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1 import os
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2 import sys
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3 from optparse import OptionParser
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4 from ConfigParser import SafeConfigParser
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5 from xml.etree import ElementTree
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6 import subprocess
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7
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8 DEBUG = False
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9
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10
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11 def main():
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12 (options, args) = _parse_args()
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13 for executable, config_path in zip(options.executables, options.configs):
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14 _run_openms(executable, config_path)
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15
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16
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17 def _run_openms(executable, config_path):
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18 _exec("%s -write_ini openms.ini" % executable)
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19 tree = ElementTree.parse("openms.ini")
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20 options = _load_options(config_path)
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21 _set_options(tree, executable, options)
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22 tree.write("openms.ini")
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23 if DEBUG:
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24 print 'With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable)
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25 _exec("%s -ini openms.ini" % executable)
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26
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27
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28 def _exec(command):
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29 proc = subprocess.Popen(args=command, shell=True)
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30 return_code = proc.wait()
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31 if return_code != 0:
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32 sys.exit(return_code)
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33
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34
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35 def _set_options(tree, executable, options):
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36 executable_node = tree.find("./NODE[@name='%s']" % executable)
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37 options_node = executable_node.find("./NODE[@name='1']")
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38 for key, raw_value in options.items("simple_options"):
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39 value = _parse_value(raw_value)
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40 _set_option(options_node, key.split("!"), value)
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41 _set_option(options_node, ["no_progress"], "true", required=False)
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42
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43
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44 def _set_option(node, key_parts, value, required=True):
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45 key = key_parts[0]
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46 if len(key_parts) == 1:
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47 item = node.find("./ITEM[@name='%s']" % key)
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48 if item is not None:
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49 item.set("value", value)
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50 elif required:
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51 raise Exception("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
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52 else:
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53 sub_node = node.find("./NODE[@name='%s']" % key)
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54 _set_option(sub_node, key_parts[1:], value, required)
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55
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56
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57 def _parse_value(raw_value):
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58 value = raw_value
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59 if raw_value in VALUE_FUNCTIONS:
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60 value = VALUE_FUNCTIONS[raw_value](raw_value)
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61 return value
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62
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63
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64 ## Special value parser for various OpenMS components
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65 def _get_pepnovo_models_path(_):
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66 pepnovo_path = _get_pepnovo_executable_path(None)
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67 pepnovo_dir = os.path.split(pepnovo_path)[0]
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68 guesses = [os.path.join(pepnovo_dir, 'Models'),
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69 os.path.join(pepnovo_dir, '..', 'Models'),
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70 os.path.join(pepnovo_dir, '..', 'share', 'pepnovo', 'Models')]
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71 models_dir = None
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72 for guess in guesses:
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73 if os.path.isdir(guess):
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74 models_dir = guess
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75 break
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76 return models_dir
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77
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78
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79 def _get_pepnovo_executable_path(_):
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80 return _which("PepNovo")
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81
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82 VALUE_FUNCTIONS = {"@PEPNOVO_MODELS_PATH@": _get_pepnovo_models_path,
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83 "@PEPNOVO_EXECUTABLE_PATH@": _get_pepnovo_executable_path}
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84
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85
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86 # http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
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87 def _which(program):
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88
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89 def is_exe(fpath):
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90 return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
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91
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92 fpath, fname = os.path.split(program)
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93 if fpath:
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94 if is_exe(program):
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95 return program
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96 else:
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97 for path in os.environ["PATH"].split(os.pathsep):
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98 exe_file = os.path.join(path, program)
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99 if is_exe(exe_file):
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100 return exe_file
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101
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102 return None
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103
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104
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105 def _parse_args():
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106 parser = OptionParser()
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107 parser.add_option("-e", "--executable", dest="executables", default=[], action="append")
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108 parser.add_option("-c", "--config", dest="configs", default=[], action="append")
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109 return parser.parse_args()
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110
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111
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112 def _load_options(config_path):
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113 config_parser = SafeConfigParser()
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114 config_parser.read(config_path)
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115 return config_parser
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116
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117 if __name__ == "__main__":
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118 main()
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