use strict;
use warnings;
-use Text::CSV_XS;
+use Text::CSV;
=head1 NAME
Text::Tradition::Parser::Tabular
+=head1 SYNOPSIS
+
+ use Text::Tradition;
+
+ my $t_from_file = Text::Tradition->new(
+ 'name' => 'my text',
+ 'input' => 'Tabular',
+ 'file' => '/path/to/collation.csv',
+ 'sep_char' => ','
+ );
+
+ my $t_from_string = Text::Tradition->new(
+ 'name' => 'my text',
+ 'input' => 'Tabular',
+ 'string' => $tab_separated_collation,
+ 'sep_char' => "\t",
+ );
+
=head1 DESCRIPTION
Parser module for Text::Tradition to read an alignment table format, such as CSV.
=head1 METHODS
-=over
+=head2 B<parse>( $tradition, $option_hash )
+
+Takes an initialized tradition and a set of options; creates the
+appropriate nodes and edges on the graph, as well as the appropriate
+witness objects. The $option_hash must contain either a 'file' or a
+'string' argument with the table to be parsed; it may also contain a
+'sep_char' argument to specify how the fields are separated.
+
+The table should have witnesses arranged in columns, with the witness sigla
+in the first row. Empty cells are interpreted as omissions (and thus
+stemmatologically relevant.) Longer lacunae in the text, to be disregarded
+in cladistic analysis, may be represented by filling the appropriate cells
+with the tag '#LACUNA#'.
+
+If a witness name ends in the collation's ac_label, it will be treated as
+an 'ante-correction' version of the 'main' witness whose sigil it shares.
+
+=begin testing
+
+use Text::Tradition;
+binmode STDOUT, ":utf8";
+binmode STDERR, ":utf8";
+eval { no warnings; binmode $DB::OUT, ":utf8"; };
+
+my $csv = 't/data/florilegium.csv';
+my $t = Text::Tradition->new(
+ 'name' => 'inline',
+ 'input' => 'Tabular',
+ 'file' => $csv,
+ 'sep_char' => ',',
+ );
+
+is( ref( $t ), 'Text::Tradition', "Parsed florilegium CSV file" );
-=item B<parse>
+### TODO Check these figures
+if( $t ) {
+ is( scalar $t->collation->readings, 311, "Collation has all readings" );
+ is( scalar $t->collation->paths, 361, "Collation has all paths" );
+ is( scalar $t->witnesses, 13, "Collation has all witnesses" );
+}
+
+# Check that we have the right witnesses
+my %seen_wits;
+map { $seen_wits{$_} = 0 } qw/ A B C D E F G H K P Q S T /;
+foreach my $wit ( $t->witnesses ) {
+ $seen_wits{$wit->sigil} = 1;
+}
+is( scalar keys %seen_wits, 13, "No extra witnesses were made" );
+foreach my $k ( keys %seen_wits ) {
+ ok( $seen_wits{$k}, "Witness $k still exists" );
+}
+
+# Check that the witnesses have the right texts
+foreach my $wit ( $t->witnesses ) {
+ my $origtext = join( ' ', @{$wit->text} );
+ my $graphtext = $t->collation->path_text( $wit->sigil );
+ is( $graphtext, $origtext, "Collation matches original for witness " . $wit->sigil );
+}
-parse( $graph, $graphml_string );
+# Check that the a.c. witnesses have the right text
+map { $seen_wits{$_} = 0 } qw/ A B C D F G H K S /;
+foreach my $k ( keys %seen_wits ) {
+ my $wit = $t->witness( $k );
+ if( $seen_wits{$k} ) {
+ ok( $wit->is_layered, "Witness $k got marked as layered" );
+ ok( $wit->has_layertext, "Witness $k has an a.c. version" );
+ my $origtext = join( ' ', @{$wit->layertext} );
+ my $acsig = $wit->sigil . $t->collation->ac_label;
+ my $graphtext = $t->collation->path_text( $acsig );
+ is( $graphtext, $origtext, "Collation matches original a.c. for witness $k" );
+ } else {
+ ok( !$wit->is_layered, "Witness $k not marked as layered" );
+ ok( !$wit->has_layertext, "Witness $k has no a.c. version" );
+ }
+}
-Takes an initialized Text::Tradition::Graph object and a string
-containing the GraphML; creates the appropriate nodes and edges on the
-graph.
+=end testing
=cut
sub parse {
- my( $tradition, $tab_str ) = @_;
- # TODO Allow setting of sep_char
+ my( $tradition, $opts ) = @_;
my $c = $tradition->collation; # shorthand
- my $csv = Text::CSV_XS->new( { binary => 1, # binary for UTF-8
- sep_char => "\t" } );
- my @lines = split( "\n", $tab_str );
- # Conveniently, we are basically receiving exactly the sort of alignment table
- # we might want to produce later. May as well save it.
+ my $csv_options = { 'binary' => 1 };
+ $csv_options->{'sep_char'} = $opts->{'sep_char'} || "\t";
+ if( $csv_options->{'sep_char'} eq "\t" ) {
+ # If it is really tab separated, nothing is an escape char.
+ $csv_options->{'quote_char'} = undef;
+ $csv_options->{'escape_char'} = undef;
+ }
+ my $csv = Text::CSV->new( $csv_options );
+
my $alignment_table;
- foreach my $l ( @lines ) {
- my $status = $csv->parse( $l );
- if( $status ) {
- push( @$alignment_table, [ $csv->fields ] );
- } else {
- warn "Could not parse line $l: " . $csv->error_input;
+ if( exists $opts->{'string' } ) {
+ my @lines = split( "\n", $opts->{'string'} );
+ foreach my $l ( @lines ) {
+ my $status = $csv->parse( $l );
+ if( $status ) {
+ push( @$alignment_table, [ $csv->fields ] );
+ } else {
+ warn "Could not parse line $l: " . $csv->error_input;
+ }
}
+ } elsif( exists $opts->{'file'} ) {
+ open( my $fh, $opts->{'file'} )
+ or warn "Could not open input file " . $opts->{'file'};
+ binmode( $fh, ':utf8' );
+ while( my $row = $csv->getline( $fh ) ) {
+ push( @$alignment_table, $row );
+ }
+ close $fh;
+ } else {
+ warn "Could not find string or file option to parse";
+ return;
}
-
+
# Set up the witnesses we find in the first line
my @witnesses;
+ my %ac_wits; # Track layered witness -> main witness mapping
+ my $aclabel = $c->ac_label;
foreach my $sigil ( @{$alignment_table->[0]} ) {
- my $wit = $tradition->add_witness( 'sigil' => $sigil );
+ if( $sigil =~ /^(.*)\Q$aclabel\E$/ ) {
+ # Sanitize the sigil name to an XML name
+ $sigil = $1 . '_layered';
+ $ac_wits{$sigil} = $1;
+ }
+ my $wit = $tradition->add_witness(
+ 'sigil' => $sigil, 'sourcetype' => 'collation' );
$wit->path( [ $c->start ] );
push( @witnesses, $wit );
+ my $aclabel = $c->ac_label;
}
+ # Save the original witness text sequences. Have to loop back through
+ # the witness columns after we have identified all the a.c. witnesses.
+ foreach my $idx ( 0 .. $#{$alignment_table->[0]} ) {
+ my @sequence = map { $_->[$idx] } @{$alignment_table};
+ my $sigil = shift @sequence;
+ my $is_layer = exists( $ac_wits{$sigil} );
+ my $wit = $tradition->witness( $is_layer ? $ac_wits{$sigil} : $sigil );
+ # Now get rid of gaps and meta-readings like #LACUNA#
+ my @words = grep { $_ && $_ !~ /^\#.*\#$/ } @sequence;
+ $is_layer ? $wit->layertext( \@words ) : $wit->text( \@words );
+ }
+
# Now for the next rows, make nodes as necessary, assign their ranks, and
# add them to the witness paths.
- $DB::single = 1;
foreach my $idx ( 1 .. $#{$alignment_table} ) {
my $row = $alignment_table->[$idx];
- my $nodes = make_nodes( $c, $row, $idx );
+ my $nodes = _make_nodes( $c, $row, $idx );
foreach my $w ( 0 .. $#{$row} ) {
# push the appropriate node onto the appropriate witness path
my $word = $row->[$w];
}
}
-
# Collapse our lacunae into a single node and
# push the end node onto all paths.
$c->end->rank( scalar @$alignment_table );
my $last_rdg = shift @$p;
my $new_p = [ $last_rdg ];
foreach my $rdg ( @$p ) {
- if( $rdg->text eq '#LACUNA#' ) {
- # If we are in a lacuna already, drop this node.
- # Otherwise make a lacuna node and drop this node.
- unless( $last_rdg->is_lacuna ) {
- my $l = $c->add_lacuna( $rdg->name );
- $l->rank( $rdg->rank );
- push( @$new_p, $l );
- $last_rdg = $l;
- }
- $c->del_reading( $rdg );
- } else {
- # No lacuna, save the reading.
- push( @$new_p, $rdg );
- }
+ # Omit the reading if we are in a lacuna already.
+ next if $rdg->is_lacuna && $last_rdg->is_lacuna;
+ # Save the reading otherwise.
+ push( @$new_p, $rdg );
+ $last_rdg = $rdg;
}
push( @$new_p, $c->end );
$wit->path( $new_p );
}
+ # Fold any a.c. witnesses into their main witness objects, and
+ # delete the independent a.c. versions.
+ foreach my $a ( keys %ac_wits ) {
+ my $ac_wit = $tradition->witness( $a );
+ my $main_wit = $tradition->witness( $ac_wits{$a} );
+ next unless $main_wit;
+ $main_wit->is_layered(1);
+ $main_wit->uncorrected_path( $ac_wit->path );
+ $tradition->del_witness( $ac_wit );
+ }
+
# Join up the paths.
$c->make_witness_paths;
-
- # Save the alignment table that was so handily provided to us.
- # TODO if we support other delimiters, we will have to re-export this
- # rather than saving the original string.
- $c->_save_csv( $tab_str );
+ # Delete our unused lacuna nodes.
+ foreach my $rdg ( grep { $_->is_lacuna } $c->readings ) {
+ $c->del_reading( $rdg ) unless $c->reading_witnesses( $rdg );
+ }
+
+ # Do a consistency check.
+ foreach my $wit ( $tradition->witnesses ) {
+ my $pathtext = $c->path_text( $wit->sigil );
+ my $origtext = join( ' ', @{$wit->text} );
+ warn "Text differs for witness " . $wit->sigil
+ unless $pathtext eq $origtext;
+ if( $wit->is_layered ) {
+ $pathtext = $c->path_text( $wit->sigil.$c->ac_label );
+ $origtext = join( ' ', @{$wit->layertext} );
+ warn "Ante-corr text differs for witness " . $wit->sigil
+ unless $pathtext eq $origtext;
+ } else {
+ warn "Text " . $wit->sigil . " has a layered text but is not marked as layered"
+ if $wit->has_layertext;
+ }
+ }
+
+ # Note that our ranks and common readings are set.
+ $c->_graphcalc_done(1);
}
-sub make_nodes {
+sub _make_nodes {
my( $collation, $row, $index ) = @_;
my %unique;
+ my $commonctr = 0; # Holds the number of unique readings + gaps, ex. lacunae.
foreach my $w ( @$row ) {
$unique{$w} = 1 if $w;
+ $commonctr +=1 unless ( $w && $w eq '#LACUNA#' );
}
my $ctr = 1;
foreach my $w ( keys %unique ) {
- my $r = $collation->add_reading( "$index,$ctr" );
- $ctr++;
- $r->rank( $index );
- $r->text( $w );
+ my $rargs = {
+ 'id' => "$index,$ctr",
+ 'rank' => $index,
+ 'text' => $w,
+ };
+ if( $w eq '#LACUNA#' ) {
+ $rargs->{'is_lacuna'} = 1;
+ } elsif( $commonctr == 1 ) {
+ $rargs->{'is_common'} = 1;
+ }
+ my $r = $collation->add_reading( $rargs );
$unique{$w} = $r;
+ $ctr++;
}
+ # Collate this sequence of readings via a single 'collation' relationship.
+ my @rankrdgs = values %unique;
+ my $collation_rel;
+ while( @rankrdgs ) {
+ my $r = shift @rankrdgs;
+ next if $r->is_meta;
+ foreach my $nr ( @rankrdgs ) {
+ if( $collation_rel ) {
+ $collation->add_relationship( $r, $nr, $collation_rel );
+ } else {
+ $collation->add_relationship( $r, $nr,
+ { 'type' => 'collated',
+ 'annotation' => "Parsed together for rank $index" } );
+ $collation_rel = $collation->get_relationship( $r, $nr );
+ }
+ }
+ }
+
return \%unique;
}
-1;
\ No newline at end of file
+1;
+
+=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>
projects / scpubgit/stemmatology.git / blobdiff