[UT GSAF] Check if sequencing job is done and download it if it is. Sed text message to notify

gistfile1.txt

#!/usr/bin/env python

from twilio.rest import TwilioRestClient
import paramiko
import os
import sys
import time

def sendMessage(job):
    #twilio
    twilio_account_sid = ''
    twilio_auth_token = ''
    client = TwilioRestClient(twilio_account_sid, twilio_auth_token)
    client.messages.create(
        to = '',
        from_ = '',
        body = 'Downloaded %s' %job,
    )
    return 0

def makedir(directory):
    if not os.path.isdir(directory):
        os.mkdir(directory)
    return 0

def checkProject(run_number, job_number):
    client = paramiko.SSHClient()
    user_name = ''
    fourierseq = 'fourierseq.icmb.utexas.edu'
    key_file = '/.ssh/id_rsa.pub'
    raw_run_path = '/raid/jcruz/corral/'
    local_storage = ''
    client.set_missing_host_key_policy(paramiko.AutoAddPolicy())
    client.connect(fourierseq, username=user_name, key_filename = key_file)
    sftp = client.open_sftp()
    print 'Connected %s' %(fourierseq)
    runs = sftp.listdir(raw_run_path)
    if run_number in runs:
        projects = sftp.listdir(raw_run_path + '/%s' %run_number)
        for job in job_number:
            project_name = 'Project_' + job
            if project_name in projects:
                remote_path = '%s/%s/%s' %(raw_run_path,run_number,project_name)
                local_path = '%s/%s' %(local_storage, job)
                makedir(local_path)
                for filename in sftp.listdir(remote_path):
                    remote_name = remote_path + '/' + filename
                    local_name = local_path + '/' + filename
                    if not os.path.isfile(local_name):
                        print 'Downloading %s to %s...' %(filename,local_path)
                        sftp.get(remote_name, local_name, callback=None)
                sendMessage(job)
    else:
        hour = time.strftime("%H:%M:%S")
        date = time.strftime("%d/%m/%Y")
        print '%s %s\t%s not finish' %(date, hour, run_number)
    return 0

def main():
    arguments = sys.argv
    if len(arguments) < 3:
        sys.exit('python %s <run_number> <job_number1> <job_number2> ...' %(arguments[0]))
    run_number = arguments[1]
    job_number = arguments[2:]
    print 'Checking %s from %s' %(','.join(job_number), run_number)
    checkProject(run_number, job_number)

if __name__ == '__main__':
    main()