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comparison openms_wrapper.py @ 2:cf0d72c7b482 draft

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Update.
author galaxyp
date Fri, 10 May 2013 17:31:05 -0400
parents ba86fd127f5a
children 1183846e70a1
comparison
equal deleted inserted replaced
1:5c65f8116244 2:cf0d72c7b482
2 import sys 2 import sys
3 from optparse import OptionParser 3 from optparse import OptionParser
4 from ConfigParser import SafeConfigParser 4 from ConfigParser import SafeConfigParser
5 from xml.etree import ElementTree 5 from xml.etree import ElementTree
6 import subprocess 6 import subprocess
7 from re import compile
7 8
8 DEBUG = False 9 DEBUG = False
9 10
10 11
11 def main(): 12 def main():
12 (options, args) = _parse_args() 13 (options, args) = _parse_args()
13 for executable, config_path in zip(options.executables, options.configs): 14 for executable, config_path in zip(options.executables, options.configs):
14 _run_openms(executable, config_path) 15 command_handler = COMMAND_HANDLERS.get(executable, _run_openms)
16 command_handler(executable, config_path)
17
18
19 def _run_shell(executable, config_path):
20 command = open(config_path, "r").read().strip()
21 if DEBUG:
22 print "Running shell command %s" % command
23 _exec(command)
15 24
16 25
17 def _run_openms(executable, config_path): 26 def _run_openms(executable, config_path):
18 _exec("%s -write_ini openms.ini" % executable) 27 _exec("%s -write_ini openms.ini" % executable)
19 tree = ElementTree.parse("openms.ini") 28 tree = ElementTree.parse("openms.ini")
22 tree.write("openms.ini") 31 tree.write("openms.ini")
23 if DEBUG: 32 if DEBUG:
24 print 'With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable) 33 print 'With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable)
25 _exec("%s -ini openms.ini" % executable) 34 _exec("%s -ini openms.ini" % executable)
26 35
36 COMMAND_HANDLERS = {
37 "__SHELL__": _run_shell,
38 }
39
40
41 def _fail(message, return_code=1):
42 print message
43 sys.exit(return_code)
44
27 45
28 def _exec(command): 46 def _exec(command):
29 proc = subprocess.Popen(args=command, shell=True) 47 proc = subprocess.Popen(args=command, shell=True)
30 return_code = proc.wait() 48 return_code = proc.wait()
31 if return_code != 0: 49 if return_code != 0:
32 sys.exit(return_code) 50 _fail("Error executing command [%s], return code is %d" % (command, return_code), return_code)
33 51
34 52
35 def _set_options(tree, executable, options): 53 def _set_options(tree, executable, options):
36 executable_node = tree.find("./NODE[@name='%s']" % executable) 54 executable_node = tree.find("./NODE[@name='%s']" % executable)
55 if executable_node is None:
56 _fail("Could not find options for executable %s" % executable)
37 options_node = executable_node.find("./NODE[@name='1']") 57 options_node = executable_node.find("./NODE[@name='1']")
38 for key, raw_value in options.items("simple_options"): 58 for key, raw_value in options.items("simple_options"):
59 if raw_value is None:
60 _fail("No value found key %s" % key)
39 value = _parse_value(raw_value) 61 value = _parse_value(raw_value)
40 _set_option(options_node, key.split("!"), value) 62 _set_option(options_node, key.split("!"), value)
41 _set_option(options_node, ["no_progress"], "true", required=False) 63 _set_option(options_node, ["no_progress"], "true", required=False)
42 64
43 65
44 def _set_option(node, key_parts, value, required=True): 66 def _set_option(node, key_parts, value, required=True):
45 key = key_parts[0] 67 key = key_parts[0]
46 if len(key_parts) == 1: 68 if len(key_parts) == 1:
47 item = node.find("./ITEM[@name='%s']" % key) 69 if not _set_item_value(node, key, value) and \
48 if item is not None: 70 not _set_list_item_value(node, key, value) and \
49 item.set("value", value) 71 required:
50 elif required: 72 _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
51 raise Exception("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
52 else: 73 else:
74 if not node:
75 _fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
53 sub_node = node.find("./NODE[@name='%s']" % key) 76 sub_node = node.find("./NODE[@name='%s']" % key)
77 if not sub_node:
78 _fail("Failed to find node for key %s" % key)
54 _set_option(sub_node, key_parts[1:], value, required) 79 _set_option(sub_node, key_parts[1:], value, required)
80
81
82 def _set_item_value(node, key, value):
83 item = node.find("./ITEM[@name='%s']" % key)
84 if item is not None:
85 item.set("value", value)
86 return item is not None
87
88
89 def _set_list_item_value(node, key, values):
90 item = node.find("./ITEMLIST[@name='%s']" % key)
91 if item is not None:
92 for value in values.split(","):
93 ElementTree.SubElement(item, "LISTITEM", {"value": value})
94 return item is not None
55 95
56 96
57 def _parse_value(raw_value): 97 def _parse_value(raw_value):
58 value = raw_value 98 value = raw_value
59 if raw_value in VALUE_FUNCTIONS: 99 for pattern, function in VALUE_FUNCTIONS.iteritems():
60 value = VALUE_FUNCTIONS[raw_value](raw_value) 100 try:
101 match = pattern.match(value)
102 except TypeError:
103 print "Invalid value found config file %s" % value
104 sys.exit(1)
105 if match:
106 value = function(*match.groups())
107 if value is None:
108 print "Failed to properly parse raw value %s" % raw_value
109 sys.exit(1)
61 return value 110 return value
62 111
63 112
64 ## Special value parser for various OpenMS components 113 ## Special value parser for various OpenMS components
65 def _get_pepnovo_models_path(_): 114 def _get_pepnovo_models_path():
66 pepnovo_path = _get_pepnovo_executable_path(None) 115 pepnovo_path = _which('PepNovo')
67 pepnovo_dir = os.path.split(pepnovo_path)[0] 116 pepnovo_dir = os.path.split(pepnovo_path)[0]
68 guesses = [os.path.join(pepnovo_dir, 'Models'), 117 guesses = [os.path.join(pepnovo_dir, 'Models'),
69 os.path.join(pepnovo_dir, '..', 'Models'), 118 os.path.join(pepnovo_dir, '..', 'Models'),
70 os.path.join(pepnovo_dir, '..', 'share', 'pepnovo', 'Models')] 119 os.path.join(pepnovo_dir, '..', 'share', 'pepnovo', 'Models')]
71 models_dir = None 120 models_dir = None
72 for guess in guesses: 121 for guess in guesses:
73 if os.path.isdir(guess): 122 if os.path.isdir(guess):
74 models_dir = guess 123 models_dir = guess
75 break 124 break
76 return models_dir 125 return models_dir
77
78
79 def _get_pepnovo_executable_path(_):
80 return _which("PepNovo")
81
82 VALUE_FUNCTIONS = {"@PEPNOVO_MODELS_PATH@": _get_pepnovo_models_path,
83 "@PEPNOVO_EXECUTABLE_PATH@": _get_pepnovo_executable_path}
84 126
85 127
86 # http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python 128 # http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
87 def _which(program): 129 def _which(program):
88 130
94 if is_exe(program): 136 if is_exe(program):
95 return program 137 return program
96 else: 138 else:
97 for path in os.environ["PATH"].split(os.pathsep): 139 for path in os.environ["PATH"].split(os.pathsep):
98 exe_file = os.path.join(path, program) 140 exe_file = os.path.join(path, program)
141 print path
99 if is_exe(exe_file): 142 if is_exe(exe_file):
100 return exe_file 143 return exe_file
101 144
102 return None 145 return None
146
147
148 VALUE_FUNCTIONS = {compile(r"\@WHICH\((.*)\)\@"): _which,
149 compile(r"\@PEPNOVO_MODELS_PATH\@"): _get_pepnovo_models_path,
150 }
103 151
104 152
105 def _parse_args(): 153 def _parse_args():
106 parser = OptionParser() 154 parser = OptionParser()
107 parser.add_option("-e", "--executable", dest="executables", default=[], action="append") 155 parser.add_option("-e", "--executable", dest="executables", default=[], action="append")
109 return parser.parse_args() 157 return parser.parse_args()
110 158
111 159
112 def _load_options(config_path): 160 def _load_options(config_path):
113 config_parser = SafeConfigParser() 161 config_parser = SafeConfigParser()
162 config_parser.optionxform = str
114 config_parser.read(config_path) 163 config_parser.read(config_path)
115 return config_parser 164 return config_parser
116 165
117 if __name__ == "__main__": 166 if __name__ == "__main__":
118 main() 167 main()