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
out = StringIO()
ctd_tree = ini_model.write_ctd(out, ini_values)
print(out.getvalue())
# therefore hardcoded params change the name of spectra:in to spectra:_in
# which is corrected here again
# TODO remove once PR is in and adapt profile accordingly
fix_underscores(args)
model = CTDModel(from_file=input_ctd)
# transform values from json that correspond to
# - old style booleans (string + restrictions) -> transformed to a str
# - new style booleans that get a string (happens for hidden parameters [-test])
# are transformed to a bool
# - unrestricted ITEMLIST which are represented as strings
# ("=quoted and space separated) in Galaxy -> transform to lists
# - optional data input parameters that have defaults and for which no
# value is given -> overwritte with the default
for p in model.get_parameters():
# check if the parameter is in the arguments from the galaxy tool
# (from the json file(s)), since advanced parameters are absent
# if the conditional is set to basic parameters
try:
getFromDict(args, p.get_lineage(name_only=True))
except KeyError:
# few tools use dashes in parameters which are automatically replaced
# by underscores by Galaxy. in these cases the dictionary needs to be
# updated (better: then dash and the underscore variant are in the dict)
# TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
try:
lineage = [
_.replace("-", "_") for _ in p.get_lineage(name_only=True)
]