package Text::Tradition::Collation;
use feature 'say';
use Encode qw( decode_utf8 );
use File::Temp;
use File::Which;
use Graph;
use IPC::Run qw( run binary );
use JSON qw/ to_json /;
use Text::CSV;
use Text::Tradition::Collation::Data;
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 _data => (
isa => 'Text::Tradition::Collation::Data',
is => 'ro',
required => 1,
handles => [ qw(
sequence
paths
_set_relations
relations
_set_start
_set_end
ac_label
has_cached_table
relationships
relationship_types
related_readings
get_relationship
del_relationship
equivalence
equivalence_graph
readings
reading
_add_reading
del_reading
has_reading
wit_list_separator
baselabel
linear
wordsep
direction
change_direction
start
end
cached_table
_graphcalc_done
has_cached_svg
wipe_table
)]
);
has 'tradition' => (
is => 'ro',
isa => 'Text::Tradition',
writer => '_set_tradition',
weak_ref => 1,
);
=encoding utf8
=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.
=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<Text::Tradition::Collation::Reading> for the available arguments.
=head2 del_reading( $object_or_id )
Removes the given reading from the collation, implicitly removing its
paths and relationships.
=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, $changed_readings )
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. If an array reference is passed in as $changed_readings,
then any readings that were altered due to the relationship creation are added to
the array.
See L<Text::Tradition::Collation::Relationship> for the available options.
=cut
sub BUILDARGS {
my ( $class, @args ) = @_;
my %args = @args == 1 ? %{ $args[0] } : @args;
# TODO determine these from the Moose::Meta object
my @delegate_attrs = qw(sequence relations readings wit_list_separator baselabel
linear wordsep direction start end cached_table _graphcalc_done);
my %data_args;
for my $attr (@delegate_attrs) {
$data_args{$attr} = delete $args{$attr} if exists $args{$attr};
}
$args{_data} = Text::Tradition::Collation::Data->new(%data_args);
return \%args;
}
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, 'init' => 1 } ) );
$self->_set_end( $self->add_reading(
{ 'collation' => $self, 'is_end' => 1, 'init' => 1 } ) );
}
=head2 register_relationship_type( %relationship_definition )
Add a relationship type definition to this collation. The argument can be either a
hash or a hashref, defining the properties of the relationship. For relationship types
and their properties, see L<Text::Tradition::Collation::RelationshipType>.
=head2 get_relationship_type( $relationship_name )
Retrieve the RelationshipType object for the relationship with the given name.
=cut
sub register_relationship_type {
my $self = shift;
my %args = @_ == 1 ? %{$_[0]} : @_;
if( $self->relations->has_type( $args{name} ) ) {
throw( 'Relationship type ' . $args{name} . ' already registered' );
}
$self->relations->add_type( %args );
}
sub get_relationship_type {
my( $self, $name ) = @_;
return $self->relations->has_type( $name )
? $self->relations->type( $name ) : undef;
}
### Reading construct/destruct functions
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->can('language') && $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 ) ) {
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 );
$self->relations->add_reading( $reading->id );
return $reading;
};
around del_reading => sub {
my $orig = shift;
my $self = shift;
my $arg = shift;
if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) {
$arg = $arg->id;
}
# Remove the reading from the graphs.
$self->_graphcalc_done(0);
$self->_clear_cache; # Explicitly clear caches to GC the reading
$self->sequence->delete_vertex( $arg );
$self->relations->delete_reading( $arg );
# Carry on.
$self->$orig( $arg );
};
=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.
=begin testing
use Test::More::UTF8;
use Text::Tradition;
use TryCatch;
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 ('unto') 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->add_relationship( 'n21', 'n22', { type => 'collated', scope => 'local' } );
$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" );
# Try to combine n21 and n21p0. This should break.
my $remaining = $c->reading('n21');
$remaining ||= $c->reading('n22'); # one of these should still exist
try {
$c->merge_readings( 'n21p0', $remaining, 1 );
ok( 0, "Bad reading merge changed the graph" );
} catch( Text::Tradition::Error $e ) {
like( $e->message, qr/neither concatenated nor collated/, "Expected exception from bad concatenation" );
} catch {
ok( 0, "Unexpected error on bad reading merge: $@" );
}
try {
$c->calculate_ranks();
ok( 1, "Graph is still evidently whole" );
} catch( Text::Tradition::Error $e ) {
ok( 0, "Caught a rank exception: " . $e->message );
}
# Test right-to-left reading merge.
my $rtl = Text::Tradition->new(
'name' => 'inline',
'input' => 'Tabular',
'sep_char' => ',',
'direction' => 'RL',
'file' => 't/data/arabic_snippet.csv'
);
my $rtlc = $rtl->collation;
is( $rtlc->reading('r8.1')->text, 'سبب', "Got target first reading in RTL text" );
my $pt = $rtlc->path_text('A');
my @path = $rtlc->reading_sequence( $rtlc->start, $rtlc->end, 'A' );
is( $rtlc->reading('r9.1')->text, 'صلاح', "Got target second reading in RTL text" );
$rtlc->merge_readings( 'r8.1', 'r9.1', 1 );
is( $rtlc->reading('r8.1')->text, 'سبب صلاح', "Got target merged reading in RTL text" );
is( $rtlc->path_text('A'), $pt, "Path text is still correct" );
is( scalar($rtlc->reading_sequence( $rtlc->start, $rtlc->end, 'A' )),
scalar(@path) - 1, "Path was shortened" );
=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 );
throw( "Cannot combine text of meta readings" ) if $combine;
}
# We can only merge readings in a linear graph if:
# - they are contiguous with only one edge between them, OR
# - they are at equivalent ranks in the graph.
if( $self->linear ) {
my @delpred = $del_obj->predecessors;
my @keptsuc = $kept_obj->successors;
unless ( @delpred == 1 && $delpred[0] eq $kept_obj
&& @keptsuc == 1 && $keptsuc[0] eq $del_obj ) {
my( $is_ok, $msg ) = $self->relations->relationship_valid(
$kept_obj, $del_obj, 'collated' );
unless( $is_ok ) {
throw( "Readings $kept_obj and $del_obj can be neither concatenated nor collated" );
}
}
}
# We only need the IDs for adding paths to the graph, not the reading
# objects themselves.
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 ) ) {
my @vector = ( $kept );
push( @vector, $path->[1] ) if $path->[0] eq $deleted;
unshift( @vector, $path->[0] ) if $path->[1] eq $deleted;
next if $vector[0] eq $vector[1]; # Don't add a self loop
my %wits = %{$self->sequence->get_edge_attributes( @$path )};
$self->sequence->add_edge( @vector );
my $fwits = $self->sequence->get_edge_attributes( @vector );
@wits{keys %$fwits} = values %$fwits;
$self->sequence->set_edge_attributes( @vector, \%wits );
}
$self->relations->merge_readings( $kept, $deleted, $combine );
# Do the deletion deed.
if( $combine ) {
# Combine the text of the readings
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->_combine( $del_obj, $joinstr );
}
$self->del_reading( $deleted );
}
=head2 merge_related( @relationship_types )
Merge all readings linked with the relationship types given. If any of the selected type(s) is not a colocation, the graph will no longer be linear. The majority/plurality reading in each case will be the one kept.
WARNING: This operation cannot be undone.
=cut
=begin testing
use Test::Warn;
use Text::Tradition;
use TryCatch;
my $t;
warnings_exist {
$t = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/legendfrag.xml' );
} [qr/Cannot set relationship on a meta reading/],
"Got expected relationship drop warning on parse";
my $c = $t->collation;
# Force the transitive propagation of all existing relationships.
$c->relations->propagate_all_relationships();
my %rdg_ids;
map { $rdg_ids{$_} = 1 } $c->readings;
$c->merge_related( 'orthographic' );
is( scalar( $c->readings ), keys( %rdg_ids ) - 9,
"Successfully collapsed orthographic variation" );
map { $rdg_ids{$_} = undef } qw/ r13.3 r11.4 r8.5 r8.2 r7.7 r7.5 r7.4 r7.3 r7.1 /;
foreach my $rid ( keys %rdg_ids ) {
my $exp = $rdg_ids{$rid};
is( !$c->reading( $rid ), !$exp, "Reading $rid correctly " .
( $exp ? "retained" : "removed" ) );
}
ok( $c->linear, "Graph is still linear" );
try {
$c->calculate_ranks; # This should succeed
ok( 1, "Can still calculate ranks on the new graph" );
} catch {
ok( 0, "Rank calculation on merged graph failed: $@" );
}
# Now add some transpositions
$c->add_relationship( 'r8.4', 'r10.4', { type => 'transposition' } );
$c->merge_related( 'transposition' );
is( scalar( $c->readings ), keys( %rdg_ids ) - 10,
"Transposed relationship is merged away" );
ok( !$c->reading('r8.4'), "Correct transposed reading removed" );
ok( !$c->linear, "Graph is no longer linear" );
try {
$c->calculate_ranks; # This should fail
ok( 0, "Rank calculation happened on nonlinear graph?!" );
} catch ( Text::Tradition::Error $e ) {
is( $e->message, 'Cannot calculate ranks on a non-linear graph',
"Rank calculation on merged graph threw an error" );
}
=end testing
=cut
# TODO: there should be a way to display merged without affecting the underlying data!
sub merge_related {
my $self = shift;
my %reltypehash;
map { $reltypehash{$_} = 1 } @_;
# Set up the filter for finding related readings
my $filter = sub {
exists $reltypehash{$_[0]->type};
};
# Go through all readings looking for related ones
foreach my $r ( $self->readings ) {
next unless $self->reading( "$r" ); # might have been deleted meanwhile
while( my @related = $self->related_readings( $r, $filter ) ) {
push( @related, $r );
@related = sort {
scalar $b->witnesses <=> scalar $a->witnesses
} @related;
my $keep = shift @related;
foreach my $delr ( @related ) {
$self->linear( 0 )
unless( $self->get_relationship( $keep, $delr )->colocated );
$self->merge_readings( $keep, $delr );
}
}
}
}
=head2 compress_readings
Where possible in the graph, compresses plain sequences of readings into a
single reading. The sequences must consist of readings with no
relationships to other readings, with only a single witness path between
them and no other witness paths from either that would skip the other. The
readings must also not be marked as nonsense or bad grammar.
WARNING: This operation cannot be undone.
=begin testing
use Text::Tradition;
my $t = Text::Tradition->new( input => 'CollateX', file => 't/data/Collatex-16.xml' );
my $c = $t->collation;
my $n = scalar $c->readings;
$c->compress_readings();
is( scalar $c->readings, $n - 6, "Compressing readings seems to work" );
# Now put in a join-word and make sure the thing still works.
my $t2 = Text::Tradition->new( input => 'CollateX', file => 't/data/Collatex-16.xml' );
my $c2 = $t2->collation;
# Split n21 ('unto') for testing purposes
my $new_r = $c2->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } );
my $old_r = $c2->reading( 'n21' );
$old_r->alter_text( 'to' );
$c2->del_path( 'n20', 'n21', 'A' );
$c2->add_path( 'n20', 'n21p0', 'A' );
$c2->add_path( 'n21p0', 'n21', 'A' );
$c2->calculate_ranks();
is( scalar $c2->readings, $n + 1, "We have our extra test reading" );
$c2->compress_readings();
is( scalar $c2->readings, $n - 6, "Compressing readings also works with join_next" );
is( $c2->reading( 'n21p0' )->text, 'unto', "The joined word has no space" );
=end testing
=cut
sub compress_readings {
my $self = shift;
# Sanity check: first save the original text of each witness.
my %origtext;
foreach my $wit ( $self->tradition->witnesses ) {
$origtext{$wit->sigil} = $self->path_text( $wit->sigil );
if( $wit->is_layered ) {
my $acsig = $wit->sigil . $self->ac_label;
$origtext{$acsig} = $self->path_text( $acsig );
}
}
# Now do the deed.
# Anywhere in the graph that there is a reading that joins only to a single
# successor, and neither of these have any relationships, just join the two
# readings.
foreach my $rdg ( sort { $a->rank <=> $b->rank } $self->readings ) {
# Now look for readings that can be joined to their successors.
next unless $rdg->is_combinable;
my %seen;
while( $self->sequence->successors( $rdg ) == 1 ) {
my( $next ) = $self->reading( $self->sequence->successors( $rdg ) );
throw( "Infinite loop" ) if $seen{$next->id};
$seen{$next->id} = 1;
last if $self->sequence->predecessors( $next ) > 1;
last unless $next->is_combinable;
say "Joining readings $rdg and $next";
$self->merge_readings( $rdg, $next, 1 );
}
}
# Finally, make sure we haven't screwed anything up.
foreach my $wit ( $self->tradition->witnesses ) {
my $pathtext = $self->path_text( $wit->sigil );
throw( "Text differs for witness " . $wit->sigil )
unless $pathtext eq $origtext{$wit->sigil};
if( $wit->is_layered ) {
my $acsig = $wit->sigil . $self->ac_label;
$pathtext = $self->path_text( $acsig );
throw( "Layered text differs for witness " . $wit->sigil )
unless $pathtext eq $origtext{$acsig};
}
}
$self->relations->rebuild_equivalence();
$self->calculate_ranks();
}
# Helper function for manipulating the graph.
sub _stringify_args {
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, @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 );
}
=head2 duplicate_reading( $reading, @witlist )
Split the given reading into two, so that the new reading is in the path for
the witnesses given in @witlist. If the result is that certain non-colocated
relationships (e.g. transpositions) are no longer valid, these will be removed.
Returns the newly-created reading.
=begin testing
use Test::More::UTF8;
use Text::Tradition;
use TryCatch;
my $st = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/collatecorr.xml' );
is( ref( $st ), 'Text::Tradition', "Got a tradition from test file" );
ok( $st->has_witness('Ba96'), "Tradition has the affected witness" );
my $sc = $st->collation;
my $numr = 17;
ok( $sc->reading('n131'), "Tradition has the affected reading" );
is( scalar( $sc->readings ), $numr, "There are $numr readings in the graph" );
is( $sc->end->rank, 14, "There are fourteen ranks in the graph" );
# Detach the erroneously collated reading
my( $newr, @del_rdgs ) = $sc->duplicate_reading( 'n131', 'Ba96' );
ok( $newr, "New reading was created" );
ok( $sc->reading('n131_0'), "Detached the bad collation with a new reading" );
is( scalar( $sc->readings ), $numr + 1, "A reading was added to the graph" );
is( $sc->end->rank, 10, "There are now only ten ranks in the graph" );
my $csucc = $sc->common_successor( 'n131', 'n131_0' );
is( $csucc->id, 'n136', "Found correct common successor to duped reading" );
# Check that the bad transposition is gone
is( scalar @del_rdgs, 1, "Deleted reading was returned by API call" );
is( $sc->get_relationship( 'n130', 'n135' ), undef, "Bad transposition relationship is gone" );
# The collation should not be fixed
my @pairs = $sc->identical_readings();
is( scalar @pairs, 0, "Not re-collated yet" );
# Fix the collation
ok( $sc->merge_readings( 'n124', 'n131_0' ), "Collated the readings correctly" );
@pairs = $sc->identical_readings( start => 'n124', end => $csucc->id );
is( scalar @pairs, 3, "Found three more identical readings" );
is( $sc->end->rank, 11, "The ranks shifted appropriately" );
$sc->flatten_ranks();
is( scalar( $sc->readings ), $numr - 3, "Now we are collated correctly" );
# Check that we can't "duplicate" a reading with no wits or with all wits
try {
my( $badr, @del_rdgs ) = $sc->duplicate_reading( 'n124' );
ok( 0, "Reading duplication without witnesses throws an error" );
} catch( Text::Tradition::Error $e ) {
like( $e->message, qr/Must specify one or more witnesses/,
"Reading duplication without witnesses throws the expected error" );
} catch {
ok( 0, "Reading duplication without witnesses threw the wrong error" );
}
try {
my( $badr, @del_rdgs ) = $sc->duplicate_reading( 'n124', 'Ba96', 'Mü11475' );
ok( 0, "Reading duplication with all witnesses throws an error" );
} catch( Text::Tradition::Error $e ) {
like( $e->message, qr/Cannot join all witnesses/,
"Reading duplication with all witnesses throws the expected error" );
} catch {
ok( 0, "Reading duplication with all witnesses threw the wrong error" );
}
try {
$sc->calculate_ranks();
ok( 1, "Graph is still evidently whole" );
} catch( Text::Tradition::Error $e ) {
ok( 0, "Caught a rank exception: " . $e->message );
}
=end testing
=cut
sub duplicate_reading {
my( $self, $r, @wits ) = @_;
# Check that we are not doing anything unwise.
throw( "Must specify one or more witnesses for the duplicated reading" )
unless @wits;
unless( ref( $r ) eq 'Text::Tradition::Collation::Reading' ) {
$r = $self->reading( $r );
}
throw( "Cannot duplicate a meta-reading" )
if $r->is_meta;
throw( "Cannot join all witnesses to the new reading" )
if scalar( @wits ) == scalar( $r->witnesses );
# Get all the reading attributes and duplicate them.
my $rmeta = Text::Tradition::Collation::Reading->meta;
my %args;
foreach my $attr( $rmeta->get_all_attributes ) {
next if $attr->name =~ /^_/;
my $acc = $attr->get_read_method;
if( !$acc && $attr->has_applied_traits ) {
my $tr = $attr->applied_traits;
if( $tr->[0] =~ /::(Array|Hash)$/ ) {
my $which = $1;
my %methods = reverse %{$attr->handles};
$acc = $methods{elements};
$args{$attr->name} = $which eq 'Array'
? [ $r->$acc ] : { $r->$acc };
}
} elsif( $acc ) {
my $attrval = $r->$acc;
if( defined $attrval ) {
$args{$attr->name} = $attrval;
}
}
}
# By definition the new reading will no longer be common.
$args{is_common} = 0;
# The new reading also needs its own ID.
$args{id} = $self->_generate_dup_id( $r->id );
# Try to make the new reading.
my $newr = $self->add_reading( \%args );
# The old reading is also no longer common.
$r->is_common( 0 );
# For each of the witnesses, dissociate from the old reading and
# associate with the new.
foreach my $wit ( @wits ) {
my $prior = $self->prior_reading( $r, $wit );
my $next = $self->next_reading( $r, $wit );
$self->del_path( $prior, $r, $wit );
$self->add_path( $prior, $newr, $wit );
$self->del_path( $r, $next, $wit );
$self->add_path( $newr, $next, $wit );
}
# If the graph is ranked, we need to look for relationships that are now
# invalid (i.e. 'non-colocation' types that might now be colocated) and
# remove them. If not, we can skip it.
my $succ;
my %rrk;
my @deleted_relations;
if( $self->end->has_rank ) {
# Find the point where we can stop checking
$succ = $self->common_successor( $r, $newr );
# Hash the existing ranks
foreach my $rdg ( $self->readings ) {
$rrk{$rdg->id} = $rdg->rank;
}
# Calculate the new ranks
$self->calculate_ranks();
# Check for invalid non-colocated relationships among changed-rank readings
# from where the ranks start changing up to $succ
my $lastrank = $succ->rank;
foreach my $rdg ( $self->readings ) {
next if $rdg->rank > $lastrank;
next if $rdg->rank == $rrk{$rdg->id};
my @noncolo = $rdg->related_readings( sub { !$_[0]->colocated } );
next unless @noncolo;
foreach my $nc ( @noncolo ) {
unless( $self->relations->verify_or_delete( $rdg, $nc ) ) {
push( @deleted_relations, [ $rdg->id, $nc->id ] );
}
}
}
}
return ( $newr, @deleted_relations );
}
sub _generate_dup_id {
my( $self, $rid ) = @_;
my $newid;
my $i = 0;
while( !$newid ) {
$newid = $rid."_$i";
if( $self->has_reading( $newid ) ) {
$newid = '';
$i++;
}
}
return $newid;
}
### Path logic
sub add_path {
my $self = shift;
# We only need the IDs for adding paths to the graph, not the reading
# objects themselves.
my( $source, $target, $wit ) = $self->_stringify_args( @_ );
$self->_graphcalc_done(0);
# Connect the readings
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;
my @args;
if( ref( $_[0] ) eq 'ARRAY' ) {
my $e = shift @_;
@args = ( @$e, @_ );
} else {
@args = @_;
}
# We only need the IDs for removing paths from the graph, not the reading
# 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( $self->sequence->has_edge_attributes( $source, $target ) ) {
$self->sequence->delete_edge( $source, $target );
$self->relations->delete_equivalence_edge( $source, $target );
}
}
# Extra graph-alike utility
sub has_path {
my $self = shift;
my( $source, $target, $wit ) = $self->_stringify_args( @_ );
return undef unless $self->sequence->has_edge( $source, $target );
return $self->sequence->has_edge_attribute( $source, $target, $wit );
}
=head2 clear_witness( @sigil_list )
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
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, $altered_readings ) = $self->_stringify_args( @_ );
my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts );
my $did_recalc;
foreach my $v ( @vectors ) {
my $rel = $self->get_relationship( $v );
next unless $rel->colocated;
my $r1 = $self->reading( $v->[0] );
my $r2 = $self->reading( $v->[1] );
# If it's a spelling or orthographic relationship, and one is marked
# as a lemma, set the normal form on the non-lemma to reflect that.
if( $r1->does( 'Text::Tradition::Morphology' ) ) {
my @changed = $r1->relationship_added( $r2, $rel );
if( ref( $altered_readings ) eq 'ARRAY' ) {
push( @$altered_readings, @changed );
}
}
next if $did_recalc;
if( $r1->has_rank && $r2->has_rank && $r1->rank ne $r2->rank ) {
$self->_graphcalc_done(0);
$self->_clear_cache;
$did_recalc = 1;
}
}
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 @stringargs = $self->_stringify_args( @args );
$self->$orig( @stringargs );
};
=head2 reading_witnesses( $reading )
Return a list of sigils corresponding to the witnesses in which the reading appears.
=cut
sub reading_witnesses {
my( $self, $reading ) = @_;
# We need only check either the incoming or the outgoing edges; I have
# arbitrarily chosen "incoming". Thus, special-case the start node.
if( $reading eq $self->start ) {
return map { $_->sigil } grep { $_->is_collated } $self->tradition->witnesses;
}
my %all_witnesses;
foreach my $e ( $self->sequence->edges_to( $reading ) ) {
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;
}
=head1 OUTPUT METHODS
=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.
=begin testing
use File::Which;
use Text::Tradition;
use XML::LibXML;
use XML::LibXML::XPathContext;
SKIP: {
skip( 'Need Graphviz installed to test graphs', 16 )
unless File::Which::which( 'dot' );
my $datafile = 't/data/Collatex-16.xml';
my $tradition = Text::Tradition->new(
'name' => 'inline',
'input' => 'CollateX',
'file' => $datafile,
);
my $collation = $tradition->collation;
# Test the svg creation
my $parser = XML::LibXML->new();
$parser->load_ext_dtd( 0 );
my $svg = $parser->parse_string( $collation->as_svg() );
is( $svg->documentElement->nodeName(), 'svg', 'Got an svg document' );
# Test for the correct number of nodes in the SVG
my $svg_xpc = XML::LibXML::XPathContext->new( $svg->documentElement() );
$svg_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
my @svg_nodes = $svg_xpc->findnodes( '//svg:g[@class="node"]' );
is( scalar @svg_nodes, 26, "Correct number of nodes in the graph" );
# Test for the correct number of edges
my @svg_edges = $svg_xpc->findnodes( '//svg:g[@class="edge"]' );
is( scalar @svg_edges, 32, "Correct number of edges in the graph" );
# Test svg creation for a subgraph
my $part_svg = $parser->parse_string( $collation->as_svg( { from => 15 } ) ); # start, no end
is( $part_svg->documentElement->nodeName(), 'svg', "Got an svg subgraph to end" );
my $part_xpc = XML::LibXML::XPathContext->new( $part_svg->documentElement() );
$part_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
@svg_nodes = $part_xpc->findnodes( '//svg:g[@class="node"]' );
is( scalar( @svg_nodes ), 9,
"Correct number of nodes in the subgraph" );
@svg_edges = $part_xpc->findnodes( '//svg:g[@class="edge"]' );
is( scalar( @svg_edges ), 10,
"Correct number of edges in the subgraph" );
$part_svg = $parser->parse_string( $collation->as_svg( { from => 10, to => 13 } ) ); # start, no end
is( $part_svg->documentElement->nodeName(), 'svg', "Got an svg subgraph in the middle" );
$part_xpc = XML::LibXML::XPathContext->new( $part_svg->documentElement() );
$part_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
@svg_nodes = $part_xpc->findnodes( '//svg:g[@class="node"]' );
is( scalar( @svg_nodes ), 9,
"Correct number of nodes in the subgraph" );
@svg_edges = $part_xpc->findnodes( '//svg:g[@class="edge"]' );
is( scalar( @svg_edges ), 11,
"Correct number of edges in the subgraph" );
$part_svg = $parser->parse_string( $collation->as_svg( { to => 5 } ) ); # start, no end
is( $part_svg->documentElement->nodeName(), 'svg', "Got an svg subgraph from start" );
$part_xpc = XML::LibXML::XPathContext->new( $part_svg->documentElement() );
$part_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
@svg_nodes = $part_xpc->findnodes( '//svg:g[@class="node"]' );
is( scalar( @svg_nodes ), 7,
"Correct number of nodes in the subgraph" );
@svg_edges = $part_xpc->findnodes( '//svg:g[@class="edge"]' );
is( scalar( @svg_edges ), 7,
"Correct number of edges in the subgraph" );
# Test a right-to-left graph
my $arabic = Text::Tradition->new(
input => 'Tabular',
sep_char => ',',
name => 'arabic',
direction => 'RL',
file => 't/data/arabic_snippet.csv' );
my $rl_svg = $parser->parse_string( $arabic->collation->as_svg() );
is( $rl_svg->documentElement->nodeName(), 'svg', "Got an svg subgraph from start" );
my $rl_xpc = XML::LibXML::XPathContext->new( $rl_svg->documentElement() );
$rl_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
my %node_cx;
foreach my $node ( $rl_xpc->findnodes( '//svg:g[@class="node"]' ) ) {
my $nid = $node->getAttribute('id');
$node_cx{$nid} = $rl_xpc->findvalue( './svg:ellipse/@cx', $node );
}
my @sorted = sort { $node_cx{$a} <=> $node_cx{$b} } keys( %node_cx );
is( $sorted[0], '__END__', "End node is the leftmost" );
is( $sorted[$#sorted], '__START__', "Start node is the rightmost" );
# Now try making it bidirectional
$arabic->collation->change_direction('BI');
my $bi_svg = $parser->parse_string( $arabic->collation->as_svg() );
is( $bi_svg->documentElement->nodeName(), 'svg', "Got an svg subgraph from start" );
my $bi_xpc = XML::LibXML::XPathContext->new( $bi_svg->documentElement() );
$bi_xpc->registerNs( 'svg', 'http://www.w3.org/2000/svg' );
my %node_cy;
foreach my $node ( $bi_xpc->findnodes( '//svg:g[@class="node"]' ) ) {
my $nid = $node->getAttribute('id');
$node_cy{$nid} = $rl_xpc->findvalue( './svg:ellipse/@cy', $node );
}
@sorted = sort { $node_cy{$a} <=> $node_cy{$b} } keys( %node_cy );
is( $sorted[0], '__START__', "Start node is the topmost" );
is( $sorted[$#sorted], '__END__', "End node is the bottom-most" );
} #SKIP
=end testing
=cut
sub as_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 );
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 );
return $svg;
}
=head2 as_dot( \%options )
Returns a string that is the collation graph expressed in dot
(i.e. GraphViz) format. Options include:
=over 4
=item * from
=item * to
=item * color_common
=back
=cut
sub as_dot {
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;
return if $startrank > $self->end->rank;
}
if( defined $endrank ) {
return if $endrank < 0;
$endrank = undef if $endrank == $self->end->rank;
}
my $graph_name = $self->tradition->name;
$graph_name =~ s/[^\w\s]//g;
$graph_name = join( '_', split( /\s+/, $graph_name ) );
my %graph_attrs = (
'bgcolor' => 'none',
);
unless( $self->direction eq 'BI' ) {
$graph_attrs{rankdir} = $self->direction;
}
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 .= "\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=\"...\",id=\"__START__\" ];\n";
}
if( $endrank ) {
$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
# 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;
# Need not output nodes without separate labels
next if $reading->id eq $reading->text;
my $rattrs;
my $label = $reading->text;
unless( $label =~ /^[[:punct:]]+$/ ) {
$label .= '-' if $reading->join_next;
$label = "-$label" if $reading->join_prior;
}
$label =~ s/\"/\\\"/g;
$rattrs->{'label'} = $label;
$rattrs->{'id'} = $reading->id;
$rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common;
$dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) );
}
# Add the real edges.
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 $label = $self->_path_display_label( $opts,
$self->path_witnesses( $edge ) );
my $variables = { %edge_attrs, 'label' => $label };
# Account for the rank gap if necessary
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;
}
# 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];
}
}
# If we are asked to, add relationship links
if( exists $opts->{show_relations} ) {
my $filter = $opts->{show_relations}; # can be 'transposition' or 'all'
if( $filter eq 'transposition' ) {
$filter =~ qr/^transposition$/;
}
my %typecolors;
my @types = sort( map { $_->name } $self->relations->types );
if( exists $opts->{graphcolors} ) {
foreach my $tdx ( 0 .. $#types ) {
$typecolors{$types[$tdx]} = $opts->{graphcolors}->[$tdx];
}
} else {
map { $typecolors{$_} = '#FFA14F' } @types;
}
foreach my $redge ( $self->relationships ) {
if( $used{$redge->[0]} && $used{$redge->[1]} ) {
my $rel = $self->get_relationship( $redge );
next unless $filter eq 'all' || $rel->type =~ /$filter/;
my $variables = {
arrowhead => 'none',
color => $typecolors{$rel->type},
constraint => 'false',
penwidth => '3',
};
unless( exists $opts->{graphcolors} ) {
$variables->{label} = uc( substr( $rel->type, 0, 4 ) ),
}
$dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n",
$redge->[0], $redge->[1], _dot_attr_string( $variables ) );
}
}
}
# Add substitute start and end edges if necessary
foreach my $node ( keys %substart ) {
my $witstr = $self->_path_display_label( $opts,
$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( $opts,
$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 ) . ' ]' );
}
=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.
if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) {
my $e = shift @edge;
@edge = @$e;
}
my @wits = keys %{$self->sequence->get_edge_attributes( @edge )};
return @wits;
}
# Helper function. Make a display label for the given witnesses, showing a.c.
# witnesses only where the main witness is not also in the list.
sub _path_display_label {
my $self = shift;
my $opts = 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 );
}
}
}
if( $opts->{'explicit_wits'} ) {
return join( ', ', sort keys %wits );
} else {
# See if we are in a majority situation.
my $maj = scalar( $self->tradition->witnesses ) * 0.6;
$maj = $maj > 5 ? $maj : 5;
if( scalar keys %wits > $maj ) {
unshift( @disp_ac, 'majority' );
return join( ', ', @disp_ac );
} else {
return join( ', ', sort keys %wits );
}
}
}
=head2 as_adjacency_list
Returns a JSON structure that represents the collation sequence graph.
=begin testing
use JSON qw/ from_json /;
use Text::Tradition;
my $t = Text::Tradition->new(
'input' => 'Self',
'file' => 't/data/florilegium_graphml.xml' );
my $c = $t->collation;
# Make a connection so we can test rank preservation
$c->add_relationship( 'w91', 'w92', { type => 'grammatical' } );
# Create an adjacency list of the whole thing; test the output.
my $adj_whole = from_json( $c->as_adjacency_list() );
is( scalar @$adj_whole, scalar $c->readings(),
"Same number of nodes in graph and adjacency list" );
my @adj_whole_edges;
map { push( @adj_whole_edges, @{$_->{adjacent}} ) } @$adj_whole;
is( scalar @adj_whole_edges, scalar $c->sequence->edges,
"Same number of edges in graph and adjacency list" );
# Find the reading whose rank should be preserved
my( $test_rdg ) = grep { $_->{id} eq 'w89' } @$adj_whole;
my( $test_edge ) = grep { $_->{id} eq 'w92' } @{$test_rdg->{adjacent}};
is( $test_edge->{minlen}, 2, "Rank of test reading is preserved" );
# Now create an adjacency list of just a portion. w76 to w122
my $adj_part = from_json( $c->as_adjacency_list(
{ from => $c->reading('w76')->rank,
to => $c->reading('w122')->rank }));
is( scalar @$adj_part, 48, "Correct number of nodes in partial graph" );
my @adj_part_edges;
map { push( @adj_part_edges, @{$_->{adjacent}} ) } @$adj_part;
is( scalar @adj_part_edges, 58,
"Same number of edges in partial graph and adjacency list" );
# Check for consistency
my %part_nodes;
map { $part_nodes{$_->{id}} = 1 } @$adj_part;
foreach my $edge ( @adj_part_edges ) {
my $testid = $edge->{id};
ok( $part_nodes{$testid}, "ID $testid referenced in edge is given as node" );
}
=end testing
=cut
sub as_adjacency_list {
my( $self, $opts ) = @_;
# Make a structure that contains all the nodes, the nodes they point to,
# and the attributes of the edges that connect them.
# [ { id: 'n0', label: 'Gallia', adjacent: [
# { id: 'n1', label: 'P Q' } ,
# { id: 'n2', label: 'R S', minlen: 2 } ] },
# { id: 'n1', label: 'est', adjacent: [ ... ] },
# ... ]
my $startrank = $opts->{'from'} || 0;
my $endrank = $opts->{'to'} || $self->end->rank;
$self->calculate_ranks()
unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear );
my $list = [];
foreach my $rdg ( $self->readings ) {
my @successors;
my $phony = '';
# Figure out what the node's successors should be.
if( $rdg eq $self->start && $startrank > 0 ) {
# Connect the start node with all the nodes at startrank.
# Lacunas should be included only if the node really has that rank.
@successors = $self->readings_at_rank( $startrank, 1 );
$phony = 'start';
} elsif( $rdg->rank < $startrank
|| $rdg->rank > $endrank && $rdg ne $self->end ) {
next;
} else {
@successors = $rdg->successors;
}
# Make sure that the end node is at the end of the successors
# list if it is needed.
if( grep { $_ eq $self->end } @successors ) {
my @ts = grep { $_ ne $self->end } @successors;
@successors = ( @ts, $self->end );
} elsif ( grep { $_->rank > $endrank } @successors ) {
push( @successors, $self->end );
}
my $listitem = { id => $rdg->id, label => $rdg->text };
my $adjacent = [];
my @endwits;
foreach my $succ ( @successors ) {
my @edgewits;
if( $phony eq 'start' ) {
@edgewits = $succ->witnesses;
} elsif( $self->sequence->has_edge( $rdg->id, $succ->id ) ) {
@edgewits = $self->path_witnesses( $rdg->id, $succ->id );
}
if( $succ eq $self->end ) {
@edgewits = @endwits;
} elsif( $succ->rank > $endrank ) {
# These witnesses will point to 'end' instead, not to the
# actual successor.
push( @endwits, @edgewits );
next;
}
my $edgelabel = $self->_path_display_label( $opts, @edgewits );
my $edgedef = { id => $succ->id, label => $edgelabel };
my $rankoffset = $succ->rank - $rdg->rank;
if( $rankoffset > 1 and $succ ne $self->end ) {
$edgedef->{minlen} = $rankoffset;
}
push( @$adjacent, $edgedef );
}
$listitem->{adjacent} = $adjacent;
push( @$list, $listitem );
}
return to_json( $list );
}
=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;
use TryCatch;
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',
'is_significant' => 'yes' } );
# 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" );
my $sigrel = $st->collation->get_relationship( 'w257', 'w262' );
is( $sigrel->is_significant, 'yes', "Ternary attribute value was restored" );
# Now add a stemma, write to GraphML, and look at the output.
SKIP: {
skip "Analysis module not present", 3 unless $tradition->can( 'add_stemma' );
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
## TODO MOVE this to Tradition.pm and modularize it better
sub as_graphml {
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';
my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' .
'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd';
# Create the document and root node
require XML::LibXML;
my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" );
my $root = $graphml->createElementNS( $graphml_ns, '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',
'Ternary' => 'string',
);
# 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 = ( 'version' => 'string' );
# Graph attributes include those of Tradition and those of Collation.
my %gattr_from;
# TODO Use meta introspection method from duplicate_reading to do this
# instead of naming custom keys.
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 unless $save_types{$attr->type_constraint->name};
$graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
}
# Extra custom keys for complex objects that should be saved in some form.
# The subroutine should return a string, or undef/empty.
if( $tmeta->has_method('stemmata') ) {
$graph_attributes{'stemmata'} = sub {
my @stemstrs;
map { push( @stemstrs, $_->editable( {linesep => ''} ) ) }
$self->tradition->stemmata;
join( "\n", @stemstrs );
};
}
if( $tmeta->has_method('user') ) {
$graph_attributes{'user'} = sub {
$self->tradition->user ? $self->tradition->user->id : undef
};
}
foreach my $datum ( sort keys %graph_attributes ) {
$graph_data_keys{$datum} = 'dg'.$gdi++;
my $key = $root->addNewChild( $graphml_ns, 'key' );
my $dtype = ref( $graph_attributes{$datum} ) ? 'string'
: $graph_attributes{$datum};
$key->setAttribute( 'attr.name', $datum );
$key->setAttribute( 'attr.type', $dtype );
$key->setAttribute( 'for', 'graph' );
$key->setAttribute( 'id', $graph_data_keys{$datum} );
}
# 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 unless $save_types{$attr->type_constraint->name};
$reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name};
}
if( $self->start->does('Text::Tradition::Morphology' ) ) {
# Extra custom key for the reading morphology
$reading_attributes{'lexemes'} = 'string';
}
my %node_data_keys;
my $ndi = 0;
foreach my $datum ( sort keys %reading_attributes ) {
$node_data_keys{$datum} = 'dn'.$ndi++;
my $key = $root->addNewChild( $graphml_ns, 'key' );
$key->setAttribute( 'attr.name', $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, 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_attributes = (
witness => 'string', # ID/label for a path
extra => 'boolean', # Path key
);
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 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', $edge_attributes{$datum} );
$key->setAttribute( 'for', 'edge' );
$key->setAttribute( 'id', $edge_data_keys{$datum} );
}
# 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', $xmlidname );
$sgraph->setAttribute( 'parse.edgeids', 'canonical' );
$sgraph->setAttribute( 'parse.edges', 0 ); # fill in later
$sgraph->setAttribute( 'parse.nodeids', 'canonical' );
$sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later
$sgraph->setAttribute( 'parse.order', 'nodesfirst' );
# Tradition/collation attribute data
foreach my $datum ( keys %graph_attributes ) {
my $value;
if( $datum eq 'version' ) {
$value = '3.2';
} elsif( ref( $graph_attributes{$datum} ) ) {
my $sub = $graph_attributes{$datum};
$value = &$sub();
} elsif( $gattr_from{$datum} eq 'Tradition' ) {
$value = $self->tradition->$datum;
} else {
$value = $self->$datum;
}
_add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value );
}
my $node_ctr = 0;
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 %reading_attributes ) {
my $nval = $n->$d;
# Custom serialization
if( $d eq 'lexemes' ) {
# If nval is a true value, we have lexemes so we need to
# serialize them. Otherwise set nval to undef so that the
# key is excluded from this reading.
$nval = $nval ? $n->_serialize_lexemes : undef;
} 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;
}
}
# Add the path edges to the sequence graph
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.
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] } );
my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' );
$edge_el->setAttribute( 'source', $from );
$edge_el->setAttribute( 'target', $to );
$edge_el->setAttribute( 'id', $id );
# It's a witness path, so add the witness
my $base = $wit;
my $key = $edge_data_keys{'witness'};
# Is this an ante-corr witness?
my $aclabel = $self->ac_label;
if( $wit =~ /^(.*)\Q$aclabel\E$/ ) {
# Keep the base witness
$base = $1;
# ...and record that this is an 'extra' reading path
_add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel );
}
_add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base );
}
}
# Report the actual number of nodes and edges that went in
$sgraph->setAttribute( 'parse.edges', $edge_ctr );
$sgraph->setAttribute( 'parse.nodes', $node_ctr );
# Add the relationship graph to the XML
map { delete $edge_data_keys{$_} } @path_attributes;
$self->relations->_as_graphml( $graphml_ns, $root, \%node_hash,
$node_data_keys{'id'}, \%edge_data_keys );
# Save and return the thing
my $result = decode_utf8( $graphml->toString(1) );
return $result;
}
sub _add_graphml_data {
my( $el, $key, $value ) = @_;
return unless defined $value;
my $data_el = $el->addNewChild( $el->namespaceURI, 'data' );
$data_el->setAttribute( 'key', $key );
$data_el->appendText( $value );
}
=head2 as_csv
Returns a CSV alignment table representation of the collation graph, one
row per witness (or witness uncorrected.)
=head2 as_tsv
Returns a tab-separated alignment table representation of the collation graph,
one row per witness (or witness uncorrected.)
=begin testing
use Text::Tradition;
use Text::CSV;
my $READINGS = 311;
my $PATHS = 361;
my $WITS = 13;
my $WITAC = 4;
my $datafile = 't/data/florilegium_tei_ps.xml';
my $tradition = Text::Tradition->new( 'input' => 'TEI',
'name' => 'test0',
'file' => $datafile,
'linear' => 1 );
my $c = $tradition->collation;
# Export the thing to CSV
my $csvstr = $c->as_csv();
# Count the columns
my $csv = Text::CSV->new({ sep_char => ',', binary => 1 });
my @lines = split(/\n/, $csvstr );
ok( $csv->parse( $lines[0] ), "Successfully parsed first line of CSV" );
is( scalar( $csv->fields ), $WITS + $WITAC, "CSV has correct number of witness columns" );
my @q_ac = grep { $_ eq 'Q'.$c->ac_label } $csv->fields;
ok( @q_ac, "Found a layered witness" );
my $t2 = Text::Tradition->new( input => 'Tabular',
name => 'test2',
string => $csvstr,
sep_char => ',' );
is( scalar $t2->collation->readings, $READINGS, "Reparsed CSV collation has all readings" );
is( scalar $t2->collation->paths, $PATHS, "Reparsed CSV collation has all paths" );
# Now do it with TSV
my $tsvstr = $c->as_tsv();
my $t3 = Text::Tradition->new( input => 'Tabular',
name => 'test3',
string => $tsvstr,
sep_char => "\t" );
is( scalar $t3->collation->readings, $READINGS, "Reparsed TSV collation has all readings" );
is( scalar $t3->collation->paths, $PATHS, "Reparsed TSV collation has all paths" );
my $table = $c->alignment_table;
my $noaccsv = $c->as_csv({ noac => 1 });
my @noaclines = split(/\n/, $noaccsv );
ok( $csv->parse( $noaclines[0] ), "Successfully parsed first line of no-ac CSV" );
is( scalar( $csv->fields ), $WITS, "CSV has correct number of witness columns" );
is( $c->alignment_table, $table, "Request for CSV did not alter the alignment table" );
my $safecsv = $c->as_csv({ safe_ac => 1});
my @safelines = split(/\n/, $safecsv );
ok( $csv->parse( $safelines[0] ), "Successfully parsed first line of safe CSV" );
is( scalar( $csv->fields ), $WITS + $WITAC, "CSV has correct number of witness columns" );
@q_ac = grep { $_ eq 'Q__L' } $csv->fields;
ok( @q_ac, "Found a sanitized layered witness" );
is( $c->alignment_table, $table, "Request for CSV did not alter the alignment table" );
# Test relationship collapse
$c->add_relationship( $c->readings_at_rank( 37 ), { type => 'spelling' } );
$c->add_relationship( $c->readings_at_rank( 60 ), { type => 'spelling' } );
my $mergedtsv = $c->as_tsv({mergetypes => [ 'spelling', 'orthographic' ] });
my $t4 = Text::Tradition->new( input => 'Tabular',
name => 'test4',
string => $mergedtsv,
sep_char => "\t" );
is( scalar $t4->collation->readings, $READINGS - 2, "Reparsed TSV merge collation has fewer readings" );
is( scalar $t4->collation->paths, $PATHS - 4, "Reparsed TSV merge collation has fewer paths" );
# Test non-ASCII sigla
my $t5 = Text::Tradition->new( input => 'Tabular',
name => 'nonascii',
file => 't/data/armexample.xlsx',
excel => 'xlsx' );
my $awittsv = $t5->collation->as_tsv({ noac => 1, ascii => 1 });
my @awitlines = split( /\n/, $awittsv );
like( $awitlines[0], qr/_A_5315622/, "Found ASCII sigil variant in TSV" );
=end testing
=cut
sub _tabular {
my( $self, $opts ) = @_;
my $table = $self->alignment_table( $opts );
my $csv_options = { binary => 1, quote_null => 0 };
$csv_options->{'sep_char'} = $opts->{fieldsep};
if( $opts->{fieldsep} eq "\t" ) {
# If it is really tab separated, nothing is an escape char.
$csv_options->{'quote_char'} = undef;
$csv_options->{'escape_char'} = '';
}
my $csv = Text::CSV->new( $csv_options );
my @result;
# Make the header row
my @witnesses = map { $_->{'witness'} } @{$table->{'alignment'}};
if( $opts->{ascii} ) {
# TODO think of a fix for this
throw( "Cannot currently produce ASCII sigla with witness layers" )
unless $opts->{noac};
my @awits = map { $self->tradition->witness( $_ )->ascii_sigil } @witnesses;
@witnesses = @awits;
}
$csv->combine( @witnesses );
push( @result, $csv->string );
# Make the rest of the rows
foreach my $idx ( 0 .. $table->{'length'} - 1 ) {
my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}};
my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs;
# Quick and dirty collapse of requested relationship types
if( ref( $opts->{mergetypes} ) eq 'ARRAY' ) {
# Now substitute the reading in the relevant index of @row
# for its merge-related reading
my %substitutes;
while( @rowobjs ) {
my $thisr = shift @rowobjs;
next unless $thisr;
next if exists $substitutes{$thisr->{t}->text};
# Make sure we don't have A <-> B substitutions.
$substitutes{$thisr->{t}->text} = $thisr->{t}->text;
foreach my $thatr ( @rowobjs ) {
next unless $thatr;
next if exists $substitutes{$thatr->{t}->text};
my $ttrel = $self->get_relationship( $thisr->{t}, $thatr->{t} );
next unless $ttrel;
next unless grep { $ttrel->type eq $_ } @{$opts->{mergetypes}};
# If we have got this far then we need to merge them.
$substitutes{$thatr->{t}->text} = $thisr->{t}->text;
}
}
@row = map { $_ && exists $substitutes{$_} ? $substitutes{$_} : $_ } @row;
}
$csv->combine( @row );
push( @result, $csv->string );
}
return join( "\n", @result );
}
sub as_csv {
my $self = shift;
my $opts = shift || {};
$opts->{fieldsep} = ',';
return $self->_tabular( $opts );
}
sub as_tsv {
my $self = shift;
my $opts = shift || {};
$opts->{fieldsep} = "\t";
return $self->_tabular( $opts );
}
=head2 alignment_table
Return a reference to an alignment table, in a slightly enhanced CollateX
format which looks like this:
$table = { alignment => [ { witness => "SIGIL",
tokens => [ { t => "TEXT" }, ... ] },
{ witness => "SIG2",
tokens => [ { t => "TEXT" }, ... ] },
... ],
length => TEXTLEN };
=cut
sub alignment_table {
my( $self, $opts ) = @_;
if( $self->has_cached_table ) {
return $self->cached_table
unless $opts->{noac} || $opts->{safe_ac};
}
# 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->_graphcalc_done && $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 ) {
# say STDERR "Making witness row(s) for " . $wit->sigil;
my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil );
my @row = _make_witness_row( \@wit_path, \@all_pos );
my $witobj = { 'witness' => $wit->sigil, 'tokens' => \@row };
$witobj->{'identifier'} = $wit->identifier if $wit->identifier;
push( @{$table->{'alignment'}}, $witobj );
if( $wit->is_layered && !$opts->{noac} ) {
my @wit_ac_path = $self->reading_sequence( $self->start, $self->end,
$wit->sigil.$self->ac_label );
my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos );
my $witlabel = $opts->{safe_ac}
? $wit->sigil . '__L' : $wit->sigil.$self->ac_label;
my $witacobj = { 'witness' => $witlabel,
'tokens' => \@ac_row };
$witacobj->{'identifier'} = $wit->identifier if $wit->identifier;
push( @{$table->{'alignment'}}, $witacobj );
}
}
unless( $opts->{noac} || $opts->{safe_ac} ) {
$self->cached_table( $table );
}
return $table;
}
sub _make_witness_row {
my( $path, $positions ) = @_;
my %char_hash;
map { $char_hash{$_} = undef } @$positions;
my $debug = 0;
foreach my $rdg ( @$path ) {
say STDERR "rank " . $rdg->rank if $debug;
# say STDERR "No rank for " . $rdg->id unless defined $rdg->rank;
$char_hash{$rdg->rank} = { 't' => $rdg };
}
my @row = map { $char_hash{$_} } @$positions;
# Fill in lacuna markers for undef spots in the row
my $last_el = shift @row;
my @filled_row = ( $last_el );
foreach my $el ( @row ) {
# If we are using node reference, make the lacuna node appear many times
# in the table. If not, use the lacuna tag.
if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) {
$el = $last_el;
}
push( @filled_row, $el );
$last_el = $el;
}
return @filled_row;
}
=head1 NAVIGATION METHODS
=head2 reading_sequence( $first, $last, $sigil, $backup )
Returns the ordered list of readings, starting with $first and ending
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 ) = @_;
$witness = $self->baselabel unless $witness;
my @readings = ( $start );
my %seen;
my $n = $start;
while( $n && $n->id ne $end->id ) {
if( exists( $seen{$n->id} ) ) {
throw( "Detected loop for $witness at " . $n->id );
}
$seen{$n->id} = 1;
my $next = $self->next_reading( $n, $witness );
unless( $next ) {
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];
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;
}
=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, $nolacuna ) = @_;
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'};
my $rdg = $e->{'t'};
next if $nolacuna && $rdg->is_lacuna && $rdg->rank ne $rank;
$readings{$e->{'t'}->id} = $e->{'t'};
}
return values %readings;
}
=head2 next_reading( $reading, $sigil );
Returns the reading that follows the given reading along the given witness
path.
=cut
sub next_reading {
# Return the successor via the corresponding path.
my $self = shift;
my $answer = $self->_find_linked_reading( 'next', @_ );
return undef unless $answer;
return $self->reading( $answer );
}
=head2 prior_reading( $reading, $sigil )
Returns the reading that precedes the given reading along the given witness
path.
=cut
sub prior_reading {
# Return the predecessor via the corresponding path.
my $self = shift;
my $answer = $self->_find_linked_reading( 'prior', @_ );
return $self->reading( $answer );
}
sub _find_linked_reading {
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 );
return undef unless scalar( @linked_paths );
# We have to find the linked path that contains all of the
# witnesses supplied in $path.
my( @path_wits, @alt_path_wits );
@path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path;
@alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path;
my $base_le;
my $alt_le;
foreach my $le ( @linked_paths ) {
if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) {
$base_le = $le;
}
my @le_wits = 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];
} elsif( _is_within( \@alt_path_wits, \@le_wits ) ) {
$alt_le = $le;
}
}
# Got this far? Return the alternate path if it exists.
return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0]
if $alt_le;
# Got this far? Return the base path if it exists.
return $direction eq 'next' ? $base_le->[1] : $base_le->[0]
if $base_le;
# Got this far? We have no appropriate path.
warn "Could not find $direction node from " . $node->id
. " along path $path";
return undef;
}
# Some set logic.
sub _is_within {
my( $set1, $set2 ) = @_;
my $ret = @$set1; # will be 0, i.e. false, if set1 is empty
foreach my $el ( @$set1 ) {
$ret = 0 unless grep { /^\Q$el\E$/ } @$set2;
}
return $ret;
}
# Return 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, $use_normal_form ] )
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. Optional specification of
$use_normal_form produces a text based on the normal form, rather than the
raw text, of the reading.
=cut
sub path_text {
my( $self, $wit, $start, $end, $normal ) = @_;
$start = $self->start unless $start;
$end = $self->end unless $end;
my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit );
return $self->known_path_text( $normal, @path );
}
=head2 known_path_text( $use_normal_form, @sequence )
Returns the text of a given sequence of readings. No attempt is made to
validate the sequence in question. If $use_normal_form is set to true, the
normal form of each reading in the sequence will be used to construct the
text.
=cut
sub known_path_text {
my( $self, $normal, @path ) = @_;
my $pathtext = '';
my $last;
foreach my $r ( @path ) {
unless ( $r->join_prior || !$last || $last->join_next ) {
$pathtext .= ' ';
}
$pathtext .= $normal ? $r->normal_form : $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.
=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.
# When we are done, clear out the witness path attributes, as they are no
# longer needed.
# TODO Find a way to replace the witness path attributes with encapsulated functions?
sub make_witness_paths {
my( $self ) = @_;
foreach my $wit ( $self->tradition->witnesses ) {
# say STDERR "Making path for " . $wit->sigil;
$self->make_witness_path( $wit );
}
}
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];
$self->add_path( $source, $target, $sig.$self->ac_label )
unless $self->has_path( $source, $target, $sig );
}
}
$wit->clear_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( 'n13', 'n23', { type => 'repetition' } );
is( $c->alignment_table, $table, "Alignment table unchanged after non-colo relationship add" );
$c->add_relationship( 'n24', 'n23', { type => 'spelling' } );
isnt( $c->alignment_table, $table, "Alignment table changed after colo relationship add" );
=end testing
=cut
sub calculate_ranks {
my $self = shift;
# Save the existing ranks, in case we need to invalidate the cached SVG.
throw( "Cannot calculate ranks on a non-linear graph" )
unless $self->linear;
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();
# Transfer our rankings from the topological graph to the real one.
foreach my $r ( $self->readings ) {
if( defined $node_ranks->{$self->equivalence( $r->id )} ) {
$r->rank( $node_ranks->{$self->equivalence( $r->id )} );
} else {
# Die. Find the last rank we calculated.
my @all_defined = sort { ( $node_ranks->{$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?" );
}
}
# Do we need to invalidate the cached data?
if( $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;
}
}
# The graph calculation information is now up to date.
$self->_graphcalc_done(1);
}
sub _clear_cache {
my $self = shift;
$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, %args ) = shift;
my %unique_rank_rdg;
my $changed;
foreach my $p ( $self->identical_readings( %args ) ) {
# say STDERR "Combining readings at same rank: @$p";
$changed = 1;
$self->merge_readings( @$p );
# TODO see if this now makes a common point.
}
# If we merged readings, the ranks are still fine but the alignment
# table is wrong. Wipe it.
$self->wipe_table() if $changed;
}
=head2 identical_readings
=head2 identical_readings( start => $startnode, end => $endnode )
=head2 identical_readings( startrank => $startrank, endrank => $endrank )
Goes through the graph identifying all pairs of readings that appear to be
identical, and therefore able to be merged into a single reading. Returns the
relevant identical pairs. Can be restricted to run over only a part of the
graph, specified either by node or by rank.
=cut
sub identical_readings {
my ( $self, %args ) = @_;
# Find where we should start and end.
my $startrank = $args{startrank} || 0;
if( $args{start} ) {
throw( "Starting reading has no rank" ) unless $self->reading( $args{start} )
&& $self->reading( $args{start} )->has_rank;
$startrank = $self->reading( $args{start} )->rank;
}
my $endrank = $args{endrank} || $self->end->rank;
if( $args{end} ) {
throw( "Ending reading has no rank" ) unless $self->reading( $args{end} )
&& $self->reading( $args{end} )->has_rank;
$endrank = $self->reading( $args{end} )->rank;
}
# Make sure the ranks are correct.
unless( $self->_graphcalc_done ) {
$self->calculate_ranks;
}
# Go through the readings looking for duplicates.
my %unique_rank_rdg;
my @pairs;
foreach my $rdg ( $self->readings ) {
next unless $rdg->has_rank;
my $rk = $rdg->rank;
next if $rk > $endrank || $rk < $startrank;
my $key = $rk . "||" . $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->is_identical( $ur ) ) {
push( @pairs, [ $ur, $rdg ] );
}
} else {
$unique_rank_rdg{$key} = $rdg;
}
}
return @pairs;
}
=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 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( 'n24', 'n23' )->id,
'__END__', "Found correct common successor" );
is( $c->common_predecessor( 'n19', 'n17' )->id,
'n16', "Found correct common predecessor for readings on same path" );
is( $c->common_successor( 'n21', 'n10' )->id,
'__END__', "Found correct common successor for readings on same path" );
=end testing
=cut
## Return the closest reading that is a predecessor of both the given readings.
sub common_predecessor {
my $self = shift;
my( $r1, $r2 ) = $self->_objectify_args( @_ );
return $self->_common_in_path( $r1, $r2, 'predecessors' );
}
sub common_successor {
my $self = shift;
my( $r1, $r2 ) = $self->_objectify_args( @_ );
return $self->_common_in_path( $r1, $r2, 'successors' );
}
# TODO think about how to do this without ranks...
sub _common_in_path {
my( $self, $r1, $r2, $dir ) = @_;
my $iter = $self->end->rank;
my @candidates;
my @last_r1 = ( $r1 );
my @last_r2 = ( $r2 );
# my %all_seen = ( $r1 => 'r1', $r2 => 'r2' );
my %all_seen;
# say STDERR "Finding common $dir for $r1, $r2";
while( !@candidates ) {
last unless $iter--; # Avoid looping infinitely
# Iterate separately down the graph from r1 and r2
my( @new_lc1, @new_lc2 );
foreach my $lc ( @last_r1 ) {
foreach my $p ( $lc->$dir ) {
if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) {
# say STDERR "Path candidate $p from $lc";
push( @candidates, $p );
} elsif( !$all_seen{$p->id} ) {
$all_seen{$p->id} = 'r1';
push( @new_lc1, $p );
}
}
}
foreach my $lc ( @last_r2 ) {
foreach my $p ( $lc->$dir ) {
if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) {
# say STDERR "Path candidate $p from $lc";
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
=over
=item * Rework XML serialization in a more modular way
=back
=head1 LICENSE
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.
=head1 AUTHOR
Tara L Andrews E<lt>aurum@cpan.orgE<gt>