Source Code for Package Bio.PopGen.Async

  1  # Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5   
  6   
  7  ''' 
  8  Support for asynchronous execution. 
  9   
 10  ''' 
 11   
 12  import os 
 13  import thread 
 14   
 15   
 16 -class Async(object): 
 17      '''Abstract Asynchronous execution class. 
 18   
 19         This is the top abstract class. 
 20         Concrete classes must implement the _run_program method. 
 21      ''' 
 22   
 23 -    def __init__(self): 
 24          '''Async constructor. 
 25   
 26             Initializes the queues, among other things. 
 27             Of notice, is the access_ds lock for controlling exclusive 
 28                 access to this object. 
 29          ''' 
 30          self.running = {} 
 31          self.waiting = [] 
 32          self.done = {} 
 33          self.id = 0 
 34          self.hooks = {} 
 35          self.access_ds = thread.allocate_lock() 
 36   
 37 -    def run_program(self, program, parameters, input_files): 
 38          '''Runs a program. 
 39   
 40             Real _run_program to be implemented by concrete classes. 
 41   
 42             parameters: 
 43             program String identifying program. 
 44             parameters List of String parameters. 
 45             input_files Hash of Input file descriptors. 
 46   
 47             returns: 
 48             Task Id. 
 49   
 50             The input_files hash key is the path that is passed 
 51             to the program. It should always be relative. 
 52             Value is a stream. 
 53          ''' 
 54          if program in self.hooks: 
 55              self.access_ds.acquire() 
 56              self.id += 1 
 57              id = self.id 
 58              self.access_ds.release() 
 59              self._run_program(id, self.hooks[program], parameters, input_files) 
 60              return id 
 61   
 62 -    def _run_program(self, id, program, parameters, input_files): 
 63          """Actually run the program, handled by a subclass (PRIVATE). 
 64   
 65          This method should be replaced by any derived class to do 
 66          something useful. It will be called by the run_program method. 
 67          """ 
 68          raise NotImplementedError("This object should be subclassed") 
 69   
 70 -    def get_result(self, id): 
 71          ''' Returns the results for a certain Id, the info for that Id is 
 72              forgotten. 
 73   
 74              parameters: 
 75              id Id of the task. 
 76   
 77              returns: 
 78              (return_code, output_files) return code and file access 
 79              object. 
 80   
 81              The output_files hash key is a relative file name, and the value a 
 82              output stream. 
 83          ''' 
 84          self.access_ds.acquire() 
 85          if id in self.done: 
 86              returnCode, fileObject = self.done[id] 
 87              del self.done[id] 
 88              self.access_ds.release() 
 89          else: 
 90              self.access_ds.release() 
 91              return None 
 92   
 93   
 94 -class FileRetriever(object): 
 95      '''An Abstract Support class to retrieve files. 
 96      ''' 
 97   
 98 -    def __init__(self): 
 99          self.file_list=[] 
100   
101 -    def get_File_list(self): 
102          '''Returns the list of available files. 
103          ''' 
104          return self.file_list 
105   
106 -    def get_file(self, name): 
107          raise NotImplementedError('Abstract method') 
108   
109   
110 -class DirectoryRetriever(FileRetriever): 
111      '''Retrieves a directory content. 
112      ''' 
113   
114 -    def __init__(self, directory): 
115          FileRetriever.__init__(self) 
116          self.directory = directory 
117          walk_list = os.walk(directory) 
118          for dir, dir_list, file_list in walk_list: 
119              for file in file_list: 
120                  self.file_list.append(file[len(directory)+1:]) 
121   
122 -    def get_file(self, name): 
123          return open(self.directory + os.sep + name) 
124