use Text::Tradition::Collation::Reading;
use Text::Tradition::Collation::RelationshipStore;
use Text::Tradition::Error;
+use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx );
use XML::LibXML;
use XML::LibXML::XPathContext;
use Moose;
related_readings => 'related_readings',
get_relationship => 'get_relationship',
del_relationship => 'del_relationship',
+ equivalence => 'equivalence',
+ equivalence_graph => 'equivalence_graph',
},
writer => '_set_relations',
);
my( $self, $reading ) = @_;
unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
my %args = %$reading;
+ if( $self->tradition->has_language && !exists $args{'language'} ) {
+ $args{'language'} = $self->tradition->language;
+ }
$reading = Text::Tradition::Collation::Reading->new(
'collation' => $self,
%args );
$self->_graphcalc_done(0);
# Connect the readings
- $self->sequence->add_edge( $source, $target );
+ unless( $self->sequence->has_edge( $source, $target ) ) {
+ $self->sequence->add_edge( $source, $target );
+ $self->relations->add_equivalence_edge( $source, $target );
+ }
# Note the witness in question
$self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
-};
+}
sub del_path {
my $self = shift;
}
unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
$self->sequence->delete_edge( $source, $target );
+ $self->relations->delete_equivalence_edge( $source, $target );
}
}
sub add_relationship {
my $self = shift;
my( $source, $target, $opts ) = $self->_stringify_args( @_ );
- my( @vectors ) = $self->relations->add_relationship( $source,
- $self->reading( $source ), $target, $self->reading( $target ), $opts );
+ my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
$self->_graphcalc_done(0);
return @vectors;
}
# Output substitute start/end readings if necessary
if( $startrank ) {
- $dot .= "\t\"#SUBSTART#\" [ label=\"...\" ];\n";
+ $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n";
}
if( $endrank ) {
- $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n";
+ $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n";
}
if( $STRAIGHTENHACK ) {
## HACK part 1
- my $startlabel = $startrank ? 'SUBSTART' : 'START';
- $dot .= "\tsubgraph { rank=same \"#$startlabel#\" \"#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
$label = "-$label" if $reading->join_prior;
$label =~ s/\"/\\\"/g;
$rattrs->{'label'} = $label;
+ $rattrs->{'id'} = $reading->id;
$rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
$dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
}
my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
my $variables = { %edge_attrs, 'label' => $witstr };
my $varopts = _dot_attr_string( $variables );
- $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;";
+ $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;";
}
foreach my $node ( keys %subend ) {
my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) );
my $variables = { %edge_attrs, 'label' => $witstr };
my $varopts = _dot_attr_string( $variables );
- $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;";
+ $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;";
}
# HACK part 2
if( $STRAIGHTENHACK ) {
- my $endlabel = $endrank ? 'SUBEND' : 'END';
- $dot .= "\t\"#$endlabel#\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
+ my $endlabel = $endrank ? '__SUBEND__' : '__END__';
+ $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n";
}
$dot .= "}\n";
is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" );
is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" );
+# Now add a stemma, write to GraphML, and parse again.
+my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" );
+is( $tradition->stemmata, 1, "Tradition now has the stemma" );
+$graphml = $c->as_graphml;
+like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" );
+
=end testing
=cut
# The readings need to be ranked for this to work.
$start = $self->start unless $start->has_rank;
$end = $self->end unless $end->has_rank;
+ my $rankoffset = 0;
+ unless( $start eq $self->start ) {
+ $rankoffset = $start->rank - 1;
+ }
my %use_readings;
# Some namespaces
'Str' => 'string',
'Int' => 'int',
'Bool' => 'boolean',
+ 'ReadingID' => 'string',
'RelationshipType' => 'string',
'RelationshipScope' => 'string',
);
next unless $save_types{$attr->type_constraint->name};
$graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
}
+ # Extra custom key for the tradition stemma(ta)
+ $graph_attributes{'stemmata'} = 'string';
foreach my $datum ( sort keys %graph_attributes ) {
$graph_data_keys{$datum} = 'dg'.$gdi++;
next unless $save_types{$attr->type_constraint->name};
$reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
}
+ # Extra custom key for the reading morphology
+ $reading_attributes{'lexemes'} = 'string';
+
my %node_data_keys;
my $ndi = 0;
foreach my $datum ( sort keys %reading_attributes ) {
$key->setAttribute( 'id', $edge_data_keys{$datum} );
}
- # Add the collation graph itself
+ # Add the collation graph itself. First, sanitize the name to a valid XML ID.
+ my $xmlidname = $self->tradition->name;
+ $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g;
+ if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) {
+ $xmlidname = '_'.$xmlidname;
+ }
my $sgraph = $root->addNewChild( $graphml_ns, 'graph' );
$sgraph->setAttribute( 'edgedefault', 'directed' );
- $sgraph->setAttribute( 'id', $self->tradition->name );
+ $sgraph->setAttribute( 'id', $xmlidname );
$sgraph->setAttribute( 'parse.edgeids', 'canonical' );
- $sgraph->setAttribute( 'parse.edges', scalar($self->paths) );
+ $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
$sgraph->setAttribute( 'parse.nodeids', 'canonical' );
- $sgraph->setAttribute( 'parse.nodes', scalar($self->readings) );
+ $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
$sgraph->setAttribute( 'parse.order', 'nodesfirst' );
- # Collation attribute data
+ # Tradition/collation attribute data
foreach my $datum ( keys %graph_attributes ) {
my $value;
if( $datum eq 'version' ) {
- $value = '3.1';
+ $value = '3.2';
+ } elsif( $datum eq 'stemmata' ) {
+ my @stemstrs;
+ map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
+ $self->tradition->stemmata;
+ $value = join( "\n", @stemstrs );
} elsif( $gattr_from{$datum} eq 'Tradition' ) {
$value = $self->tradition->$datum;
} else {
$node_el->setAttribute( 'id', $node_xmlid );
foreach my $d ( keys %reading_attributes ) {
my $nval = $n->$d;
+ # Custom serialization
+ if( $d eq 'lexemes' ) {
+ # If nval is a true value, we have lexemes so we need to
+ # serialize them. Otherwise set nval to undef so that the
+ # key is excluded from this reading.
+ $nval = $nval ? $n->_serialize_lexemes : undef;
+ }
+ if( $rankoffset && $d eq 'rank' && $n ne $self->start ) {
+ # Adjust the ranks within the subgraph.
+ $nval = $n eq $self->end ? $end->rank - $rankoffset + 1
+ : $nval - $rankoffset;
+ }
_add_graphml_data( $node_el, $node_data_keys{$d}, $nval )
if defined $nval;
}
# We add an edge in the graphml for every witness in $e.
next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} );
my @edge_wits = sort $self->path_witnesses( $e );
- $e->[0] = $self->start unless $use_readings{$e->[0]};
- $e->[1] = $self->end unless $use_readings{$e->[1]};
+ $e->[0] = $self->start->id unless $use_readings{$e->[0]};
+ $e->[1] = $self->end->id unless $use_readings{$e->[1]};
+ # Skip any path from start to end; that witness is not in the subgraph.
+ next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id );
foreach my $wit ( @edge_wits ) {
my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
$node_hash{ $e->[0] },
}
}
+ # Report the actual number of nodes and edges that went in
+ $sgraph->setAttribute( 'parse.edges', $edge_ctr );
+ $sgraph->setAttribute( 'parse.nodes', $node_ctr );
+
# Add the relationship graph to the XML
map { delete $edge_data_keys{$_} } @path_attributes;
$self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
my $pathtext = '';
my $last;
foreach my $r ( @path ) {
- if( $r->join_prior || !$last || $last->join_next ) {
- $pathtext .= $r->text;
- } else {
- $pathtext .= ' ' . $r->text;
- }
+ unless ( $r->join_prior || !$last || $last->join_next ) {
+ $pathtext .= ' ';
+ }
+ $pathtext .= $r->text;
$last = $r;
}
return $pathtext;
my $self = shift;
# Save the existing ranks, in case we need to invalidate the cached SVG.
my %existing_ranks;
- # Walk a version of the graph where every node linked by a relationship
- # edge is fundamentally the same node, and do a topological ranking on
- # the nodes in this graph.
- my $topo_graph = Graph->new();
- my %rel_containers;
- my $rel_ctr = 0;
- # Add the nodes
- foreach my $r ( $self->readings ) {
- next if exists $rel_containers{$r->id};
- my @rels = $r->related_readings( 'colocated' );
- if( @rels ) {
- # Make a relationship container.
- push( @rels, $r );
- my $rn = 'rel_container_' . $rel_ctr++;
- $topo_graph->add_vertex( $rn );
- foreach( @rels ) {
- $rel_containers{$_->id} = $rn;
- }
- } else {
- # Add a new node to mirror the old node.
- $rel_containers{$r->id} = $r->id;
- $topo_graph->add_vertex( $r->id );
- }
- }
+ map { $existing_ranks{$_} = $_->rank } $self->readings;
- # Add the edges.
- foreach my $r ( $self->readings ) {
- $existing_ranks{$r} = $r->rank;
- foreach my $n ( $self->sequence->successors( $r->id ) ) {
- my( $tfrom, $tto ) = ( $rel_containers{$r->id},
- $rel_containers{$n} );
- # $DB::single = 1 unless $tfrom && $tto;
- $topo_graph->add_edge( $tfrom, $tto );
- }
- }
-
- # Now do the rankings, starting with the start node.
- my $topo_start = $rel_containers{$self->start->id};
+ # Do the rankings based on the relationship equivalence graph, starting
+ # with the start node.
+ my $topo_start = $self->equivalence( $self->start->id );
my $node_ranks = { $topo_start => 0 };
my @curr_origin = ( $topo_start );
# A little iterative function.
while( @curr_origin ) {
- @curr_origin = _assign_rank( $topo_graph, $node_ranks, @curr_origin );
+ @curr_origin = _assign_rank( $self->equivalence_graph,
+ $node_ranks, @curr_origin );
}
# Transfer our rankings from the topological graph to the real one.
foreach my $r ( $self->readings ) {
- if( defined $node_ranks->{$rel_containers{$r->id}} ) {
- $r->rank( $node_ranks->{$rel_containers{$r->id}} );
+ if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
+ $r->rank( $node_ranks->{$self->equivalence( $r->id )} );
} else {
# Die. Find the last rank we calculated.
- my @all_defined = sort { ( $node_ranks->{$rel_containers{$a->id}}||-1 )
- <=> ( $node_ranks->{$rel_containers{$b->id}}||-1 ) }
+ my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 )
+ <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) }
$self->readings;
my $last = pop @all_defined;
throw( "Ranks not calculated after $last - do you have a cycle in the graph?" );
=head2 common_predecessor( $reading_a, $reading_b )
Find the last reading that occurs in sequence before both the given readings.
+At the very least this should be $self->start.
=head2 common_successor( $reading_a, $reading_b )
Find the first reading that occurs in sequence after both the given readings.
+At the very least this should be $self->end.
=begin testing
is( $c->common_predecessor( 'n24', 'n23' )->id,
'n20', "Found correct common predecessor" );
is( $c->common_successor( 'n24', 'n23' )->id,
- '#END#', "Found correct common successor" );
+ '__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', 'n10' )->id,
- '#END#', "Found correct common successor for readings on same path" );
+ '__END__', "Found correct common successor for readings on same path" );
=end testing
return $self->_common_in_path( $r1, $r2, 'successors' );
}
+
+# TODO think about how to do this without ranks...
sub _common_in_path {
my( $self, $r1, $r2, $dir ) = @_;
- my $iter = $r1->rank > $r2->rank ? $r1->rank : $r2->rank;
- $iter = $self->end->rank - $iter if $dir eq 'successors';
+ my $iter = $self->end->rank;
my @candidates;
- my @last_checked = ( $r1, $r2 );
+ my @last_r1 = ( $r1 );
+ my @last_r2 = ( $r2 );
+ # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
my %all_seen;
+ # print STDERR "Finding common $dir for $r1, $r2\n";
while( !@candidates ) {
- my @new_lc;
- foreach my $lc ( @last_checked ) {
+ last unless $iter--; # Avoid looping infinitely
+ # Iterate separately down the graph from r1 and r2
+ my( @new_lc1, @new_lc2 );
+ foreach my $lc ( @last_r1 ) {
+ foreach my $p ( $lc->$dir ) {
+ if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
+ # print STDERR "Path candidate $p from $lc\n";
+ push( @candidates, $p );
+ } elsif( !$all_seen{$p->id} ) {
+ $all_seen{$p->id} = 'r1';
+ push( @new_lc1, $p );
+ }
+ }
+ }
+ foreach my $lc ( @last_r2 ) {
foreach my $p ( $lc->$dir ) {
- if( $all_seen{$p->id} ) {
+ if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
+ # print STDERR "Path candidate $p from $lc\n";
push( @candidates, $p );
- } else {
- $all_seen{$p->id} = 1;
- push( @new_lc, $p );
+ } elsif( !$all_seen{$p->id} ) {
+ $all_seen{$p->id} = 'r2';
+ push( @new_lc2, $p );
}
}
}
- @last_checked = @new_lc;
+ @last_r1 = @new_lc1;
+ @last_r2 = @new_lc2;
}
my @answer = sort { $a->rank <=> $b->rank } @candidates;
return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer );
projects / scpubgit/stemmatology.git / blobdiff