def wait_and_notify(app, email, tag, sid, url):
with app.app_context():
print(sf.func_name())
status = {'status': 'xxx'}
while status['status'] != "finished":
time.sleep(30)
print(sf.func_name() + " update")
status = update_status(sid)
if status['error'] == '0':
mess = "completed successfully"
else:
mess = "failed"
send_email(email, tag, mess, url)
def send_email_upon_termination(email, tag, sid):
print(sf.func_name())
# create new thread to send to background
url = url_for('results', user=email, job_id=tag, _external=True)
thr = Thread(target=wait_and_notify, args=[app, email, tag, sid, url])
thr.start()
return thr
def download(job_id, user, file_name):
data = app.config['USER_DATA_DIR']
feil = data + "/" + user + "/" + job_id + "/protein_prompt.txt"
print(sf.func_name() + " " + feil)
try:
return send_file(feil, attachment_filename='results.txt')
except Exception as e:
return str(e)
def results(job_id, user="******"):
user = sf.QuickFix(user)
data = app.config['USER_DATA_DIR']
print(sf.func_name() + " datadir: " + str(data))
feil = data + "/" + user + "/" + job_id + "/protein_prompt.txt"
all_lines = sf.WriteLines(feil)
feil = "../../downloads/" + user + "/" + job_id + "/result.txt"
return render_template('results.html',
lines=all_lines,
user=user,
job_id=job_id,
result=feil)
def update_status(jiddle):
print(sf.func_name())
connector = sql.connect("jobs.db")
cursor = connector.cursor()
status = subprocess.check_output(["tsp", "-s", str(jiddle)]).strip()
error = ""
if status == "finished":
error = subprocess.check_output(["tsp", "-i", str(jiddle)])
print(sf.func_name() + " " + error)
id1 = error.find("exit code") + 10
id2 = error.find('\n')
error = error[id1:id2].strip()
print(sf.func_name() + " error-code: <" + error + ">")
cmd = "UPDATE jobs SET status = '" + status + "' WHERE id = '" + str(
jiddle) + "'"
print(cmd)
cursor.execute(cmd)
connector.commit()
connector.close()
return {'status': status, 'error': error}
def send_email(email, tag, mess, url):
with app.app_context():
print(sf.func_name())
subject = tag + " " + mess
template = 'mail/link'
msg = Message(app.config['FLASKY_MAIL_SUBJECT_PREFIX'] + ' ' + subject,
sender=app.config['FLASKY_MAIL_SENDER'],
recipients=[email])
msg.body = render_template(template + '.txt',
email=email,
tag=tag,
mess=mess,
url=url)
msg.html = render_template(template + '.html',
email=email,
tag=tag,
mess=mess,
url=url)
mail.send(msg)
def update_all():
print(sf.func_name())
connector = sql.connect("jobs.db")
cursor = connector.cursor()
status = {}
lines = subprocess.check_output(["tsp"]).split('\n')
print(str(len(lines)) + " entries")
for l in lines:
print(l)
l = l.strip()
if len(l) < 5 or "ID" in l: continue
c = l.split()
status[c[0]] = c[1]
for k, v in status.iteritems():
cmd = "UPDATE jobs SET status = '" + v + "' WHERE id = '" + k + "'"
print(cmd)
cursor.execute(cmd)
connector.commit()
connector.close()
return status
def submit(email, tag, sequence, db):
print("now entered submit:" + current_app.name)
# os.chdir( app.config['APP_PATH'] )
pwd = os.getcwd()
print(pwd)
if email == '':
email = "anonymous"
else:
email = sf.QuickFix(email)
print(email)
sequence = sf.CleanSequence(sequence)
print(sequence)
tag = sf.QuickFix(tag)
print(tag)
user_dir = app.config['USER_DATA_DIR']
connector = sql.connect("jobs.db")
cursor = connector.cursor()
# os.chdir( user_dir )
job_dir = user_dir + "/" + email + "/" + tag
print(job_dir)
if os.path.isdir(job_dir):
print("dir exists")
return {'status': 'exists', 'id': '-99999', 'error': '-99999'}
else:
os.makedirs(job_dir)
print(job_dir + " created")
# os.chdir( job_dir )
with open(job_dir + '/protein_prompt.txt', 'w') as f:
f.write("fake.fa 15 AABCDEABCDEBCDE 0.4 \n")
f.write(
"cake.fa 105 ABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDEABCDE 0.5 \n"
)
f.write("bake.fa 5 ABCDE 1.5 \n")
print(sf.func_name() + " send to queue")
#cmd = "tsp rf -seq " + sequence + " -db " + db + " -out " + job_dir + "/protein_prompt.txt"
cmd = ["tsp", "sleep", "10"]
jiddle = subprocess.check_output(cmd).strip()
print("job id: " + jiddle)
status = subprocess.check_output(["tsp", "-s", str(jiddle)]).strip()
print("status " + status)
date = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime())
print(date)
print("INSERT INTO jobs (user,tag,id,date,status) VALUES (?,?,?,?,?)",
(email, tag, jiddle, date, status))
cursor.execute(
"INSERT INTO jobs (user,tag,id,date,status) VALUES (?,?,?,?,?)",
(email, tag, jiddle, date, status))
connector.commit()
# os.chdir( pwd)
print("now: " + os.getcwd() + " should have retured to base dir")
connector.close()
return {'status': status, 'id': jiddle}
def taskstatus(task_id):
print(sf.func_name() + " id: " + task_id)
status = update_status(task_id)
return jsonify(status)
def index():
print(sf.func_name() + " go")
form = RequestForm()
# form = RequestForm(db='1')
if request.method == 'GET':
form.email.data = session.get('email', '')
form.sequence.data = session.get('sequence', '')
form.tag.data = session.get('tag', '')
form.db.data = session.get('db', '1')
print(sf.func_name() + " get")
print(sf.func_name() + " " + form.email.data)
print(sf.func_name() + " " + form.tag.data)
print(sf.func_name() + " " + form.sequence.data)
print(sf.func_name() + " " + form.db.data)
return render_template('form.html', form=form)
print(sf.func_name() + " post ")
if form.validate() == False:
print(sf.func_name() + " errors ")
flash('errors in input (see detailed information above)')
return render_template('form.html', form=form)
# email = request.form['email']
session['email'] = form.email.data
session['tag'] = form.tag.data
session['sequence'] = form.sequence.data
session['db'] = form.db.data
print(sf.func_name() + " redirect")
print(sf.func_name() + " " + session.get('email'))
print(sf.func_name() + " " + session.get('tag'))
print(sf.func_name() + " " + session.get('sequence'))
print(sf.func_name() + " " + session.get('db'))
# return render_template( 'wait.html', form = form, serialize=Serialize)
status = submit(form.email.data, form.tag.data, form.sequence.data,
form.db.data)
print(sf.func_name() + " submit send to background, id: " +
str(status['id']))
print(sf.func_name() + " forward status location: " +
url_for('taskstatus', task_id=status['id']))
joburl = url_for('taskstatus', task_id=status['id'])
if int(status['id']) < 0:
flash("submission failed")
return render_template('form.html', form=form)
# start background process waiting for termination of calculation to send email
if form.email.data != "anonymous":
send_email_upon_termination(form.email.data, form.tag.data,
status['id'])
return render_template('wait.html', form=form, joburl=joburl)