to = form.email.data if form.email.data else ''
if email_to != '':
email_handler.send_email(email_to, result_url)
return redirect(url_for('status', job_id=job_id))
return render_template('index.html', form=form)
@app.route('/help')
def help():
return render_template('help.html')
@app.route('/status/<job_id>')
def status(job_id):
result_url = get_result_url(request, job_id)
return render_template('status.html', result_url=result_url)
@app.route('/results/<path:path>')
def browser(path=None):
uploads_dir = app.config['UPLOADS_DIRECTORY']
path_join = op.join(uploads_dir, path)
# if path is toplevel output dir, check for result tarball
# if tarball exists, trigger output download
if path.endswith('-output'):
result_targz = '{0}.tar.gz'.format(path)
result_path = op.join(uploads_dir, result_targz)
if op.exists(result_path):
return redirect(url_for('download', path=result_targz))
# if result file not ready yet, let user browse the run directory
if op.isdir(path_join):
folder = Folder(uploads_dir, path)
folder.read()
return render_template('folder.html', folder=folder)
else:
my_file = File(uploads_dir, path)
context = my_file.apply_action(View)
folder = Folder(uploads_dir, my_file.get_path())
if context == None:
return render_template('file_unreadable.html', folder=folder)
return render_template('file_view.html', text=context['text'], file=my_file, folder=folder)
@app.route('/download/<path:path>')
def download(path=''):
return send_from_directory(app.config['UPLOADS_DIRECTORY'], path)
@app.route('/download_sample_data')
def sample_data():
from shutil import make_archive
sample_data_dir = 'Sample_Data'
sample_data_path = op.join(SCRIPT_PATH, 'pipeline', sample_data_dir)
sample_data_zip_base = op.join(app.config['UPLOADS_DIRECTORY'], sample_data_dir)
make_archive(sample_data_zip_base, format="gztar", root_dir=sample_data_path)
return redirect(url_for('download', path='{0}.tar.gz'.format(sample_data_dir)))
return app
if __name__ == '__main__':
create_app(configfile='site.cfg').run(host='0.0.0.0')