Hi,
just fixed the print() issue locally and ran into the next problems
which were easy to fix:
- ConfigParser -> configparser
- iteritems -> items
(The modified sources are attached if they are of interest)
Now I have an error that seems to be deeper:
Failed to find specific OpenMS option [shuffle] in node [<Element 'NODE'
at 0x2b96a3b1c048>]
Any ideas?
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
import os
import sys
from optparse import OptionParser
from configparser import SafeConfigParser
from xml.etree import ElementTree
import subprocess
from re import compile
DEBUG = False
def main():
(options, args) = _parse_args()
for executable, config_path in zip(options.executables, options.configs):
command_handler = COMMAND_HANDLERS.get(executable, _run_openms)
command_handler(executable, config_path)
def _run_shell(executable, config_path):
command = open(config_path, "r").read().strip()
if DEBUG:
print( "Running shell command %s" % command)
_exec(command)
def _run_openms(executable, config_path):
_exec("%s -write_ini openms.ini" % executable)
tree = ElementTree.parse("openms.ini")
options = _load_options(config_path)
_set_options(tree, executable, options)
tree.write("openms.ini")
if DEBUG:
print('With openms.ini as:\n%s\n, calling: %s -ini openms.ini' % (open("openms.ini", "r").read(), executable))
_exec("%s -ini openms.ini" % executable)
COMMAND_HANDLERS = {
"__SHELL__": _run_shell,
}
def _fail(message, return_code=1):
print( message )
sys.exit(return_code)
def _exec(command):
proc = subprocess.Popen(args=command, shell=True)
return_code = proc.wait()
if return_code != 0:
_fail("Error executing command [%s], return code is %d" % (command, return_code), return_code)
def _set_options(tree, executable, options):
executable_node = tree.find("./NODE[@name='%s']" % executable)
if executable_node is None:
_fail("Could not find options for executable %s" % executable)
options_node = executable_node.find("./NODE[@name='1']")
for key, raw_value in options.items("simple_options"):
if raw_value is None:
_fail("No value found key %s" % key)
value = _parse_value(raw_value)
_set_option(options_node, key.split("!"), value)
_set_option(options_node, ["no_progress"], "true", required=False)
def _set_option(node, key_parts, value, required=True):
key = key_parts[0]
if len(key_parts) == 1:
if not _set_item_value(node, key, value) and \
not _set_list_item_value(node, key, value) and \
required:
_fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
else:
if node is None:
_fail("Failed to find specific OpenMS option [%s] in node [%s]" % (key, node))
sub_node = node.find("./NODE[@name='%s']" % key)
if sub_node is None:
_fail("Failed to find node for key %s" % key)
_set_option(sub_node, key_parts[1:], value, required)
def _set_item_value(node, key, value):
item = node.find("./ITEM[@name='%s']" % key)
if item is not None:
item.set("value", value)
return item is not None
def _set_list_item_value(node, key, values):
item = node.find("./ITEMLIST[@name='%s']" % key)
if item is not None:
for value in values.split(","):
ElementTree.SubElement(item, "LISTITEM", {"value": value})
return item is not None
def _parse_value(raw_value):
value = raw_value
for pattern, function in VALUE_FUNCTIONS.items():
try:
match = pattern.match(value)
except TypeError:
print( "Invalid value found config file %s" % value )
sys.exit(1)
if match:
value = function(*match.groups())
if value is None:
print( "Failed to properly parse raw value %s" % raw_value )
sys.exit(1)
return value
## Special value parser for various OpenMS components
def _get_pepnovo_models_path():
pepnovo_path = _which('PepNovo')
pepnovo_dir = os.path.split(pepnovo_path)[0]
guesses = [os.path.join(pepnovo_dir, 'Models'),
os.path.join(pepnovo_dir, '..', 'Models'),
os.path.join(pepnovo_dir, '..', 'share', 'pepnovo', 'Models')]
models_dir = None
for guess in guesses:
if os.path.isdir(guess):
models_dir = guess
break
return models_dir
# http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
def _which(program):
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
print( path )
if is_exe(exe_file):
return exe_file
return None
def _mapped_outputs(output_directory, inputs):
inputs = inputs.split(",")
os.makedirs(output_directory)
outputs = [os.path.join(output_directory, os.path.basename(input)) for input in inputs]
return ",".join(outputs)
VALUE_FUNCTIONS = {compile(r"\@WHICH\((.*)\)\@"): _which,
compile(r"\@PEPNOVO_MODELS_PATH\@"): _get_pepnovo_models_path,
compile(r"\@MULTI_OUTPUT\(([^,]*),(.*)\)\@"): _mapped_outputs,
}
def _parse_args():
parser = OptionParser()
parser.add_option("-e", "--executable", dest="executables", default=[], action="append")
parser.add_option("-c", "--config", dest="configs", default=[], action="append")
return parser.parse_args()
def _load_options(config_path):
config_parser = SafeConfigParser()
config_parser.optionxform = str
config_parser.read(config_path)
return config_parser
if __name__ == "__main__":
main()
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