tok2WikiFormat.pl
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A tok2WikiFormat.pl is a Perl-based Token-to-Wiki program.
- See: Perl Program, Tokenization System.
References
#!/usr/bin/perl
use strict ;
my $PROGRAM = "_tokToWikiFormat.pl" ;
my $CONTACT = '_tokToWikiFormat@at@gabormelli.com' ;
my $VERSION = '1.1' ;
my $VERSIONDATE = "2009.11.11" ;
#########################################################################################
# == SYNOPSIS:
# * Convert tokenFile format to wikiFile format.
#
# == USAGE
# * Input: tokenFile
# * Input: SynonymToConceptId (hardcoded)
#
# == TODO
# * support the reading of a header (with column names)
#########################################################################################
#use warnings ;
# PACKAGES
use lib '..' ;
use lib './lib' ;
use lib '../lib' ;
use TABularDataFileMgmt ;
use TGQueryDataMgmt ;
use Getopt::Long;
#########################################################################################
# GLOBAL SCALARS
my $debug = 2 ;
$TABularDataFileMgmt::debug = $debug ;
TABularDataFileMgmt::settimestamp() ;
my $runningSeconds_=TABularDataFileMgmt::getrunningseconds() ;
my $SynonymToConceptIdFile="SynonymToConceptId.dat" ;
my $removeDocumentId ;
# GLOBAL ARRAYS
my @Token ;
my @Document ;
my @Sentence ;
# Some standard column configurations
my @TokFileAttrsType ;
$TokFileAttrsType[1] ="Token POS Parse ConceptType ConceptId OntologyId BaseVerb SRL1 SRL2 SRL3 SRL4 SRL5 SRL6 SRL7 SRL8" ;
$TokFileAttrsType[2] ="DocumentExtId Token POS Parse ConceptType ConceptId OntologyId BaseVerb SRL1 SRL2 SRL3 SRL4 SRL5 SRL6 SRL7 SRL8" ;
$TokFileAttrsType[3] ="Token BaseWord POS Parse ConceptType ConceptId OntologyId BaseVerb SRL1 SRL2 SRL3 SRL4 SRL5 SRL6 SRL7 SRL8" ;
$TokFileAttrsType[4] ="DocumentExtId Token BaseWord POS Parse ConceptType ConceptId OntologyId BaseVerb SRL1 SRL2 SRL3 SRL4 SRL5 SRL6 SRL7 SRL8" ;
$TokFileAttrsType[5] ="Token POS Parse BIO ConceptType ConceptId" ;
$TokFileAttrsType[7] ="Token POS Parse Oe1 Oe2 Og2 ChrCntCat CapsCnt NumCnt SpeChrCnt BIO" ;
$TokFileAttrsType[8] ="Token POS Parse Oe1 Oe2 Og2 ChrCntCat CapsCnt NumCnt SpeChrCnt BIO ConceptType ConceptId" ;
$TokFileAttrsType[9] ="Token POS Oe1 Oe2 Og2 ChrCntCat CapsCnt NumCnt SpeChrCnt BIO BIOp" ;
$TokFileAttrsType[10]="Token POS Oe1 Oe2 Og2 ChrCntCat CapsCnt NumCnt SpeChrCnt BIO ConceptType ConceptId" ;
# Token input file description
my $inputTokFileAttrs ; # will eventually hold the attribute names for the (token) input file
my @InputTokFileAttrs ;
my $inputTokFileAttrsTypeId = 10 ; # the default configuration
my $inputTokFile = "-" ;
my $outputFile = "-" ;
my $verbose = 0 ;
my $help = 0 ;
GetOptions (
'f|inputTokFile=s' => \$inputTokFile,
'o|outputFile:s' => \$outputFile,
'removeDocumentId=s' => \$removeDocumentId,
'inputTokFileAttrsTypeId:s' => \$inputTokFileAttrsTypeId ,
'inputTokFileAttrs:s' => \$inputTokFileAttrs ,
'd|debug=i' => \$debug,
'v|verbose+' => \$verbose,
'h|help' => \$help
);
my $USAGE ;
$USAGE .= "USAGE:\n" ;
$USAGE .= " Program info: Version: $VERSION($VERSIONDATE) Contact: $CONTACT\n" ;
$USAGE .= " Example: ./$PROGRAM -r=svml -f=All -d=1 -p train\n" ;
$USAGE .= " PARAMS:\n" ;
$USAGE .= " inputTokFile:s def[$inputTokFile]\n" ;
$USAGE .= " inputTokFileAttrsTypeId:s def[$inputTokFileAttrsTypeId]\n" ;
$USAGE .= " inputTokFileAttrs:s def[$inputTokFileAttrs]\n" ;
$USAGE .= " outputFile:s def[$outputFile]\n" ;
$USAGE .= " d|debug:i def[$debug]\n" ;
$USAGE .= " v|verbose+\n" ;
$USAGE .= " h|help\n" ;
if ($help) {
print $USAGE ;
exit ;
}
#########################################################################################
# Process inputed attributes
$debug=$debug+$verbose ;
if ($debug>0) {
print "DEBUG: Debugging enabled and set to level: $debug.\n" ;
}
# Test the inputTokFile parameter
if (not defined($inputTokFile) ) {
print $USAGE ;
die ("ERROR a0djla: requires that --inputTokFile parameter be provided.\n\n") ;
}
if (-d $inputTokFile ) {
die("\nERROR aolkdj: The InputFile parameter must be a file not a directory [$inputTokFile].\n") ;
}
if (not open (INPUTFILE, “< $inputTokFile") ) {
die("\nERROR oxlkkd: could not open input file [$inputTokFile].\n") ;
}
close(INPUTFILE) ; # leave the opening to the subroutine
# Test the outputFile parameter
my $outputFileHandle ;
if (defined($outputFile) and not ($outputFile =~ /\-/)) {
if (-d $outputFile ) {
die("\nERROR lasjii: The OutputFile parameter must be a file not a directory [$outputFile].\n") ;
}
if (not open ($outputFileHandle, ">", $outputFile) ) {
die("\nERROR aanxks: could not open output file [$outputFile].\n") ;
}
}
if (not defined $inputTokFileAttrs) {
$inputTokFileAttrs = $TokFileAttrsType[$inputTokFileAttrsTypeId] ;
}
@InputTokFileAttrs = split ('\s+', $inputTokFileAttrs) ; # array of attribute names
print "DEBUG: inputTokFileAttrs=[@InputTokFileAttrs]\n" if $debug>=3 ;
##############
# not using TAB module ... yet
print "DEBUG: Read in the SynonymToConceptIdFile[$SynonymToConceptIdFile]\n" if $debug>=1 ;
my %ConceptIdToPreferredName ;
if (-e $SynonymToConceptIdFile ) {
open FILEH, “<$SynonymToConceptIdFile" or die "ERROR: Could not open [$SynonymToConceptIdFile] !*\n" ;
while (<FILEH>) {
print "." if $debug>=4 ;
my @R_ = split /\t/;
##ConceptName ConceptId Preferred
#- 5302 0
#1-Nearest Neighbor Range Search Task 4080 1
next if $R_[2] != "1" ; # We only need the preferred name
my $conceptId_ = $R_[1] ;
my $conceptPrefName_ = $R_[0] ;
$ConceptIdToPreferredName{$conceptId_} = $conceptPrefName_ ;
print "DEBUG: ConceptIdToPreferredName{$conceptId_} = $conceptPrefName_\n" if $debug>=4 ;
}
}
else {
print "DEBUG: not found [$SynonymToConceptIdFile]\n" if $debug>=0 ;
}
print "\n" if $debug>=4 ;
################################################################
################################################################
# Read-in the token input file and populate some prelim structures
$runningSeconds_=TABularDataFileMgmt::getrunningseconds() ;
print "DEBUG: [$runningSeconds_]s READ IN OUR DOCUMENT [$inputTokFile] with [" if $debug>=1 ;
TABularDataFileMgmt::ReadTabularFileIntoArrayOfHashes($inputTokFile, \@Token, \@InputTokFileAttrs) ;
print $#Token . “] records.\n" if $debug>=1 ;
if ($debug>=3) {
print "\nTokens :\n" ;
TABularDataFileMgmt::WriteArrayOfHashesToTabularFile("-", \@Token, \@InputTokFileAttrs );
}
# Populate the @Sentence structure
$runningSeconds_=TABularDataFileMgmt::getrunningseconds() ;
print "DEBUG: [$runningSeconds_]secs EXTRACT THE DOCUMENT AND SENTENCE INFORMATION\n" if $debug>=2 ;
# This is an overkill.
TGQueryDataMgmt::PopulateDocumentSentence(\@Token, \@Document, \@Sentence) ;
if ($debug>=2) {
print "DEBUG: COMPLETED: Documents=[" ;
print 1+$#Document;
print "] Sentences=[" ;
print 1+$#Sentence;
print "]\n" ;
}
##############
my $rawRestiched = "" ; # will contain the initial raw restiched results.
my $documentId ; # currently just for debugging
my $docSectionFlag=0 ; # special handling when a documentId is encountered.
$docSectionFlag=3 if $removeDocumentId ;
my $prevBioTag='O' ;
my $prevConceptId ;
my $cMAnchorText = "" ;
my $rawTokenId_ = 0 ;
print "DEBUG: PROCESS the inputTokFile\n" if $debug>=1 ;
for my $tokenId_ (0 .. $#Token) {
$rawTokenId_++ ;
my $token_ = $Token[$tokenId_]{Token} ;
my $bioTag_ = $Token[$tokenId_]{BIO} ;
my $conceptIdTxt_ = $Token[$tokenId_]{ConceptId} ;
my $conceptId_ = $conceptIdTxt_ ;
$conceptId_ =~ s/[\(\)\s\-]//g ;
undef $conceptId_ if ($conceptId_ =~ m/UNLINKED/) ;
print "DEBUG: token[$token_] bioTag[$bioTag_] conceptId[$conceptId_] cMAnchorText[$cMAnchorText] prevConceptId[$prevConceptId] docSectionFlag[$docSectionFlag]\n" if $debug>=2 ;
my $nextBioTag_ = $Token[$tokenId_+1]{BIO} ;
######## HANDLE DOCUMENT IDENTIFICATION SECTION #########
if ($token_ =~ m/^(\d\d\d\d_[^\s]+)/ or $token_ =~ m/^(10.\d\d\d\d[^\s]+)/) { # the pattern to detect a new document and extract the document identifier
$rawRestiched .= "\n$token_\t";
$documentId = $1 ;
$documentId =~ s/\//_/g ;
print "DEBUG: Found document start [$documentId]\n" if $debug>=3;
$docSectionFlag=2 ;
next ;
}
# test whether we need to skip the document section.
if ($removeDocumentId and $docSectionFlag) {
if ($docSectionFlag > 1) {
$docSectionFlag = 1 if ($token_ =~ /[\s]*/ and $token_ =~ /[^\w\d]/) ;
next ;
}
if ($token_ =~ /[^\s]/) { # Look for the first content token.
$docSectionFlag=0 ;
print "DEBUG: In document content section\n" if $debug>=3;
}
else {
next ;
}
}
############################################################
# Mark the end of a concept mention (on the previous token).
if ($bioTag_ =~ m/[^I]/ and $prevBioTag =~ m/[^O]/) { # if we are not in a continued span (bioTag==I) and the previous one is not in a span (prevBioTag==O).
print "DEBUG: End of a concept mention\n" if $debug>=3 ;
my $conceptName_ ;
if ($prevConceptId) {
$conceptName_ = $ConceptIdToPreferredName{$prevConceptId} ;
print "DEBUG: prevConceptId[$prevConceptId] => prevConceptName[$conceptName_]\n" if $debug>=2 ;
die "ERROR: unrecog concept name for conceptId[$prevConceptId]\n" if (not defined $conceptName_) ;
undef $prevConceptId ;
}
if (defined $conceptName_) { $rawRestiched .= $conceptName_ . “|" . $cMAnchorText }
else { $rawRestiched .= $cMAnchorText }
$rawRestiched .= "]]”
undef $cMAnchorText ;
}
# Can now commit to a conceptId in the current token (if present).
$prevConceptId = $conceptId_ if ($conceptId_ =~ m/\d/ and not $conceptId_ =~ m/\w/) ;
if ($bioTag_ =~ m/B/) { # Mark the start of a concept mention
$rawRestiched .= " [[" if $bioTag_ =~ m/B/ ;
$prevConceptId = $conceptId_ if ($conceptId_ =~ m/\d/) ;
$cMAnchorText = $token_ ;
print "DEBUG: mark the start of a concept mention (token[$token_]/bioTag=[$bioTag_])\n" if $debug>=4 ;
}
elsif ($bioTag_ =~ m/O/) { # Commit the token (insert appropriate spacing)
# if (not $cMAnchorText ) {
print "DEBUG: commit the token [$token_] (not [$cMAnchorText])\n" if $debug>=3 ;
my $space_ = " " ;
$rawRestiched .= "$space_$token_"
}
elsif ($bioTag_ =~ m/I/) {
$cMAnchorText .= " $token_" if defined $cMAnchorText ;
my $space_ = " " ;
$rawRestiched .= $space_ ;
print "DEBUG: insert the space between [$cMAnchorText])\n" if $debug>=3 ;
}
elsif (not defined $bioTag_) { # Mark an end of sentence.
$rawRestiched .= " <\/s> " ;
print "DEBUG: mark the end of a sentence (token[$token_]/bioTag=[$bioTag_])\n" if $debug>=3 ;
}
else {
die "ERROR(laks0hs): bioTag[$bioTag_]\n" ;
}
$prevBioTag=$bioTag_ ;
}
####################################
$_ = $rawRestiched ;
# recreate the typographical look&feel (e.g. periods, commas, ...)
s/ +/ /g ;
s/ \. <\/s>/. <\/s>/g ;
s/[ ]+([\,:;"\)])/$1/g ;
s/(\() /$1/g ;
s/\[\ [[]*?<([\/]*?)i>/<$1i>[[/gi ;
s/<([\/])*?i>[ ]*?\]\]/]]<$1i>/gi ;
s/\[\ [[]+?/[[/g ;
s/[ ]+?\]\]/]]/g ;
s/\[\ [[]*?\]\]//g ;
# reproduce the items that were reformated for convinience (e.g. _BR_ Yahoo_)
s/_BR_/<BR>/g ;
s/_sq_/``/g ;
s/_eq_/''/g ;
s/_#_/ # /g ;
s/_7_(.+?)_7_/&#$1;/g ;
s/Yahoo_/Yahoo!/g ;
# fixup some simple mistakes
# remove brackets around zero or one characters
s/\[\[(.{0,1})\]\]/$1/g ;
# ?? (stale?)
# append a <tab> after
s/2008_(\d+?)\. [\s]+?<\/s>[\s]*?/\n2008_$1\t/g ;
if (defined $outputFileHandle) {
print $outputFileHandle $_ ;
} else {
print STDOUT $_ ;
}