From: Tara L Andrews <tla\@mit.edu>
Date: Tue, 20 Dec 2011 13:39:27 +0000 (+0100)
Subject: cope with some parsing niggles
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=a7fb313395e449d44e91da2bb6a217451cae57ec;p=scpubgit%2Fstemmatology.git

cope with some parsing niggles
---

diff --git a/META.yml b/META.yml
index 18a6c3b..64a5c0f 100644
--- a/META.yml
+++ b/META.yml
@@ -1,13 +1,14 @@
 ---
-abstract: ~
+abstract: 'a software model for a set of collated texts'
 author:
   - 'Tara L Andrews <aurum@cpan.org>'
 build_requires:
-  ExtUtils::MakeMaker: 6.42
+  ExtUtils::MakeMaker: 6.56
 configure_requires:
-  ExtUtils::MakeMaker: 6.42
+  ExtUtils::MakeMaker: 6.56
 distribution_type: module
-generated_by: 'Module::Install version 0.91'
+dynamic_config: 1
+generated_by: 'Module::Install version 1.00'
 license: perl
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -35,7 +36,7 @@ requires:
   Text::CSV_XS: 0
   XML::LibXML: 0
   XML::LibXML::XPathContext: 0
-  perl: 5.010
+  perl: 5.12.0
 resources:
   license: http://dev.perl.org/licenses/
-version: undef
+version: 0.1
diff --git a/lib/Text/Tradition/Parser/TEI.pm b/lib/Text/Tradition/Parser/TEI.pm
index a86adf7..db18da6 100644
--- a/lib/Text/Tradition/Parser/TEI.pm
+++ b/lib/Text/Tradition/Parser/TEI.pm
@@ -129,7 +129,7 @@ sub parse {
     map { $text->{$_->sigil} = [] } $tradition->witnesses;
 
     # Look for all word/seg node IDs and note their pre-existence.
-    my @attrs = $xpc->findnodes( "//$W|$SEG/attribute::xml:id" );
+    my @attrs = $xpc->findnodes( "//$W/attribute::xml:id" );
     _save_preexisting_nodeids( @attrs );
 
     # Count up how many apps we have.
@@ -147,7 +147,6 @@ sub parse {
     # Join them up.
     my $c = $tradition->collation;
     foreach my $sig ( keys %$text ) {
-        next if $sig eq 'base';  # Skip base text readings with no witnesses.
         # Determine the list of readings for 
         my $sequence = $text->{$sig};
         my @real_sequence = ( $c->start );
@@ -186,7 +185,7 @@ sub parse {
     }
     
     # Calculate the ranks for the nodes.
-    $tradition->collation->calculate_ranks();
+	$tradition->collation->calculate_ranks();
     
     # Now that we have ranks, see if we have distinct nodes with identical
     # text and identical rank that can be merged.
@@ -335,7 +334,7 @@ sub _return_rdg {
             # TODO handle p.c. and s.l. designations too
             $ac = $xn->getAttribute( 'type' ) && $xn->getAttribute( 'type' ) eq 'a.c.';
             my @rdg_wits = _get_sigla( $xn );
-            @rdg_wits = ( 'base' ) unless @rdg_wits;  # Allow for editorially-supplied readings
+            return unless @rdg_wits;  # Skip readings that appear in no witnesses
             my @words;
             foreach ( $xn->childNodes ) {
                 my @rdg_set = _get_readings( $tradition, $_, 1, $ac, @rdg_wits );
@@ -388,7 +387,8 @@ sub _return_rdg {
                     push( @{$text->{$w}}, $l );
                 }
             }
-        } elsif( $xn->nodeName eq 'witDetail' ) {
+        } elsif( $xn->nodeName eq 'witDetail' 
+        		 || $xn->nodeName eq 'note' ) {
             # Ignore these for now.
             return;
         } else {
@@ -433,6 +433,7 @@ sub _get_sigla {
     my @wits;
     if( ref( $rdg ) eq 'XML::LibXML::Element' ) {
         my $witstr = $rdg->getAttribute( 'wit' );
+        return () unless $witstr;
         $witstr =~ s/^\s+//;
         $witstr =~ s/\s+$//;
         @wits = split( /\s+/, $witstr );
diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index e241d56..28a9109 100644
--- a/lib/Text/Tradition/Stemma.pm
+++ b/lib/Text/Tradition/Stemma.pm
@@ -145,14 +145,25 @@ sub convert_characters {
     my %unique = ( '__UNDEF__' => 'X',
                    '#LACUNA#'  => '?',
                  );
+    my %count;
     my $ctr = 0;
     foreach my $word ( @$row ) {
         if( $word && !exists $unique{$word} ) {
             $unique{$word} = chr( 65 + $ctr );
             $ctr++;
         }
+        $count{$word}++ if $word;
     }
+    # Try to keep variants under 8 by lacunizing any singletons.
     if( scalar( keys %unique ) > 8 ) {
+		foreach my $word ( keys %count ) {
+			if( $count{$word} == 1 ) {
+				$unique{$word} = '?';
+			}
+		}
+    }
+    my %u = reverse %unique;
+    if( scalar( keys %u ) > 8 ) {
         warn "Have more than 8 variants on this location; phylip will break";
     }
     my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
diff --git a/script/make_tradition.pl b/script/make_tradition.pl
index f928c33..bb7cb33 100755
--- a/script/make_tradition.pl
+++ b/script/make_tradition.pl
@@ -11,8 +11,8 @@ binmode STDERR, ":utf8";
 binmode STDOUT, ":utf8";
 eval { no warnings; binmode $DB::OUT, ":utf8"; };
 
-my( $informat, $inbase, $outformat, $help, $linear, $name, $HACK ) 
-    = ( '', '', '', '', 1, 'Tradition', 0 );
+my( $informat, $inbase, $outformat, $help, $linear, $name, $HACK, $sep ) 
+    = ( '', '', '', '', 1, 'Tradition', 0, ',' );
 
 GetOptions( 'i|in=s'    => \$informat,
             'b|base=s'  => \$inbase,
@@ -20,6 +20,7 @@ GetOptions( 'i|in=s'    => \$informat,
             'l|linear!' => \$linear,
             'n|name'    => \$name,
             'h|help'    => \$help,
+            'sep=s'		=> \$sep,
             'hack'      => \$HACK,
     );
 
@@ -57,6 +58,7 @@ my %args = ( 'input' => $informat,
              'linear' => $linear );
 $args{'base'} = $inbase if $inbase;
 $args{'name'} = $name if $name;
+$args{'sep_char'} = $sep if $informat eq 'Tabular';
 ### Custom hacking for Stone
 if( $informat eq 'CollateText' ) {
     $args{'sigla'} = [ qw/ S M X V Z Bb B K W L / ];