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1 #!/usr/bin/env python3
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2 import os
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3 import atexit
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4 import socket
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5 import time
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6 import config
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7 import pyRserve
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8
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9 def shutdown(port):
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10 try:
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11 conn = pyRserve.connect(port=port)
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12 print("Shutting down Rserv...", end="")
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13 conn.shutdown()
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14 print("Done")
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15 except pyRserve.rexceptions.RConnectionRefused:
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16 print("connection to Rserve refused, server is probably already down")
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17
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18 def get_open_port():
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19 s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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20 s.bind(("", 0))
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21 s.listen(1)
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22 port = s.getsockname()[1]
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23 s.close()
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24 return port
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25
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26 # find free port
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27 def create_connection():
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28 '''Start R Rserver and test connection, port is
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29 stored in config.RSERVE_PORT
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30 '''
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31 config.RSERVE_PORT = get_open_port()
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32 print('Trying to start Rserve...',)
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33 os.system(
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34 "R CMD Rserve --RS-port {} -q --no-save ".format(config.RSERVE_PORT))
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35 # wait for server to start accepting connections
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36 time.sleep(1)
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37 try:
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38 conn = pyRserve.connect(port=config.RSERVE_PORT)
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39 print("connection OK")
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40 conn.close()
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41 atexit.register(shutdown, config.RSERVE_PORT)
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42 return config.RSERVE_PORT
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43 except:
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44 print("Connection with Rserve was not established!")
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45 raise
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46
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47
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48 class setFunctionName():
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49 # decorator
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50
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51 def __init__(self, f, name):
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52 self.f = f
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53 self.name = name
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54
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55 def __call__(self, *args, **kwargs):
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56 return self.f(self.name, *args, **kwargs)
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57
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58
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59 def convert_types(fn):
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60 ''' decorator function to convert type for r2py'''
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61 allowed_classes = [str, int, float, list, bool, type(None)]
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62 # everything else is converted to str
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63
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64 def fn_wrapper(*args, **kwargs):
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65 new_args = list(args)
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66 new_kwargs = kwargs
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67 for i, value in enumerate(args):
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68 if any(type(value) is i for i in allowed_classes):
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69 new_args[i] = value
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70 else:
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71 new_args[i] = str(value)
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72 for i, value in kwargs.items():
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73 if any(type(value) is i for i in allowed_classes):
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74 new_kwargs[i] = value
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75 else:
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76 new_kwargs[i] = str(value)
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77 return fn(*new_args, **new_kwargs)
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78
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79 return fn_wrapper
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80
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81
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82 class R():
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83
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84 def __init__(self, source, verbose=False):
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85 ''' Code in file should defined R functions which will be linked to python function
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86 purpose of this is to make it memory efficient - rserve connection will be closed
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87 after every exetion so memory is released.
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88 warning - Source code is executed each time function is used so it should only
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89 contain function definition!!
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90
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91 '''
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92 self.source = os.path.realpath(source)
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93 conn = pyRserve.connect(port=config.RSERVE_PORT)
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94 conn.voidEval("source('{}', chdir=TRUE)".format(self.source))
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95 # if single object is define then fn return str! conversion neccessary
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96 object_names = list(conn.r.ls())
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97 if verbose:
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98 print("R function loaded:", end=" ")
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99 for i in object_names:
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100 ## skip these objects - not compatible with older version of rserve
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101 ## and not needed to be accessed from python
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102 if i in ['DT_OPTIONS', 'HTMLHEADER', 'WD', 'options',
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103 'htmlheader', 'options', 'xcolor_code', 'TANDEM_RANKS', 'RANKS_TANDEM',]:
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104 continue
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105 try:
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106 obj = getattr(conn.r, i)
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107 if isinstance(obj, pyRserve.rconn.RFuncProxy):
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108 if verbose:
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109 print(i, end=" ")
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110 @convert_types
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111 def rwrapper(fname, *args, **kwargs):
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112 c = pyRserve.connect(port=config.RSERVE_PORT)
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113 c.r.setwd(os.getcwd())
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114 c.voidEval("source('{}',chdir=TRUE)".format(self.source))
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115 fn = getattr(c.r, fname)
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116 out = fn(*args, **kwargs)
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117 c.close()
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118 return out
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119 rwrapper = setFunctionName(rwrapper, i)
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120 setattr(self, i, rwrapper)
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121 del(rwrapper)
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122 except:
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123 print("skipping :", i)
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124 pass
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125 if verbose:
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126 print("\r")
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