From: Tara L Andrews <tla\@mit.edu>
Date: Thu, 22 Dec 2011 13:30:31 +0000 (+0100)
Subject: stop saving duplicate path arrays in witnesses; get rid of relationship
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=b74d89f9e926466ba4ded77746fd0f98912cc17a;p=scpubgit%2Fstemmatology.git

stop saving duplicate path arrays in witnesses; get rid of relationship
vectors that we don't use
---

diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm
index 236a9bd..5f94dfb 100644
--- a/lib/Text/Tradition/Collation.pm
+++ b/lib/Text/Tradition/Collation.pm
@@ -438,6 +438,7 @@ sub as_graphml {
         _add_graphml_data( $node_el, $node_data_keys{'rank'}, $n->rank )
             if $n->has_rank;
         _add_graphml_data( $node_el, $node_data_keys{'class'}, $n->sub_class );
+        $DB::single = 1 if $n->has_primary && $n->primary ne $n;
         _add_graphml_data( $node_el, $node_data_keys{'identical'}, $n->primary->name )
             if $n->has_primary && $n->primary ne $n;
     }
@@ -530,11 +531,14 @@ sub make_alignment_table {
     my @all_pos = ( 0 .. $self->end->rank - 1 );
     foreach my $wit ( $self->tradition->witnesses ) {
         # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
-        my @row = _make_witness_row( $wit->path, \@all_pos, $noderefs );
+        my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
+        my @row = _make_witness_row( \@wit_path, \@all_pos, $noderefs );
         unshift( @row, $wit->sigil );
         push( @$table, \@row );
-        if( $wit->has_ante_corr ) {
-            my @ac_row = _make_witness_row( $wit->uncorrected_path, \@all_pos, $noderefs );
+        if( $wit->is_layered ) {
+        	my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, 
+        		$wit->sigil.$self->ac_label, $wit->sigil );
+            my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos, $noderefs );
             unshift( @ac_row, $wit->sigil . $self->ac_label );
             push( @$table, \@ac_row );
         }           
@@ -861,69 +865,12 @@ sub _is_within {
 
 
 ## INITIALIZATION METHODS - for use by parsers
-# Walk the paths for each witness in the graph, and return the nodes
-# that the graph has in common.  If $using_base is true, some 
-# different logic is needed.
-# NOTE This does not create paths; it merely finds common readings.
-
-sub walk_witness_paths {
-    my( $self ) = @_;
-    # For each witness, walk the path through the graph.
-    # Then we need to find the common nodes.  
-    # TODO This method is going to fall down if we have a very gappy 
-    # text in the collation.
-    my $paths = {};
-    my @common_readings;
-    foreach my $wit ( $self->tradition->witnesses ) {
-        my $curr_reading = $self->start;
-        my @wit_path = $self->reading_sequence( $self->start, $self->end, 
-                                                $wit->sigil );
-        $wit->path( \@wit_path );
-
-        # Detect the common readings.
-        @common_readings = _find_common( \@common_readings, \@wit_path );
-    }
-
-    # Mark all the nodes as either common or not.
-    foreach my $cn ( @common_readings ) {
-        print STDERR "Setting " . $cn->name . " / " . $cn->label 
-            . " as common node\n";
-        $cn->make_common;
-    }
-    foreach my $n ( $self->readings() ) {
-        $n->make_variant unless $n->is_common;
-    }
-    # Return an array of the common nodes in order.
-    return @common_readings;
-}
-
-sub _find_common {
-    my( $common_readings, $new_path ) = @_;
-    my @cr;
-    if( @$common_readings ) {
-        foreach my $n ( @$new_path ) {
-            push( @cr, $n ) if grep { $_ eq $n } @$common_readings;
-        }
-    } else {
-        push( @cr, @$new_path );
-    }
-    return @cr;
-}
-
-sub _remove_common {
-    my( $common_readings, $divergence ) = @_;
-    my @cr;
-    my %diverged;
-    map { $diverged{$_->name} = 1 } @$divergence;
-    foreach( @$common_readings ) {
-        push( @cr, $_ ) unless $diverged{$_->name};
-    }
-    return @cr;
-}
-
 
 # For use when a collation is constructed from a base text and an apparatus.
 # We have the sequences of readings and just need to add path edges.
+# When we are done, clear out the witness path attributes, as they are no
+# longer needed.
+# TODO Find a way to replace the witness path attributes with encapsulated functions?
 
 sub make_witness_paths {
     my( $self ) = @_;
@@ -940,7 +887,7 @@ sub make_witness_path {
     foreach my $idx ( 0 .. $#chain-1 ) {
         $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
     }
-    if( $wit->has_ante_corr ) {
+    if( $wit->is_layered ) {
         @chain = @{$wit->uncorrected_path};
         foreach my $idx( 0 .. $#chain-1 ) {
             my $source = $chain[$idx];
@@ -949,6 +896,8 @@ sub make_witness_path {
                 unless $self->has_path( $source, $target, $sig );
         }
     }
+    $wit->clear_path;
+    $wit->clear_uncorrected_path;
 }
 
 sub calculate_ranks {
diff --git a/lib/Text/Tradition/Collation/Relationship.pm b/lib/Text/Tradition/Collation/Relationship.pm
index c2ad3ae..9c6e80e 100644
--- a/lib/Text/Tradition/Collation/Relationship.pm
+++ b/lib/Text/Tradition/Collation/Relationship.pm
@@ -12,19 +12,6 @@ extends 'Graph::Easy::Edge';
 
 enum 'RelationshipType' => qw( spelling orthographic grammatical repetition lexical );
 
-subtype 'RelationshipVector',
-    => as 'ArrayRef',
-    => where { @$_ == 2
-	       && $_->[0]->isa( 'Graph::Easy::Node' )
-	       && $_->[1]->isa( 'Graph::Easy::Node' )
-	     },
-    message { 'Argument should be [ SourceReading, TargetReading ]' };
-
-subtype 'RelationshipTokenVector',
-    => as 'ArrayRef',
-    => where { @$_ == 2 },
-    message { 'Argument should be [ \'source\', \'target\' ]' };
-
 no Moose::Util::TypeConstraints;  ## see comment above
 		   
 has 'type' => (
@@ -33,17 +20,6 @@ has 'type' => (
     required => 1,
 );
 
-has 'this_relation' => (
-    is => 'rw',
-    isa => 'RelationshipVector',
-    required => 1,
-);
-
-has 'primary_relation' => (
-    is => 'rw',
-    isa => 'RelationshipTokenVector',
-);
-
 has 'global' => (
     is => 'rw',
     isa => 'Bool',
@@ -82,10 +58,6 @@ sub BUILD {
 
     $self->set_attribute( 'class', 'relationship' );
 
-    unless( $self->primary_relation ) {
-	$self->primary_relation( [ $self->this_relation->[0]->label,
-				   $self->this_relation->[1]->label ] );
-    }
 }
 
 no Moose;
diff --git a/lib/Text/Tradition/Parser/CollateX.pm b/lib/Text/Tradition/Parser/CollateX.pm
index 62123fe..f2dac33 100644
--- a/lib/Text/Tradition/Parser/CollateX.pm
+++ b/lib/Text/Tradition/Parser/CollateX.pm
@@ -2,7 +2,7 @@ package Text::Tradition::Parser::CollateX;
 
 use strict;
 use warnings;
-use Text::Tradition::Parser::GraphML qw/ graphml_parse populate_witness_path /;
+use Text::Tradition::Parser::GraphML qw/ graphml_parse /;
 
 =head1 NAME
 
@@ -163,9 +163,6 @@ sub parse {
         }
     }
     
-    # Set the $witness->path arrays for each wit.
-    populate_witness_path( $tradition );
-
     # Rank the readings.
     $collation->calculate_ranks() if $collation->linear;
 }
diff --git a/lib/Text/Tradition/Parser/GraphML.pm b/lib/Text/Tradition/Parser/GraphML.pm
index 9fe2911..fbc0d3a 100644
--- a/lib/Text/Tradition/Parser/GraphML.pm
+++ b/lib/Text/Tradition/Parser/GraphML.pm
@@ -8,7 +8,7 @@ use vars qw/ @EXPORT_OK $xpc /;
 use XML::LibXML;
 use XML::LibXML::XPathContext;
 
-@EXPORT_OK = qw/ graphml_parse populate_witness_path /;
+@EXPORT_OK = qw/ graphml_parse /;
 
 =head1 NAME
 
@@ -130,28 +130,6 @@ sub graphml_parse {
     return $graph_hash;
 }
 
-=head2 B<populate_witness_path>( $tradition )
-
-Given a tradition, populate the 'path' and 'uncorrected_path' attributes
-of all of its witnesses.  Useful for all formats based on the graph itself.
-
-=cut
-
-sub populate_witness_path {
-    my ( $tradition, $ante_corr ) = @_;
-    my $c = $tradition->collation;
-    print STDERR "Walking paths for witnesses\n";
-    foreach my $wit ( $tradition->witnesses ) {
-    	my @path = $c->reading_sequence( $c->start, $c->end, $wit->sigil );
-    	$wit->path( \@path );
-    	if( $ante_corr->{$wit->sigil} ) {
-    		# Get the uncorrected path too
-    		my @uc = $c->reading_sequence( $c->start, $c->end, 
-    			$wit->sigil . $c->ac_label, $wit->sigil );
-    		$wit->uncorrected_path( \@uc );
-    	}
-    }
-}
 
 sub _lookup_node_data {
     my( $xmlnode, $key ) = @_;
diff --git a/lib/Text/Tradition/Parser/Self.pm b/lib/Text/Tradition/Parser/Self.pm
index a34c9f5..7bc2c6d 100644
--- a/lib/Text/Tradition/Parser/Self.pm
+++ b/lib/Text/Tradition/Parser/Self.pm
@@ -2,7 +2,7 @@ package Text::Tradition::Parser::Self;
 
 use strict;
 use warnings;
-use Text::Tradition::Parser::GraphML qw/ graphml_parse populate_witness_path /;
+use Text::Tradition::Parser::GraphML qw/ graphml_parse /;
 
 =head1 NAME
 
@@ -171,7 +171,6 @@ sub parse {
         
     # Now add the edges.
     print STDERR "Adding graph edges\n";
-    my $has_ante_corr = {};
     foreach my $e ( @{$graph_data->{'edges'}} ) {
         my $from = $e->{$SOURCE_KEY};
         my $to = $e->{$TARGET_KEY};
@@ -190,7 +189,7 @@ sub parse {
 				$tradition->add_witness( sigil => $wit );
 				$witnesses{$wit} = 1;
 			}
-			$has_ante_corr->{$wit} = 1 if $extra;
+			$tradition->witness( $wit )->is_layered( 1 ) if $extra;
         } elsif( $class eq 'relationship' ) {
         	# We need the metadata about the relationship.
         	my $opts = { 'type' => $e->{$RELATIONSHIP_KEY} };
@@ -222,9 +221,6 @@ sub parse {
             }
         }
     }
-    
-    # Set the $witness->path arrays for each wit.
-    populate_witness_path( $tradition, $has_ante_corr );
 }
 
 1;
diff --git a/lib/Text/Tradition/Parser/TEI.pm b/lib/Text/Tradition/Parser/TEI.pm
index db18da6..6eb5541 100644
--- a/lib/Text/Tradition/Parser/TEI.pm
+++ b/lib/Text/Tradition/Parser/TEI.pm
@@ -158,7 +158,6 @@ sub parse {
             $c->add_path( $source, $rdg, $sig );
             $source = $rdg;
         }
-        $tradition->witness( $sig )->path( \@real_sequence );
         # See if we need to make an a.c. version of the witness.
         if( exists $app_ac->{$sig} ) {
             my @uncorrected;
@@ -180,7 +179,7 @@ sub parse {
                 $source = $rdg;
             }
             print STDERR "Adding a.c. version for witness $sig\n";
-            $tradition->witness( $sig )->uncorrected_path( \@uncorrected );
+            $tradition->witness( $sig )->is_layered( 1 );
         }
     }
     
diff --git a/lib/Text/Tradition/Witness.pm b/lib/Text/Tradition/Witness.pm
index 5010ffe..dc38c05 100644
--- a/lib/Text/Tradition/Witness.pm
+++ b/lib/Text/Tradition/Witness.pm
@@ -65,15 +65,10 @@ Accessor method for the witness identifier.
 
 Accessor method for the general witness description.
 
-=head2 path
+=head2 is_layered
 
-An array of Text::Tradition::Collation::Reading objects which, taken in
-sequence, represent the text.
-
-=head2 uncorrected_path
-
-An array of Text::Tradition::Collation::Reading objects which, taken in
-sequence, represent the text before any scribal corrections were made.
+Boolean method to note whether the witness has layers (e.g. pre-correction 
+readings) in the collation.
 
 =begin testing
 
@@ -118,18 +113,24 @@ has 'source' => (
 	predicate => 'has_source',
 	);
 
-# Path.	 This is an array of Reading nodes that should mirror the
-# text above.
+# Path.	 This is an array of Reading nodes that can be saved during
+# initialization, but should be cleared before saving in a DB.
 has 'path' => (
 	is => 'rw',
 	isa => 'ArrayRef[Text::Tradition::Collation::Reading]',
 	predicate => 'has_path',
+	clearer => 'clear_path',
 	);		   
 
 has 'uncorrected_path' => (
 	is => 'rw',
 	isa => 'ArrayRef[Text::Tradition::Collation::Reading]',
-	predicate => 'has_ante_corr',
+	clearer => 'clear_uncorrected_path',
+	);
+	
+has 'is_layered' => (
+	is => 'rw',
+	isa => 'Bool',
 	);
 
 # Manuscript name or similar
@@ -144,6 +145,14 @@ has 'other_info' => (
 	isa => 'Str',
 	);
 	
+# If we set an uncorrected path, ever, remember that we did so.
+around 'uncorrected_path' => sub {
+	my $orig = shift;
+	my $self = shift;
+	
+	$self->is_layered( 1 );
+	$self->$orig( @_ );
+};
 
 sub BUILD {
 	my $self = shift;
@@ -202,6 +211,7 @@ around text => sub {
 	$self->$orig( @_ );
 };
 
+
 no Moose;
 __PACKAGE__->meta->make_immutable;
 
diff --git a/script/save_to_db.pl b/script/save_to_db.pl
index 45ebb17..497c723 100644
--- a/script/save_to_db.pl
+++ b/script/save_to_db.pl
@@ -36,24 +36,27 @@ if( $dir ) {
 	opendir( DIR, $dir ) or die "Could not open directory $dir";
 	while( readdir DIR ) {
 		next unless /\.xml$/;
-		my $stemmafile = "$dir/" . $stemma_map{$_};	
+		print STDERR "Looking at $_\n";
 		my $tradition = Text::Tradition->new( 
 			'input' => 'Self',
 			'file' => "$dir/$_",
 			'linear' => 1,
 			);
-		open my $stemma_fh, '<', $stemmafile or die "Could not read stemma file $stemmafile";		
-		my $stemma = Text::Tradition::Stemma->new(
-			'collation' => $tradition->collation,
-			'dot' => $stemma_fh,
-			);
+		my $stemma;
+		if( exists $stemma_map{$_} ) {
+			my $stemmafile = "$dir/" . $stemma_map{$_};	
+			open my $stemma_fh, '<', $stemmafile or die "Could not read stemma file $stemmafile";		
+			$stemma = Text::Tradition::Stemma->new(
+				'collation' => $tradition->collation,
+				'dot' => $stemma_fh,
+				);
+		}
 			
 		my $scope = $kdb->new_scope;
 		my $tid = $kdb->store( $tradition );
-		my $sid = $kdb->store( $stemma );
-		
-		print STDERR "Stored tradition and stemma for " . $tradition->name 
-			. ", got $tid / $sid as the ref\n";
+		my $sid = $kdb->store( $stemma ) if $stemma;
+		print STDERR "Stored tradition for " . $tradition->name . " at $tid\n";
+		print STDERR "\tand stemma at $sid\n" if $stemma;
 	}
 }