biblicit 1.0 → 2.0.3

data/parscit/lib/ParsCit/Citation.pm

@@ -0,0 +1,737 @@
+package ParsCit::Citation;
+###
+# Container object for citation data.  Stores all metadata fields
+# associated with a citation and utility methods for data access
+# and transformation.
+#
+# Isaac Councill, 7/19/07
+###
+
+use strict;
+use CSXUtil::SafeText qw(cleanAll cleanXML);
+
+sub new 
+{
+  	my ($class)		= @_;
+
+  	my @authors		= ();
+  	my @contexts	= ();
+	###
+	# Huydhn: volume is now an array of subvolume
+	###
+	my @volumes		= ();
+  	########## modified by Nick Friedrich
+  	### added array @positions for storing position of the marker of a context
+  	#
+  	# HISTORY: Nick (v081201)
+  	#
+  	# As Joran wrote I added functionality to find the position of a
+  	# reference (context) in the (body)text. I added an array "positions"
+  	# and also an add-method und get-method to Citation.pm. To find the
+  	# positions I modified CitationContext::getCitationContext. When a
+  	# context is found, the position of the match (subtract the context
+  	# radius) is stored in an array. The method returns an array with the
+  	# positions in addition to the array with the
+  	# contexts.Controller::extractCitationsImpl is modified accordingly.
+  	my @positions	= ();
+  	my @citStrs		= (); # Thang Nov 09 add in-text citation strings e.g. Brown et al., 1990 which might differ from the marker Brown, Pietra, deSouza, Lai, Mercer, 1990
+
+  	#	Thang May 10 add positions (word unit, 0-based) for in-text citation strings
+  	my @startWordPositions = ();   my @endWordPositions = ();
+
+  	my $self =	{
+			'_rawString' 	=> undef,
+	      	'_markerType' 	=> undef,
+	      	'_marker' 		=> undef,
+	      	'_authors' 		=> \@authors,
+	      	'_title' 		=> undef,
+	      	'_year' 		=> undef,
+	      	'_publisher' 	=> undef,
+	      	'_location' 	=> undef,
+	      	'_booktitle' 	=> undef,
+	      	'_journal' 		=> undef,
+	      	'_pages' 		=> undef,
+	      	'_volume' 		=> \@volumes,
+	      	'_number' 		=> undef,
+	      	'_contexts' 	=> \@contexts,
+	      	'_tech'			=> undef,
+	      	'_institution'	=> undef,
+	      	'_editor'		=> undef,
+	      	'_note'			=> undef,
+	      	'_positions'	=> \@positions,
+			# Thang Nov 09 add in-text citation strings
+	      	'_citStrs'		=> \@citStrs, 	      
+			# Thang May 10
+	      	'_startWordPositions'	=> \@startWordPositions, 
+	      	'_endWordPositions'		=> \@endWordPositions
+				};
+
+	bless $self, $class;
+	# Our work here is done
+  	return $self;
+}
+
+###
+# Looks for various combinations of data that could be used to
+# uniquely identify a citation.  If too much data is missing,
+# returns 0; otherwise, returns 1.
+###
+sub isValid 
+{
+    my ($self) = @_;
+
+    my @authors	= $self->getAuthors();
+    my $title	= $self->getTitle();
+    my $venue	= $self->getJournal();
+    my $date	= $self->getDate();
+
+	###
+	# Modified by Artemy Kolchinsky (v090625)
+	# added extra checks to subroutine 'isValid' in lib/ParsCit/Citation.pm.
+	# It helps to eliminate a lot of mis-parsed citations
+	###
+    my $rawString = $self->getString();
+
+	# Date not found in citation
+    if (!defined $date) { return 0; }
+
+	# Citation string over 400 characters --- probably a mistake in parsing somewhere
+    if (length($rawString) > 400) { return 0; }
+	###
+	# End modified by Artemy Kolchinsky (v090625)
+	###
+
+    if (!defined $venue) { $venue = $self->getBooktitle(); }
+
+    if ($#authors>=0 && (defined $title || defined $date)) { return 1; }
+
+    if (defined $venue && defined $date) { return 1; }
+
+    if (defined $title) { return 1; }
+
+	# Not a valid citation
+    return 0;
+}
+
+###
+# Utility for loading in a datum based on a tag from Tr2crfpp output.
+###
+sub loadDataItem 
+{
+    my ($self, $tag, $data) = @_;
+
+    if ($tag eq "authors") 
+	{
+		my @authors = @$data;
+		foreach my $auth (@authors) 
+		{
+	    	$self->addAuthor($auth);
+		}
+    }
+
+    if ($tag eq "contexts") 
+	{
+		my @contexts = @$data;
+		foreach my $context (@contexts) 
+		{
+	    	$self->addContext($context);
+		}
+    }
+
+    if ($tag eq "title") 
+	{
+		$self->setTitle($data);
+    }
+	
+    if ($tag eq "date") 
+	{
+		$self->setDate($data);
+    }
+
+    if ($tag eq "journal") 
+	{
+		$self->setJournal($data);
+    }
+
+    if ($tag eq "booktitle") 
+	{
+		$self->setBooktitle($data);
+    }
+
+    if ($tag eq "tech") 
+	{
+		$self->setTech($data);
+    }
+
+    if ($tag eq "location") 
+	{
+		$self->setLocation($data);
+    }
+	
+    if ($tag eq "volume") 
+	{
+		my @volumes = @$data;
+		foreach my $vol (@volumes) 
+		{
+	    	$self->addVolume($vol);
+		}
+    }
+
+    if ($tag eq "note") 
+	{
+		$self->setNote($data);
+    }
+
+    if ($tag eq "editor") 
+	{
+		$self->setEditor($data);
+    }
+
+    if ($tag eq "publisher") 
+	{
+		$self->setPublisher($data);
+    }
+
+    if ($tag eq "pages") 
+	{
+		$self->setPages($data);
+    }
+
+    if ($tag eq "institution") 
+	{
+		$self->setInstitution($data);
+    }
+
+    if ($tag eq "marker") 
+	{
+		$self->setMarker($data);
+    }
+}
+
+##
+# Returns a well-formed XML snippet containing all the data
+# in a citation object.
+##
+sub toXML 
+{
+    my $self = shift;
+
+    my $valid = $self->isValid();
+
+	if ($valid>0)
+	{
+		$valid = "true";
+    } 
+	else 
+	{
+		$valid = "false";
+    }
+
+	# Begin citation tag
+    my $xml = "<citation valid=\"$valid\">\n";
+
+	my @authors = $self->getAuthors();
+    map { $_ =~ s/_/ /g } @authors;
+
+	# Authors
+    if ($#authors >= 0) 
+	{
+		$xml .= "<authors>\n";
+		
+		foreach my $auth (@authors) 
+		{
+	    	cleanAll(\$auth);
+	    	$xml .= "<author>" . $auth . "</author>\n";
+		}
+
+		$xml .= "</authors>\n";
+    }
+
+	# Title
+    my $title = $self->getTitle();
+    if (defined $title) 
+	{
+		cleanAll(\$title);
+		$xml .= "<title>" . $title . "</title>\n";
+    }
+
+	# Date
+    my $date = $self->getDate();
+    if (defined $date) 
+	{
+		cleanAll(\$date);
+		$xml .= "<date>" . $date . "</date>\n";
+    }
+
+	# Journal name
+    my $journal = $self->getJournal();
+    if (defined $journal) 
+	{
+		cleanAll(\$journal);
+		$xml .= "<journal>" . $journal . "</journal>\n";
+    }
+
+	# Book title
+    my $booktitle = $self->getBooktitle();
+    if (defined $booktitle) 
+	{
+		cleanAll(\$booktitle);
+		$xml .= "<booktitle>" . $booktitle . "</booktitle>\n";
+    }
+
+	# What' title is it?
+    my $tech = $self->getTech();
+    if (defined $tech) 
+	{
+		cleanAll(\$tech);
+		$xml .= "<tech>" . $tech . "</tech>\n";
+    }
+
+    my @volumes = $self->getVolumes();
+    if (scalar(@volumes) > 0)
+	{
+		# Main volume
+		cleanAll(\$volumes[ 0 ]);
+		$xml .= "<volume>" . $volumes[ 0 ] . "</volume>\n";
+
+		# Sub-volume, issue
+		for (my $i = 1; $i < scalar(@volumes); $i++)
+		{
+			cleanAll(\$volumes[ $i ]);
+			$xml .= "<issue>" . $volumes[ $i ] . "</issue>\n";
+		}
+    }
+
+    my $pages = $self->getPages();
+    if (defined $pages) 
+	{
+		cleanAll(\$pages);
+		$xml .= "<pages>" . $pages . "</pages>\n";
+    }
+
+    my $editor = $self->getEditor();
+    if (defined $editor) 
+	{
+		cleanAll(\$editor);
+		$xml .= "<editor>" . $editor . "</editor>\n";
+    }
+
+    my $publisher = $self->getPublisher();
+    if (defined $publisher) 
+	{
+		cleanAll(\$publisher);
+		$xml .= "<publisher>" . $publisher . "</publisher>\n";
+    }
+
+    my $institution = $self->getInstitution();
+    if (defined $institution) 
+	{
+		cleanAll(\$institution);
+		$xml .= "<institution>" . $institution . "</institution>\n";
+    }
+
+    my $location = $self->getLocation();
+    if (defined $location) 
+	{
+		cleanAll(\$location);
+		$xml .= "<location>" . $location . "</location>\n";
+    }
+
+    my $note = $self->getNote();
+    if (defined $note) 
+	{
+		cleanAll(\$note);
+		$xml .= "<note>" . $note . "</note>\n";
+    }
+	
+	###
+	# Modified by Nick Friedrich (v081201)
+	# the xml-element "context" contains now an attribute "position"
+	####
+    my @contexts	= $self->getContexts();
+    my @positions	= $self->getPositions();
+	# Thang Nov 09
+    my @cit_strs	= $self->getCitStrs(); 
+
+    # Thang May 10
+    my @start_wd_positions	= $self->getStartWordPositions(); 
+    my @end_wd_positions	= $self->getEndWordPositions(); 
+
+    if ($#contexts >= 0) 
+	{
+		$xml .= "<contexts>\n";
+
+		# Print out citation's context
+		foreach my $context (@contexts) 
+		{
+	    	cleanAll(\$context);
+	    	
+			my $pos		= shift(@positions);
+			# Thang Nov 09
+	    	my $cit_str	= shift(@cit_strs);
+			cleanAll(\$cit_str);
+
+		    # Thang May 10
+		    my $start_wd_position	= shift(@start_wd_positions); 
+	    	my $end_wd_position		= shift(@end_wd_positions);
+
+		    $xml .= "<context";
+		    $xml .= " position=\"" . $pos . "\"";
+			# Thang Nov 09
+	    	$xml .= " citStr=\"" . $cit_str . "\""; 
+
+	    	# Thang May 10
+	    	$xml .= " startWordPosition=\"" . $start_wd_position . "\""; 
+	    	$xml .= " endWordPosition=\"" . $end_wd_position . "\"";
+
+		    $xml .= ">" . $context . "</context>\n";
+		}
+
+		$xml .= "</contexts>\n";
+	}
+	###
+	# End modified by Nick Friedrich (v081201)
+	###
+
+    my $marker = $self->getMarker();
+    if (defined $marker) 
+	{
+		cleanAll(\$marker);
+		$xml .= "<marker>" . $marker . "</marker>\n";
+    }
+
+    my $rawString = $self->getString();
+    if (defined $rawString) 
+	{
+		cleanXML(\$rawString);
+		$xml .= "<rawString>" . $rawString . "</rawString>\n";
+    }
+
+    $xml .= "</citation>\n";
+	# Our work here is done
+    return $xml;
+
+} # toXML
+
+
+sub getPositions 
+{
+    my ($self) = @_;
+    return @{$self->{'_positions'}};
+}
+
+sub addPosition 
+{
+    my ($self, $position) = @_;
+    my @positions = @{$self->{'_positions'}};
+    push @positions, $position;
+    $self->{'_positions'} = \@positions;
+}
+
+###
+# Thang Nov 09 add in-text citation strings
+###
+sub getCitStrs 
+{
+    my ($self) = @_;
+    return @{$self->{'_citStrs'}};
+}
+
+sub addCitStr 
+{
+    my ($self, $cit_str) = @_;
+    my @cit_strs = @{$self->{'_citStrs'}};
+    push @cit_strs, $cit_str;
+    $self->{ '_citStrs' } = \@cit_strs;
+}
+###
+# End Thang Nov 09 add in-text citation strings
+###
+
+###
+# Thang May 10 add positions (in word unit, 0-based) for in-text citation strings
+###
+sub getStartWordPositions 
+{
+    my ($self) = @_;
+    return @{$self->{'_startWordPositions'}};
+}
+
+sub addStartWordPosition 
+{
+    my ($self, $start_wd_position) = @_;
+    my @start_wd_positions = @{ $self->{ '_startWordPositions' } };
+    push @start_wd_positions, $start_wd_position;
+    $self->{ '_startWordPositions' } = \@start_wd_positions;
+}
+
+sub getEndWordPositions 
+{
+    my ($self) = @_;
+    return @{ $self->{ '_endWordPositions' } };
+}
+
+sub addEndWordPosition 
+{
+    my ($self, $end_wd_position) = @_;
+    my @end_wd_positions = @{ $self->{ '_endWordPositions' } };
+    push @end_wd_positions, $end_wd_position;
+    $self->{ '_endWordPositions' } = \@end_wd_positions;
+}
+###
+# End Thang May 10 add positions (in word unit) for in-text citation strings
+###
+
+sub getString 
+{
+    my ($self) = @_;
+    return $self->{ '_rawString' };
+}
+
+sub setString 
+{
+    my ($self, $str) = @_;
+    $self->{ '_rawString' } = $str;
+}
+
+sub getMarkerType 
+{
+    my ($self) = @_;
+    return $self->{ '_markerType' };
+}
+
+sub setMarkerType 
+{
+    my ($self, $marker_type) = @_;
+    $self->{ '_markerType' } = $marker_type;
+}
+
+sub getMarker 
+{
+    my ($self) = @_;
+    return $self->{ '_marker' };
+}
+
+sub setMarker 
+{
+    my ($self, $marker) = @_;
+    $self->{ '_marker' } = $marker;
+}
+
+sub addAuthor 
+{
+    my ($self, $author) = @_;
+    my @authors = @{ $self->{ '_authors' } };
+    push @authors, $author;
+    $self->{ '_authors' } = \@authors;
+}
+
+sub getAuthors 
+{
+    my ($self) = @_;
+    return @{ $self->{ '_authors' } };
+}
+
+sub addContext 
+{
+    my ($self, $context) = @_;
+    my @contexts = @{ $self->{ '_contexts' } };
+    push @contexts, $context;
+    $self->{ '_contexts' } = \@contexts;
+}
+
+sub getContexts 
+{
+    my ($self) = @_;
+    return @{ $self->{ '_contexts' } };
+}
+
+sub getTitle 
+{
+    my ($self) = @_;
+    return $self->{ '_title' };
+}
+
+sub setTitle 
+{
+    my ($self, $title) = @_;
+    $self->{ '_title' } = $title;
+}
+
+sub getDate 
+{
+    my $self = shift;
+    return $self->{ '_year' };
+}
+
+sub setDate 
+{
+    my ($self, $year) = @_;
+    $self->{ '_year' } = $year;
+}
+
+sub getPublisher 
+{
+    my $self = shift;
+    return $self->{ '_publisher' };
+}
+
+sub setPublisher 
+{
+    my ($self, $publisher) = @_;
+    $self->{ '_publisher' } = $publisher;
+}
+
+sub getLocation 
+{
+    my $self = shift;
+    return $self->{ '_location' };
+}
+
+sub setLocation 
+{
+    my ($self, $location) = @_;
+    $self->{ '_location' } = $location;
+}
+
+sub getBooktitle 
+{
+    my $self = shift;
+    return $self->{ '_booktitle' };
+}
+
+sub setBooktitle 
+{
+    my ($self, $booktitle) = @_;
+    $self->{ '_booktitle' } = $booktitle;
+}
+
+sub getJournal 
+{
+    my $self = shift;
+    return $self->{ '_journal' };
+}
+
+sub setJournal 
+{
+    my ($self, $journal) = @_;
+    $self->{ '_journal' } = $journal;
+}
+
+sub getPages 
+{
+    my $self = shift;
+    return $self->{ '_pages' };
+}
+
+sub setPages 
+{
+    my ($self, $pages) = @_;
+    $self->{ '_pages' } = $pages;
+}
+
+sub addVolume
+{
+    my ($self, $volume) = @_;
+    my @volumes = @{ $self->{ '_volume' } };
+    push @volumes, $volume;
+    $self->{ '_volume' } = \@volumes;
+}
+
+sub getVolumes 
+{
+    my $self = shift;
+	###
+	# Huydhn: volume is now an array of sub-volume
+	# 18 Jan 2011
+	###
+    return @{ $self->{ '_volume' } };
+}
+
+###
+# Huydhn: remove because volume is now an array of sub-volumes
+###
+#sub setVolume 
+#{
+#    my ($self, $volume) = @_;
+#    $self->{'_volume'} = $volume;
+#}
+#
+#sub getVolume {
+#    my $self = shift;
+#    return $self->{'_volume'};
+#}
+
+sub getTech 
+{
+    my $self = shift;
+    return $self->{ '_tech' };
+}
+
+sub setTech 
+{
+    my ($self, $tech) = @_;
+    $self->{ '_tech' } = $tech;
+}
+
+sub getInstitution 
+{
+    my $self = shift;
+    return $self->{ '_institution' };
+}
+
+sub setInstitution 
+{
+    my ($self, $institution) = @_;
+    $self->{ '_institution' } = $institution;
+}
+
+sub getEditor 
+{
+    my $self = shift;
+    return $self->{ '_editor' };
+}
+
+sub setEditor 
+{
+    my ($self, $editor) = @_;
+    $self->{ '_editor' } = $editor;
+}
+
+sub getNote 
+{
+    my $self = shift;
+    return $self->{ '_note' };
+}
+
+sub setNote 
+{
+    my ($self, $note) = @_;
+    $self->{ '_note' } = $note;
+}
+
+
+###
+# Build a marker based on the author list and publication year.
+# This should be used when no marker was found during citation
+# segmentation.
+###
+sub buildAuthYearMarker 
+{
+    my $self = shift;
+
+	my @authors		= $self->getAuthors();
+    my @last_names	= ();
+
+    foreach my $auth (@authors) 
+	{
+		my @toks = split " +", $auth;
+		push @last_names, $toks[ $#toks ];
+    }
+
+    my $year = $self->getDate();
+    map { $_ =~ s/_/ /g } @last_names;
+    return join ", ", @last_names, $year;
+}
+
+1;