biblicit 1.0 → 2.0.3

data/perl/ParsCit/lib/ParsCit/CitationContext.pm

@@ -1,132 +0,0 @@
-package ParsCit::CitationContext;
-#
-# Utility functions for finding citation contexts after citation
-# parsing.  The idea is to build regular expressions that could match
-# citation references in the body text and scan the body text for
-# occurrences.  The size of the context returned can be configured
-# in ParsCit::Config::contextRadius.
-#
-# Isaac Councill, 7/20/07
-#
-use ParsCit::Config;
-use utf8;
-
-my $contextRadius = $ParsCit::Config::contextRadius;
-my $maxContexts = $ParsCit::Config::maxContexts;
-my $premark = $ParsCit::Config::context_premark;
-my $postmark = $ParsCit::Config::context_postmark;
-
-##
-# Build a list of potential regular expressions based on the supplied
-# citation marker and applies the expressions to the specified body text.
-# Returns a reference to a list of strings that match the expressions,
-# expanded to radius $contextRadius.
-##
-sub getCitationContext {
-    my ($rBodyText, $marker) = @_;
-
-    my ($prioritize, @markers) = guessPossibleMarkers($marker);
-    my @matches = ();
-
-    my $contextsFound = 0;
-    foreach my $mark (@markers) {
-	while (($contextsFound < $maxContexts) &&
-	       $$rBodyText =~ m/(.{$contextRadius}$mark.{$contextRadius})/gs) {
-	    my $match = $1;
-	    $match =~ s/^(.*?)($mark)(.*)$/$1$premark$2$postmark$+/;
-	    push @matches, $match;
-	    $contextsFound++;
-	}
-	if (($prioritize > 0) && ($#matches >= 0)) {
-	    last;
-	}
-    }
-    return \@matches;
-
-}  # getCitationContext
-
-
-##
-# Builds a list of regular expressions based on the supplied
-# citation marker that may indicate a citation reference in
-# body text.  The first value returned is a parameter indicating
-# whether the list should be prioritized (i.e., if matches to
-# one element are found, don't try to match subsquent expressions),
-# with 0 indicating no prioritization and 1 indicating otherwise.
-##
-sub guessPossibleMarkers {
-    my $marker = shift;
-    if ($marker =~ m/^([\[\(])([\p{IsUpper}\p{IsLower}\-\d]+)([\]\)])/) {
-	my $open = makeSafe($1);
-	my $mark = makeSafe($2);
-	my $close = makeSafe($3);
-	my $refIndicator = "$open([\p{IsUpper}\p{IsLower}\\-\\d]+[;,] *)*$mark([;,] *[\p{IsUpper}\p{IsLower}\\-\\d]+)*$close";
-	return (0, $refIndicator);
-    }
-    if ($marker =~ m/^(\d+)\.?/) {
-	my $square = "\\[(\\d+[,;] *)*$1([;,] *\\d+)*\\]";
-	my $paren = "\\((\\d+[,;] *)*$1([,;] *\\d+)*\\)";
-	return (1, $square, $paren);
-    }
-    if ($marker =~ m/^([\p{IsUpper}\p{IsLower}\-\.\']+(, )*)+\d{4}/) {
-	my @tokens = split ", ", $marker;
-	my $year = $tokens[$#tokens];
-	my @names = @tokens[0..$#tokens-1];
-	my @possibleMarkers = ();
-	if ($#names == 0) {
-	    push @possibleMarkers, $names[0].",? $year";
-	}
-	if ($#names == 1) {
-	    push @possibleMarkers, $names[0]." and ".$names[1].",? $year";
-	    push @possibleMarkers, $names[0]." & ".$names[1].",? $year";
-	}
-	if ($#names > 1) {
-	    map { $_ = makeSafe($_) } $names;
-	    map { $_ = $_."," } @names;
-	    my $lastAuth1 = "and ".$names[$#names];
-	    my $lastAuth2 = "& ".$names[$#names];
-	    push @possibleMarkers,
-	      join " ", @names[0..$#names-1], $lastAuth1, $year;
-	    push @possibleMarkers,
-	      join " ", @names[0..$#names-1], $lastAuth2, $year;
-
-	    push @possibleMarkers, $names[0]."? et al\\\.?,? $year";
-	}
-	for (my $i=0; $i<=$#possibleMarkers; $i++) {
-	    my $safeMarker = $possibleMarkers[$i];
-	    $safeMarker =~ s/\-/\\\-/g;
-	    $possibleMarkers[$i] = $safeMarker;
-	}
-	return (0, @possibleMarkers);
-    }
-    return makeSafe($marker);
-
-}  # guessPossibleMarkers
-
-
-##
-# Prepare strings for safe inclusion within a regular expression,
-# escaping control characters.
-##
-sub makeSafe {
-    my $marker = shift;
-    $marker =~ s/\\/\\\\/g;
-    $marker =~ s/\-/\\\-/g;
-    $marker =~ s/\[/\\\[/g;
-    $marker =~ s/\]/\\\]/g;
-    $marker =~ s/\(/\\\(/g;
-    $marker =~ s/\)/\\\)/g;
-    $marker =~ s/\'/\\\'/g;
-    $marker =~ s/\"/\\\"/g;
-    $marker =~ s/\+//g;
-    $marker =~ s/\?//g;
-    $marker =~ s/\*//g;
-    $marker =~ s/\^//g;
-    $marker =~ s/\$//g;
-    $marker =~ s/\./\\\./g;
-    return $marker;
-
-} # makeSafe
-
-
-1;

data/perl/ParsCit/lib/ParsCit/Config.pm

@@ -1,46 +0,0 @@
-package ParsCit::Config;
-
-
-## Global
-
-$algorithmName = "ParsCit";
-$algorithmVersion = "1.0";
-
-
-## Repository Mappings
-
-%repositories = ('rep1' => '/repositories/rep1',
-                 'example1' => '/',
-		 'example2' => '/home',
-		 );
-
-
-## WS settings
-
-$serverURL = '130.203.133.46';
-$serverPort = 10555;
-$URI = 'http://citeseerx.org/algorithms/parscit/wsdl';
-
-
-## Tr2crfpp
-## Paths relative to ParsCit root dir ($FindBin::Bin/..)
-
-$tmpDir = "tmp";
-$dictFile = "resources/parsCitDict.txt";
-$modelFile = "resources/parsCit.model";
-
-$crf_test = "crf_test"; # assumes crfpp is installed in the system path
-
-## Citation Context
-
-$contextRadius = 200;
-$maxContexts = 5;
-$context_premark = "=-=";
-$context_postmark = "-=-";
-
-## Write citation and body file components
-
-$bWriteSplit = 1;
-
-
-1;

data/perl/ParsCit/lib/ParsCit/Controller.pm

@@ -1,306 +0,0 @@
-package ParsCit::Controller;
-#
-# This package is used to pull together various citation
-# processing modules in the ParsCit distribution, serving
-# as a script for handling the entire citation processing
-# control flow.  The extractCitations subroutine should be
-# the only needed API element if XML output is desired;
-# however, the extractCitationsImpl subroutine can be used
-# to get direct access to the list of citation objects.
-#
-# Isaac Councill, 07/23/07
-#
-use strict;
-use ParsCit::PreProcess;
-use ParsCit::PostProcess;
-use ParsCit::Tr2crfpp;
-use ParsCit::CitationContext;
-use ParsCit::Config;
-use CSXUtil::SafeText qw(cleanXML);
-
-
-##
-# Main API method for generating an XML document including all
-# citation data.  Returns a reference XML document and a
-# reference to the article body text.
-##
-sub extractCitations {
-    my ($textFile) = @_;
-    my ($status, $msg, $rCitations, $rBodyText)
-	= extractCitationsImpl($textFile);
-    if ($status > 0) {
-	return buildXMLResponse($rCitations);
-    } else {
-	my $error = "Error: $msg";
-	return \$error;
-    }
-
-} # extractCitations
-
-
-##
-# Main script for actually walking through the steps of
-# citation processing.  Returns a status code (0 for failure),
-# an error message (may be blank if no error), a reference to
-# an array of citation objects and a reference to the body
-# text of the article being processed.
-##
-sub extractCitationsImpl {
-    my ($textFile, $bWriteSplit) = @_;
-
-    if (!defined $bWriteSplit) {
-	$bWriteSplit = $ParsCit::Config::bWriteSplit;
-    }
-
-    my ($status, $msg) = (1, "");
-
-    if (!open (IN, "<:utf8", "$textFile")) {
-	return (-1, "Could not open text file $textFile: $!");
-    }
-
-    my $text;
-    {
-	local $/ = undef;
-	$text = <IN>;
-    }
-    close IN;
-
-    my ($rCiteText, $rNormBodyText, $rBodyText) =
-	ParsCit::PreProcess::findCitationText(\$text);
-    my ($citeFile, $bodyFile) = ("", "");
-    if ($bWriteSplit > 0) {
-	($citeFile, $bodyFile) =
-	    writeSplit($textFile, $rCiteText, $rBodyText);
-    }
-
-    my $rRawCitations = ParsCit::PreProcess::segmentCitations($rCiteText);
-    my @citations = ();
-    my @validCitations = ();
-
-    my $normalizedCiteText;
-    foreach my $citation (@{$rRawCitations}) {
-	# Tr2cfpp needs an enclosing tag for initial class seed.
-	my $citeString = $citation->getString();
-	if (defined $citeString && $citeString !~ m/^\s*$/) {
-	    $normalizedCiteText .=
-		"<title> ".$citation->getString() . " </title>\n";
-	    push @citations, $citation;
-	}
-    }
-
-    if ($#citations < 0) {
-	# Stop - nothing left to do.
-	return ($status, $msg, \@validCitations, $rNormBodyText);
-    }
-
-    my $tmpFile = ParsCit::Tr2crfpp::prepData(\$normalizedCiteText, $textFile);
-    my $outFile = $tmpFile."_dec";
-
-    if (ParsCit::Tr2crfpp::decode($tmpFile, $outFile)) {
-	my ($rRawXML, $rCiteInfo, $tstatus, $tmsg) =
-	    ParsCit::PostProcess::readAndNormalize($outFile);
-	if ($tstatus <= 0) {
-	    return ($tstatus, $msg, undef, undef);
-	}
-	my @citeInfo = @{$rCiteInfo};
-	if ($#citations == $#citeInfo) {
-	    for (my $i=0; $i<=$#citations; $i++) {
-		my $citation = $citations[$i];
-		my %citeInfo = %{$citeInfo[$i]};
-		foreach my $key (keys %citeInfo) {
-		    $citation->loadDataItem($key, $citeInfo{$key});
-		}
-		my $marker = $citation->getMarker();
-		if (!defined $marker) {
-		    $marker = $citation->buildAuthYearMarker();
-		    $citation->setMarker($marker);
-		}
-		my $rContexts =
-		    ParsCit::CitationContext::getCitationContext($rNormBodyText,
-								 $marker);
-		foreach my $context (@{$rContexts}) {
-		    $citation->addContext($context);
-		}
-		push @validCitations, $citation;
-	    }
-	} else {
-	    $status = -1;
-	    $msg = "Mismatch between expected citations and cite info";
-	}
-    }
-
-    unlink($tmpFile);
-    unlink($outFile);
-
-    return ($status, $msg, \@validCitations,
-	    $rBodyText, $citeFile, $bodyFile);
-
-} # extractCitationsImpl
-
-
-##
-# Quickly hacked copy of extractCitationsImpl used for testing a
-# parscit with pre-segmented reference strings.  This method
-# will be collapsed with the main Impl method in future versions.
-##
-sub extractCitationsAlreadySegmented {
-    my ($textFile) = @_;
-
-    my ($status, $msg) = (1, "");
-
-    if (!open(IN, "<:utf8", $textFile)) {
-	return (-1, "Could not open file $textFile: $!");
-    }
-
-    my @rawCitations = ();
-    my $currentCitation;
-    while(<IN>) {
-	chomp();
-	if (m/^\s*$/ && defined $currentCitation) {
-	    my $cite = new ParsCit::Citation();
-	    $cite->setString($currentCitation);
-	    push @rawCitations, $cite;
-	    $currentCitation = undef;
-	    next;
-	}
-	if (!defined $currentCitation) {
-	    $currentCitation = $_;
-	} else {
-	    $currentCitation .= " ".$_;
-	}
-    }
-    close IN;
-    if (defined $currentCitation) {
-	my $cite = new ParsCit::Citation();
-	push @rawCitations, $cite;
-    }
-
-    my @citations;
-    my @validCitations = ();
-    my $normalizedCiteText;
-    foreach my $citation (@rawCitations) {
-	# Tr2cfpp needs an enclosing tag for initial class seed.
-	my $citeString = $citation->getString();
-	if (defined $citeString && $citeString !~ m/^\s*$/) {
-	    $normalizedCiteText .=
-		"<title> ".$citation->getString() . " </title>\n";
-	    push @citations, $citation;
-	}
-    }
-
-    if ($#citations < 0) {
-	# Stop - nothing left to do.
-	return ($status, $msg, \@validCitations);
-    }
-
-    my $tmpFile = ParsCit::Tr2crfpp::prepData(\$normalizedCiteText, $textFile);
-    my $outFile = $tmpFile."_dec";
-
-    if (ParsCit::Tr2crfpp::decode($tmpFile, $outFile)) {
-	my ($rRawXML, $rCiteInfo, $tstatus, $tmsg) =
-	    ParsCit::PostProcess::readAndNormalize($outFile);
-	if ($tstatus <= 0) {
-	    return ($tstatus, $msg, undef, undef);
-	}
-	my @citeInfo = @{$rCiteInfo};
-	if ($#citations == $#citeInfo) {
-	    for (my $i=0; $i<=$#citations; $i++) {
-		my $citation = $citations[$i];
-		my %citeInfo = %{$citeInfo[$i]};
-		foreach my $key (keys %citeInfo) {
-		    $citation->loadDataItem($key, $citeInfo{$key});
-		}
-#		unless ($citation->isValid()>0) {
-#		    next;
-#		}
-		my $marker = $citation->getMarker();
-		if (!defined $marker) {
-		    $marker = $citation->buildAuthYearMarker();
-		    $citation->setMarker($marker);
-		}
-		push @validCitations, $citation;
-	    }
-	} else {
-	    $status = -1;
-	    $msg = "Mismatch between expected citations and cite info";
-	}
-    }
-
-    unlink($tmpFile);
-    unlink($outFile);
-
-    return buildXMLResponse(\@validCitations);
-
-} # extractCitationsAlreadySegmented
-
-
-sub buildXMLResponse {
-    my ($rCitations) = @_;
-    my $l_algName = $ParsCit::Config::algorithmName;
-    my $l_algVersion = $ParsCit::Config::algorithmVersion;
-    cleanXML(\$l_algName);
-    cleanXML(\$l_algVersion);
-
-    my $xml = "<algorithm name=\"$l_algName\" ".
-	"version=\"$l_algVersion\">\n";
-    $xml .= "<citationList>\n";
-
-    foreach my $citation (@$rCitations) {
-	$xml .= $citation->toXML();
-    }
-
-    $xml .= "</citationList>\n";
-    $xml .= "</algorithm>\n";
-
-    return \$xml;
-
-} # buildXMLResponse
-
-
-##
-# Writes separated citation and body text to disk.
-##
-sub writeSplit {
-    my ($textFile, $rCiteText, $rBodyText) = @_;
-
-    my $citeFile = changeExtension($textFile, "cite");
-    my $bodyFile = changeExtension($textFile, "body");
-
-    if (open(OUT, ">$citeFile")) {
-	binmode OUT, ":utf8";
-	print OUT $$rCiteText;
-	close OUT;
-    } else {
-	print STDERR "Could not open .cite file for writing: $!\n";
-    }
-
-    if (open(OUT, ">$bodyFile")) {
-	binmode OUT, ":utf8";
-	print OUT $$rBodyText;
-	close OUT;
-    } else {
-	print STDERR "Could not open .body file for writing: $!\n";
-    }
-
-    return ($citeFile, $bodyFile);
-
-} # writeSplit
-
-
-##
-# Utility to replace the extension of a file name.  Parameter
-# $ext should be just the alphanumeric extension, without the
-# preceeding ".".  If no extension is present on the file name,
-# $ext will be appended.
-##
-sub changeExtension {
-    my ($fn, $ext) = @_;
-    unless ($fn =~ s/^(.*)\..*$/$1\.$ext/) {
-	$fn .= ".$ext";
-    }
-    return $fn;
-
-} # changeExtension
-
-
-1;