<s> from __future__ import with_statement <EOL> import sys <EOL> import re <EOL> import os <EOL> from collections import namedtuple <EOL> from os import path <EOL> from subprocess import Popen , PIPE <EOL> from cStringIO import StringIO <EOL> sys . path . append ( os . path . join ( os . path . dirname ( __file__ ) , '<STR_LIT>' ) ) <EOL> sys . path . append ( '<STR_LIT:.>' ) <EOL> from sentencesplit import sentencebreaks_to_newlines <EOL> options = None <EOL> EMPTY_LINE_RE = re . compile ( r'<STR_LIT>' ) <EOL> CONLL_LINE_RE = re . compile ( r'<STR_LIT>' ) <EOL> class FormatError ( Exception ) : <EOL> pass <EOL> def argparser ( ) : <EOL> import argparse <EOL> ap = argparse . ArgumentParser ( description = '<STR_LIT>' + <EOL> '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT>' , '<STR_LIT>' , default = "<STR_LIT>" , <EOL> help = '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT:-c>' , '<STR_LIT>' , default = None , <EOL> help = '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT>' , '<STR_LIT>' , default = False , action = '<STR_LIT:store_true>' , <EOL> help = '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT>' , '<STR_LIT>' , default = "<STR_LIT>" , <EOL> help = '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT>' , '<STR_LIT>' , default = False , action = '<STR_LIT:store_true>' , <EOL> help = '<STR_LIT>' ) <EOL> ap . add_argument ( '<STR_LIT:text>' , metavar = '<STR_LIT>' , nargs = '<STR_LIT:+>' , <EOL> help = '<STR_LIT>' ) <EOL> return ap <EOL> def read_sentence ( f ) : <EOL> """<STR_LIT>""" <EOL> lines = [ ] <EOL> for l in f : <EOL> lines . append ( l ) <EOL> if EMPTY_LINE_RE . match ( l ) : <EOL> break <EOL> if not CONLL_LINE_RE . search ( l ) : <EOL> raise FormatError ( '<STR_LIT>' % l . rstrip ( '<STR_LIT:\n>' ) ) <EOL> return lines <EOL> def strip_labels ( lines ) : <EOL> """<STR_LIT>""" <EOL> labels , stripped = [ ] , [ ] <EOL> labels = [ ] <EOL> for l in lines : <EOL> if EMPTY_LINE_RE . match ( l ) : <EOL> labels . append ( None ) <EOL> stripped . append ( l ) <EOL> else : <EOL> fields = l . split ( '<STR_LIT:\t>' ) <EOL> labels . append ( fields [ <NUM_LIT:0> ] ) <EOL> stripped . append ( '<STR_LIT:\t>' . join ( fields [ <NUM_LIT:1> : ] ) ) <EOL> return labels , stripped <EOL> def attach_labels ( labels , lines ) : <EOL> """<STR_LIT>""" <EOL> assert len ( labels ) == len ( lines ) , "<STR_LIT>" % ( len ( labels ) , len ( lines ) ) <EOL> attached = [ ] <EOL> for label , line in zip ( labels , lines ) : <EOL> empty = EMPTY_LINE_RE . match ( line ) <EOL> assert ( label is None and empty ) or ( label is not None and not empty ) <EOL> if empty : <EOL> attached . append ( line ) <EOL> else : <EOL> attached . append ( '<STR_LIT>' % ( label , line ) ) <EOL> return attached <EOL> TOKENIZATION_REGEX = re . compile ( r'<STR_LIT>' ) <EOL> NEWLINE_TERM_REGEX = re . compile ( r'<STR_LIT>' ) <EOL> def text_to_conll ( f ) : <EOL> """<STR_LIT>""" <EOL> global options <EOL> if options . nosplit : <EOL> sentences = f . readlines ( ) <EOL> else : <EOL> sentences = [ ] <EOL> for l in f : <EOL> l = sentencebreaks_to_newlines ( l ) <EOL> sentences . extend ( [ s for s in NEWLINE_TERM_REGEX . split ( l ) if s ] ) <EOL> lines = [ ] <EOL> offset = <NUM_LIT:0> <EOL> for s in sentences : <EOL> nonspace_token_seen = False <EOL> tokens = [ t for t in TOKENIZATION_REGEX . split ( s ) if t ] <EOL> for t in tokens : <EOL> if not t . isspace ( ) : <EOL> lines . append ( [ '<STR_LIT:O>' , offset , offset + len ( t ) , t ] ) <EOL> nonspace_token_seen = True <EOL> offset += len ( t ) <EOL> if nonspace_token_seen : <EOL> lines . append ( [ ] ) <EOL> if options . annsuffix : <EOL> lines = relabel ( lines , get_annotations ( f . name ) ) <EOL> lines = [ [ l [ <NUM_LIT:0> ] , str ( l [ <NUM_LIT:1> ] ) , str ( l [ <NUM_LIT:2> ] ) , l [ <NUM_LIT:3> ] ] if l else l for l in lines ] <EOL> return StringIO ( '<STR_LIT:\n>' . join ( ( '<STR_LIT:\t>' . join ( l ) for l in lines ) ) ) <EOL> def relabel ( lines , annotations ) : <EOL> global options <EOL> offset_label = { } <EOL> for tb in annotations : <EOL> for i in range ( tb . start , tb . end ) : <EOL> if i in offset_label : <EOL> print >> sys . stderr , "<STR_LIT>" <EOL> offset_label [ i ] = tb <EOL> prev_label = None <EOL> for i , l in enumerate ( lines ) : <EOL> if not l : <EOL> prev_label = None <EOL> continue <EOL> tag , start , end , token = l <EOL> label = None <EOL> for o in range ( start , end ) : <EOL> if o in offset_label : <EOL> if o != start : <EOL> print >> sys . stderr , '<STR_LIT>' % ( token , offset_label [ o ] . text ) <EOL> label = offset_label [ o ] . type <EOL> break <EOL> if label is not None : <EOL> if label == prev_label : <EOL> tag = '<STR_LIT>' + label <EOL> else : <EOL> tag = '<STR_LIT>' + label <EOL> prev_label = label <EOL> lines [ i ] = [ tag , start , end , token ] <EOL> if options . singleclass : <EOL> for l in lines : <EOL> if l and l [ <NUM_LIT:0> ] != '<STR_LIT:O>' : <EOL> l [ <NUM_LIT:0> ] = l [ <NUM_LIT:0> ] [ : <NUM_LIT:2> ] + options . singleclass <EOL> return lines <EOL> def process ( f ) : <EOL> return text_to_conll ( f ) <EOL> def process_files ( files ) : <EOL> global options <EOL> nersuite_proc = [ ] <EOL> try : <EOL> for fn in files : <EOL> try : <EOL> if fn == '<STR_LIT:->' : <EOL> lines = process ( sys . stdin ) <EOL> else : <EOL> with open ( fn , '<STR_LIT>' ) as f : <EOL> lines = process ( f ) <EOL> if lines is None : <EOL> raise FormatError <EOL> if fn == '<STR_LIT:->' or not options . outsuffix : <EOL> sys . stdout . write ( '<STR_LIT>' . join ( lines ) ) <EOL> else : <EOL> ofn = path . splitext ( fn ) [ <NUM_LIT:0> ] + options . outsuffix <EOL> with open ( ofn , '<STR_LIT>' ) as of : <EOL> of . write ( '<STR_LIT>' . join ( lines ) ) <EOL> except : <EOL> raise <EOL> except Exception , e : <EOL> for p in nersuite_proc : <EOL> p . kill ( ) <EOL> if not isinstance ( e , FormatError ) : <EOL> raise <EOL> TEXTBOUND_LINE_RE = re . compile ( r'<STR_LIT>' ) <EOL> Textbound = namedtuple ( '<STR_LIT>' , '<STR_LIT>' ) <EOL> def parse_textbounds ( f ) : <EOL> """<STR_LIT>""" <EOL> textbounds = [ ] <EOL> for l in f : <EOL> l = l . rstrip ( '<STR_LIT:\n>' ) <EOL> if not TEXTBOUND_LINE_RE . search ( l ) : <EOL> continue <EOL> id_ , type_offsets , text = l . split ( '<STR_LIT:\t>' ) <EOL> type_ , start , end = type_offsets . split ( ) <EOL> start , end = int ( start ) , int ( end ) <EOL> textbounds . append ( Textbound ( start , end , type_ , text ) ) <EOL> return textbounds <EOL> def eliminate_overlaps ( textbounds ) : <EOL> eliminate = { } <EOL> for t1 in textbounds : <EOL> for t2 in textbounds : <EOL> if t1 is t2 : <EOL> continue <EOL> if t2 . start >= t1 . end or t2 . end <= t1 . start : <EOL> continue <EOL> if t1 . end - t1 . start > t2 . end - t2 . start : <EOL> print >> sys . stderr , "<STR_LIT>" % ( t2 , t1 ) <EOL> eliminate [ t2 ] = True <EOL> else : <EOL> print >> sys . stderr , "<STR_LIT>" % ( t1 , t2 ) <EOL> eliminate [ t1 ] = True <EOL> return [ t for t in textbounds if not t in eliminate ] <EOL> def get_annotations ( fn ) : <EOL> global options <EOL> annfn = path . splitext ( fn ) [ <NUM_LIT:0> ] + options . annsuffix <EOL> with open ( annfn , '<STR_LIT>' ) as f : <EOL> textbounds = parse_textbounds ( f ) <EOL> textbounds = eliminate_overlaps ( textbounds ) <EOL> return textbounds <EOL> def main ( argv = None ) : <EOL> if argv is None : <EOL> argv = sys . argv <EOL> global options <EOL> options = argparser ( ) . parse_args ( argv [ <NUM_LIT:1> : ] ) <EOL> if options . outsuffix and options . outsuffix [ <NUM_LIT:0> ] != '<STR_LIT:.>' : <EOL> options . outsuffix = '<STR_LIT:.>' + options . outsuffix <EOL> if options . annsuffix and options . annsuffix [ <NUM_LIT:0> ] != '<STR_LIT:.>' : <EOL> options . annsuffix = '<STR_LIT:.>' + options . annsuffix <EOL> process_files ( options . text ) <EOL> if __name__ == "<STR_LIT:__main__>" : <EOL> sys . exit ( main ( sys . argv ) ) </s>
