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cron_rdahmm_scripps_raw.py
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cron_rdahmm_scripps_raw.py
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#!/usr/local/bin/python
#==========================================================================
# Download, ingest, and execute rdahmm evaluation for updated scripps datasets
# Set up a cron job to run nightly
#
# usage: cron_rdahmm.py
#
#===========================================================================
import os, subprocess, sys, glob
import urllib,string
import re
from threading import Thread
from properties import properties
cron_path = properties('cron_path') + "/SCRIPPS_RAW/"
download_path = properties('download_path') + "/SCRIPPS_RAW/"
#model_path = properties('model_path')
scripps_data = properties('cron_path') + "/SCRIPPS_RAW/*.tar"
scripps_cmd = properties('script_path') + "/scripps_ingest_single_raw.py"
eval_cmd = properties('script_path') + "/rdahmm_eval_single.py"
xml_cmd = properties('script_path') + "/create_summary_xmls.py"
json_cmd = properties('script_path') + "/create_summary_jsons.py"
class ThreadJob(Thread):
def __init__(self, tarball):
Thread.__init__(self)
self.tarball = tarball
self.dataset = string.split(tarball, "/")[-1][:-13]
def run(self):
# ingest a given tar ball
print "+++Starting process ", self.tarball, " ..."
cmd = scripps_cmd
#cmd = "echo"
p = subprocess.Popen([cmd, self.tarball], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(stdout, stderr) = p.communicate()
if p.returncode != 0:
print p.stderr
print "+++Finished process ", self.tarball
# run rdahmm evaluation on the corresponding dataset
print "+++Starting process ", self.dataset, " ..."
cmd = eval_cmd
#cmd = "echo"
p = subprocess.Popen([cmd, self.dataset], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(stdout, stderr) = p.communicate()
if p.returncode != 0:
print p.stderr
print "+++Finished process ", self.dataset
# create summary xml on the corresponding dataset
print "+++creating summary xml for ", self.dataset, " ..."
cmd = xml_cmd
#cmd = "echo"
p = subprocess.Popen([cmd, self.dataset], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(stdout, stderr) = p.communicate()
if p.returncode != 0:
print p.stderr
print "+++Finished creating summary xml for ", self.dataset
# create summary json on the corresponding dataset
print "+++creating summary json for ", self.dataset, " ..."
cmd = json_cmd
#cmd = "echo"
p = subprocess.Popen([cmd, self.dataset], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(stdout, stderr) = p.communicate()
if p.returncode != 0:
print p.stderr
print "+++Finished creating summary json for ", self.dataset
# update download_path with the latest tarball
oldtars = download_path + self.dataset + "*.tar"
if len(glob.glob(oldtars)) > 0:
cmd = "rm " + oldtars
os.system(cmd)
#print cmd
cmd = "cp " + self.tarball + " " + download_path
os.system(cmd)
#print cmd
# Get current SCRIPPS raw datasets
# http://garner.ucsd.edu/pub/timeseries/measures/rawNeuTimeSeries.MEASURES_Combination.20130616.tar
# We will compare tars available on the web site with the ones we already have.
# We will only download the differences.
def list_tars(url, username="anonymous", password="[email protected]" ):
"""download html with login"""
newurl = "http://" + username + ":" + password + "@" + string.replace(url,"http://","")
opener = urllib.urlopen(newurl)
html = opener.read()
opener.close()
r = re.compile('(?<=href=").*?(?=")')
links = r.findall(html)
tars = [name for name in links if name[-4:]=='.tar' ]
return tars
url = 'http://garner.ucsd.edu/pub/timeseries/measures/'
tars = list_tars(url)
datasets = os.listdir(download_path)
#datasets = glob.glob(download_path + "*.tar")
#datasets = [string.split(name,"/")[-1] for name in datasets]
#print datasets
# newdatasets is the list of all updated tarballs from SCRIPPS site
newdatasets = []
for tarball in tars:
#Currently we only want rawNeuTimeSeries
if not "rawNeuTimeSeries" in tarball:
continue
if not tarball in datasets:
newdatasets.append(tarball)
if len(newdatasets) == 0:
sys.exit("No new scripps raw dataset available today.")
# clear working directory cron_path
cmd = "rm -r " + cron_path + "/*"
os.system(cmd)
wgetcmd = "wget -nv --user=anonymous --password='[email protected]' -P " + cron_path + " -r -nH --cut-dirs=4 --no-parent --reject 'index.html*' " + url + "%s"
for tarball in newdatasets:
cmd = wgetcmd % tarball
#print cmd
os.system(cmd)
#break
#threadjobs = []
for tarball in glob.glob(cron_path + "*.tar"):
#print tarball
t = ThreadJob(tarball)
t.start()
#threadjobs.append(t)
#sys.exit()
# wait for all processing threads to finish before generating the XML
#for t in threadjobs:
# t.join()
# Create the summary XML command
#print "Finally, create the summary XML files."
#os.system(xml_cmd)