X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FCollation.pm;h=62972954d06a49db2708d7f7ed0c884c80fedb00;hb=1dd07bda1ca984d1218473cf165da01c214d555f;hp=85c23603cd5a7e79ab8832532b3b7cfbb7fd0267;hpb=f1b3b33a5366c738cab39c57a1f26679a876668e;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Collation.pm b/lib/Text/Tradition/Collation.pm index 85c2360..6297295 100644 --- a/lib/Text/Tradition/Collation.pm +++ b/lib/Text/Tradition/Collation.pm @@ -7,7 +7,9 @@ use IPC::Run qw( run binary ); use Text::CSV_XS; use Text::Tradition::Collation::Reading; use Text::Tradition::Collation::RelationshipStore; +use Text::Tradition::Error; use XML::LibXML; +use XML::LibXML::XPathContext; use Moose; has 'sequence' => ( @@ -65,7 +67,7 @@ has 'linear' => ( isa => 'Bool', default => 1, ); - + has 'ac_label' => ( is => 'rw', isa => 'Str', @@ -85,21 +87,161 @@ 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', + ); + +=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.)'. + +=back + +=head1 ACCESSORS + +=head2 tradition + +=head2 linear + +=head2 wit_list_separator + +=head2 baselabel + +=head2 ac_label + +Simple accessors for collation attributes. + +=head2 start + +The meta-reading at the start of every witness path. + +=head2 end + +The meta-reading at the end of every witness path. + +=head2 readings -# 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. +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 ) + +Merges the $second reading into the $main one. +The 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; @@ -110,6 +252,12 @@ sub BUILD { ### Reading construct/destruct functions +sub _clear_cache { + my $self = shift; + $self->wipe_svg if $self->has_cached_svg; + $self->wipe_table if $self->has_cached_table; +} + sub add_reading { my( $self, $reading ) = @_; unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) { @@ -120,9 +268,9 @@ sub add_reading { } # 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->_clear_cache; $self->_add_reading( $reading->id => $reading ); # Once the reading has been added, put it in both graphs. $self->sequence->add_vertex( $reading->id ); @@ -139,6 +287,7 @@ around del_reading => sub { $arg = $arg->id; } # Remove the reading from the graphs. + $self->_clear_cache; $self->sequence->delete_vertex( $arg ); $self->relations->delete_reading( $arg ); @@ -154,6 +303,7 @@ sub merge_readings { # We only need the IDs for adding paths to the graph, not the reading # objects themselves. my( $kept, $deleted, $combine_char ) = $self->_stringify_args( @_ ); + $self->_clear_cache; # The kept reading should inherit the paths and the relationships # of the deleted reading. @@ -191,6 +341,15 @@ sub _stringify_args { return( $first, $second, $arg ); } +# 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 { @@ -200,6 +359,7 @@ sub add_path { # objects themselves. my( $source, $target, $wit ) = $self->_stringify_args( @_ ); + $self->_clear_cache; # Connect the readings $self->sequence->add_edge( $source, $target ); # Note the witness in question @@ -220,6 +380,7 @@ sub del_path { # objects themselves. my( $source, $target, $wit ) = $self->_stringify_args( @args ); + $self->_clear_cache; if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) { $self->sequence->delete_edge_attribute( $source, $target, $wit ); } @@ -237,25 +398,42 @@ 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->_clear_cache; + # 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, + my( @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 ); + $self->calculate_ranks() if $self->end->has_rank; + $self->_clear_cache; + return @vectors; } =head2 reading_witnesses( $reading ) @@ -279,82 +457,62 @@ sub reading_witnesses { return keys %all_witnesses; } -=head2 Output method(s) - -=over +=head1 OUTPUT METHODS -=item B - -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. =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 ) = @_; + my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'}; + if( !$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 ) +=head2 as_dot( \%options ) -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. - -=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; + # Check the arguments if( $startrank ) { return if $endrank && $startrank > $endrank; @@ -365,15 +523,29 @@ 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 ) { @@ -382,61 +554,137 @@ sub as_dot { if( $endrank ) { $dot .= "\t\"#SUBEND#\" [ label=\"...\" ];\n"; } + if( $STRAIGHTENHACK ) { + ## HACK part 1 + $dot .= "\tsubgraph { rank=same \"#START#\" \"#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 $rattrs; my $label = $reading->text; $label =~ s/\"/\\\"/g; - $dot .= sprintf( "\t\"%s\" [ label=\"%s\" ];\n", $reading->id, $label ); + $rattrs->{'label'} = $label; + $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]} = 1; + } elsif( $used{$edge->[1]} ) { + $substart{$edge->[1]} = 1; } } - + # Add substitute start and end edges if necessary + foreach my $node ( keys %substart ) { + my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); + my $variables = { %edge_attrs, 'label' => $witstr }; + my $varopts = _dot_attr_string( $variables ); + $dot .= "\t\"#SUBSTART#\" -> \"$node\" $varopts;"; + } + foreach my $node ( keys %subend ) { + my $witstr = $self->_path_display_label ( $self->reading_witnesses( $self->reading( $node ) ) ); + my $variables = { %edge_attrs, 'label' => $witstr }; + my $varopts = _dot_attr_string( $variables ); + $dot .= "\t\"$node\" -> \"#SUBEND#\" $varopts;"; + } + # HACK part 2 + if( $STRAIGHTENHACK ) { + $dot .= "\t\"#END#\" -> \"#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( $self, @edge ) = @_; # If edge is an arrayref, cope. @@ -445,29 +693,74 @@ sub path_witnesses { @edge = @$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 ); +sub _path_display_label { + my $self = shift; + my @wits = sort @_; my $maj = scalar( $self->tradition->witnesses ) * 0.6; if( scalar @wits > $maj ) { + # TODO break out a.c. wits return 'majority'; } else { return join( ', ', @wits ); } } - -=item B +=head2 witnesses_at_rank + +Returns a list of witnesses that are not lacunose, for a given rank. + +=cut -print $collation->as_graphml( $recalculate ) +sub witnesses_at_rank { + my( $self, $rank ) = @_; +} -Returns a GraphML representation of the collation graph, with -transposition information and position information. Unless -$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. +=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; + +my $datafile = 't/data/florilegium_tei_ps.xml'; +my $tradition = Text::Tradition->new( 'input' => 'TEI', + 'name' => 'test0', + 'file' => $datafile, + 'linear' => 1 ); + +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" ); + +=end testing =cut @@ -528,7 +821,7 @@ sub as_graphml { witness => 'string', # ID/label for a path relationship => 'string', # ID/label for a relationship extra => 'boolean', # Path key - colocated => 'boolean', # Relationship key + scope => 'string', # Relationship key non_correctable => 'boolean', # Relationship key non_independent => 'boolean', # Relationship key ); @@ -577,7 +870,7 @@ 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 ) ) { + foreach my $wit ( sort $self->path_witnesses( $e ) ) { my( $id, $from, $to ) = ( 'e'.$edge_ctr++, $node_hash{ $e->[0] }, $node_hash{ $e->[1] } ); @@ -603,7 +896,8 @@ sub as_graphml { } # Add the relationship graph to the XML - $self->relations->as_graphml( $root ); + $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, + $node_data_keys{'id'}, \%edge_data_keys ); # Save and return the thing my $result = decode_utf8( $graphml->toString(1) ); @@ -618,9 +912,7 @@ 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.) @@ -629,7 +921,7 @@ row per witness (or witness uncorrected.) sub as_csv { my( $self ) = @_; - my $table = $self->make_alignment_table; + my $table = $self->alignment_table; my $csv = Text::CSV_XS->new( { binary => 1, quote_null => 0 } ); my @result; # Make the header row @@ -638,40 +930,43 @@ 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 ) = @_; + my $include; # see if we can ditch this + 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 ) { @@ -680,22 +975,23 @@ sub make_alignment_table { } # 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; @@ -704,8 +1000,7 @@ 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 @@ -714,8 +1009,8 @@ 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; @@ -723,63 +1018,23 @@ 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 +=head1 NAVIGATION METHODS -my $beginning = $collation->start(); - -Returns the beginning of the collation, a meta-reading with label '#START#'. - -=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 ); @@ -787,31 +1042,27 @@ 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. @@ -826,9 +1077,7 @@ 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. @@ -843,7 +1092,15 @@ 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 ); @@ -852,15 +1109,15 @@ 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]; @@ -892,8 +1149,61 @@ 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, $mainsigil [, $start, $end ] ) -## INITIALIZATION METHODS - for use by parsers +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 ); + return join( ' ', map { $_->text } @path ); +} + +=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. + +=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. @@ -929,8 +1239,41 @@ 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 $svg = $c->as_svg; +is( substr( $svg, 0, 5 ), 'has_cached_svg, "SVG was cached" ); +is( $c->as_svg, $svg, "Cached SVG returned upon second call" ); +$c->calculate_ranks; +is( $c->as_svg, $svg, "Cached SVG retained with no rank change" ); +$c->add_relationship( 'n9', 'n23', { 'type' => 'spelling' } ); +isnt( $c->as_svg, $svg, "SVG changed after relationship add" ); + +=end testing + +=cut + sub calculate_ranks { my $self = shift; + # Save the existing ranks, in case we need to invalidate the cached SVG. + my %existing_ranks; # Walk a version of the graph where every node linked by a relationship # edge is fundamentally the same node, and do a topological ranking on # the nodes in this graph. @@ -958,10 +1301,11 @@ sub calculate_ranks { # Add the edges. foreach my $r ( $self->readings ) { + $existing_ranks{$r} = $r->rank; foreach my $n ( $self->sequence->successors( $r->id ) ) { my( $tfrom, $tto ) = ( $rel_containers{$r->id}, $rel_containers{$n} ); - $DB::single = 1 unless $tfrom && $tto; + # $DB::single = 1 unless $tfrom && $tto; $topo_graph->add_edge( $tfrom, $tto ); } } @@ -979,11 +1323,22 @@ sub calculate_ranks { 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?"; + # Die. Find the last rank we calculated. + my @all_defined = sort { $node_ranks->{$rel_containers{$a->id}} + <=> $node_ranks->{$rel_containers{$b->id}} } + $self->readings; + my $last = pop @all_defined; + throw( "Ranks not calculated after $last - do you have a cycle in the graph?" ); } } + # Do we need to invalidate the cached SVG? + if( $self->has_cached_svg ) { + foreach my $r ( $self->readings ) { + next if $existing_ranks{$r} == $r->rank; + $self->wipe_svg; + last; + } + } } sub _assign_rank { @@ -1021,8 +1376,13 @@ sub _assign_rank { 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. +=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; @@ -1031,26 +1391,139 @@ sub flatten_ranks { my $key = $rdg->rank . "||" . $rdg->text; if( exists $unique_rank_rdg{$key} ) { # Combine! - # print STDERR "Combining readings at same rank: $key\n"; + # print STDERR "Combining readings at same rank: $key\n"; $self->merge_readings( $unique_rank_rdg{$key}, $rdg ); + # TODO see if this now makes a common point. } else { $unique_rank_rdg{$key} = $rdg; } } } +=head2 remove_collations -## 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; -} +Another convenience method for parsing. Removes all 'collation' relationships +that were defined in order to get the reading ranks to be correct. + +=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; + +isnt( $c->reading('n23')->rank, $c->reading('n9')->rank, "Rank skew exists" ); +$c->add_relationship( 'n23', 'n9', { 'type' => 'collated', 'scope' => 'local' } ); +is( scalar $c->relationships, 4, "Found all expected relationships" ); +$c->remove_collations; +is( scalar $c->relationships, 3, "Collated relationships now gone" ); +is( $c->reading('n23')->rank, $c->reading('n9')->rank, "Aligned ranks were preserved" ); + +=end testing + +=cut + +sub remove_collations { + my $self = shift; + foreach my $reledge ( $self->relationships ) { + my $relobj = $self->relations->get_relationship( $reledge ); + if( $relobj && $relobj->type eq 'collated' ) { + $self->relations->delete_relationship( $reledge ); + } + } +} + + +=head2 calculate_common_readings + +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 + +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 @common = $c->calculate_common_readings(); +is( scalar @common, 8, "Found correct number of common readings" ); +my @marked = sort $c->common_readings(); +is( scalar @common, 8, "All common readings got marked as such" ); +my @expected = qw/ n1 n12 n16 n19 n20 n5 n6 n7 /; +is_deeply( \@marked, \@expected, "Found correct list of common readings" ); + +=end testing + +=cut + +sub calculate_common_readings { + my $self = shift; + my @common; + my $table = $self->alignment_table; + foreach my $idx ( 0 .. $table->{'length'} - 1 ) { + my @row = map { $_->{'tokens'}->[$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 @text = split( /\s+/, + $self->reading_sequence( $self->start, $self->end, $wit->sigil ) ); + $wit->text( \@text ); + if( $wit->is_layered ) { + my @uctext = split( /\s+/, + $self->reading_sequence( $self->start, $self->end, + $wit->sigil.$self->ac_label ) ); + $wit->text( \@uctext ); + } + } +} + +=head1 UTILITY FUNCTIONS + +=head2 common_predecessor( $reading_a, $reading_b ) + +Find the last reading that occurs in sequence before both the given readings. + +=head2 common_successor( $reading_a, $reading_b ) + +Find the first reading that occurs in sequence after both the given readings. + =begin testing use Text::Tradition; @@ -1063,14 +1536,14 @@ my $t = Text::Tradition->new( ); my $c = $t->collation; -is( $c->common_predecessor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_predecessor( 'n9', 'n23' )->id, 'n20', "Found correct common predecessor" ); -is( $c->common_successor( $c->reading('n9'), $c->reading('n23') )->id, +is( $c->common_successor( 'n9', '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, +is( $c->common_successor( 'n21', 'n26' )->id, '#END#', "Found correct common successor for readings on same path" ); =end testing @@ -1080,15 +1553,17 @@ 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 { +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'; @@ -1113,13 +1588,22 @@ sub common_in_path { 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