Source Code for Module Bio.Restriction._Update.Update

  1  #!/usr/bin/env python 
  2  # 
  3  #      Restriction Analysis Libraries. 
  4  #      Copyright (C) 2004. Frederic Sohm. 
  5  # 
  6  # This code is part of the Biopython distribution and governed by its 
  7  # license.  Please see the LICENSE file that should have been included 
  8  # as part of this package. 
  9  # 
 10   
 11  """Update the Rebase emboss files used by Restriction to build the 
 12  Restriction_Dictionary.py module.""" 
 13   
 14  import os 
 15  import sys 
 16  import time 
 17  from urllib import FancyURLopener 
 18   
 19  from Bio.Restriction.RanaConfig import * 
 20   
 21   
 22 -class RebaseUpdate(FancyURLopener): 
 23   
 24 -    def __init__(self, e_mail='', ftpproxy=''): 
 25          """RebaseUpdate([e_mail[, ftpproxy]]) -> new RebaseUpdate instance. 
 26   
 27          if e_mail and ftpproxy are not given RebaseUpdate uses the corresponding 
 28          variable from RanaConfig. 
 29   
 30          e_mail is the password for the anonymous ftp connection to Rebase. 
 31          ftpproxy is the proxy to use if any.""" 
 32          proxy = {'ftp' : ftpproxy or ftp_proxy} 
 33          global Rebase_password 
 34          Rebase_password = e_mail or Rebase_password 
 35          if not Rebase_password: 
 36              raise FtpPasswordError('Rebase') 
 37          if not Rebase_name: 
 38              raise FtpNameError('Rebase') 
 39          FancyURLopener.__init__(self, proxy) 
 40   
 41 -    def prompt_user_passwd(self, host, realm): 
 42          return (Rebase_name, Rebase_password) 
 43   
 44 -    def openRebase(self, name = ftp_Rebase): 
 45          print '\n Please wait, trying to connect to Rebase\n' 
 46          try: 
 47              self.open(name) 
 48          except: 
 49              raise ConnectionError('Rebase') 
 50          return 
 51   
 52 -    def getfiles(self, *files): 
 53          print '\n', 
 54          for file in self.update(*files): 
 55              print 'copying', file 
 56              fn = os.path.basename(file) 
 57              #filename = os.path.join(Rebase, fn) 
 58              filename = os.path.join(os.getcwd(), fn) 
 59              print 'to', filename 
 60              self.retrieve(file, filename) 
 61          self.close() 
 62          return 
 63   
 64 -    def localtime(self): 
 65          t = time.gmtime() 
 66          year = str(t.tm_year)[-1] 
 67          month = str(t.tm_mon) 
 68          if len(month) == 1: 
 69              month = '0' + month 
 70          return year+month 
 71   
 72 -    def update(self, *files): 
 73          if not files: 
 74              files = [ftp_emb_e, ftp_emb_s, ftp_emb_r] 
 75          return [x.replace('###', self.localtime()) for x in files] 
 76   
 77 -    def __del__(self): 
 78          if hasattr(self, 'tmpcache'): 
 79              self.close() 
 80          # 
 81          #   self.tmpcache is created by URLopener.__init__ method. 
 82          # 
 83          return 
 84   
 85   
 86 -class FtpNameError(ValueError): 
 87   
 88 -    def __init__(self, which_server): 
 89          print " In order to connect to %s ftp server, you must provide a name.\ 
 90          \n Please edit Bio.Restriction.RanaConfig\n" % which_server 
 91          sys.exit() 
 92   
 93   
 94 -class FtpPasswordError(ValueError): 
 95   
 96 -    def __init__(self, which_server): 
 97          print "\n\ 
 98          \n In order to connect to %s ftp server, you must provide a password.\ 
 99          \n Use the --e-mail switch to enter your e-mail address.\ 
100          \n\n" % which_server 
101          sys.exit() 
102   
103   
104 -class ConnectionError(IOError): 
105   
106 -    def __init__(self, which_server): 
107          print '\ 
108          \n Unable to connect to the %s ftp server, make sure your computer\ 
109          \n is connected to the internet and that you have correctly configured\ 
110          \n the ftp proxy.\ 
111          \n Use the --proxy switch to enter the address of your proxy\ 
112          \n' % which_server 
113          sys.exit() 
114   
115   
116  __all__ = ['RebaseUpdate', 'FtpNameError', 'FtpPasswordError'] 
117