package Text::Tradition::Collation;
-use Graph::Easy;
+use Encode qw( decode_utf8 );
+use File::Temp;
+use Graph;
use IPC::Run qw( run binary );
-use Module::Load;
+use Text::CSV_XS;
use Text::Tradition::Collation::Reading;
+use XML::LibXML;
use Moose;
-has 'graph' => (
+has 'sequence' => (
is => 'ro',
- isa => 'Graph::Easy',
+ isa => 'Graph',
+ default => sub { Graph->new() },
handles => {
- add_reading => 'add_node',
- del_reading => 'del_node',
- add_path => 'add_edge',
- del_path => 'del_edge',
- reading => 'node',
- path => 'edge',
- readings => 'nodes',
- paths => 'edges',
+ paths => 'edges',
},
- default => sub { Graph::Easy->new( undirected => 0 ) },
);
-
+
+has 'relations' => (
+ is => 'ro',
+ isa => 'Graph',
+ default => sub { Graph->new( undirected => 1 ) },
+ handles => {
+ relationships => 'edges',
+ },
+ );
has 'tradition' => (
- is => 'rw',
+ is => 'ro',
isa => 'Text::Tradition',
+ weak_ref => 1,
);
-has 'svg' => (
- is => 'ro',
+has 'readings' => (
+ isa => 'HashRef[Text::Tradition::Collation::Reading]',
+ traits => ['Hash'],
+ handles => {
+ reading => 'get',
+ _add_reading => 'set',
+ del_reading => 'delete',
+ has_reading => 'exists',
+ readings => 'values',
+ },
+ default => sub { {} },
+ );
+
+has 'wit_list_separator' => (
+ is => 'rw',
isa => 'Str',
- writer => '_save_svg',
- predicate => 'has_svg',
+ default => ', ',
);
-has 'graphviz' => (
- is => 'ro',
+has 'baselabel' => (
+ is => 'rw',
isa => 'Str',
- writer => '_save_graphviz',
- predicate => 'has_graphviz',
+ default => 'base text',
);
-has 'graphml' => (
- is => 'ro',
- isa => 'XML::LibXML::Document',
- writer => '_save_graphml',
- predicate => 'has_graphml',
+has 'linear' => (
+ is => 'rw',
+ isa => 'Bool',
+ default => 1,
);
+has 'ac_label' => (
+ is => 'rw',
+ isa => 'Str',
+ default => ' (a.c.)',
+ );
+
+has 'start' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_start',
+ weak_ref => 1,
+ );
+
+has 'end' => (
+ is => 'ro',
+ isa => 'Text::Tradition::Collation::Reading',
+ writer => '_set_end',
+ weak_ref => 1,
+ );
+
# The collation can be created two ways:
# 1. Collate a set of witnesses (with CollateX I guess) and process
# the results as in 2.
# come through option 1.
sub BUILD {
- my( $self, $args ) = @_;
+ my $self = shift;
+ $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) );
+ $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) );
+}
- # Call the appropriate parser on the given data
- my @formats = grep { /^(GraphML|CSV|CTE|TEI)$/ } keys( %$args );
- my $format = shift( @formats );
- unless( $format ) {
- warn "No data given to create a graph; will initialize an empty one";
- }
- if( $format && $format =~ /^(CSV|CTE)$/ && !exists $args->{'base'} ) {
- warn "Cannot make a graph from $format without a base text";
- return;
- }
+### Reading construct/destruct functions
- # Initialize our graph object.
- $self->graph->use_class('node', 'Text::Tradition::Collation::Reading');
- $self->graph->set_attribute( 'node', 'shape', 'ellipse' );
- # Starting point for all texts
- my $last_node = $self->add_reading( '#START#' );
-
- # Now do the parsing.
- my @sigla;
- if( $format ) {
- my @parseargs;
- if( $format =~ /^(CSV|CTE)$/ ) {
- @parseargs = ( 'base' => $args->{'base'},
- 'data' => $args->{$format},
- 'format' => $format );
- $format = 'BaseText';
- } else {
- @parseargs = ( $args->{ $format } );
+sub add_reading {
+ my( $self, $reading ) = @_;
+ unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+ my %args = %$reading;
+ $reading = Text::Tradition::Collation::Reading->new(
+ 'collation' => $self,
+ %args );
}
- my $mod = "Text::Tradition::Parser::$format";
- load( $mod );
- # TODO parse needs to return witness IDs
- @sigla = $mod->can('parse')->( $self, @parseargs );
- }
+ # First check to see if a reading with this ID exists.
+ if( $self->reading( $reading->id ) ) {
+ warn "Collation already has a reading with id " . $reading->id;
+ return undef;
+ }
+ $self->_add_reading( $reading->id => $reading );
+ # Once the reading has been added, put it in both graphs.
+ $self->sequence->add_vertex( $reading->id );
+ $self->relations->add_vertex( $reading->id );
+ return $reading;
+};
+
+around del_reading => sub {
+ my $orig = shift;
+ my $self = shift;
+ my $arg = shift;
+
+ if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
+ $arg = $arg->id;
+ }
+
+ # Remove the reading from the graphs.
+ $self->sequence->delete_vertex( $arg );
+ $self->relations->delete_vertex( $arg );
+
+ # Carry on.
+ $self->$orig( $arg );
+};
+
+# merge_readings( $main, $to_be_deleted );
+
+sub merge_readings {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $kept, $deleted ) = $self->_stringify_args( @_ );
+
+ # The kept reading should inherit the paths and the relationships
+ # of the deleted reading.
+ foreach my $path ( $self->sequence->edges_at( $deleted ) ) {
+ my @vector = ( $kept );
+ push( @vector, $path->[1] ) if $path->[0] eq $deleted;
+ unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
+ my %wits = %{$self->sequence->get_edge_attributes( @$path )};
+ $self->sequence->add_edge( @vector );
+ my $fwits = $self->sequence->get_edge_attributes( @vector );
+ @wits{keys %$fwits} = values %$fwits;
+ $self->sequence->set_edge_attributes( @vector, \%wits );
+ }
+ foreach my $rel ( $self->relations->edges_at( $deleted ) ) {
+ my @vector = ( $kept );
+ push( @vector, $rel->[0] eq $deleted ? $rel->[1] : $rel->[0] );
+ # Is there a relationship here already? If so, keep it.
+ # TODO Warn about conflicting relationships
+ next if $self->relations->has_edge( @vector );
+ # If not, adopt the relationship that would be deleted.
+ $self->relations->add_edge( @vector );
+ my $attr = $self->relations->get_edge_attributes( @$rel );
+ $self->relations->set_edge_attributes( @vector, $attr );
+ }
+
+ # Do the deletion deed.
+ $self->del_reading( $deleted );
+}
+
+
+# Helper function for manipulating the graph.
+sub _stringify_args {
+ my( $self, $first, $second, $arg ) = @_;
+ $first = $first->id
+ if ref( $first ) eq 'Text::Tradition::Collation::Reading';
+ $second = $second->id
+ if ref( $second ) eq 'Text::Tradition::Collation::Reading';
+ return( $first, $second, $arg );
+}
+
+### Path logic
+
+sub add_path {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+
+ # Connect the readings
+ $self->sequence->add_edge( $source, $target );
+ # Note the witness in question
+ $self->sequence->set_edge_attribute( $source, $target, $wit, 1 );
+};
+
+sub del_path {
+ my $self = shift;
+
+ # We only need the IDs for adding paths to the graph, not the reading
+ # objects themselves.
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
- # Do we need to initialize the witnesses?
- unless( $args->{'have_witnesses'} ) {
- # initialize Witness objects for all our witnesses
- my @witnesses;
- foreach my $sigil ( @sigla ) {
- push( @witnesses, Text::Tradition::Witness->new( 'sigil' => $sigil ) );
+ if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) {
+ $self->sequence->del_edge_attribute( $source, $target, $wit );
}
- $self->tradition->witnesses( \@witnesses );
+ unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) {
+ $self->sequence->delete_edge( $source, $target );
+ }
+}
+
+
+# Extra graph-alike utility
+sub has_path {
+ my $self = shift;
+ my( $source, $target, $wit ) = $self->_stringify_args( @_ );
+ return undef unless $self->sequence->has_edge( $source, $target );
+ return $self->sequence->has_edge_attribute( $source, $target, $wit );
+}
+
+### Relationship logic
+
+=head2 add_relationship( $reading1, $reading2, $definition )
+
+Adds the specified relationship between the two readings. A relationship
+is transitive (i.e. undirected), and must have the following attributes
+specified in the hashref $definition:
+
+=over 4
+
+=item * type - Can be one of spelling, orthographic, grammatical, meaning, repetition, transposition. The first three are only valid relationships between readings that occur at the same point in the text.
+
+=item * non_correctable - (Optional) True if the reading would not have been corrected independently.
+
+=item * non_independent - (Optional) True if the variant is unlikely to have occurred independently in unrelated witnesses.
+
+=item * global - (Optional) A meta-attribute, to set the same relationship between readings with the same text whenever they occur in the same place.
+
+=back
+
+=cut
+
+# Wouldn't it be lovely if edges could be objects, and all this type checking
+# and attribute management could be done via Moose?
+
+sub add_relationship {
+ my $self = shift;
+ my( $source, $target, $options ) = $self->_stringify_args( @_ );
+
+ # Check the options
+ if( !defined $options->{'type'} ||
+ $options->{'type'} !~ /^(spelling|orthographic|grammatical|meaning|repetition|transposition)$/i ) {
+ my $t = $options->{'type'} ? $options->{'type'} : '';
+ return( undef, "Invalid or missing type" . $options->{'type'} );
+ }
+ if( $options->{'type'} =~ /^(spelling|orthographic|grammatical|meaning)$/ ) {
+ $options->{'colocated'} = 1;
+ }
+
+ # Make sure there is not another relationship between these two
+ # readings already
+ if( $self->relations->has_edge( $source, $target ) ) {
+ return ( undef, "Relationship already exists between these readings" );
+ }
+ if( $options->{'colocated'} && !$self->relationship_valid( $source, $target ) ) {
+ return ( undef, 'Relationship creates witness loop' );
}
+
+ my @vector = ( $source, $target );
+ $self->relations->add_edge( @vector );
+ $self->relations->set_edge_attributes( @vector, $options );
+
+ # TODO Handle global relationship setting
+
+ return( 1, @vector );
}
-# Wrappers around some methods
+sub relationship_valid {
+ my( $self, $source, $target ) = @_;
+ # Check that linking the source and target in a relationship won't lead
+ # to a path loop for any witness. First make a lookup table of all the
+ # readings related to either the source or the target.
+ my @proposed_related = ( $source, $target );
+ push( @proposed_related, $source->related_readings( 'colocated' ) );
+ push( @proposed_related, $target->related_readings( 'colocated' ) );
+ my %pr_ids;
+ map { $pr_ids{ $_->id } = 1 } @proposed_related;
-sub merge_readings {
- my $self = shift;
- my $first_node = shift;
- my $second_node = shift;
- $first_node->merge_from( $second_node );
- unshift( @_, $first_node, $second_node );
- return $self->graph->merge_nodes( @_ );
+ # None of these proposed related readings should have a neighbor that
+ # is also in proposed_related.
+ foreach my $pr ( keys %pr_ids ) {
+ foreach my $neighbor( $self->sequence->neighbors( $pr ) ) {
+ return 0 if exists $pr_ids{$neighbor};
+ }
+ }
+
+ return 1;
+}
+
+sub related_readings {
+ my( $self, $reading, $colocated ) = @_;
+ my $return_object;
+ if( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) {
+ $reading = $reading->id;
+ $return_object = 1;
+# print STDERR "Returning related objects\n";
+# } else {
+# print STDERR "Returning related object names\n";
+ }
+ my @related = $self->relations->all_reachable( $reading );
+ if( $colocated ) {
+ my @colo = grep { $self->relations->has_edge_attribute( $reading, $_, 'colocated' ) } @related;
+ @related = @colo;
+ }
+ return $return_object ? map { $self->reading( $_ ) } @related : @related;
}
=head2 Output method(s)
print $graph->as_svg( $recalculate );
Returns an SVG string that represents the graph. Uses GraphViz to do
-this, because Graph::Easy doesn't cope well with long graphs. Unless
+this, because Graph::Easy doesn\'t cope well with long graphs. Unless
$recalculate is passed (and is a true value), the method will return a
cached copy of the SVG after the first call to the method.
=cut
sub as_svg {
- my( $self, $recalc ) = @_;
- return $self->svg if $self->has_svg;
-
- $self->_save_graphviz( $self->graph->as_graphviz() )
- unless( $self->has_graphviz && !$recalc );
-
+ my( $self ) = @_;
+
my @cmd = qw/dot -Tsvg/;
my( $svg, $err );
- my $in = $self->graphviz;
- run( \@cmd, \$in, ">", binary(), \$svg );
- $self->{'svg'} = $svg;
+ my $dotfile = File::Temp->new();
+ ## TODO REMOVE
+ # $dotfile->unlink_on_destroy(0);
+ binmode $dotfile, ':utf8';
+ print $dotfile $self->as_dot();
+ push( @cmd, $dotfile->filename );
+ run( \@cmd, ">", binary(), \$svg );
+ $svg = decode_utf8( $svg );
return $svg;
}
+=item B<as_dot>
+
+print $graph->as_dot( $view, $recalculate );
+
+Returns a string that is the collation graph expressed in dot
+(i.e. GraphViz) format. The 'view' argument determines what kind of
+graph is produced.
+ * 'path': a graph of witness paths through the collation (DEFAULT)
+ * 'relationship': a graph of how collation readings relate to
+ each other
+
+=cut
+
+sub as_dot {
+ my( $self, $view ) = @_;
+ $view = 'sequence' unless $view;
+ # TODO consider making some of these things configurable
+ my $graph_name = $self->tradition->name;
+ $graph_name =~ s/[^\w\s]//g;
+ $graph_name = join( '_', split( /\s+/, $graph_name ) );
+ my $dot = sprintf( "digraph %s {\n", $graph_name );
+ $dot .= "\tedge [ arrowhead=open ];\n";
+ $dot .= "\tgraph [ rankdir=LR ];\n";
+ $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n",
+ 11, "white", "filled", "ellipse" );
+
+ foreach my $reading ( $self->readings ) {
+ # Need not output nodes without separate labels
+ next if $reading->id eq $reading->text;
+ $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $reading->text );
+ }
+
+ # TODO do something sensible for relationships
+
+ my @edges = $self->paths;
+ foreach my $edge ( @edges ) {
+ my %variables = ( 'color' => '#000000',
+ 'fontcolor' => '#000000',
+ 'label' => join( ', ', $self->path_witnesses( $edge ) ),
+ );
+ my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables );
+ $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n",
+ $edge->[0], $edge->[1], $varopts );
+ }
+ $dot .= "}\n";
+ return $dot;
+}
+
+sub path_witnesses {
+ my( $self, @edge ) = @_;
+ # If edge is an arrayref, cope.
+ if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
+ my $e = shift @edge;
+ @edge = @$e;
+ }
+ my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
+ return sort @wits;
+}
+
=item B<as_graphml>
print $graph->as_graphml( $recalculate )
=cut
sub as_graphml {
- my( $self, $recalc ) = @_;
- return $self->graphml if $self->has_graphml;
+ my( $self ) = @_;
# Some namespaces
my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns';
my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance';
my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
- 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
+ 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
# Create the document and root node
my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
$root->setNamespace( $xsi_ns, 'xsi', 0 );
$root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema );
+ # Add the data keys for the graph
+ my %graph_data_keys;
+ my $gdi = 0;
+ my @graph_attributes = qw/ wit_list_separator baselabel linear ac_label /;
+ foreach my $datum ( @graph_attributes ) {
+ $graph_data_keys{$datum} = 'dg'.$gdi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $key eq 'linear' ? 'boolean' : 'string' );
+ $key->setAttribute( 'for', 'graph' );
+ $key->setAttribute( 'id', $graph_data_keys{$datum} );
+ }
+
# Add the data keys for nodes
- my @node_data = ( 'name', 'token', 'identical', 'position' );
- foreach my $ndi ( 0 .. $#node_data ) {
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $node_data[$ndi] );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'node' );
- $key->setAttribute( 'id', 'd'.$ndi );
+ my %node_data_keys;
+ my $ndi = 0;
+ my %node_data = (
+ id => 'string',
+ reading => 'string',
+ rank => 'string',
+ is_start => 'boolean',
+ is_end => 'boolean',
+ is_lacuna => 'boolean',
+ );
+ foreach my $datum ( keys %node_data ) {
+ $node_data_keys{$datum} = 'dn'.$ndi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $node_data{$datum} );
+ $key->setAttribute( 'for', 'node' );
+ $key->setAttribute( 'id', $node_data_keys{$datum} );
}
- # Add the data keys for edges
- my %wit_hash;
- my $wit_ctr = 0;
- foreach my $wit ( $self->getWitnessList ) {
- my $wit_key = 'w' . $wit_ctr++;
- $wit_hash{$wit} = $wit_key;
- my $key = $root->addNewChild( $graphml_ns, 'key' );
- $key->setAttribute( 'attr.name', $wit );
- $key->setAttribute( 'attr.type', 'string' );
- $key->setAttribute( 'for', 'edge' );
- $key->setAttribute( 'id', $wit_key );
+ # Add the data keys for edges, i.e. witnesses
+ my $edi = 0;
+ my %edge_data_keys;
+ my %edge_data = (
+ class => 'string', # Path or relationship?
+ witness => 'string', # ID/label for a path
+ relationship => 'string', # ID/label for a relationship
+ extra => 'boolean', # Path key
+ colocated => 'boolean', # Relationship key
+ non_correctable => 'boolean', # Relationship key
+ non_independent => 'boolean', # Relationship key
+ );
+ foreach my $datum ( keys %edge_data ) {
+ $edge_data_keys{$datum} = 'de'.$edi++;
+ my $key = $root->addNewChild( $graphml_ns, 'key' );
+ $key->setAttribute( 'attr.name', $datum );
+ $key->setAttribute( 'attr.type', $edge_data{$datum} );
+ $key->setAttribute( 'for', 'edge' );
+ $key->setAttribute( 'id', $edge_data_keys{$datum} );
}
- # Add the graph, its nodes, and its edges
+ # Add the collation graph itself
my $graph = $root->addNewChild( $graphml_ns, 'graph' );
$graph->setAttribute( 'edgedefault', 'directed' );
- $graph->setAttribute( 'id', 'g0' ); # TODO make this meaningful
+ $graph->setAttribute( 'id', $self->tradition->name );
$graph->setAttribute( 'parse.edgeids', 'canonical' );
- $graph->setAttribute( 'parse.edges', $self->edges() );
+ $graph->setAttribute( 'parse.edges', scalar($self->paths) );
$graph->setAttribute( 'parse.nodeids', 'canonical' );
- $graph->setAttribute( 'parse.nodes', $self->nodes() );
+ $graph->setAttribute( 'parse.nodes', scalar($self->readings) );
$graph->setAttribute( 'parse.order', 'nodesfirst' );
+
+ # Collation attribute data
+ foreach my $datum ( @graph_attributes ) {
+ _add_graphml_data( $graph, $graph_data_keys{$datum}, $self->$datum );
+ }
my $node_ctr = 0;
my %node_hash;
- foreach my $n ( $self->readings ) {
- my %this_node_data = ();
- foreach my $ndi ( 0 .. $#node_data ) {
- my $value;
- $this_node_data{'d'.$ndi} = $n->name if $node_data[$ndi] eq 'name';
- $this_node_data{'d'.$ndi} = $n->label
- if $node_data[$ndi] eq 'token';
- $this_node_data{'d'.$ndi} = $n->primary->name if $n->has_primary;
- $this_node_data{'d'.$ndi} =
- $self->{'positions'}->node_position( $n )
- if $node_data[$ndi] eq 'position';
- }
- my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
- my $node_xmlid = 'n' . $node_ctr++;
- $node_hash{ $n->name } = $node_xmlid;
- $node_el->setAttribute( 'id', $node_xmlid );
-
- foreach my $dk ( keys %this_node_data ) {
- my $d_el = $node_el->addNewChild( $graphml_ns, 'data' );
- $d_el->setAttribute( 'key', $dk );
- $d_el->appendTextChild( $this_node_data{$dk} );
+ # Add our readings to the graph
+ foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) {
+ my $node_el = $graph->addNewChild( $graphml_ns, 'node' );
+ my $node_xmlid = 'n' . $node_ctr++;
+ $node_hash{ $n->id } = $node_xmlid;
+ $node_el->setAttribute( 'id', $node_xmlid );
+ _add_graphml_data( $node_el, $node_data_keys{'id'}, $n->id );
+ _add_graphml_data( $node_el, $node_data_keys{'reading'}, $n->text );
+ _add_graphml_data( $node_el, $node_data_keys{'rank'}, $n->rank )
+ if $n->has_rank;
+ }
+
+ # Add the path edges
+ my $edge_ctr = 0;
+ foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) {
+ # We add an edge in the graphml for every witness in $e.
+ foreach my $wit ( $self->path_witnesses( $e ) ) {
+ my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+ $node_hash{ $e->[0] },
+ $node_hash{ $e->[1] } );
+ my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+ # Add the edge class
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'path' );
+
+ # It's a witness path, so add the witness
+ my $base = $wit;
+ my $key = $edge_data_keys{'witness'};
+ # Is this an ante-corr witness?
+ my $aclabel = $self->ac_label;
+ if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
+ # Keep the base witness
+ $base = $1;
+ # ...and record that this is an 'extra' reading path
+ _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
+ }
+ _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
+ }
}
+
+ # Add the relationship edges
+ foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->relationships ) {
+ my( $id, $from, $to ) = ( 'e'.$edge_ctr++,
+ $node_hash{ $e->[0] },
+ $node_hash{ $e->[1] } );
+ my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
+ $edge_el->setAttribute( 'source', $from );
+ $edge_el->setAttribute( 'target', $to );
+ $edge_el->setAttribute( 'id', $id );
+ # Add the edge class
+ _add_graphml_data( $edge_el, $edge_data_keys{'class'}, 'relationship' );
+
+ my $data = $self->relations->get_edge_attributes( @$e );
+ # It's a relationship, so save the relationship data
+ _add_graphml_data( $edge_el, $edge_data_keys{'relationship'}, $data->{type} );
+ _add_graphml_data( $edge_el, $edge_data_keys{'colocated'}, $data->{colocated} );
+ if( exists $data->{non_correctable} ) {
+ _add_graphml_data( $edge_el, $edge_data_keys{'non_correctable'},
+ $data->{non_correctable} );
+ }
+ if( exists $data->{non_independent} ) {
+ _add_graphml_data( $edge_el, $edge_data_keys{'non_independent'},
+ $data->{non_independent} );
+ }
+ }
+
+ # Save and return the thing
+ my $result = decode_utf8( $graphml->toString(1) );
+ return $result;
+}
+
+sub _add_graphml_data {
+ my( $el, $key, $value ) = @_;
+ return unless defined $value;
+ my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
+ $data_el->setAttribute( 'key', $key );
+ $data_el->appendText( $value );
+}
+
+=item B<as_csv>
+
+print $graph->as_csv( $recalculate )
+
+Returns a CSV alignment table representation of the collation graph, one
+row per witness (or witness uncorrected.) Unless $recalculate is passed
+(and is a true value), the method will return a cached copy of the CSV
+after the first call to the method.
+
+=cut
+
+sub as_csv {
+ my( $self ) = @_;
+ my $table = $self->make_alignment_table;
+ my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } );
+ my @result;
+ foreach my $row ( @$table ) {
+ $csv->combine( @$row );
+ push( @result, decode_utf8( $csv->string ) );
+ }
+ return join( "\n", @result );
+}
+
+# Make an alignment table - $noderefs controls whether the objects
+# in the table are the nodes or simply their readings.
+
+sub make_alignment_table {
+ my( $self, $noderefs, $include ) = @_;
+ unless( $self->linear ) {
+ warn "Need a linear graph in order to make an alignment table";
+ return;
+ }
+ my $table;
+ my @all_pos = ( 1 .. $self->end->rank - 1 );
+ foreach my $wit ( $self->tradition->witnesses ) {
+ # print STDERR "Making witness row(s) for " . $wit->sigil . "\n";
+ 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->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 );
+ }
}
- foreach my $e ( $self->edges() ) {
- my( $name, $from, $to ) = ( $e->name,
- $node_hash{ $e->from()->name() },
- $node_hash{ $e->to()->name() } );
- my $edge_el = $graph->addNewChild( $graphml_ns, 'edge' );
- $edge_el->setAttribute( 'source', $from );
- $edge_el->setAttribute( 'target', $to );
- $edge_el->setAttribute( 'id', $name );
- # TODO Got to add the witnesses
+ if( $include ) {
+ my $winnowed = [];
+ # Winnow out the rows for any witness not included.
+ foreach my $row ( @$table ) {
+ next unless $include->{$row->[0]};
+ push( @$winnowed, $row );
+ }
+ $table = $winnowed;
}
- # Return the thing
- $self->_save_graphml( $graphml );
- return $graphml;
+ # Return a table where the witnesses read in columns rather than rows.
+ my $turned = _turn_table( $table );
+ # TODO We should really go through and delete empty rows.
+ return $turned;
+}
+
+sub _make_witness_row {
+ my( $path, $positions, $noderefs ) = @_;
+ my %char_hash;
+ map { $char_hash{$_} = undef } @$positions;
+ foreach my $rdg ( @$path ) {
+ my $rtext = $rdg->text;
+ $rtext = '#LACUNA#' if $rdg->is_lacuna;
+ # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank;
+ $char_hash{$rdg->rank} = $noderefs ? $rdg : $rtext;
+ }
+ my @row = map { $char_hash{$_} } @$positions;
+ # Fill in lacuna markers for undef spots in the row
+ my $last_el = shift @row;
+ my @filled_row = ( $last_el );
+ foreach my $el ( @row ) {
+ # If we are using node reference, make the lacuna node appear many times
+ # in the table. If not, use the lacuna tag.
+ if( $last_el && _el_is_lacuna( $last_el ) && !defined $el ) {
+ $el = $noderefs ? $last_el : '#LACUNA#';
+ }
+ push( @filled_row, $el );
+ $last_el = $el;
+ }
+ return @filled_row;
+}
+
+# Tiny utility function to say if a table element is a lacuna
+sub _el_is_lacuna {
+ my $el = shift;
+ return 1 if $el eq '#LACUNA#';
+ return 1 if ref( $el ) eq 'Text::Tradition::Collation::Reading'
+ && $el->is_lacuna;
+ return 0;
+}
+
+# Helper to turn the witnesses along columns rather than rows. Assumes
+# equal-sized rows.
+sub _turn_table {
+ my( $table ) = @_;
+ my $result = [];
+ return $result unless scalar @$table;
+ my $nrows = scalar @{$table->[0]};
+ foreach my $idx ( 0 .. $nrows - 1 ) {
+ foreach my $wit ( 0 .. $#{$table} ) {
+ $result->[$idx]->[$wit] = $table->[$wit]->[$idx];
+ }
+ }
+ return $result;
}
=back
+=head2 Navigation methods
+
+=over
+
=item B<start>
my $beginning = $collation->start();
Returns the beginning of the collation, a meta-reading with label '#START#'.
+=item B<end>
+
+my $end = $collation->end();
+
+Returns the end of the collation, a meta-reading with label '#END#'.
+
+
+=item B<reading_sequence>
+
+my @readings = $graph->reading_sequence( $first, $last, $path[, $alt_path] );
+
+Returns the ordered list of readings, starting with $first and ending
+with $last, along the given witness path. If no path is specified,
+assume that the path is that of the base text (if any.)
+
=cut
-sub start {
- # Return the beginning node of the graph.
- my $self = shift;
- my( $new_start ) = @_;
- if( $new_start ) {
- $self->del_reading( '#START#' );
- $self->graph->rename_node( $new_start, '#START#' );
+# TODO Think about returning some lazy-eval iterator.
+
+sub reading_sequence {
+ my( $self, $start, $end, $witness, $backup ) = @_;
+
+ $witness = $self->baselabel unless $witness;
+ my @readings = ( $start );
+ my %seen;
+ my $n = $start;
+ while( $n && $n->id ne $end->id ) {
+ if( exists( $seen{$n->id} ) ) {
+ warn "Detected loop at " . $n->id;
+ last;
+ }
+ $seen{$n->id} = 1;
+
+ my $next = $self->next_reading( $n, $witness, $backup );
+ $DB::single = 1 if $next->id eq $end->id;
+ unless( $next ) {
+ warn "Did not find any path for $witness from reading " . $n->id;
+ last;
+ }
+ push( @readings, $next );
+ $n = $next;
}
- return $self->reading('#START#');
+ # Check that the last reading is our end reading.
+ my $last = $readings[$#readings];
+ warn "Last reading found from " . $start->text .
+ " for witness $witness is not the end!"
+ unless $last->id eq $end->id;
+
+ return @readings;
}
-=item B<next_word>
+=item B<next_reading>
-my $next_node = $graph->next_word( $node, $path );
+my $next_reading = $graph->next_reading( $reading, $witpath );
-Returns the node that follows the given node along the given witness
-path. TODO These are badly named.
+Returns the reading that follows the given reading along the given witness
+path.
=cut
-sub next_word {
- # Return the successor via the corresponding edge.
+sub next_reading {
+ # Return the successor via the corresponding path.
my $self = shift;
- return $self->_find_linked_word( 'next', @_ );
+ my $answer = $self->_find_linked_reading( 'next', @_ );
+ return $self->reading( $answer );
}
-=item B<prior_word>
+=item B<prior_reading>
-my $prior_node = $graph->prior_word( $node, $path );
+my $prior_reading = $graph->prior_reading( $reading, $witpath );
-Returns the node that precedes the given node along the given witness
-path. TODO These are badly named.
+Returns the reading that precedes the given reading along the given witness
+path.
=cut
-sub prior_word {
- # Return the predecessor via the corresponding edge.
+sub prior_reading {
+ # Return the predecessor via the corresponding path.
my $self = shift;
- return $self->_find_linked_word( 'prior', @_ );
+ my $answer = $self->_find_linked_reading( 'prior', @_ );
+ return $self->reading( $answer );
}
-sub _find_linked_word {
- my( $self, $direction, $node, $edge ) = @_;
- $edge = 'base text' unless $edge;
- my @linked_edges = $direction eq 'next'
- ? $node->outgoing() : $node->incoming();
- return undef unless scalar( @linked_edges );
+sub _find_linked_reading {
+ my( $self, $direction, $node, $path, $alt_path ) = @_;
+ my @linked_paths = $direction eq 'next'
+ ? $self->sequence->edges_from( $node )
+ : $self->sequence->edges_to( $node );
+ return undef unless scalar( @linked_paths );
- # We have to find the linked edge that contains all of the
- # witnesses supplied in $edge.
- my @edge_wits = split( /, /, $edge );
- foreach my $le ( @linked_edges ) {
- my @le_wits = split( /, /, $le->name() );
- if( _is_within( \@edge_wits, \@le_wits ) ) {
- # This is the right edge.
- return $direction eq 'next' ? $le->to() : $le->from();
- }
+ # We have to find the linked path that contains all of the
+ # witnesses supplied in $path.
+ my( @path_wits, @alt_path_wits );
+ @path_wits = sort( $self->witnesses_of_label( $path ) ) if $path;
+ @alt_path_wits = sort( $self->witnesses_of_label( $alt_path ) ) if $alt_path;
+ my $base_le;
+ my $alt_le;
+ foreach my $le ( @linked_paths ) {
+ if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
+ $base_le = $le;
+ }
+ my @le_wits = $self->path_witnesses( $le );
+ if( _is_within( \@path_wits, \@le_wits ) ) {
+ # This is the right path.
+ return $direction eq 'next' ? $le->[1] : $le->[0];
+ } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
+ $alt_le = $le;
+ }
}
+ # Got this far? Return the alternate path if it exists.
+ return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
+ if $alt_le;
+
+ # Got this far? Return the base path if it exists.
+ return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
+ if $base_le;
+
+ # Got this far? We have no appropriate path.
warn "Could not find $direction node from " . $node->label
- . " along edge $edge";
+ . " along path $path";
return undef;
}
-sub create_witnesses {
- # TODO Given a new collation, make a bunch of Witness objects.
+# Some set logic.
+sub _is_within {
+ my( $set1, $set2 ) = @_;
+ my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
+ foreach my $el ( @$set1 ) {
+ $ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
+ }
+ return $ret;
+}
+
- return [];
+## INITIALIZATION METHODS - for use by parsers
+
+# 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 ) = @_;
+ foreach my $wit ( $self->tradition->witnesses ) {
+ print STDERR "Making path for " . $wit->sigil . "\n";
+ $self->make_witness_path( $wit );
+ }
}
+sub make_witness_path {
+ my( $self, $wit ) = @_;
+ my @chain = @{$wit->path};
+ my $sig = $wit->sigil;
+ foreach my $idx ( 0 .. $#chain-1 ) {
+ $self->add_path( $chain[$idx], $chain[$idx+1], $sig );
+ }
+ if( $wit->is_layered ) {
+ @chain = @{$wit->uncorrected_path};
+ foreach my $idx( 0 .. $#chain-1 ) {
+ my $source = $chain[$idx];
+ my $target = $chain[$idx+1];
+ $self->add_path( $source, $target, $sig.$self->ac_label )
+ unless $self->has_path( $source, $target, $sig );
+ }
+ }
+ $wit->clear_path;
+ $wit->clear_uncorrected_path;
+}
+
+sub calculate_ranks {
+ my $self = shift;
+ # 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 );
+ }
+ }
+
+ # Add the edges.
+ foreach my $r ( $self->readings ) {
+ foreach my $n ( $self->sequence->successors( $r->id ) ) {
+ my( $tfrom, $tto ) = ( $rel_containers{$r->id},
+ $rel_containers{$n} );
+ $topo_graph->add_edge( $tfrom, $tto );
+ }
+ }
+
+ # Now do the rankings, starting with the start node.
+ my $topo_start = $rel_containers{$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 );
+ }
+ # 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}} );
+ } else {
+ $DB::single = 1;
+ die "No rank calculated for node " . $r->id
+ . " - do you have a cycle in the graph?";
+ }
+ }
+}
+
+sub _assign_rank {
+ my( $graph, $node_ranks, @current_nodes ) = @_;
+ # Look at each of the children of @current_nodes. If all the child's
+ # parents have a rank, assign it the highest rank + 1 and add it to
+ # @next_nodes. Otherwise skip it; we will return when the highest-ranked
+ # parent gets a rank.
+ my @next_nodes;
+ foreach my $c ( @current_nodes ) {
+ warn "Current reading $c has no rank!"
+ unless exists $node_ranks->{$c};
+ # print STDERR "Looking at child of node $c, rank "
+ # . $node_ranks->{$c} . "\n";
+ foreach my $child ( $graph->successors( $c ) ) {
+ next if exists $node_ranks->{$child};
+ my $highest_rank = -1;
+ my $skip = 0;
+ foreach my $parent ( $graph->predecessors( $child ) ) {
+ if( exists $node_ranks->{$parent} ) {
+ $highest_rank = $node_ranks->{$parent}
+ if $highest_rank <= $node_ranks->{$parent};
+ } else {
+ $skip = 1;
+ last;
+ }
+ }
+ next if $skip;
+ my $c_rank = $highest_rank + 1;
+ # print STDERR "Assigning rank $c_rank to node $child \n";
+ $node_ranks->{$child} = $c_rank;
+ push( @next_nodes, $child );
+ }
+ }
+ return @next_nodes;
+}
+
+# Another method to make up for rough collation methods. If the same reading
+# appears multiple times at the same rank, collapse the nodes.
+sub flatten_ranks {
+ my $self = shift;
+ my %unique_rank_rdg;
+ 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";
+ $self->merge_readings( $unique_rank_rdg{$key}, $rdg );
+ } else {
+ $unique_rank_rdg{$key} = $rdg;
+ }
+ }
+}
+
+
+## Utility functions
+
+# Return the string that joins together a list of witnesses for
+# display on a single path.
+sub witnesses_of_label {
+ my( $self, $label ) = @_;
+ my $regex = $self->wit_list_separator;
+ my @answer = split( /\Q$regex\E/, $label );
+ return @answer;
+}
+
no Moose;
__PACKAGE__->meta->make_immutable;
+
+=head1 BUGS / TODO
+
+=over
+
+=item * Rationalize edge classes
+
+=item * Port the internal graph from Graph::Easy to Graph
+
+=back
projects / scpubgit/stemmatology.git / blobdiff