text: # Copyright 2001 by Katharine Lindner.  All rights reserved.
  # This code is part of the Biopython distribution and governed by its
  # license.  Please see the LICENSE file that should have been included
  # as part of this package.
  
  # standard library
  import sys
  import string
  import copy
  import array
  import os
  import re
  import sgmllib
  import urlparse
  
  # XML from python 2.0
  from xml.sax import handler
  
  # Martel
  import Martel
  from Martel import RecordReader
  
  from Bio.ParserSupport import EventGenerator
  from Bio.ParserSupport import AbstractConsumer
  from Bio import File
  from Bio.Align.Generic import Alignment
  import Bio.Alphabet
  import ecell_format
  import Record
  
  """
  Ecell converts the ECell input from spreadsheet format to an intermediate format, described in
  http://www.e-cell.org/manual/chapter2E.html#3.2.  It provides an alternative to the perl script
  supplied with the Ecell2 distribution at http://bioinformatics.org/project/?group_id=49.
  
  ECell expects a spreadsheet exported in delimited text format. The file should be read with
  FilteredReader using the default filter chain to remove extraneous characters.
  """
  
  class Error( Exception ):
      """
      """
      def __init__( self ):
          pass
  
  class ECellError( Error ):
  
      """
          message - description of error
      """
  
      def __init__( self, message ):
          self.message = message
  
  
  
  class Iterator:
      """Iterator interface to move over a file of ecell entries one at a time.
      """
      def __init__(self, handle, parser = None):
          """Initialize the iterator.
  
          Arguments:
          o handle - A handle with ECell entries to iterate through.
          o parser - An optional parser to pass the entries through before
          returning them. If None, then the raw entry will be returned.
          """
          self.handle = File.UndoHandle( handle )
          self._reader = RecordReader.Everything( self.handle )
          self._parser = parser
  
      def next(self):
          """Return the next ecell record from the handle.
  
          Will return None if we ran out of records.
          """
          data = self._reader.next()
  
          if self._parser is not None:
              if data:
                  dumpfile = open( 'dump', 'w' )
                  dumpfile.write( data )
                  dumpfile.close()
                  return self._parser.parse(File.StringHandle(data))
  
          return data
  
      def __iter__(self):
          return iter(self.next, None)
  
  
  
  class _Scanner:
      """Start up Martel to do the scanning of the file.
  
      This initialzes the Martel based parser and connects it to a handler
      that will generate events for a Feature Consumer.
      """
      def __init__(self, debug = 0):
          """Initialize the scanner by setting up our caches.
  
          Creating the parser takes a long time, so we want to cache it
          to reduce parsing time.
  
          Arguments:
          o debug - The level of debugging that the parser should
          display. Level 0 is no debugging, Level 2 displays the most
          debugging info (but is much slower). See Martel documentation
          for more info on this.
          """
          # a listing of all tags we are interested in scanning for
          # in the MartelParser
          self.interest_tags = [ 'header_line', 'system_line', 'substance_multiline', \
              'reactor_multiline', 'include_line' ]
  
          # make a parser that returns only the tags we are interested in
          expression = Martel.select_names( ecell_format.ecell_record, self.interest_tags)
          self._parser = expression.make_parser(debug_level = debug)
  
      def feed(self, handle, consumer):
          """Feed a set of data into the scanner.
  
          Arguments:
          o handle - A handle with the information to parse.
          o consumer - The consumer that should be informed of events.
          """
          self._parser.setContentHandler( EventGenerator(consumer,
                                                         self.interest_tags))
  #        self._parser.setErrorHandler(handle.ErrorHandler())
  
          self._parser.parseFile(handle)
  
  class _RecordConsumer:
      """Create an ECell Record object from scanner generated information.
      """
      def __init__(self):
          self.data = Record.Record()
          self._header = []
          self._database = {}
          self._state = ''
  
      def include_line( self, line ):
          self.data.include_buf = self.data.include_buf + line
  
      def header_line( self, lines ):
          for line in lines:
              items = line.split( '\t')
              items[ 0 ] = items[ 0 ].lower()
              self._header = []
              self._state = items[ 0 ]
              for item in items:
                  item = item.strip()
                  self._header.append( item.lower() )
  
  
      def system_line( self, lines ):
          for line in lines:
              line_dict = self._make_line_dict( line )
              if( not self._check_missing_header( line_dict ) ):
                  raise EcellError( "invalid header" )
              self.data.num_systems = self.data.num_systems + 1
              _set_defaults( line_dict )
              self._build_system_entry( line_dict )
  
  
      def substance_multiline( self, multiline ):
          for line in multiline:
              self.parse_substance_lines( line )
  
      def parse_substance_lines( self, multiline ):
          lines = multiline.splitlines()
          line_no = 0
          for line in lines:
              line_dict = self._make_line_dict( line )
              try:
                  if( not _is_valid_substance( line_dict ) ):
                      raise ECellError( "quantity and concentration are mutually exclusive" )
              except ECellError, e:
                  print sys.stderr, e.message
  
              qty = Record.get_entry( line_dict, 'qty' )
              conc = Record.get_entry( line_dict, 'conc' )
              if( ( qty.lower() != 'fix' ) and ( conc.lower() != 'fix' ) ):
                  self.data.num_substances = self.data.num_substances + 1
              else:
                  line_no = line_no + 1
              if( line.lower().startswith( 'substance' ) ):
                  _set_defaults( line_dict )
                  self._convert_conc( line_dict )
  
              self._build_substance_entry( line_dict, line_no )
  
      def reactor_multiline( self, multiline ):
          for line in multiline:
              self.parse_reactor_lines( line )
  
      def parse_reactor_lines( self, multiline ):
          lines = multiline.splitlines()
          for line in lines:
              line_dict = self._make_line_dict( line )
              if( line.lower().startswith( 'reactor' ) ):
                  if( not self._check_missing_header( line_dict ) ):
                      raise ECellError( "invalid header" )
              try:
                  if( not is_only_digits( line_dict[ 's_coeff' ] ) ):
                      raise ECellError( 's_coeff must contain only digits' )
                  if( not is_only_digits( line_dict[ 'p_coeff' ] ) ):
                      raise ECellError( 'p_coeff must contain only digits' )
              except KeyError:
                  pass
              if( line.lower().startswith( 'reactor' ) ):
                  _set_reactor_defaults( line_dict )
              line_dict = self._remove_if_inconsistent( line_dict )
  
              if( line_dict.has_key( 'class' ) ):
                  self.data.num_reactors = self.data.num_reactors + 1
                  num_substrates = 0
                  num_products = 0
                  num_catalysts = 0
                  num_effectors = 0
                  num_options = 0
                  num_args = 0
              if( line_dict.has_key( 's_id' ) ): num_substrates = num_substrates + 1
              if( line_dict.has_key( 'p_id' ) ): num_products = num_products + 1
              if( line_dict.has_key( 'c_id' ) ): num_catalysts = num_catalysts + 1
              if( line_dict.has_key( 'e_id' ) ): num_effectors = num_effectors + 1
              if( line_dict.has_key( 'o_type' ) ): num_options = num_options + 1
              if( line_dict.has_key( 'arg_tag' ) ): num_args = num_args + 1
              counter_dict = { \
                  's_' : num_substrates, \
                  'p_' : num_products, \
                  'c_' : num_catalysts, \
                  'e_' : num_effectors, \
                  'o_' : num_options, \
                  'arg_tag' : num_args
              }
              self._set_max( counter_dict )
              self._build_reactor_entry( line_dict, counter_dict )
  
  
      def _set_max( self, counter_dict ):
          num_reactors = self.data.num_reactors
          for key in counter_dict.keys():
              composite_key = key + str( num_reactors )
              self.data._max_dict[ composite_key ] = counter_dict[ key ]
  
      def _build_system_entry( self, line_dict ):
          for key in line_dict.keys():
              item = line_dict[ key ]
              composite_key = 'system' + str( self.data.num_systems ) + key + '0'
  
              if( not self.data.cell_dict.has_key( composite_key ) ):
                  self.data.cell_dict[ composite_key ] = item
  
      def _build_substance_entry( self, line_dict, line_no ):
          for key in line_dict.keys():
              item = line_dict[ key ]
              composite_key = 'substance' + str( self.data.num_substances ) + key + \
                  str( line_no )
              if( not self.data.cell_dict.has_key( composite_key ) ):
                  self.data.cell_dict[ composite_key ] = item
  
      def _convert_conc( self, line_dict ):
          if( line_dict.has_key( 'conc' ) ):
              if( not line_dict.has_key( 'qty' ) ):
                  contents = 'QTY(%s,%s)' % ( line_dict[ 'conc' ], line_dict[ 'path' ] )
                  composite_key = 'substance' + str( self.data.num_substances ) + 'qty' + '0'
                  self.data.cell_dict[ composite_key ] = contents
                  self.data.contains_concentration = 1
  
      def _build_reactor_entry( self, line_dict, counter_dict ):
          for key in line_dict.keys():
              item = line_dict[ key ]
              prefix = key[ :2 ]
              if( key.startswith( 'arg_' ) ):
                  index = counter_dict[ 'arg_tag' ]
              elif( counter_dict.has_key( prefix ) ):
                  index = counter_dict[ prefix ]
              else:
                  index = '0'
              composite_key = 'reactor' + str( self.data.num_reactors ) + str( key ) + str( index )
              if( not self.data.cell_dict.has_key( composite_key ) ):
                  self.data.cell_dict[ composite_key ] = item
  
  
      def _check_missing_header( self, line_dict ):
          ok = 1
          items = [ 'id', 'path', 'class' ]
          for item in items:
              if( line_dict.has_key( item ) == 0 ):
                  others = copy.deepcopy( items )
                  others.remove( item )
                  for other in others:
                      if( line_dict.has_key( other ) ):
                          if( item.lower() != 'class' ):
                              ok = 0
                              break
          return ok
  
      def _remove_if_inconsistent( self, list_dict ):
          valid_keys = list_dict.keys()
          for label in [ 'id', 'path', 'type' ]:
              for prefix in [ 's_', 'p_', 'c_', 'e_' ]:
                  node = prefix + label
                  valid_keys = self._consistency_filter( prefix, node, valid_keys )
          for key in list_dict.keys():
              if( not key in valid_keys ):
                  del list_dict[ key ]
          return list_dict
  
      def _consistency_filter( self, prefix, tag, valid_keys ):
          block = []
          for suffix in [ 'id', 'path', 'coeff', 'type' ]:
              node = prefix + suffix
              block.append( node )
          for node in block:
              if( ( not tag in valid_keys ) and ( node in valid_keys ) ):
                  if( ( prefix == 'o_' ) or ( not tag.endswith( 'type' ) ) ):
                      valid_keys.remove( node )
          return valid_keys
  
      def _make_line_dict( self, line ):
          line_dict = {}
          items = line.split( '\t' )
          num = 0
          for item in items:
              item = item.strip()
              if( item != '' ):
                  line_dict[ self._header[ num ] ] = item
              num = num + 1
          return line_dict
  
  def _clear_bad_block( block, items ):
      for label in block:
          items = items.remove( items.index( label ) )
      return items
  
  def _is_valid_substance( line_dict ):
      ok = 1
      if( line_dict.has_key( 'qty' ) and line_dict.has_key( 'conc' ) ):
          if( not ( line_dict[ 'qty' ] == 'QTY' ) ):
              ok = 0
      return ok
  
  def is_only_digits( line ):
      ok = 1
      text = line.strip()
      if( text != '' ):
          if( not text.isdigit() ):
              ok = 0
      return ok
  
  def _set_reactor_defaults( line_dict ):
      line_dict = _set_defaults( line_dict )
      for item in [ 's_', 'p_', 'c_', 'e_' ]:
          id = item + 'id'
          coeff = item + 'coeff'
          path = item + 'path'
          if( line_dict.has_key( id ) ):
              if( not line_dict.has_key( coeff ) ):
                  line_dict[ coeff ] = 1
          if( not line_dict.has_key( path ) ):
              line_dict[ path ] = line_dict[ 'path' ]
  
      return( line_dict )
  
  def _set_defaults( line_dict ):
      if( not line_dict.has_key( 'name' ) ):
          line_dict[ 'name' ] = line_dict[ 'id' ]
      if( line_dict.has_key( 'arg_tag' ) ):
          if( not line_dict.has_key( 'arg_coeff' ) ):
              line_dict[ 'arg_coeff' ] = 0
  
      return( line_dict )
  
  
  
  
  
  
  
  class RecordParser:
      """Parse ECell files into Record objects
      """
      def __init__(self, debug_level = 0):
          """Initialize the parser.
  
          Arguments:
          o debug_level - An optional argument that specifies the amount of
          debugging information Martel should spit out. By default we have
          no debugging info (the fastest way to do things), but if you want
          you can set this as high as two and see exactly where a parse fails.
          """
          self._scanner = _Scanner(debug_level)
  
      def parse(self, handle):
          """Parse the specified handle into an ECell record.
          """
          self._consumer = _RecordConsumer()
          self._scanner.feed(handle, self._consumer)
          return self._consumer.data
  
  