def sam_logout():
"""Log out of the session and delete all session files."""
if 'id' in session:
delete_files('sam', session['id'])
session.pop('id', None)
flash('Session was reset.', 'success')
return render_template('sam.html', showHidden=False)
def sam_delete_allbam():
"""Delete all the non-fasta files that were uploaded in this session."""
if 'id' not in session:
return json_notauth()
exts = ('.bam', '.bam.bai', '.sam')
if delete_files('sam', session['id'], None, exts):
return json_success()
return json_notfound()
def sam_delete():
"""Delete a specified file and its similar extensions via AJAX."""
if 'id' not in session:
return json_notauth()
# Fetch queried filename from JSON request
filename = request.json['file']
# Delete a bam file and associated files
if filename.endswith(('.bam')):
front = os.path.splitext(filename)[0]
exts = ('.bam', '.bam.bai', '.sam')
if delete_files('sam', session['id'], front, exts):
return json_success()
return json_notfound()
# Delete some other kind of file
if delete_file('sam', filename, session['id']):
return json_success()
return json_notfound()
def sam_upload():
"""Render the file manager for handling SAM and FASTA files.
Methods:
GET: Render the File Management Page with form.
POST: Process the form upload and redirect user.
"""
# Quick shortcut method so I don't have to rewrite this code
def render_form(session_id, samfiles=None, fastafile=None):
"""Render the form associated with this route."""
return render_template('sam/upload.html',
session_id=escape(session_id),
samfiles=basename(samfiles, session_id),
fastafile=basename(fastafile, session_id))
# Generate a new session ID if it doesn't already exist
if 'id' not in session:
session['id'] = random_id()
# Get all files associated with this session id
oldbams = list_dir('sam', session['id'], ('.bam'))
oldfasta = get_firstfile('sam', session['id'], ('.fa', '.fasta'))
# Render an empty form for a GET request
if request.method == 'GET':
return render_form(session['id'], oldbams, oldfasta)
# Otherwise validate the form on a POST request
if request.method == 'POST':
sams = request.files.getlist('sam')
fasta = request.files['fasta']
# Throw error if entire form is empty
if not fasta and not sams[0]:
flash('No files were selected for upload.', 'alert-warning')
return render_form(session['id'], oldbams, oldfasta)
# Throw error if any file does not have the appropriate extension
abort = False
for sam in sams:
if len(sam.filename) > 0:
ext = os.path.splitext(secure_filename(sam.filename))[1]
if ext.lower() not in ['.bam', '.sam']:
abort = True
if fasta:
ext = os.path.splitext(secure_filename(fasta.filename))[1]
if ext.lower() not in ['.fa', '.fasta']:
abort = True
if abort:
flash('Invalid file types were uploaded', 'alert-warning')
return render_form(session['id'], oldbams, oldfasta)
# Upload SAM files
if sams:
error_count = 0
for sam in sams:
if len(sam.filename) > 0:
try:
upload_sam(sam, sam.filename, escape(session['id']))
except IOError, message:
flash(message, 'alert-warning')
error_count = error_count + 1
if len(sams) == error_count:
return render_form(session['id'], oldbams, oldfasta)
# Upload Fasta file; first delete old fasta files if they exist
if fasta:
delete_files('sam', session['id'], None, ('.fa', '.fasta'))
fa = upload(fasta, fasta.filename, 'sam', escape(session['id']))
try:
Fasta(fa)
except:
flash(message, 'alert-warning')
if not sams:
return render_form(session['id'], oldbams, oldfasta)
flash('Files were successfully uploaded.', 'alert-success')
return render_template('sam.html', showHidden=True)
from flask import Flask
__author__ = 'Jeffrey Zhou'
__copyright__ = 'Copyright (C) 2017, EpigenDx Inc.'
__credits__ = ['Jeffrey Zhou', 'Eric Zhou']
__version__ = '0.1.1'
__status__ = 'Production'
UPLOAD_FOLDER = os.path.join(os.path.dirname(__file__), 'tmp')
app = Flask(__name__)
app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
app.config['MAX_FILE_AGE'] = 7200
app.secret_key = os.environ.get('SECRET', 'Big Secret!')
app.logger.addHandler(logging.StreamHandler(sys.stdout))
app.logger.setLevel(logging.ERROR)
# Clean temporary file folders
from biotin_flask.models.disk_io import delete_files
delete_files('sam')
import biotin_flask.views.application
import biotin_flask.views.partek_transpose_view
import biotin_flask.views.psq_view
import biotin_flask.views.genotyping_view
import biotin_flask.views.cov_view
import biotin_flask.views.sam
import biotin_flask.views.epic_view
import biotin_flask.views.bed_view
import biotin_flask.views.cpg_view