Codebase list ctdconverter / ed044c3
Added extra parameters to allow more control over the generation of Galaxy stubs Luis de la Garza 9 years ago
1 changed file(s) with 55 addition(s) and 18 deletion(s). Raw diff Collapse all Expand all
+55
-18
galaxyconfiggenerator/generator.py less more
3232 return self.msg
3333 def __unicode__(self):
3434 return self.msg
35
36 class ExitCode:
37 def __init__(self, code_range="", level="", description=""):
38 self.range = code_range
39 self.level = level
40 self.description = description
3541
3642 def main(argv=None): # IGNORE:C0111
3743 '''Command line options.'''
7783
7884 try:
7985 # Setup argument parser
80 parser = ArgumentParser(description=program_license, formatter_class=RawDescriptionHelpFormatter, add_help=True)
86 parser = ArgumentParser(prog="GalaxyConfigGenerator", description=program_license, formatter_class=RawDescriptionHelpFormatter, add_help=True)
8187 parser.add_argument("-i", "--input-file", dest="input_file", help="provide a single input CTD file to convert", required=True)
8288 parser.add_argument("-o", "--output-file", dest="output_file", help="provide a single output Galaxy wrapper file", required=True)
8389 parser.add_argument("-a", "--add-to-command-line", dest="add_to_command_line", help="adds content to the command line", default="", required=False)
8692 "validated against emptiness or being equal to 'None'", required=False)
8793 parser.add_argument("-q", "--quote-parameters", dest="quote_parameters", action="store_true", default=False,
8894 help="if true, each parameter in the generated command line will be quoted", required=False)
89 parser.add_argument("-b", "--blacklisted-parameters", dest="blacklisted_parameters", default="",
90 help="comma separated list of parameters that will be ignored and won't appear on the galaxy stub", required=False)
91 parser.add_argument("-p", "--package-requirements", dest="package_requirements", default="",
92 help="comma separated list of required galaxy packages", required=False)
95 parser.add_argument("-b", "--blacklisted-parameter", dest="blacklisted_parameters", default=[], nargs="+", action="append",
96 help="list of parameters that will be ignored and won't appear on the galaxy stub", required=False)
97 parser.add_argument("-p", "--package-requirement", dest="package_requirements", default=[], nargs="+", action="append",
98 help="list of required galaxy packages", required=False)
99 parser.add_argument("-x", "--exit-code", dest="exit_codes", default=[], nargs="+", action="append",
100 help="list of <stdio> galaxy exit codes, in the following format: range=<range>,level=<level>,description=<description>,\n" +
101 "example: --exit-codes \"range=3:4,level=fatal,description=Out of memory\"")
93102 # verbosity will be added later on, will not waste time on this now
94103 # parser.add_argument("-v", "--verbose", dest="verbose", action="count", help="set verbosity level [default: %(default)s]")
95104 parser.add_argument("-V", "--version", action='version', version=program_version_message)
103112
104113 #if verbose > 0:
105114 # print("Verbose mode on")
106 convert(
107 input_file,
115 convert(input_file,
108116 output_file,
109117 add_to_command_line=args.add_to_command_line,
110118 whitespace_validation=args.whitespace_validation,
111119 quote_parameters=args.quote_parameters,
112 blacklisted_parameters=map(strip, args.blacklisted_parameters.split(",")),
113 package_requirements=map(strip, args.package_requirements.split(",")))
120 # remember that blacklisted_parameters, package_requirements and exit_codes are lists of lists of strings
121 blacklisted_parameters=[item for sublist in args.blacklisted_parameters for item in sublist],
122 package_requirements=[item for sublist in args.package_requirements for item in sublist],
123 exit_codes=convert_exit_codes([item for sublist in args.exit_codes for item in sublist]))
114124 return 0
115125
116126 except KeyboardInterrupt:
133143 traceback.print_exc()
134144 return 2
135145
146 def convert_exit_codes(exit_codes_raw):
147 # input is in the format:
148 # range=3:4,level=fatal,description=Out of memory
149 exit_codes = []
150 for exit_code_raw in exit_codes_raw:
151 exit_code = ExitCode()
152 for key_value in exit_code_raw.split(","):
153 # each key_value contains something like range=3 or description=whatever
154 # so we can split again by using "="
155 key_value_split = key_value.split("=")
156 setattr(exit_code, key_value_split[0], key_value_split[1].strip())
157 exit_codes.append(exit_code)
158 return exit_codes
159
136160 def convert(input_file, output_file, **kwargs):
137161 # first, generate a model
138162 print("Parsing CTD from [%s]" % input_file)
144168 create_description(doc, tool, model)
145169 create_requirements(doc, tool, model, kwargs["package_requirements"])
146170 create_command(doc, tool, model, **kwargs)
147 create_inputs(doc, tool, model, **kwargs)
148 create_outputs(doc, tool, model, **kwargs)
171 create_inputs(doc, tool, model, kwargs["blacklisted_parameters"])
172 create_outputs(doc, tool, model, kwargs["blacklisted_parameters"])
173 create_exit_codes(doc, tool, model, kwargs["exit_codes"])
149174 create_help(doc, tool, model)
150175
151176 # finally, serialize the tool
244269 def get_galaxy_parameter_name(param_name):
245270 return "param_%s" % param_name
246271
247 def create_inputs(doc, tool, model, **kwargs):
272 def create_inputs(doc, tool, model, blacklisted_parameters):
248273 inputs_node = doc.createElement("inputs")
249274 # treat all non output-file parameters as inputs
250275 for param in extract_parameters(model):
251 if param.name in kwargs["blacklisted_parameters"]:
276 if param.name in blacklisted_parameters:
252277 # let's not use an extra level of indentation and use NOP
253278 continue
254279 if param.type is not _OutFile:
377402 checked_value = "true"
378403 param_node.setAttribute("checked", checked_value)
379404
380 def create_outputs(doc, tool, model, **kwargs):
405 def create_outputs(doc, tool, model, blacklisted_parameters):
381406 outputs_node = doc.createElement("outputs")
382407 for param in extract_parameters(model):
383 if param.name in kwargs["blacklisted_parameters"]:
408 if param.name in blacklisted_parameters:
384409 # let's not use an extra level of indentation and use NOP
385410 continue
386411 if param.type is _OutFile:
403428
404429 return data_node
405430
431 def create_exit_codes(doc, tool, model, exit_codes):
432 if len(exit_codes) > 0:
433 stdio_node = doc.createElement("stdio")
434 for exit_code in exit_codes:
435 exit_code_node = doc.createElement("exit_code")
436 exit_code_node.setAttribute("range", exit_code.range)
437 exit_code_node.setAttribute("level", exit_code.level)
438 exit_code_node.setAttribute("description", exit_code.description)
439 stdio_node.appendChild(exit_code_node)
440 tool.appendChild(stdio_node)
441
406442 def create_help(doc, tool, model):
407443 manual = None
408444 doc_url = None
409445 if 'manual' in model.opt_attribs.keys():
410 model.opt_attribs["manual"]
446 manual = model.opt_attribs["manual"]
411447 if 'docurl' in model.opt_attribs.keys():
412 model.opt_attribs["docurl"]
448 doc_url = model.opt_attribs["docurl"]
413449 help_text = "No help available"
414450 if manual is not None:
415451 help_text = manual
416452 if doc_url is not None:
417 help_text = ("" if manual is None else manual) + " For more information, visit %s" % doc_url
453 help_text = ("" if manual is None else manual) + "\nFor more information, visit %s" % doc_url
418454
419455 help_node = doc.createElement("help")
456 # TODO: do we need CDATA Section here?
420457 help_node.appendChild(doc.createTextNode(help_text))
421458 tool.appendChild(help_node)
422459