def login():
"""Checks the user credentials
and logs him in
"""
form = LogInForm()
if form.validate_on_submit():
import hashlib
user = models.User.query.get(request.form["username"])
if user != None and \
user.password == hashlib.sha512(request.form["password"]).hexdigest():
login_user(user)
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Logged in"
db.session.add(log_entry)
db.session.commit()
return redirect(url_for('index'))
else:
flash("Invalid login", "danger")
return redirect(url_for('login'))
return render_template('login.html', form=form)
def delete_project(id):
"""Delete a project and
all associated data.
"""
project = models.Project.query.filter_by(project_id=id).one()
if project.owner == g.user.user_name:
memship = models.Membership.query.filter_by(project=id).delete()
db.session.commit()
genotypes = models.Genotype.query.filter_by(project_id=id).delete()
db.session.commit()
phenotypes = models.Phenotype.query.filter_by(project_id=id).delete()
db.session.commit()
individuals = models.Individual.query.filter_by(project_id=id).delete()
db.session.commit()
groups = models.Group.query.filter_by(project_id=id).delete()
db.session.commit()
db.session.delete(project)
db.session.commit()
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Deleted project " + project.name
db.session.add(log_entry)
db.session.commit()
flash('Project deleted successfuly.', 'success')
else:
flash('You do not have the premision to do that.', 'danger')
return redirect(url_for('projects'))
def add_user():
"""Add a new user to the system.
Only the master administrator can do that.
"""
# Check if this is the master administrator
if g.user.user_name != gen_app.config['ADMIN_USER']:
flash("You should not be here", "danger")
return redirect(url_for('index'))
user = models.User()
if request.method == 'POST':
import hashlib
user.password = hashlib.sha512(request.form["password"]).hexdigest()
user.user_name = request.form['username']
user.email = request.form['email']
db.session.add(user)
db.session.commit()
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Created user " + request.form['username']
db.session.add(log_entry)
db.session.commit()
return redirect(url_for('users'))
def add_project():
"""Create a new project.
No duplicate names are allowed.
"""
form = AddProject()
project = models.Project()
memship = models.Membership()
nm = models.Project.query.filter_by(name=form.project_name.data).all()
if form.validate_on_submit():
if nm:
flash("A project with that name already exists", "danger")
return redirect(url_for('projects'))
project.name = form.project_name.data
project.description = form.project_description.data
project.owner = g.user.user_name
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Created project " + form.project_name.data
db.session.add(log_entry)
db.session.add(project)
db.session.commit()
memship.user_name = g.user.user_name
memship.project = project.project_id
db.session.add(memship)
db.session.commit()
return redirect(url_for('projects'))
return render_template('add_project.html',
title="New Project",
ap=form)
def download_dat(filename,project_id):
"""Generate and serve
the DAT file
"""
geno = models.Genotype.query.filter_by(project_id=project_id).all()
pheno = db.engine.execute('SELECT name FROM phenotype where project_id=' + \
str(project_id) +' group by name;')
gen_list = {}
phn_list = list()
for row in geno:
gen_list[row.snp] = row.snp
for row in pheno:
phn_list.append(row.name)
with open(gen_app.config['UPLOAD_FOLDER'] + filename, 'w+') as f:
writer = csv.writer(f, delimiter=',')
for row in gen_list:
r = [] + ["M"] + [gen_list[row]]
writer.writerow(r)
for row in phn_list:
r = [] + ["T"] + [row]
writer.writerow(r)
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Downloaded DAT file."
db.session.add(log_entry)
db.session.commit()
return send_from_directory(gen_app.config['UPLOAD_FOLDER'], filename=filename)
def single_geno():
"""Upload a file containing information
for a single genotype.
The file format is the following:
ID - column with genotype IDs
SNP - SNP name column
Call - call column
No header is required.
"""
abort_commit = False
csv.field_size_limit(sys.maxsize)
num_rows = 0
current_geno_q = models.Genotype.query.\
filter_by(project_id=request.form['id']).all()
current_geno = set()
duplicate = set()
for row in current_geno_q:
current_geno.add(row.snp)
# Upload file and parse it
if request.method == 'POST':
single_geno = request.files['single_geno']
# Check if this is the correct file type
if single_geno and allowed_file(single_geno.filename):
filename = secure_filename(single_geno.filename)
single_geno.save(os.path.join(gen_app.config['UPLOAD_FOLDER'], filename))
flash("Genotype file uploaded successfully", "success")
try:
with open(gen_app.config['UPLOAD_FOLDER'] + filename, 'rb') as csvfile:
header=csvfile.readline()
# Determine delimiter
dell = ","
if header.find(" ") !=- 1:
dell = " "
elif header.find("\t") != -1:
dell = "\t"
elif header.find(",") != -1:
dell = ","
sr = csv.reader(csvfile, delimiter=dell)
csvfile.seek(0)
# List of IDs for when it crashes
future = []
for row in sr:
future.append(row[0])
# Perform checks
csvfile.seek(0)
for row in sr:
num_rows = num_rows+1
if len(row) > 4:
flash("Ivalid file format", "danger")
return redirect(url_for('project_page', id=request.form['id']))
gen = models.Genotype()
gen.individual_id = row[0]
if row[1] in current_geno:
duplicate.add(row[1])
abort_commit = True
gen.snp = row[1]
if len(row) == 4:
gen.call = row[2] + "/" + row[3]
else:
gen.call = row[2]
gen.project_id = request.form['id']
db.session.add(gen)
if abort_commit:
flash("Duplicate genotypes detected", "danger")
flash(list(duplicate), "info")
return redirect(url_for('project_page', id=request.form['id']))
# Generate a list of missing IDs
inds = models.Individual.query.filter_by(project_id=request.form['id']).all()
current = []
missing = []
for row in inds:
current.append(row.new_id)
for row in future:
if row not in current:
missing.append(row)
if len(missing) != 0:
flash("Error: missing or misspelled IDs.", "danger")
flash(missing, "info")
db.session.rollback()
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
return redirect(url_for('project_page', id=request.form['id']))
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Upload Genotype file for project "\
+ request.form['proname']
db.session.add(log_entry)
"""
Commit changes to DB
"""
db.session.commit()
except exc.IntegrityError, e:
db.session.rollback()
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
def bulk_geno():
"""Bulk upload of genotype information
The file format is the following:
IDs - column containing all the IDs
Gen1 - first genotype
Gen2 - second genotype
Gen3 - etc...
GenN - ...
This file REQUIRES a header:
ID - the first cell can be anything
Gen Name 1 - coresponding genotype name
Gen Name 2 - ...
Gen Name 3 - ...
Gen Name N - ...
"""
csv.field_size_limit(sys.maxsize)
num_rows = 0
if request.method == 'POST':
bulk_geno = request.files['bulk_geno']
if bulk_geno and allowed_file(bulk_geno.filename):
filename = secure_filename(bulk_geno.filename)
bulk_geno.save(os.path.join(gen_app.config['UPLOAD_FOLDER'], filename))
flash("Genotype file uploaded successfuly", "success")
try:
with open(gen_app.config['UPLOAD_FOLDER'] + filename, 'rb') as csvfile:
header=csvfile.readline()
dell = ","
if header.find(" ") !=- 1:
dell = " "
elif header.find("\t") != -1:
dell = "\t"
elif header.find(",") != -1:
dell = ","
# List of IDs for when it crashes
csvfile.seek(0)
future = []
for row in sr:
future.append(row[0])
sr = csv.reader(csvfile, delimiter=dell)
header = sr.next()
csvfile.seek(0)
for row in sr:
num_rows = num_rows+1
num_cols = len(row)
for i in range(1,num_cols):
gen = models.Genotype()
gen.individual_id = row[0]
gen.snp = header[i]
gen.call = row[i]
gen.project_id = request.form['id']
db.session.add(gen)
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Upload Genotype file for project " + request.form['proname']
db.session.add(log_entry)
"""
Commit changes to DB
"""
db.session.commit()
except exc.IntegrityError, e:
db.session.rollback()
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
# Generate a list of missing IDs
inds = models.Individual.query.filter_by(project_id=request.form['id']).all()
current = []
missing = []
for row in inds:
current.append(row.new_id)
for row in future:
if row not in current:
missing.append(row)
flash("Error: missing or misspelled IDs", "danger")
flash(missing, "info")
return redirect(url_for('project_page', id=request.form['id']))
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
def upload_individual():
"""Upload a file containing a list of individuals.
The file format is the following:
ID - a column containing all the individual IDs
Gender - a column containing gender information
No header is required.
"""
csv.field_size_limit(sys.maxsize)
num_rows = 0
if request.method == 'POST':
ind_file = request.files['individuals']
if ind_file and allowed_file(ind_file.filename):
filename = secure_filename(ind_file.filename)
ind_file.save(os.path.join(gen_app.config['UPLOAD_FOLDER'], filename))
flash("Individuals file uploaded successfully", "success")
try:
with open(gen_app.config['UPLOAD_FOLDER'] + '/' + filename, 'rb') as csvfile:
sr = csv.reader(csvfile, delimiter=',')
for row in sr:
num_rows = num_rows+1
if len(row) != 2:
flash("Ivalid file format. Only two column with \
IDs and gender are required", "danger")
return redirect(url_for('project_page', id=request.form['id']))
ind = models.Individual()
ind.new_id = row[0]
ind.gender = row[1]
ind.project_id = request.form['id']
db.session.add(ind)
"""
Create log entry
"""
log_entry = models.Log()
import time
log_entry.timestamp = int(time.time())
log_entry.user_id = g.user.user_name
log_entry.action = "Upload Individual file for project "\
+ request.form['proname']
db.session.add(log_entry)
"""
Commit changes to DB
"""
db.session.commit()
# clean up
except exc.IntegrityError, e:
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)
flash("Error: missing or misspelled IDs", "danger")
return redirect(url_for('project_page', id=request.form['id']))
try:
os.remove(gen_app.config['UPLOAD_FOLDER'] + '/' +filename)
except OSError,e :
print str(e)