--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sift_web/sift_web.py	Thu Sep 04 17:46:51 2014 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+import requests
+import argparse
+import sys
+from functools import wraps
+import time
+from bs4 import BeautifulSoup
+
+__url__ = 'http://provean.jcvi.org/genome_prg_2.php'
+
+
+def stop_err(msg, err=1):
+    sys.stderr.write('%s\n' % msg)
+    sys.exit(err)
+
+
+def retry(ExceptionToCheck, tries=10, delay=3, backoff=2, logger=None):
+    """Retry calling the decorated function using an exponential backoff.
+
+    http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
+    original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
+
+    :param ExceptionToCheck: the exception to check. may be a tuple of
+        exceptions to check
+    :type ExceptionToCheck: Exception or tuple
+    :param tries: number of times to try (not retry) before giving up
+    :type tries: int
+    :param delay: initial delay between retries in seconds
+    :type delay: int
+    :param backoff: backoff multiplier e.g. value of 2 will double the delay
+        each retry
+    :type backoff: int
+    :param logger: logger to use. If None, print
+    :type logger: logging.Logger instance
+    """
+    def deco_retry(f):
+
+        @wraps(f)
+        def f_retry(*args, **kwargs):
+            mtries, mdelay = tries, delay
+            while mtries > 1:
+                try:
+                    return f(*args, **kwargs)
+                except ExceptionToCheck, e:
+                    #msg = '%s, Retrying in %d seconds...' % (str(e), mdelay)
+                    msg = 'Retrying in %d seconds...' % (mdelay)
+                    if logger:
+                        logger.warning(msg)
+                    else:
+                        # print msg
+                        pass
+                    time.sleep(mdelay)
+                    mtries -= 1
+                    mdelay *= backoff
+            return f(*args, **kwargs)
+
+        return f_retry  # true decorator
+
+    return deco_retry
+
+
+class SIFTWeb:
+
+    def __init__(self):
+        self.full_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.tsv'
+        self.condensed_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.one.tsv'
+        self.summary_download_url = 'http://provean.jcvi.org/serve_file.php?VAR=g%s/%s.result.summary.tsv'
+        self.url_dict = {'full': self.full_download_url,
+                         'condensed': self.condensed_download_url,
+                         'summary': self.summary_download_url}
+
+    def upload(self, inputpath):
+        payload = {'table': 'human37_66'}
+        in_txt = open(inputpath, 'rb').read()
+        payload['CHR'] = in_txt
+        request = requests.post( __url__, data=payload)#, files={'CHR_file': open(path)})
+        return request.text
+
+    @retry(requests.exceptions.HTTPError)
+    def get_full_data(self, job_id, full_output):
+        r = requests.request(
+            'GET', (self.full_download_url) % (job_id, job_id))
+        if r.text != 'No file exists':
+            with open(full_output, 'wb') as f:
+                f.write(r.text)
+        else:
+            return requests.HTTPError()
+
+    @retry(requests.exceptions.HTTPError)
+    def get_condensed_data(self, job_id, condensed_output):
+        r = requests.request(
+            'GET', (self.condensed_download_url) % (job_id, job_id))
+        if r.text != 'No file exists':
+            with open(condensed_output, 'wb') as f:
+                f.write(r.text)
+        else:
+            raise(requests.HTTPError())
+
+    @retry(requests.exceptions.HTTPError)
+    def get_summary_data(self, job_id, summary_output):
+        r = requests.request(
+            'GET', (self.summary_download_url) % (job_id, job_id))
+        if r.text != 'No file exists':
+            with open(summary_output, 'wb') as f:
+                f.write(r.text)
+        else:
+            raise(requests.HTTPError())
+
+
+def main(params):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input', type=str, required=True)
+    parser.add_argument('--output1', type=str, required=True)
+    parser.add_argument('--output2', type=str, required=True)
+    parser.add_argument('--output3', type=str, required=True)
+    args = parser.parse_args(params)
+    sift_web = SIFTWeb()
+    content = sift_web.upload(args.input)
+    soup = BeautifulSoup(content)
+    p = soup.findAll('p')
+    job_id = p[1].string.split(':')[-1].replace(' ', '').replace(').', '')
+    sift_web.get_full_data(job_id, args.output1)
+    sift_web.get_condensed_data(job_id, args.output2)
+    sift_web.get_summary_data(job_id, args.output3)
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])