annotate corebio/utils/deoptparse.py @ 9:f3462128e87c

Minor alterations to the galaxy interface with some better examples and error messages added.

#  Copyright (c) 2004 Gavin E. Crooks <[e-mail]>
#
#  This software is distributed under the MIT Open Source License.
#  <http://www.opensource.org/licenses/mit-license.html>
#
#  Permission is hereby granted, free of charge, to any person obtaining a 
#  copy of this software and associated documentation files (the "Software"),
#  to deal in the Software without restriction, including without limitation
#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
#  and/or sell copies of the Software, and to permit persons to whom the
#  Software is furnished to do so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included
#  in all copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
#  THE SOFTWARE.
#

"""Custom extensions to OptionParse for parsing command line options."""
# FIXME: Docstring

# TODO: Add profiling option

# DeOptionParser : 
# 
#  http://docs.python.org/lib/module-optparse.html
#
# Random_options : 
#   Set random generator and seed. Use options.random as
#   source of random numbers
# Copyright :
#   print copyright information

# Documentation :
#   print extended document information
#
# Additional file_in and file_out types

import sys
from copy import copy
from optparse import Option
from optparse import OptionParser
from optparse import IndentedHelpFormatter
from optparse import OptionValueError
import random



def _copyright_callback(option, opt, value, parser):
    if option or  opt or  value or parser: pass # Shut up lint checker
    print parser.copyright
    sys.exit()

def _doc_callback(option, opt, value, parser):
    if option or  opt or  value or parser: pass # Shut up lint checker
    print parser.long_description
    sys.exit()


class DeHelpFormatter(IndentedHelpFormatter) :
    def __init__ (self,
                  indent_increment=2,
                  max_help_position=32, 
                  width=78,
                  short_first=1):
        IndentedHelpFormatter.__init__(
            self, indent_increment, max_help_position,
            width, short_first)

    def format_option_strings (self, option):
        """Return a comma-separated list of option strings & metavariables."""
        if option.takes_value():
            metavar = option.metavar or option.dest.upper()
            short_opts = option._short_opts
            long_opts = [lopt + " " + metavar for lopt in option._long_opts]
        else:
            short_opts = option._short_opts
            long_opts = option._long_opts
            
        if not short_opts : short_opts = ["  ",]

        if self.short_first:
            opts = short_opts + long_opts
        else:
            opts = long_opts + short_opts

        return " ".join(opts)



def _check_file_in(option, opt, value):
    if option or  opt or  value : pass # Shut up lint checker 
    try:
        return file(value, "r")
    except IOError:
        raise OptionValueError(
            "option %s: cannot open file: %s" % (opt, value) )

def _check_file_out(option, opt, value):
    if option or  opt or  value : pass # Shut up lint checker 
    try:
        return file(value, "w+")
    except IOError:
        raise OptionValueError(
            "option %s: cannot open file: %s" % (opt, value) )
    
def _check_boolean(option, opt, value) :
    if option or  opt or  value : pass # Shut up lint checker 
    v = value.lower()
    choices = {'no': False, 'false':False, '0': False,
            'yes': True, 'true': True, '1':True }   
    try:
        return choices[v]
    except KeyError:
        raise OptionValueError(
            "option %s: invalid choice: '%s' " \
            "(choose from 'yes' or 'no', 'true' or 'false')" %  (opt, value))

def _check_dict(option, opt, value) :
    if option or  opt or  value : pass # Shut up lint checker 
    v = value.lower()
    choices = option.choices
    try:
        return choices[v]
    except KeyError:
        raise OptionValueError(
            "option %s: invalid choice: '%s' " \
            "(choose from '%s')" %  (opt, value, "', '".join(choices)))
 

                    
class DeOption(Option):
    TYPES = Option.TYPES + ("file_in","file_out", "boolean", "dict")
    TYPE_CHECKER = copy(Option.TYPE_CHECKER)
    TYPE_CHECKER["file_in"] = _check_file_in
    TYPE_CHECKER["file_out"] = _check_file_out
    TYPE_CHECKER["boolean"] = _check_boolean
    TYPE_CHECKER["dict"] = _check_dict
    choices = None

    def _new_check_choice(self):
        if self.type == "dict":
            if self.choices is None:
                raise OptionValueError(
                    "must supply a dictionary of choices for type 'dict'")
            elif not isinstance(self.choices, dict):
                raise OptionValueError(
                    "choices must be a dictinary ('%s' supplied)"
                    % str(type(self.choices)).split("'")[1])
            return
        self._check_choice()
 
    # Have to override _check_choices so that we can parse
    # a dict through to check_dict
    CHECK_METHODS = Option.CHECK_METHODS
    CHECK_METHODS[2] = _new_check_choice
    




class DeOptionParser(OptionParser) :
    def __init__(self,
                usage=None,
                option_list=None,
                option_class=DeOption,
                version=None,
                conflict_handler="error",
                description=None,
                long_description = None,
                formatter=DeHelpFormatter(),
                add_help_option=True,
                prog=None,
                copyright=None,
                add_verbose_options=True,
                add_random_options=False
                ):

        OptionParser.__init__(self,
                              usage,
                              option_list,
                              option_class,
                              version,
                              conflict_handler,
                              description,
                              formatter,
                              add_help_option,
                              prog )
       
        if long_description :
            self.long_description = long_description
            self.add_option("--doc",
                            action="callback",
                            callback=_doc_callback,
                            help="Detailed documentation")
    
        if copyright :
            self.copyright = copyright
            self.add_option("--copyright",
                            action="callback",
                            callback=_copyright_callback,
                            help="") 
               
        if add_verbose_options :
            self.add_option("-q", "--quite",
                action="store_false",
                dest="verbose",
                default=False,
                help="Run quietly (default)")
            
            self.add_option("-v", "--verbose",
                action="store_true",
                dest="verbose",
                default=False,
                help="Verbose output (Not quite)")
    
        self.random_options = False
        if add_random_options :
            self.random_options = True
            self.add_option("--seed",
                action="store",
                type = "int",
                dest="random_seed",
                help="Initial seed for pseudo-random number generator. (default: System time)",
                metavar="INTEGER" )
                            
            self.add_option("--generator",
                action="store",
                dest="random_generator",
                default="MersenneTwister",
                help="Select MersenneTwister (default) or WichmannHill pseudo-random number generator", 
                metavar="TYPE" )

    def parse_args(self,args, values=None) :
        (options, args) = OptionParser.parse_args(self, args, values)
        
        if self.random_options :
            if options.random_generator is None or options.random_generator =="MersenneTwister" :
                r = random.Random()
            elif options.random_generator == "WichmannHill" :
                r = random.WichmannHill()
            else :
                self.error("Acceptible generators are MersenneTwister (default) or WichmannHill")
            if options.random_seed :
                r.seed(options.random_seed)
        
            options.__dict__["random"] = r        
                
        
        return (options, args)