X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=ac750ea3793a939acf36b7fe2a0dd85fb8c795f0;hb=82fa4d574ae69634563ea89a5fd973f49b2d435c;hp=8344288f7118986a3f286bf671eef291b46e3804;hpb=4e483aa5bae680511b62d9c77984f732ae699066;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm index 8344288..ac750ea 100644 --- a/lib/Text/Tradition/Collation.pm +++ b/lib/Text/Tradition/Collation.pm @@ -5,7 +5,7 @@ use File::Temp; use File::Which; use Graph; use IPC::Run qw( run binary ); -use Text::CSV_XS; +use Text::CSV; use Text::Tradition::Collation::Reading; use Text::Tradition::Collation::RelationshipStore; use Text::Tradition::Error; @@ -338,15 +338,15 @@ $c->flatten_ranks(); ok( $c->reading( 'n21p0' ), "New reading exists" ); is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" ); -# Combine n3 and n4 +# Combine n3 and n4 ( with his ) $c->merge_readings( 'n3', 'n4', 1 ); ok( !$c->reading('n4'), "Reading n4 is gone" ); is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" ); -# Collapse n25 and n26 -$c->merge_readings( 'n25', 'n26' ); -ok( !$c->reading('n26'), "Reading n26 is gone" ); -is( $c->reading('n25')->text, 'rood', "Reading n25 has an unchanged word" ); +# Collapse n9 and n10 ( rood / root ) +$c->merge_readings( 'n9', 'n10' ); +ok( !$c->reading('n10'), "Reading n10 is gone" ); +is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" ); # Combine n21 and n21p0 my $remaining = $c->reading('n21'); @@ -594,6 +594,7 @@ sub as_dot { my $color_common = $opts->{'color_common'} if $opts; my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank && $self->end->rank > 100; + $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs # Check the arguments if( $startrank ) { @@ -638,7 +639,8 @@ sub as_dot { } if( $STRAIGHTENHACK ) { ## HACK part 1 - $dot .= "\tsubgraph { rank=same \"#START#\" \"#SILENT#\" }\n"; + my $startlabel = $startrank ? 'SUBSTART' : 'START'; + $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#SILENT#\" }\n"; $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];" } my %used; # Keep track of the readings that actually appear in the graph @@ -719,7 +721,8 @@ sub as_dot { } # HACK part 2 if( $STRAIGHTENHACK ) { - $dot .= "\t\"#END#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; + my $endlabel = $endrank ? 'SUBEND' : 'END'; + $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; } $dot .= "}\n"; @@ -780,26 +783,55 @@ sub path_witnesses { return @wits; } +# Helper function. Make a display label for the given witnesses, showing a.c. +# witnesses only where the main witness is not also in the list. sub _path_display_label { my $self = shift; - my @wits = sort @_; + my %wits; + map { $wits{$_} = 1 } @_; + + # If an a.c. wit is listed, remove it if the main wit is also listed. + # Otherwise keep it for explicit listing. + my $aclabel = $self->ac_label; + my @disp_ac; + foreach my $w ( sort keys %wits ) { + if( $w =~ /^(.*)\Q$aclabel\E$/ ) { + if( exists $wits{$1} ) { + delete $wits{$w}; + } else { + push( @disp_ac, $w ); + } + } + } + + # See if we are in a majority situation. my $maj = scalar( $self->tradition->witnesses ) * 0.6; - if( scalar @wits > $maj ) { - # TODO break out a.c. wits - return 'majority'; + if( scalar keys %wits > $maj ) { + unshift( @disp_ac, 'majority' ); + return join( ', ', @disp_ac ); } else { - return join( ', ', @wits ); + return join( ', ', sort keys %wits ); } } -=head2 witnesses_at_rank +=head2 readings_at_rank( $rank ) -Returns a list of witnesses that are not lacunose, for a given rank. +Returns a list of readings at a given rank, taken from the alignment table. =cut -sub witnesses_at_rank { +sub readings_at_rank { my( $self, $rank ) = @_; + my $table = $self->alignment_table; + # Table rank is real rank - 1. + my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}}; + my %readings; + foreach my $e ( @elements ) { + next unless ref( $e ) eq 'HASH'; + next unless exists $e->{'t'}; + $readings{$e->{'t'}->id} = $e->{'t'}; + } + return values %readings; } =head2 as_graphml @@ -864,61 +896,90 @@ sub as_graphml { $graphml->setDocumentElement( $root ); $root->setNamespace( $xsi_ns, 'xsi', 0 ); $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema ); + + # List of attribute types to save on our objects and their corresponding + # GraphML types + my %save_types = ( + 'Str' => 'string', + 'Int' => 'int', + 'Bool' => 'boolean', + 'RelationshipType' => 'string', + 'RelationshipScope' => 'string', + ); + + # List of attribute names *not* to save on our objects. + # We will also not save any attribute beginning with _. + my %skipsave; + map { $skipsave{$_} = 1 } qw/ cached_svg /; - # Add the data keys for the graph + # Add the data keys for the graph. Include an extra key 'version' for the + # GraphML output version. my %graph_data_keys; my $gdi = 0; - my @graph_attributes = qw/ version wit_list_separator baselabel linear ac_label /; - foreach my $datum ( @graph_attributes ) { + my %graph_attributes = ( 'version' => 'string' ); + # Graph attributes include those of Tradition and those of Collation. + my %gattr_from; + my $tmeta = $self->tradition->meta; + my $cmeta = $self->meta; + map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes; + map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes; + foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) { + next if $attr->name =~ /^_/; + next if $skipsave{$attr->name}; + next unless $save_types{$attr->type_constraint->name}; + $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; + } + + foreach my $datum ( sort keys %graph_attributes ) { $graph_data_keys{$datum} = 'dg'.$gdi++; my $key = $root->addNewChild( $graphml_ns, 'key' ); $key->setAttribute( 'attr.name', $datum ); - $key->setAttribute( 'attr.type', $datum eq 'linear' ? 'boolean' : 'string' ); + $key->setAttribute( 'attr.type', $graph_attributes{$datum} ); $key->setAttribute( 'for', 'graph' ); $key->setAttribute( 'id', $graph_data_keys{$datum} ); } - # Add the data keys for nodes + # Add the data keys for reading nodes + my %reading_attributes; + my $rmeta = Text::Tradition::Collation::Reading->meta; + foreach my $attr( $rmeta->get_all_attributes ) { + next if $attr->name =~ /^_/; + next if $skipsave{$attr->name}; + next unless $save_types{$attr->type_constraint->name}; + $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; + } my %node_data_keys; my $ndi = 0; - my %node_data = ( - id => 'string', - text => 'string', - rank => 'string', - is_start => 'boolean', - is_end => 'boolean', - is_lacuna => 'boolean', - is_common => 'boolean', - join_prior => 'boolean', - join_next => 'boolean', - ); - foreach my $datum ( keys %node_data ) { + foreach my $datum ( sort keys %reading_attributes ) { $node_data_keys{$datum} = 'dn'.$ndi++; my $key = $root->addNewChild( $graphml_ns, 'key' ); $key->setAttribute( 'attr.name', $datum ); - $key->setAttribute( 'attr.type', $node_data{$datum} ); + $key->setAttribute( 'attr.type', $reading_attributes{$datum} ); $key->setAttribute( 'for', 'node' ); $key->setAttribute( 'id', $node_data_keys{$datum} ); } - # Add the data keys for edges, i.e. witnesses + # Add the data keys for edges, that is, paths and relationships. Path + # data does not come from a Moose class so is here manually. my $edi = 0; my %edge_data_keys; - my %edge_data = ( - class => 'string', # Class, deprecated soon + my %edge_attributes = ( witness => 'string', # ID/label for a path - relationship => 'string', # ID/label for a relationship extra => 'boolean', # Path key - scope => 'string', # Relationship key - annotation => 'string', # Relationship key - non_correctable => 'boolean', # Relationship key - non_independent => 'boolean', # Relationship key ); - foreach my $datum ( keys %edge_data ) { + my @path_attributes = keys %edge_attributes; # track our manual additions + my $pmeta = Text::Tradition::Collation::Relationship->meta; + foreach my $attr( $pmeta->get_all_attributes ) { + next if $attr->name =~ /^_/; + next if $skipsave{$attr->name}; + next unless $save_types{$attr->type_constraint->name}; + $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; + } + foreach my $datum ( sort keys %edge_attributes ) { $edge_data_keys{$datum} = 'de'.$edi++; my $key = $root->addNewChild( $graphml_ns, 'key' ); $key->setAttribute( 'attr.name', $datum ); - $key->setAttribute( 'attr.type', $edge_data{$datum} ); + $key->setAttribute( 'attr.type', $edge_attributes{$datum} ); $key->setAttribute( 'for', 'edge' ); $key->setAttribute( 'id', $edge_data_keys{$datum} ); } @@ -934,8 +995,15 @@ sub as_graphml { $sgraph->setAttribute( 'parse.order', 'nodesfirst' ); # Collation attribute data - foreach my $datum ( @graph_attributes ) { - my $value = $datum eq 'version' ? '3.0' : $self->$datum; + foreach my $datum ( keys %graph_attributes ) { + my $value; + if( $datum eq 'version' ) { + $value = '3.1'; + } elsif( $gattr_from{$datum} eq 'Tradition' ) { + $value = $self->tradition->$datum; + } else { + $value = $self->$datum; + } _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value ); } @@ -948,7 +1016,7 @@ sub as_graphml { my $node_xmlid = 'n' . $node_ctr++; $node_hash{ $n->id } = $node_xmlid; $node_el->setAttribute( 'id', $node_xmlid ); - foreach my $d ( keys %node_data ) { + foreach my $d ( keys %reading_attributes ) { my $nval = $n->$d; _add_graphml_data( $node_el, $node_data_keys{$d}, $nval ) if defined $nval; @@ -980,11 +1048,11 @@ sub as_graphml { _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel ); } _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base ); - _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' ); } } # Add the relationship graph to the XML + map { delete $edge_data_keys{$_} } @path_attributes; $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, $node_data_keys{'id'}, \%edge_data_keys ); @@ -1011,7 +1079,7 @@ row per witness (or witness uncorrected.) sub as_csv { my( $self ) = @_; my $table = $self->alignment_table; - my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } ); + my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } ); my @result; # Make the header row $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} ); @@ -1257,7 +1325,7 @@ sub common_readings { return @common; } -=head2 path_text( $sigil, $mainsigil [, $start, $end ] ) +=head2 path_text( $sigil, [, $start, $end ] ) Returns the text of a witness (plus its backup, if we are using a layer) as stored in the collation. The text is returned as a string, where the @@ -1319,11 +1387,16 @@ sub make_witness_path { my( $self, $wit ) = @_; my @chain = @{$wit->path}; my $sig = $wit->sigil; + # Add start and end if necessary + unshift( @chain, $self->start ) unless $chain[0] eq $self->start; + push( @chain, $self->end ) unless $chain[-1] eq $self->end; foreach my $idx ( 0 .. $#chain-1 ) { $self->add_path( $chain[$idx], $chain[$idx+1], $sig ); } if( $wit->is_layered ) { @chain = @{$wit->uncorrected_path}; + unshift( @chain, $self->start ) unless $chain[0] eq $self->start; + push( @chain, $self->end ) unless $chain[-1] eq $self->end; foreach my $idx( 0 .. $#chain-1 ) { my $source = $chain[$idx]; my $target = $chain[$idx+1]; @@ -1358,7 +1431,7 @@ ok( $c->has_cached_table, "Alignment table was cached" ); is( $c->alignment_table, $table, "Cached table returned upon second call" ); $c->calculate_ranks; is( $c->alignment_table, $table, "Cached table retained with no rank change" ); -$c->add_relationship( 'n9', 'n23', { 'type' => 'spelling' } ); +$c->add_relationship( 'n24', 'n23', { 'type' => 'spelling' } ); isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" ); =end testing @@ -1494,18 +1567,23 @@ with the same text at the same rank, and merges any that are found. sub flatten_ranks { my $self = shift; my %unique_rank_rdg; + my $changed; foreach my $rdg ( $self->readings ) { next unless $rdg->has_rank; my $key = $rdg->rank . "||" . $rdg->text; if( exists $unique_rank_rdg{$key} ) { # Combine! # print STDERR "Combining readings at same rank: $key\n"; + $changed = 1; $self->merge_readings( $unique_rank_rdg{$key}, $rdg ); # TODO see if this now makes a common point. } else { $unique_rank_rdg{$key} = $rdg; } } + # If we merged readings, the ranks are still fine but the alignment + # table is wrong. Wipe it. + $self->wipe_table() if $changed; } @@ -1531,7 +1609,7 @@ my @common = $c->calculate_common_readings(); is( scalar @common, 8, "Found correct number of common readings" ); my @marked = sort $c->common_readings(); is( scalar @common, 8, "All common readings got marked as such" ); -my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /; +my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /; is_deeply( \@marked, \@expected, "Found correct list of common readings" ); =end testing @@ -1576,14 +1654,22 @@ original texts. sub text_from_paths { my $self = shift; foreach my $wit ( $self->tradition->witnesses ) { - my @text = split( /\s+/, - $self->reading_sequence( $self->start, $self->end, $wit->sigil ) ); + my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); + my @text; + foreach my $r ( @readings ) { + next if $r->is_meta; + push( @text, $r->text ); + } $wit->text( \@text ); if( $wit->is_layered ) { - my @uctext = split( /\s+/, - $self->reading_sequence( $self->start, $self->end, - $wit->sigil.$self->ac_label ) ); - $wit->text( \@uctext ); + my @ucrdgs = $self->reading_sequence( $self->start, $self->end, + $wit->sigil.$self->ac_label ); + my @uctext; + foreach my $r ( @ucrdgs ) { + next if $r->is_meta; + push( @uctext, $r->text ); + } + $wit->layertext( \@uctext ); } } } @@ -1610,14 +1696,14 @@ my $t = Text::Tradition->new( ); my $c = $t->collation; -is( $c->common_predecessor( 'n9', 'n23' )->id, +is( $c->common_predecessor( 'n24', 'n23' )->id, 'n20', "Found correct common predecessor" ); -is( $c->common_successor( 'n9', 'n23' )->id, +is( $c->common_successor( 'n24', 'n23' )->id, '#END#', "Found correct common successor" ); is( $c->common_predecessor( 'n19', 'n17' )->id, 'n16', "Found correct common predecessor for readings on same path" ); -is( $c->common_successor( 'n21', 'n26' )->id, +is( $c->common_successor( 'n21', 'n10' )->id, '#END#', "Found correct common successor for readings on same path" ); =end testing