def parseCTDCommandLine(argv, model, openms_param):
# Configure CTDOpt to use OpenMS style on the command line.
directives = parse_cl_directives(argv,
input_ctd='ini',
write_tool_ctd='write_ini',
prefix='-')
if directives[
"write_tool_ctd"] is not None: # triggered if -write_ini was provided on CML
# if called with -write_ini write CTD
model.write_ctd(directives["write_tool_ctd"])
exit(0)
elif directives["input_ctd"] is not None: # read ctd/ini file
model = CTDModel(from_file=directives["input_ctd"])
# print(model.get_defaults())
param = pms.Param()
fh = pms.ParamXMLFile()
fh.load(directives["input_ctd"], param)
openms_param.update(param, True)
return model.get_defaults(), openms_param
else: # only command line options provided
temp = tempfile.NamedTemporaryFile(
suffix='ini') # makes sure we get a writable file
tmp_name = temp.name
temp.close() # removes the file
model.write_ctd(tmp_name)
param = pms.Param()
fh = pms.ParamXMLFile()
fh.load(tmp_name, param)
openms_param.update(param)
os.remove(tmp_name)
return model.parse_cl_args(argv), openms_param
# load CTDModel
ini_model = None
try:
ini_model = CTDModel(from_file=args.ini_file)
except ModelTypeError:
pass
try:
ini_model = Parameters(from_file=args.ini_file)
except ModelTypeError:
pass
assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (
args.ini_file)
# get a dictionary of the ctd arguments where the values of the parameters
# given on the command line are overwritten
ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
if args.ctd_file:
ctd_model = CTDModel(from_file=args.ctd_file)
ctd_values = ctd_model.get_defaults()
for param in ini_model.get_parameters():
if not param.required and (param.default is None
or type(param.default) is _Null):
lineage = param.get_lineage(name_only=True)
try:
default = getFromDict(ctd_values, lineage)
except KeyError:
continue
setInDict(ini_values, lineage, default)
# write the ctd with the values taken from the dictionary
description='Only adds results to entries with decoy set to true. DEFAULT: false'
)
pout2mzidparams.add(
'validate',
type=bool,
description='This is a flag: Type 1 to set flag. Sets that validation of XML schema should not be performed. Faster parsing.'
)
pout2mzidparams.add(
'warning',
type=bool,
description='This is a flag: Type 1 to set flag. Sets that upon warning the software should terminate'
)
args = msgf_percolator_model.parse_cl_args()
try:
args = args_from_file(args['ctd'])
print "try to load ctd"
### MZID2PIN Parameter ###
try:
args['mzid2pin']['mzid2pin_path']
args['mzid2pin']['target_input']
args['mzid2pin']['decoy_input']
except:
print "Path or decoy/target-files missing!"
str = ''
try:
if args['mzid2pin']['outputXML'] != '':
print ("One might want to combine arguments loaded from a CTD file with arguments coming from elsewhere, like the command line."
"In that case, the method CTDopts.override_args(*arg_dicts) creates a combined argument dictionary where argument values "
"are always taken from the rightmost (last) dictionary that has them. Let's override a few parameters:")
override = {
'this_that': 'that',
'positive_int': 777
}
overridden = override_args(validated, override)
pretty_print(overridden)
print()
print ("So how to deal with command line arguments? If we have a model, we can look for its arguments. "
"Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. "
"By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'."
"Grouped parameters are expected in --group:subgroup:param_x format.")
cl_args = model.parse_cl_args('--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --input_files a.fastq b.fastq')
pretty_print(cl_args)
print()
# # you can get unmatchable command line arguments with get_remaining=True like:
# cl_args, unparsed = model.parse_cl_args('--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --unrelated_stuff abc', get_remaining=True)
print ("Override other parameters with them, and validate it against the model:")
overridden_with_cl = override_args(validated, cl_args)
validated_3 = model.validate_args(overridden_with_cl)
pretty_print(validated_3)
print()
print ("One last thing: certain command line directives that are specific to CTD functionality can be parsed for, "
"to help your script performing common tasks. These are CTD argument input, CTD model file writing and CTD argument "
"file writing. CTDopts.parse_cl_directives() can also be customized as to what directives to look for if the defaults "
"--input_ctd, --write_tool_ctd and --write_param_ctd respectively don't satisfy you.")
"One might want to combine arguments loaded from a CTD file with arguments coming from elsewhere, like the command line."
"In that case, the method CTDopts.override_args(*arg_dicts) creates a combined argument dictionary where argument values "
"are always taken from the rightmost (last) dictionary that has them. Let's override a few parameters:"
)
override = {'this_that': 'that', 'positive_int': 777}
overridden = override_args(validated, override)
pretty_print(overridden)
print()
print(
"So how to deal with command line arguments? If we have a model, we can look for its arguments. "
"Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. "
"By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'."
"Grouped parameters are expected in --group:subgroup:param_x format.")
cl_args = model.parse_cl_args(
'--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --input_files a.fastq b.fastq --output out_dir/'
)
pretty_print(cl_args)
print()
# # you can get unmatchable command line arguments with get_remaining=True like:
# cl_args, unparsed = model.parse_cl_args('--positive_int 44 --subparams:param_2 5.0 5.5 6.0 --unrelated_stuff abc', get_remaining=True)
print(
"Override other parameters with them, and validate it against the model:")
overridden_with_cl = override_args(validated, cl_args)
validated_3 = model.validate_args(overridden_with_cl)
pretty_print(validated_3)
print
print(
"One last thing: certain command line directives that are specific to CTD functionality can be parsed for, "
add_help=False,
allow_abbrev=False)
parser.add_argument("--ctd",
dest="ctd",
help="input ctd file",
metavar='CTD',
default=None,
required=True)
args, cliargs = parser.parse_known_args()
# load CTDModel
model = None
try:
model = CTDModel(from_file=args.ctd)
except ModelTypeError:
pass
try:
model = Parameters(from_file=args.ctd)
except ModelTypeError:
pass
assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (
args.ctd)
# get a dictionary of the ctd arguments where the values of the parameters
# given on the command line are overwritten
margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True)
# write the ctd with the values taken from the dictionary
out = StringIO()
ctd_tree = model.write_ctd(out, margs)
print(out.getvalue())