#!/usr/bin/env python
"""
Creates the moiety_structure section of the SBMLLint
configuration file. The user declares all moieties.
The moiety structure for a molecule is the number of
occurrences of each moiety string in the molecule.
Substrings are handled by looking first for the longest
moiety names.
"""

from SBMLLint.common.simple_sbml import SimpleSBML
from SBMLLint.common.moiety import MoietyStoichiometry
from SBMLLint.common import msgs

import argparse
import sys
import yaml


MOIETY_COUNT_SEPARATOR = ", "


def getMoieties(moiety_fid):
  """
  Creates the YAML configuration file.
  :param IOWrappter moiety_fid: 
  :return list-str: list of moiety names
  :raises ValueError: if one moiety is a substring of another
  """
  return yaml.safe_load(moiety_fid)

# TODO: Extend to do recursive checks of moiety names for
# their substructures
def findMoietyStoichiometries(molecule_name, moiety_names,
    is_check_error=True):
  """
  Finds the moieties and their stoichiometries for each molecule.
  Handles substrings by looking for largest strings first.
  :param str molecule:
  :param list-str moiety_names:
  :return list-MoietyStoichiometry:
  """
  result = []
  sorted_moiety_names = sorted(
      moiety_names, key=lambda n: len(str(n)), reverse=True)
  current_name = molecule_name
  for moiety_name in sorted_moiety_names:
    moiety_name = str(moiety_name)
    count = current_name.count(moiety_name)
    if count > 0:
      current_name = current_name.replace(moiety_name, "")
      result.append(MoietyStoichiometry(moiety_name, count,
          MOIETY_COUNT_SEPARATOR))
  current_name = current_name.replace("_", "")
  if is_check_error and len(current_name) > 0:
    msg = "Moieties specified do not completely express %s" % molecule_name
    msgs.error(msg)
  return result

# TODO: Look for moieties from largest string to smallest,
# eliminating those found.
def main(xml_fid, moiety_fid, otfile_fid):
  """
  Creates the YAML configuration file.
  :param IOWrapper xml_fid: xml file:
  :param IOWrapper moiety_fid: 
  :param IOWrapper otfile_fid: file to write
  """
  # Acquire and validate moieties
  moiety_names = getMoieties(moiety_fid)
  # Create the configuration file
  config_dct = {} 
  simple = SimpleSBML()
  simple.initialize(xml_fid)
  for molecule in simple.molecules:
    moiety_stoichiometries = findMoietyStoichiometries(
       molecule.name, moiety_names)
    config_dct[molecule.name] =  \
        [str(ms) for ms in moiety_stoichiometries]
  dct = {"moiety_structure": config_dct}
  yaml.dump(dct, otfile_fid)
  for fid in [xml_fid, moiety_fid, otfile_fid]:
    fid.close()

    
if __name__ == '__main__':
  def open_write(path):
    return open(path, "w")
  #
  parser = argparse.ArgumentParser(
      description='Creates configuration file for BioModels 147.')
  parser.add_argument('xml_file', 
      type=open, 
      help='SBML file from which species names are obtained.')
  parser.add_argument('moiety_file', 
      type=open, 
      help='YAML file the specifies moieties for the XML model.')
  parser.add_argument('--output', type=open_write,
      help="Generated configuration file. Defaults to config.yml.")
  args = parser.parse_args()
  if args.output is None:
    otfile_fid = sys.stdout
  else:
    otfile_fid = args.output
  main(args.xml_file, args.moiety_file, otfile_fid)

#!/usr/bin/env python
"""
Creates the moiety_structure section of the SBMLLint
configuration file. The user declares all moieties.
The moiety structure for a molecule is the number of
occurrences of each moiety string in the molecule.
Substrings are handled by looking first for the longest
moiety names.
"""

from SBMLLint.common.simple_sbml import SimpleSBML
from SBMLLint.common.moiety import MoietyStoichiometry
from SBMLLint.common import msgs

import argparse
import sys
import yaml


MOIETY_COUNT_SEPARATOR = ", "


def getMoieties(moiety_fid):
  """
  Creates the YAML configuration file.
  :param IOWrappter moiety_fid: 
  :return list-str: list of moiety names
  :raises ValueError: if one moiety is a substring of another
  """
  return yaml.safe_load(moiety_fid)

# TODO: Extend to do recursive checks of moiety names for
# their substructures
def findMoietyStoichiometries(molecule_name, moiety_names,
    is_check_error=True):
  """
  Finds the moieties and their stoichiometries for each molecule.
  Handles substrings by looking for largest strings first.
  :param str molecule:
  :param list-str moiety_names:
  :return list-MoietyStoichiometry:
  """
  result = []
  sorted_moiety_names = sorted(
      moiety_names, key=lambda n: len(str(n)), reverse=True)
  current_name = molecule_name
  for moiety_name in sorted_moiety_names:
    moiety_name = str(moiety_name)
    count = current_name.count(moiety_name)
    if count > 0:
      current_name = current_name.replace(moiety_name, "")
      result.append(MoietyStoichiometry(moiety_name, count,
          MOIETY_COUNT_SEPARATOR))
  current_name = current_name.replace("_", "")
  if is_check_error and len(current_name) > 0:
    msg = "Moieties specified do not completely express %s" % molecule_name
    msgs.error(msg)
  return result

# TODO: Look for moieties from largest string to smallest,
# eliminating those found.
def main(xml_fid, moiety_fid, otfile_fid):
  """
  Creates the YAML configuration file.
  :param IOWrapper xml_fid: xml file:
  :param IOWrapper moiety_fid: 
  :param IOWrapper otfile_fid: file to write
  """
  # Acquire and validate moieties
  moiety_names = getMoieties(moiety_fid)
  # Create the configuration file
  config_dct = {} 
  simple = SimpleSBML()
  simple.initialize(xml_fid)
  for molecule in simple.molecules:
    moiety_stoichiometries = findMoietyStoichiometries(
       molecule.name, moiety_names)
    config_dct[molecule.name] =  \
        [str(ms) for ms in moiety_stoichiometries]
  dct = {"moiety_structure": config_dct}
  yaml.dump(dct, otfile_fid)
  for fid in [xml_fid, moiety_fid, otfile_fid]:
    fid.close()

    
if __name__ == '__main__':
  def open_write(path):
    return open(path, "w")
  #
  parser = argparse.ArgumentParser(
      description='Creates configuration file for BioModels 147.')
  parser.add_argument('xml_file', 
      type=open, 
      help='SBML file from which species names are obtained.')
  parser.add_argument('moiety_file', 
      type=open, 
      help='YAML file the specifies moieties for the XML model.')
  parser.add_argument('--output', type=open_write,
      help="Generated configuration file. Defaults to config.yml.")
  args = parser.parse_args()
  if args.output is None:
    otfile_fid = sys.stdout
  else:
    otfile_fid = args.output
  main(args.xml_file, args.moiety_file, otfile_fid)

#!/usr/bin/env python Creates the moiety_structure section of the SBMLLint configuration file. The user declares all moieties. The moiety structure for a molecule is the number of occurrences of each moiety string in the molecule. Substrings are handled by looking first for the longest moiety names. Creates the YAML configuration file.   :param IOWrappter moiety_fid:    :return list-str: list of moiety names   :raises ValueError: if one moiety is a substring of another # TODO: Extend to do recursive checks of moiety names for # their substructures Finds the moieties and their stoichiometries for each molecule.   Handles substrings by looking for largest strings first.   :param str molecule:   :param list-str moiety_names:   :return list-MoietyStoichiometry: # TODO: Look for moieties from largest string to smallest, # eliminating those found. Creates the YAML configuration file.   :param IOWrapper xml_fid: xml file:   :param IOWrapper moiety_fid:    :param IOWrapper otfile_fid: file to write # Acquire and validate moieties # Create the configuration file #