X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?p=scpubgit%2Fstemmatology.git;a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=d3a8567cdcd80a3ebcae936b3807bcce26bd6db8;hp=00b48b7b21d6705dca542ffa826ac2548a28c978;hb=96ba0418c65f3450b419aea78db41bf697612b63;hpb=2626f7099a2e4f00962f6b33dd2ff66a7b41c5a1 diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm index 00b48b7..d3a8567 100644 --- a/lib/Text/Tradition/Collation.pm +++ b/lib/Text/Tradition/Collation.pm @@ -2,12 +2,16 @@ package Text::Tradition::Collation; use Encode qw( decode_utf8 ); 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; +use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx ); use XML::LibXML; +use XML::LibXML::XPathContext; use Moose; has 'sequence' => ( @@ -25,6 +29,10 @@ has 'relations' => ( handles => { relationships => 'relationships', related_readings => 'related_readings', + get_relationship => 'get_relationship', + del_relationship => 'del_relationship', + equivalence => 'equivalence', + equivalence_graph => 'equivalence_graph', }, writer => '_set_relations', ); @@ -32,6 +40,7 @@ has 'relations' => ( has 'tradition' => ( is => 'ro', isa => 'Text::Tradition', + writer => '_set_tradition', weak_ref => 1, ); @@ -66,18 +75,18 @@ has 'linear' => ( default => 1, ); -has 'collapse_punctuation' => ( - is => 'rw', - isa => 'Bool', - default => 1, - ); - has 'ac_label' => ( is => 'rw', isa => 'Str', default => ' (a.c.)', ); +has 'wordsep' => ( + is => 'rw', + isa => 'Str', + default => ' ', + ); + has 'start' => ( is => 'ro', isa => 'Text::Tradition::Collation::Reading', @@ -91,27 +100,184 @@ has 'end' => ( writer => '_set_end', weak_ref => 1, ); + +has 'cached_svg' => ( + is => 'rw', + isa => 'Str', + predicate => 'has_cached_svg', + clearer => 'wipe_svg', + ); + +has 'cached_table' => ( + is => 'rw', + isa => 'HashRef', + predicate => 'has_cached_table', + clearer => 'wipe_table', + ); + +has '_graphcalc_done' => ( + is => 'rw', + isa => 'Bool', + default => undef, + ); + +=head1 NAME + +Text::Tradition::Collation - a software model for a text collation + +=head1 SYNOPSIS + + use Text::Tradition; + my $t = Text::Tradition->new( + 'name' => 'this is a text', + 'input' => 'TEI', + 'file' => '/path/to/tei_parallel_seg_file.xml' ); + + my $c = $t->collation; + my @readings = $c->readings; + my @paths = $c->paths; + my @relationships = $c->relationships; + + my $svg_variant_graph = $t->collation->as_svg(); + +=head1 DESCRIPTION + +Text::Tradition is a library for representation and analysis of collated +texts, particularly medieval ones. The Collation is the central feature of +a Tradition, where the text, its sequence of readings, and its relationships +between readings are actually kept. + +=head1 CONSTRUCTOR + +=head2 new + +The constructor. Takes a hash or hashref of the following arguments: + +=over + +=item * tradition - The Text::Tradition object to which the collation +belongs. Required. + +=item * linear - Whether the collation should be linear; that is, whether +transposed readings should be treated as two linked readings rather than one, +and therefore whether the collation graph is acyclic. Defaults to true. + +=item * baselabel - The default label for the path taken by a base text +(if any). Defaults to 'base text'. + +=item * wit_list_separator - The string to join a list of witnesses for +purposes of making labels in display graphs. Defaults to ', '. + +=item * ac_label - The extra label to tack onto a witness sigil when +representing another layer of path for the given witness - that is, when +a text has more than one possible reading due to scribal corrections or +the like. Defaults to ' (a.c.)'. + +=item * wordsep - The string used to separate words in the original text. +Defaults to ' '. + +=back + +=head1 ACCESSORS + +=head2 tradition + +=head2 linear + +=head2 wit_list_separator + +=head2 baselabel + +=head2 ac_label + +=head2 wordsep + +Simple accessors for collation attributes. + +=head2 start + +The meta-reading at the start of every witness path. -# The collation can be created two ways: -# 1. Collate a set of witnesses (with CollateX I guess) and process -# the results as in 2. -# 2. Read a pre-prepared collation in one of a variety of formats, -# and make the graph from that. - -# The graph itself will (for now) be immutable, and the positions -# within the graph will also be immutable. We need to calculate those -# positions upon graph construction. The equivalences between graph -# nodes will be mutable, entirely determined by the user (or possibly -# by some semantic pre-processing provided by the user.) So the -# constructor should just make an empty equivalences object. The -# constructor will also need to make the witness objects, if we didn't -# come through option 1. +=head2 end + +The meta-reading at the end of every witness path. + +=head2 readings + +Returns all Reading objects in the graph. + +=head2 reading( $id ) + +Returns the Reading object corresponding to the given ID. + +=head2 add_reading( $reading_args ) + +Adds a new reading object to the collation. +See L for the available arguments. + +=head2 del_reading( $object_or_id ) + +Removes the given reading from the collation, implicitly removing its +paths and relationships. + +=head2 merge_readings( $main, $second, $concatenate, $with_str ) + +Merges the $second reading into the $main one. If $concatenate is true, then +the merged node will carry the text of both readings, concatenated with either +$with_str (if specified) or a sensible default (the empty string if the +appropriate 'join_*' flag is set on either reading, or else $self->wordsep.) + +The first two arguments may be either readings or reading IDs. + +=head2 has_reading( $id ) + +Predicate to see whether a given reading ID is in the graph. + +=head2 reading_witnesses( $object_or_id ) + +Returns a list of sigils whose witnesses contain the reading. + +=head2 paths + +Returns all reading paths within the document - that is, all edges in the +collation graph. Each path is an arrayref of [ $source, $target ] reading IDs. + +=head2 add_path( $source, $target, $sigil ) + +Links the given readings in the collation in sequence, under the given witness +sigil. The readings may be specified by object or ID. + +=head2 del_path( $source, $target, $sigil ) + +Links the given readings in the collation in sequence, under the given witness +sigil. The readings may be specified by object or ID. + +=head2 has_path( $source, $target ); + +Returns true if the two readings are linked in sequence in any witness. +The readings may be specified by object or ID. + +=head2 relationships + +Returns all Relationship objects in the collation. + +=head2 add_relationship( $reading, $other_reading, $options ) + +Adds a new relationship of the type given in $options between the two readings, +which may be specified by object or ID. Returns a value of ( $status, @vectors) +where $status is true on success, and @vectors is a list of relationship edges +that were ultimately added. +See L for the available options. + +=cut sub BUILD { my $self = shift; $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) ); - $self->_set_start( $self->add_reading( { 'collation' => $self, 'is_start' => 1 } ) ); - $self->_set_end( $self->add_reading( { 'collation' => $self, 'is_end' => 1 } ) ); + $self->_set_start( $self->add_reading( + { 'collation' => $self, 'is_start' => 1, 'init' => 1 } ) ); + $self->_set_end( $self->add_reading( + { 'collation' => $self, 'is_end' => 1, 'init' => 1 } ) ); } ### Reading construct/destruct functions @@ -120,15 +286,22 @@ sub add_reading { my( $self, $reading ) = @_; unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) { my %args = %$reading; + if( $args{'init'} ) { + # If we are initializing an empty collation, don't assume that we + # have set a tradition. + delete $args{'init'}; + } elsif( $self->tradition->has_language && !exists $args{'language'} ) { + $args{'language'} = $self->tradition->language; + } $reading = Text::Tradition::Collation::Reading->new( 'collation' => $self, %args ); } # 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; + throw( "Collation already has a reading with id " . $reading->id ); } + $self->_graphcalc_done(0); $self->_add_reading( $reading->id => $reading ); # Once the reading has been added, put it in both graphs. $self->sequence->add_vertex( $reading->id ); @@ -145,6 +318,8 @@ around del_reading => sub { $arg = $arg->id; } # Remove the reading from the graphs. + $self->_graphcalc_done(0); + $self->_clear_cache; # Explicitly clear caches to GC the reading $self->sequence->delete_vertex( $arg ); $self->relations->delete_reading( $arg ); @@ -152,15 +327,71 @@ around del_reading => sub { $self->$orig( $arg ); }; -# merge_readings( $main, $to_be_deleted ); +=begin testing + +use Text::Tradition; + +my $cxfile = 't/data/Collatex-16.xml'; +my $t = Text::Tradition->new( + 'name' => 'inline', + 'input' => 'CollateX', + 'file' => $cxfile, + ); +my $c = $t->collation; + +my $rno = scalar $c->readings; +# Split n21 for testing purposes +my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } ); +my $old_r = $c->reading( 'n21' ); +$old_r->alter_text( 'to' ); +$c->del_path( 'n20', 'n21', 'A' ); +$c->add_path( 'n20', 'n21p0', 'A' ); +$c->add_path( 'n21p0', 'n21', 'A' ); +$c->flatten_ranks(); +ok( $c->reading( 'n21p0' ), "New reading exists" ); +is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" ); + +# Combine n3 and n4 ( with his ) +$c->merge_readings( 'n3', 'n4', 1 ); +ok( !$c->reading('n4'), "Reading n4 is gone" ); +is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" ); + +# Collapse n9 and n10 ( rood / root ) +$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 = $c->reading('n21'); +$remaining ||= $c->reading('n22'); # one of these should still exist +$c->merge_readings( 'n21p0', $remaining, 1 ); +ok( !$c->reading('n21'), "Reading $remaining is gone" ); +is( $c->reading('n21p0')->text, 'unto', "Reading n21p0 merged correctly" ); + +=end testing + +=cut sub merge_readings { my $self = shift; + # Sanity check + my( $kept_obj, $del_obj, $combine, $combine_char ) = $self->_objectify_args( @_ ); + my $mergemeta = $kept_obj->is_meta; + throw( "Cannot merge meta and non-meta reading" ) + unless ( $mergemeta && $del_obj->is_meta ) + || ( !$mergemeta && !$del_obj->is_meta ); + if( $mergemeta ) { + throw( "Cannot merge with start or end node" ) + if( $kept_obj eq $self->start || $kept_obj eq $self->end + || $del_obj eq $self->start || $del_obj eq $self->end ); + } # We only need the IDs for adding paths to the graph, not the reading # objects themselves. - my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ ); - + my $kept = $kept_obj->id; + my $deleted = $del_obj->id; + $self->_graphcalc_done(0); + # The kept reading should inherit the paths and the relationships # of the deleted reading. foreach my $path ( $self->sequence->edges_at( $deleted ) ) { @@ -174,14 +405,16 @@ sub merge_readings { @wits{keys %$fwits} = values %$fwits; $self->sequence->set_edge_attributes( @vector, \%wits ); } - $self->relations->merge_readings( $kept, $deleted, $combine_char ); + $self->relations->merge_readings( $kept, $deleted, $combine ); # Do the deletion deed. - if( $combine_char ) { - my $kept_obj = $self->reading( $kept ); - my $new_text = join( $combine_char, $kept_obj->text, - $self->reading( $deleted )->text ); - $kept_obj->alter_text( $new_text ); + if( $combine ) { + my $joinstr = $combine_char; + unless( defined $joinstr ) { + $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior; + $joinstr = $self->wordsep unless defined $joinstr; + } + $kept_obj->alter_text( join( $joinstr, $kept_obj->text, $del_obj->text ) ); } $self->del_reading( $deleted ); } @@ -189,14 +422,23 @@ sub merge_readings { # Helper function for manipulating the graph. sub _stringify_args { - my( $self, $first, $second, $arg ) = @_; + my( $self, $first, $second, @args ) = @_; $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 ); + return( $first, $second, @args ); } +# Helper function for manipulating the graph. +sub _objectify_args { + my( $self, $first, $second, $arg ) = @_; + $first = $self->reading( $first ) + unless ref( $first ) eq 'Text::Tradition::Collation::Reading'; + $second = $self->reading( $second ) + unless ref( $second ) eq 'Text::Tradition::Collation::Reading'; + return( $first, $second, $arg ); +} ### Path logic sub add_path { @@ -206,11 +448,15 @@ sub add_path { # objects themselves. my( $source, $target, $wit ) = $self->_stringify_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; @@ -226,11 +472,13 @@ sub del_path { # objects themselves. my( $source, $target, $wit ) = $self->_stringify_args( @args ); + $self->_graphcalc_done(0); if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) { $self->sequence->delete_edge_attribute( $source, $target, $wit ); } unless( keys %{$self->sequence->get_edge_attributes( $source, $target )} ) { $self->sequence->delete_edge( $source, $target ); + $self->relations->delete_equivalence_edge( $source, $target ); } } @@ -243,27 +491,52 @@ sub has_path { return $self->sequence->has_edge_attribute( $source, $target, $wit ); } -=head2 add_relationship( $reading1, $reading2, $definition ) +=head2 clear_witness( @sigil_list ) -Adds the specified relationship between the two readings. A relationship -is transitive (i.e. undirected); the options for its definition may be found -in Text::Tradition::Collation::Relationship. +Clear the given witnesses out of the collation entirely, removing references +to them in paths, and removing readings that belong only to them. Should only +be called via $tradition->del_witness. =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 clear_witness { + my( $self, @sigils ) = @_; + + $self->_graphcalc_done(0); + # Clear the witness(es) out of the paths + foreach my $e ( $self->paths ) { + foreach my $sig ( @sigils ) { + $self->del_path( $e, $sig ); + } + } + + # Clear out the newly unused readings + foreach my $r ( $self->readings ) { + unless( $self->reading_witnesses( $r ) ) { + $self->del_reading( $r ); + } + } +} sub add_relationship { my $self = shift; my( $source, $target, $opts ) = $self->_stringify_args( @_ ); - my( $ret, @vectors ) = $self->relations->add_relationship( $source, - $self->reading( $source ), $target, $self->reading( $target ), $opts ); - # Force a full rank recalculation every time. Yuck. - $self->calculate_ranks() if $ret && $self->end->has_rank; - return( $ret, @vectors ); + my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts ); + $self->_graphcalc_done(0); + return @vectors; } +around qw/ get_relationship del_relationship / => sub { + my $orig = shift; + my $self = shift; + my @args = @_; + if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) { + @args = @{$_[0]}; + } + my( $source, $target ) = $self->_stringify_args( @args ); + $self->$orig( $source, $target ); +}; + =head2 reading_witnesses( $reading ) Return a list of sigils corresponding to the witnesses in which the reading appears. @@ -282,85 +555,74 @@ sub reading_witnesses { my $wits = $self->sequence->get_edge_attributes( @$e ); @all_witnesses{ keys %$wits } = 1; } + my $acstr = $self->ac_label; + foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) { + delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit}; + } return keys %all_witnesses; } -=head2 Output method(s) - -=over - -=item B +=head1 OUTPUT METHODS -print $collation->as_svg(); +=head2 as_svg( \%options ) Returns an SVG string that represents the graph, via as_dot and graphviz. +See as_dot for a list of options. Must have GraphViz (dot) installed to run. =cut sub as_svg { - my( $self ) = @_; - - my @cmd = qw/dot -Tsvg/; - my( $svg, $err ); - 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; + my( $self, $opts ) = @_; + throw( "Need GraphViz installed to output SVG" ) + unless File::Which::which( 'dot' ); + my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'}; + $self->calculate_ranks() + unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear ); + if( !$self->has_cached_svg || $opts->{'recalc'} || $want_subgraph ) { + my @cmd = qw/dot -Tsvg/; + my( $svg, $err ); + my $dotfile = File::Temp->new(); + ## USE FOR DEBUGGING + # $dotfile->unlink_on_destroy(0); + binmode $dotfile, ':utf8'; + print $dotfile $self->as_dot( $opts ); + push( @cmd, $dotfile->filename ); + run( \@cmd, ">", binary(), \$svg ); + $svg = decode_utf8( $svg ); + $self->cached_svg( $svg ) unless $want_subgraph; + return $svg; + } else { + return $self->cached_svg; + } } -=item B - -print $collation->svg_subgraph( $from, $to ) -Returns an SVG string that represents the portion of the graph given by the -specified range. The $from and $to variables refer to ranks within the graph. +=head2 as_dot( \%options ) -=cut +Returns a string that is the collation graph expressed in dot +(i.e. GraphViz) format. Options include: -sub svg_subgraph { - my( $self, $from, $to ) = @_; - - my $dot = $self->as_dot( $from, $to ); - unless( $dot ) { - warn "Could not output a graph with range $from - $to"; - return; - } - - my @cmd = qw/dot -Tsvg/; - my( $svg, $err ); - my $dotfile = File::Temp->new(); - ## TODO REMOVE - # $dotfile->unlink_on_destroy(0); - binmode $dotfile, ':utf8'; - print $dotfile $dot; - push( @cmd, $dotfile->filename ); - run( \@cmd, ">", binary(), \$svg ); - $svg = decode_utf8( $svg ); - return $svg; -} +=over 4 +=item * from -=item B +=item * to -print $collation->as_dot(); +=item * color_common -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 +=back =cut sub as_dot { - my( $self, $startrank, $endrank ) = @_; - + my( $self, $opts ) = @_; + my $startrank = $opts->{'from'} if $opts; + my $endrank = $opts->{'to'} if $opts; + 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 ) { return if $endrank && $startrank > $endrank; @@ -371,78 +633,178 @@ sub as_dot { $endrank = undef if $endrank == $self->end->rank; } - # 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 %graph_attrs = ( + 'rankdir' => 'LR', + 'bgcolor' => 'none', + ); + my %node_attrs = ( + 'fontsize' => 14, + 'fillcolor' => 'white', + 'style' => 'filled', + 'shape' => 'ellipse' + ); + my %edge_attrs = ( + 'arrowhead' => 'open', + 'color' => '#000000', + 'fontcolor' => '#000000', + ); + my $dot = sprintf( "digraph %s {\n", $graph_name ); - $dot .= "\tedge [ arrowhead=open ];\n"; - $dot .= "\tgraph [ rankdir=LR,bgcolor=none ];\n"; - $dot .= sprintf( "\tnode [ fontsize=%d, fillcolor=%s, style=%s, shape=%s ];\n", - 11, "white", "filled", "ellipse" ); + $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n"; + $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n"; # 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"; + $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];" } my %used; # Keep track of the readings that actually appear in the graph - my %subedges; - my %subend; - foreach my $reading ( $self->readings ) { + # Sort the readings by rank if we have ranks; this speeds layout. + my @all_readings = $self->end->has_rank + ? sort { $a->rank <=> $b->rank } $self->readings + : $self->readings; + # TODO Refrain from outputting lacuna nodes - just grey out the edges. + foreach my $reading ( @all_readings ) { # Only output readings within our rank range. next if $startrank && $reading->rank < $startrank; next if $endrank && $reading->rank > $endrank; $used{$reading->id} = 1; - $subedges{$reading->id} = '#SUBSTART#' - if $startrank && $startrank == $reading->rank; - $subedges{$reading->id} = '#SUBEND#' - if $endrank && $endrank == $reading->rank; # Need not output nodes without separate labels next if $reading->id eq $reading->text; - my $label = $reading->punctuated_form; + my $rattrs; + my $label = $reading->text; + $label .= '-' if $reading->join_next; + $label = "-$label" if $reading->join_prior; $label =~ s/\"/\\\"/g; - $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label ); + $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 ) ); } - # Add substitute start and end edges if necessary - foreach my $node ( keys %subedges ) { - my @vector = ( $subedges{$node}, $node ); - @vector = reverse( @vector ) if $vector[0] =~ /END/; - my $witstr = join( ', ', sort $self->reading_witnesses( $self->reading( $node ) ) ); - my %variables = ( 'color' => '#000000', - 'fontcolor' => '#000000', - 'label' => $witstr, - ); - my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables ); - $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", @vector, $varopts ); - } - - # Add the real edges + # Add the real edges. Need to weight one edge per rank jump, in a + # continuous line. + # my $weighted = $self->_add_edge_weights; my @edges = $self->paths; + my( %substart, %subend ); foreach my $edge ( @edges ) { # Do we need to output this edge? - if( $used{$edge->[0]} && $used{$edge->[1]} ) {; - my %variables = ( 'color' => '#000000', - 'fontcolor' => '#000000', - 'label' => join( ', ', $self->path_display_label( $edge ) ), - ); - my $varopts = join( ', ', map { $_.'="'.$variables{$_}.'"' } sort keys %variables ); + if( $used{$edge->[0]} && $used{$edge->[1]} ) { + my $label = $self->_path_display_label( $self->path_witnesses( $edge ) ); + my $variables = { %edge_attrs, 'label' => $label }; + # Account for the rank gap if necessary - my $rankgap = $self->reading( $edge->[1] )->rank - - $self->reading( $edge->[0] )->rank; - $varopts .= ", minlen=$rankgap" if $rankgap > 1; - $dot .= sprintf( "\t\"%s\" -> \"%s\" [ %s ];\n", - $edge->[0], $edge->[1], $varopts ); + my $rank0 = $self->reading( $edge->[0] )->rank + if $self->reading( $edge->[0] )->has_rank; + my $rank1 = $self->reading( $edge->[1] )->rank + if $self->reading( $edge->[1] )->has_rank; + if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) { + $variables->{'minlen'} = $rank1 - $rank0; + } + + # Add the calculated edge weights + # if( exists $weighted->{$edge->[0]} + # && $weighted->{$edge->[0]} eq $edge->[1] ) { + # # $variables->{'color'} = 'red'; + # $variables->{'weight'} = 3.0; + # } + + # EXPERIMENTAL: make edge width reflect no. of witnesses + my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2; + $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit + + my $varopts = _dot_attr_string( $variables ); + $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n", + $edge->[0], $edge->[1], $varopts ); + } elsif( $used{$edge->[0]} ) { + $subend{$edge->[0]} = $edge->[1]; + } elsif( $used{$edge->[1]} ) { + $substart{$edge->[1]} = $edge->[0]; } } - + # Add substitute start and end edges if necessary + foreach my $node ( keys %substart ) { + my $witstr = $self->_path_display_label ( $self->path_witnesses( $substart{$node}, $node ) ); + my $variables = { %edge_attrs, 'label' => $witstr }; + my $nrdg = $self->reading( $node ); + if( $nrdg->has_rank && $nrdg->rank > $startrank ) { + # Substart is actually one lower than $startrank + $variables->{'minlen'} = $nrdg->rank - ( $startrank - 1 ); + } + my $varopts = _dot_attr_string( $variables ); + $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;\n"; + } + foreach my $node ( keys %subend ) { + my $witstr = $self->_path_display_label ( $self->path_witnesses( $node, $subend{$node} ) ); + my $variables = { %edge_attrs, 'label' => $witstr }; + my $varopts = _dot_attr_string( $variables ); + $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;\n"; + } + # HACK part 2 + if( $STRAIGHTENHACK ) { + my $endlabel = $endrank ? '__SUBEND__' : '__END__'; + $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; + } + $dot .= "}\n"; return $dot; } +sub _dot_attr_string { + my( $hash ) = @_; + my @attrs; + foreach my $k ( sort keys %$hash ) { + my $v = $hash->{$k}; + push( @attrs, $k.'="'.$v.'"' ); + } + return( '[ ' . join( ', ', @attrs ) . ' ]' ); +} + +sub _add_edge_weights { + my $self = shift; + # Walk the graph from START to END, choosing the successor node with + # the largest number of witness paths each time. + my $weighted = {}; + my $curr = $self->start->id; + my $ranked = $self->end->has_rank; + while( $curr ne $self->end->id ) { + my $rank = $ranked ? $self->reading( $curr )->rank : 0; + my @succ = sort { $self->path_witnesses( $curr, $a ) + <=> $self->path_witnesses( $curr, $b ) } + $self->sequence->successors( $curr ); + my $next = pop @succ; + my $nextrank = $ranked ? $self->reading( $next )->rank : 0; + # Try to avoid lacunae in the weighted path. + while( @succ && + ( $self->reading( $next )->is_lacuna || + $nextrank - $rank > 1 ) ){ + $next = pop @succ; + } + $weighted->{$curr} = $next; + $curr = $next; + } + return $weighted; +} + +=head2 path_witnesses( $edge ) + +Returns the list of sigils whose witnesses are associated with the given edge. +The edge can be passed as either an array or an arrayref of ( $source, $target ). + +=cut + sub path_witnesses { my( $self, @edge ) = @_; # If edge is an arrayref, cope. @@ -451,35 +813,134 @@ sub path_witnesses { @edge = @$e; } my @wits = keys %{$self->sequence->get_edge_attributes( @edge )}; - return sort @wits; + return @wits; } -sub path_display_label { - my( $self, $edge ) = @_; - my @wits = $self->path_witnesses( $edge ); +# 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; + 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 ) { - return 'majority'; + $maj = $maj > 5 ? $maj : 5; + if( scalar keys %wits > $maj ) { + unshift( @disp_ac, 'majority' ); + return join( ', ', @disp_ac ); } else { - return join( ', ', @wits ); + return join( ', ', sort keys %wits ); } } - -=item B +=head2 readings_at_rank( $rank ) + +Returns a list of readings at a given rank, taken from the alignment table. + +=cut + +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 + +Returns a GraphML representation of the collation. The GraphML will contain +two graphs. The first expresses the attributes of the readings and the witness +paths that link them; the second expresses the relationships that link the +readings. This is the native transfer format for a tradition. + +=begin testing + +use Text::Tradition; + +my $READINGS = 311; +my $PATHS = 361; -print $collation->as_graphml( $recalculate ) +my $datafile = 't/data/florilegium_tei_ps.xml'; +my $tradition = Text::Tradition->new( 'input' => 'TEI', + 'name' => 'test0', + 'file' => $datafile, + 'linear' => 1 ); -Returns a GraphML representation of the collation graph, with -transposition information and position information. Unless -$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. +ok( $tradition, "Got a tradition object" ); +is( scalar $tradition->witnesses, 13, "Found all witnesses" ); +ok( $tradition->collation, "Tradition has a collation" ); + +my $c = $tradition->collation; +is( scalar $c->readings, $READINGS, "Collation has all readings" ); +is( scalar $c->paths, $PATHS, "Collation has all paths" ); +is( scalar $c->relationships, 0, "Collation has all relationships" ); + +# Add a few relationships +$c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } ); +$c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } ); +$c->add_relationship( 'w257', 'w262', { 'type' => 'transposition' } ); + +# Now write it to GraphML and parse it again. + +my $graphml = $c->as_graphml; +my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml ); +is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" ); +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 sub as_graphml { - my( $self ) = @_; - + my( $self, $options ) = @_; + $self->calculate_ranks unless $self->_graphcalc_done; + + my $start = $options->{'from'} + ? $self->reading( $options->{'from'} ) : $self->start; + my $end = $options->{'to'} + ? $self->reading( $options->{'to'} ) : $self->end; + if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) { + throw( 'Start node must be before end node' ); + } + # 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 my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns'; my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance'; @@ -492,74 +953,130 @@ 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', + 'ReadingID' => 'string', + '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}; + } + # 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++; my $key = $root->addNewChild( $graphml_ns, 'key' ); $key->setAttribute( 'attr.name', $datum ); - $key->setAttribute( 'attr.type', $key 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}; + } + # Extra custom key for the reading morphology + $reading_attributes{'lexemes'} = 'string'; + 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', - ); - 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 - 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} ); } - # 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 - foreach my $datum ( @graph_attributes ) { - my $value = $datum eq 'version' ? '3.0' : $self->$datum; + # Tradition/collation attribute data + foreach my $datum ( keys %graph_attributes ) { + my $value; + if( $datum eq 'version' ) { + $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 { + $value = $self->$datum; + } _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value ); } @@ -567,14 +1084,30 @@ sub as_graphml { my %node_hash; # Add our readings to the graph foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) { + next if $n->has_rank && $n ne $self->start && $n ne $self->end && + ( $n->rank < $start->rank || $n->rank > $end->rank ); + $use_readings{$n->id} = 1; # Add to the main graph my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' ); 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; - $nval = $n->punctuated_form if $d eq 'text'; + # 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; + } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) { + $nval = 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; } @@ -584,7 +1117,13 @@ sub as_graphml { 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 ) ) { + next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} ); + my @edge_wits = sort $self->path_witnesses( $e ); + $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] }, $node_hash{ $e->[1] } ); @@ -605,12 +1144,16 @@ 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' ); } } + # 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 - $self->relations->as_graphml( $graphml_ns, $root, \%node_hash, + map { delete $edge_data_keys{$_} } @path_attributes; + $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, $node_data_keys{'id'}, \%edge_data_keys ); # Save and return the thing @@ -626,9 +1169,7 @@ sub _add_graphml_data { $data_el->appendText( $value ); } -=item B - -print $collation->as_csv( $recalculate ) +=head2 as_csv Returns a CSV alignment table representation of the collation graph, one row per witness (or witness uncorrected.) @@ -637,8 +1178,8 @@ row per witness (or witness uncorrected.) sub as_csv { my( $self ) = @_; - my $table = $self->make_alignment_table; - my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } ); + my $table = $self->alignment_table; + my $csv = Text::CSV->new( { binary => 1, quote_null => 0 } ); my @result; # Make the header row $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} ); @@ -646,64 +1187,65 @@ sub as_csv { # Make the rest of the rows foreach my $idx ( 0 .. $table->{'length'} - 1 ) { my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}}; - my @row = map { $_ ? $_->{'t'} : $_ } @rowobjs; + my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs; $csv->combine( @row ); push( @result, decode_utf8( $csv->string ) ); } return join( "\n", @result ); } -=item B - -my $table = $collation->make_alignment_table( $use_refs, \@wits_to_include ) +=head2 alignment_table( $use_refs, $include_witnesses ) Return a reference to an alignment table, in a slightly enhanced CollateX format which looks like this: $table = { alignment => [ { witness => "SIGIL", - tokens => [ { t => "READINGTEXT" }, ... ] }, + tokens => [ { t => "TEXT" }, ... ] }, { witness => "SIG2", - tokens => [ { t => "READINGTEXT" }, ... ] }, + tokens => [ { t => "TEXT" }, ... ] }, ... ], length => TEXTLEN }; If $use_refs is set to 1, the reading object is returned in the table instead of READINGTEXT; if not, the text of the reading is returned. -If $wits_to_include is set to a hashref, only the witnesses whose sigil + +If $include_witnesses is set to a hashref, only the witnesses whose sigil keys have a true hash value will be included. =cut -sub make_alignment_table { - my( $self, $noderefs, $include ) = @_; - unless( $self->linear ) { - warn "Need a linear graph in order to make an alignment table"; - return; - } +sub alignment_table { + my( $self ) = @_; + $self->calculate_ranks() unless $self->_graphcalc_done; + return $self->cached_table if $self->has_cached_table; + + # Make sure we can do this + throw( "Need a linear graph in order to make an alignment table" ) + unless $self->linear; + $self->calculate_ranks unless $self->end->has_rank; + my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 }; my @all_pos = ( 1 .. $self->end->rank - 1 ); foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) { - if( $include ) { - next unless $include->{$wit->sigil}; - } # 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, $noderefs ); + my @row = _make_witness_row( \@wit_path, \@all_pos ); push( @{$table->{'alignment'}}, { 'witness' => $wit->sigil, 'tokens' => \@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 ); + $wit->sigil.$self->ac_label ); + my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos ); push( @{$table->{'alignment'}}, { 'witness' => $wit->sigil.$self->ac_label, 'tokens' => \@ac_row } ); } } - return $table; + $self->cached_table( $table ); + return $table; } sub _make_witness_row { - my( $path, $positions, $noderefs ) = @_; + my( $path, $positions ) = @_; my %char_hash; map { $char_hash{$_} = undef } @$positions; my $debug = 0; @@ -712,8 +1254,7 @@ sub _make_witness_row { $rtext = '#LACUNA#' if $rdg->is_lacuna; print STDERR "rank " . $rdg->rank . "\n" if $debug; # print STDERR "No rank for " . $rdg->id . "\n" unless defined $rdg->rank; - $char_hash{$rdg->rank} = $noderefs ? { 't' => $rdg } - : { 't' => $rtext }; + $char_hash{$rdg->rank} = { 't' => $rdg }; } my @row = map { $char_hash{$_} } @$positions; # Fill in lacuna markers for undef spots in the row @@ -722,8 +1263,8 @@ sub _make_witness_row { 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 : { 't' => '#LACUNA#' }; + if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) { + $el = $last_el; } push( @filled_row, $el ); $last_el = $el; @@ -731,63 +1272,23 @@ sub _make_witness_row { 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->{'t'} eq '#LACUNA#'; - return 1 if ref( $el->{'t'} ) eq 'Text::Tradition::Collation::Reading' - && $el->{'t'}->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 - -my $beginning = $collation->start(); - -Returns the beginning of the collation, a meta-reading with label '#START#'. +=head1 NAVIGATION METHODS -=item B - -my $end = $collation->end(); - -Returns the end of the collation, a meta-reading with label '#END#'. - - -=item B - -my @readings = $collation->reading_sequence( $first, $last, $path[, $alt_path] ); +=head2 reading_sequence( $first, $last, $sigil, $backup ) 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.) +with $last, for the witness given in $sigil. If a $backup sigil is +specified (e.g. when walking a layered witness), it will be used wherever +no $sigil path exists. If there is a base text reading, that will be +used wherever no path exists for $sigil or $backup. =cut # TODO Think about returning some lazy-eval iterator. +# TODO Get rid of backup; we should know from what witness is whether we need it. sub reading_sequence { - my( $self, $start, $end, $witness, $backup ) = @_; + my( $self, $start, $end, $witness ) = @_; $witness = $self->baselabel unless $witness; my @readings = ( $start ); @@ -795,31 +1296,27 @@ sub reading_sequence { my $n = $start; while( $n && $n->id ne $end->id ) { if( exists( $seen{$n->id} ) ) { - warn "Detected loop at " . $n->id; - last; + throw( "Detected loop for $witness at " . $n->id ); } $seen{$n->id} = 1; - my $next = $self->next_reading( $n, $witness, $backup ); + my $next = $self->next_reading( $n, $witness ); unless( $next ) { - warn "Did not find any path for $witness from reading " . $n->id; - last; + throw( "Did not find any path for $witness from reading " . $n->id ); } push( @readings, $next ); $n = $next; } # 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!" + throw( "Last reading found from " . $start->text . + " for witness $witness is not the end!" ) # TODO do we get this far? unless $last->id eq $end->id; return @readings; } -=item B - -my $next_reading = $collation->next_reading( $reading, $witpath ); +=head2 next_reading( $reading, $sigil ); Returns the reading that follows the given reading along the given witness path. @@ -834,9 +1331,7 @@ sub next_reading { return $self->reading( $answer ); } -=item B - -my $prior_reading = $collation->prior_reading( $reading, $witpath ); +=head2 prior_reading( $reading, $sigil ) Returns the reading that precedes the given reading along the given witness path. @@ -851,7 +1346,15 @@ sub prior_reading { } sub _find_linked_reading { - my( $self, $direction, $node, $path, $alt_path ) = @_; + my( $self, $direction, $node, $path ) = @_; + + # Get a backup if we are dealing with a layered witness + my $alt_path; + my $aclabel = $self->ac_label; + if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) { + $alt_path = $1; + } + my @linked_paths = $direction eq 'next' ? $self->sequence->edges_from( $node ) : $self->sequence->edges_to( $node ); @@ -860,15 +1363,15 @@ sub _find_linked_reading { # 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; + @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 ); + my @le_wits = sort $self->path_witnesses( $le ); if( _is_within( \@path_wits, \@le_wits ) ) { # This is the right path. return $direction eq 'next' ? $le->[1] : $le->[0]; @@ -900,8 +1403,70 @@ sub _is_within { return $ret; } +# 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; +} + +=head2 common_readings + +Returns the list of common readings in the graph (i.e. those readings that are +shared by all non-lacunose witnesses.) + +=cut + +sub common_readings { + my $self = shift; + my @common = grep { $_->is_common } $self->readings; + return @common; +} + +=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 +individual readings are joined with spaces and the meta-readings (e.g. +lacunae) are omitted. Optional specification of $start and $end allows +the generation of a subset of the witness text. + +=cut + +sub path_text { + my( $self, $wit, $start, $end ) = @_; + $start = $self->start unless $start; + $end = $self->end unless $end; + my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit ); + my $pathtext = ''; + my $last; + foreach my $r ( @path ) { + unless ( $r->join_prior || !$last || $last->join_next ) { + $pathtext .= ' '; + } + $pathtext .= $r->text; + $last = $r; + } + return $pathtext; +} + +=head1 INITIALIZATION METHODS + +These are mostly for use by parsers. + +=head2 make_witness_path( $witness ) + +Link the array of readings contained in $witness->path (and in +$witness->uncorrected_path if it exists) into collation paths. +Clear out the arrays when finished. -## INITIALIZATION METHODS - for use by parsers +=head2 make_witness_paths + +Call make_witness_path for all witnesses in the tradition. + +=cut # 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. @@ -921,11 +1486,16 @@ 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]; @@ -937,127 +1507,126 @@ sub make_witness_path { $wit->clear_uncorrected_path; } +=head2 calculate_ranks + +Calculate the reading ranks (that is, their aligned positions relative +to each other) for the graph. This can only be called on linear collations. + +=begin testing + +use Text::Tradition; + +my $cxfile = 't/data/Collatex-16.xml'; +my $t = Text::Tradition->new( + 'name' => 'inline', + 'input' => 'CollateX', + 'file' => $cxfile, + ); +my $c = $t->collation; + +# Make an svg +my $table = $c->alignment_table; +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( 'n24', 'n23', { 'type' => 'spelling' } ); +isnt( $c->alignment_table, $table, "Alignment table changed after relationship add" ); + +=end testing + +=cut + 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 ); - } - } + # Save the existing ranks, in case we need to invalidate the cached SVG. + my %existing_ranks; + map { $existing_ranks{$_} = $_->rank } $self->readings; + + # Do the rankings based on the relationship equivalence graph, starting + # with the start node. + my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks(); - # 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} ); - $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}; - 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}} ); + if( defined $node_ranks->{$self->equivalence( $r->id )} ) { + $r->rank( $node_ranks->{$self->equivalence( $r->id )} ); } else { - $DB::single = 1; - die "No rank calculated for node " . $r->id - . " - do you have a cycle in the graph?"; + # Die. Find the last rank we calculated. + 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?" ); } } -} - -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 ); - } + # Do we need to invalidate the cached data? + if( $self->has_cached_svg || $self->has_cached_table ) { + foreach my $r ( $self->readings ) { + next if defined( $existing_ranks{$r} ) + && $existing_ranks{$r} == $r->rank; + # Something has changed, so clear the cache + $self->_clear_cache; + # ...and recalculate the common readings. + $self->calculate_common_readings(); + last; + } } - return @next_nodes; + # The graph calculation information is now up to date. + $self->_graphcalc_done(1); } -# Another method to make up for rough collation methods. If the same reading -# appears multiple times at the same rank, collapse the nodes. +sub _clear_cache { + my $self = shift; + $self->wipe_svg if $self->has_cached_svg; + $self->wipe_table if $self->has_cached_table; +} + + +=head2 flatten_ranks + +A convenience method for parsing collation data. Searches the graph for readings +with the same text at the same rank, and merges any that are found. + +=cut + 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} ) { + # Make sure they don't have different grammatical forms + my $ur = $unique_rank_rdg{$key}; + if( $rdg->disambiguated && $ur->disambiguated ) { + my $rform = join( '//', map { $_->form->to_string } $rdg->lexemes ); + my $uform = join( '//', map { $_->form->to_string } $ur->lexemes ); + next unless $rform eq $uform; + } elsif( $rdg->disambiguated xor $ur->disambiguated ) { + next; + } # Combine! - # print STDERR "Combining readings at same rank: $key\n"; + #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; } + +=head2 calculate_common_readings -## 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; -} +Goes through the graph identifying the readings that appear in every witness +(apart from those with lacunae at that spot.) Marks them as common and returns +the list. =begin testing @@ -1071,15 +1640,108 @@ my $t = Text::Tradition->new( ); my $c = $t->collation; -is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id, +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 n11 n16 n19 n20 n5 n6 n7 /; +is_deeply( \@marked, \@expected, "Found correct list of common readings" ); + +=end testing + +=cut + +sub calculate_common_readings { + my $self = shift; + my @common; + map { $_->is_common( 0 ) } $self->readings; + # Implicitly calls calculate_ranks + my $table = $self->alignment_table; + foreach my $idx ( 0 .. $table->{'length'} - 1 ) { + my @row = map { $_->{'tokens'}->[$idx] + ? $_->{'tokens'}->[$idx]->{'t'} : '' } + @{$table->{'alignment'}}; + my %hash; + foreach my $r ( @row ) { + if( $r ) { + $hash{$r->id} = $r unless $r->is_meta; + } else { + $hash{'UNDEF'} = $r; + } + } + if( keys %hash == 1 && !exists $hash{'UNDEF'} ) { + my( $r ) = values %hash; + $r->is_common( 1 ); + push( @common, $r ); + } + } + return @common; +} + +=head2 text_from_paths + +Calculate the text array for all witnesses from the path, for later consistency +checking. Only to be used if there is no non-graph-based way to know the +original texts. + +=cut + +sub text_from_paths { + my $self = shift; + foreach my $wit ( $self->tradition->witnesses ) { + 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 @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 ); + } + } +} + +=head1 UTILITY FUNCTIONS + +=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 + +use Text::Tradition; + +my $cxfile = 't/data/Collatex-16.xml'; +my $t = Text::Tradition->new( + 'name' => 'inline', + 'input' => 'CollateX', + 'file' => $cxfile, + ); +my $c = $t->collation; + +is( $c->common_predecessor( 'n24', 'n23' )->id, 'n20', "Found correct common predecessor" ); -is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id, - '#END#', "Found correct common successor" ); +is( $c->common_successor( 'n24', 'n23' )->id, + '__END__', "Found correct common successor" ); -is( $c->common_predecessor( $c->reading('n19'), $c->reading('n17') )->id, +is( $c->common_predecessor( 'n19', 'n17' )->id, 'n16', "Found correct common predecessor for readings on same path" ); -is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, - '#END#', "Found correct common successor for readings on same path" ); +is( $c->common_successor( 'n21', 'n10' )->id, + '__END__', "Found correct common successor for readings on same path" ); =end testing @@ -1088,46 +1750,76 @@ is( $c->common_successor( $c->reading('n21'), $c->reading('n26') )->id, ## Return the closest reading that is a predecessor of both the given readings. sub common_predecessor { my $self = shift; - return $self->common_in_path( @_, 'predecessors' ); + my( $r1, $r2 ) = $self->_objectify_args( @_ ); + return $self->_common_in_path( $r1, $r2, 'predecessors' ); } sub common_successor { my $self = shift; - return $self->common_in_path( @_, 'successors' ); + my( $r1, $r2 ) = $self->_objectify_args( @_ ); + return $self->_common_in_path( $r1, $r2, 'successors' ); } -sub common_in_path { + +# 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} ) { + if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) { + # 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} = 'r1'; + push( @new_lc1, $p ); } } } - @last_checked = @new_lc; + foreach my $lc ( @last_r2 ) { + foreach my $p ( $lc->$dir ) { + if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) { + # print STDERR "Path candidate $p from $lc\n"; + push( @candidates, $p ); + } elsif( !$all_seen{$p->id} ) { + $all_seen{$p->id} = 'r2'; + push( @new_lc2, $p ); + } + } + } + @last_r1 = @new_lc1; + @last_r2 = @new_lc2; } my @answer = sort { $a->rank <=> $b->rank } @candidates; return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer ); } +sub throw { + Text::Tradition::Error->throw( + 'ident' => 'Collation error', + 'message' => $_[0], + ); +} + no Moose; __PACKAGE__->meta->make_immutable; -=head1 BUGS / TODO +=head1 LICENSE -=over +This package is free software and is provided "as is" without express +or implied warranty. You can redistribute it and/or modify it under +the same terms as Perl itself. -=item * Think about making Relationship objects again +=head1 AUTHOR -=back +Tara L Andrews Eaurum@cpan.orgE