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1 import sys
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2 sys.path.insert(0, '/home/saket/requests-new-urllib3-api/requests/packages/')
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3 sys.path.insert(0, '/home/saket/requests-new-urllib3-api')
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4
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5
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6 import requests
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7 from functools import wraps
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8 import tempfile, shutil,time
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9 import os,csv
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10 #__url__="http://mutationassessor.org/?cm=var&var=%s&frm=txt&fts=all"
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11 __url__="http://mutationassessor.org"
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12 def stop_err( msg ):
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13 sys.stderr.write( '%s\n' % msg )
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14 sys.exit()
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15
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16 def retry(ExceptionToCheck, tries=4, delay=3, backoff=2, logger=None):
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17
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18 """Retry calling the decorated function using an exponential backoff.
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19
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20 http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
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21 original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
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22
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23 :param ExceptionToCheck: the exception to check. may be a tuple of
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24 exceptions to check
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25 :type ExceptionToCheck: Exception or tuple
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26 :param tries: number of times to try (not retry) before giving up
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27 :type tries: int
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28 :param delay: initial delay between retries in seconds
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29 :type delay: int
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30 :param backoff: backoff multiplier e.g. value of 2 will double the delay
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31 each retry
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32 :type backoff: int
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33 :param logger: logger to use. If None, print
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34 :type logger: logging.Logger instance
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35 """
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36 def deco_retry(f):
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37
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38 @wraps(f)
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39
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40 def f_retry(*args, **kwargs):
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41 mtries, mdelay = tries, delay
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42 while mtries > 1:
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43 try:
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44 return f(*args, **kwargs)
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45 except ExceptionToCheck, e:
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46 #msg = "%s, Retrying in %d seconds..." % (str(e), mdelay)
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47 msg = "Retrying in %d seconds..." % (mdelay)
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48 if logger:
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49 logger.warning(msg)
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50 else:
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51 #print msg
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52 pass
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53 time.sleep(mdelay)
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54 mtries -= 1
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55 mdelay *= backoff
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56 return f(*args, **kwargs)
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57
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58 return f_retry # true decorator
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59
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60 return deco_retry
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61 def main(params):
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62 with open(params[0],"r") as f:
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63 for i,sequence in enumerate(f):
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64 #print sequence
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65 sequence=sequence.replace("\t",",").replace(" ",",")
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66 call=requests.get((__url__)%(sequence))
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67 with open(params[1],"a") as w:
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68 text = call.content.replace("\\t","\t")
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69 if i>1:
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70 text_split=text.split("\n")
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71 text="\t".join(text_split[1])
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72 w.write(text)
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73 time.sleep(1)
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74 return True
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75
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76 def main_web(params):
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77 tmp_dir = tempfile.mkdtemp()
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78 path = os.path.join(tmp_dir,"csv_file")
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79 in_txt = csv.reader(open(params[0],"rb"), delimiter="\t")
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80 with open(path,"wb") as fp:
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81 out_csv = csv.writer(fp,delimiter=",")
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82 out_csv.writerows(in_txt)
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83 fh = open(path,"rb")
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84 readfile=fh.read()
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85 fh.close()
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86 payload = {"vars":readfile,"tableQ":"","protres":""}
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87 request = requests.post(__url__,data=payload)
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88 response = request.text
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89 temp_file = os.path.join(tmp_dir,"int_file")
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90 with open(temp_file,"wb") as w:
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91 w.write(response)
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92
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93 in_txt = csv.reader(open(temp_file,"rb"), delimiter=",")
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94 with open(params[1],"wb") as fp:
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95 out_csv = csv.writer(fp,delimiter="\t")
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96 out_csv.writerows(in_txt)
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97 shutil.rmtree(tmp_dir)
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98 return True
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99 if __name__=="__main__":
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100 main_web(sys.argv[1:])
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