[scpubgit/stemmatology.git] / lib / Text / Tradition / Parser / Tabular.pm

package Text::Tradition::Parser::Tabular;

use strict;
use warnings;
use Text::CSV_XS;

=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

=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" );

### 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 );
}

# 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" );
	}
}	

=end testing

=cut

sub parse {
    my( $tradition, $opts ) = @_;
    my $c = $tradition->collation; # shorthand
    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_XS->new( $csv_options );
    
    my $alignment_table;
    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
    foreach my $sigil ( @{$alignment_table->[0]} ) {
        my $wit = $tradition->add_witness( 'sigil' => $sigil );
        $wit->path( [ $c->start ] );
        push( @witnesses, $wit );
        my $aclabel = $c->ac_label;
        if( $sigil =~ /^(.*)\Q$aclabel\E$/ ) {
            $ac_wits{$sigil} = $1;
        }
    }
    
    # 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.
    foreach my $idx ( 1 .. $#{$alignment_table} ) {
        my $row = $alignment_table->[$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];
            if( $word ) {
                my $reading = $nodes->{$word};
                my $wit = $witnesses[$w];
                push( @{$wit->path}, $reading );
            } # else skip it for empty readings.
        }
    }
    
    # Collapse our lacunae into a single node and
    # push the end node onto all paths.
    $c->end->rank( scalar @$alignment_table );
    foreach my $wit ( @witnesses ) {
        my $p = $wit->path;
        my $last_rdg = shift @$p;
        my $new_p = [ $last_rdg ];
        foreach my $rdg ( @$p ) {
        	# 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;
    # 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 {
    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 $rargs = {
    		'id' => "$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++;
    }
    return \%unique;
}

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>
Commit	Line	Data
d9e873d0	1	package Text::Tradition::Parser::Tabular;
	2
	3	use strict;
	4	use warnings;
	5	use Text::CSV_XS;
	6
	7	=head1 NAME
	8
	9	Text::Tradition::Parser::Tabular
	10
3b853983	11	=head1 SYNOPSIS
	12
	13	use Text::Tradition;
	14
	15	my $t_from_file = Text::Tradition->new(
	16	'name' => 'my text',
	17	'input' => 'Tabular',
	18	'file' => '/path/to/collation.csv',
	19	'sep_char' => ','
	20	);
	21
	22	my $t_from_string = Text::Tradition->new(
	23	'name' => 'my text',
	24	'input' => 'Tabular',
	25	'string' => $tab_separated_collation,
	26	'sep_char' => "\t",
	27	);
	28
d9e873d0	29	=head1 DESCRIPTION
	30
	31	Parser module for Text::Tradition to read an alignment table format, such as CSV.
	32
	33	=head1 METHODS
	34
e867486f	35	=head2 B<parse>( $tradition, $option_hash )
3b853983	36
	37	Takes an initialized tradition and a set of options; creates the
	38	appropriate nodes and edges on the graph, as well as the appropriate
	39	witness objects. The $option_hash must contain either a 'file' or a
	40	'string' argument with the table to be parsed; it may also contain a
	41	'sep_char' argument to specify how the fields are separated.
	42
	43	The table should have witnesses arranged in columns, with the witness sigla
	44	in the first row. Empty cells are interpreted as omissions (and thus
	45	stemmatologically relevant.) Longer lacunae in the text, to be disregarded
	46	in cladistic analysis, may be represented by filling the appropriate cells
	47	with the tag '#LACUNA#'.
	48
	49	If a witness name ends in the collation's ac_label, it will be treated as
	50	an 'ante-correction' version of the 'main' witness whose sigil it shares.
	51
	52	=begin testing
	53
	54	use Text::Tradition;
	55	binmode STDOUT, ":utf8";
	56	binmode STDERR, ":utf8";
	57	eval { no warnings; binmode $DB::OUT, ":utf8"; };
	58
	59	my $csv = 't/data/florilegium.csv';
	60	my $t = Text::Tradition->new(
	61	'name' => 'inline',
	62	'input' => 'Tabular',
	63	'file' => $csv,
	64	'sep_char' => ',',
	65	);
d9e873d0	66
3b853983	67	is( ref( $t ), 'Text::Tradition', "Parsed florilegium CSV file" );
d9e873d0	68
3b853983	69	### TODO Check these figures
3b853983	70	if( $t ) {
0e47f4f6	71	is( scalar $t->collation->readings, 311, "Collation has all readings" );
0e47f4f6	72	is( scalar $t->collation->paths, 361, "Collation has all paths" );
3b853983	73	is( scalar $t->witnesses, 13, "Collation has all witnesses" );
	74	}
	75
b0b4421a	76	# Check that we have the right witnesses
	77	my %seen_wits;
	78	map { $seen_wits{$_} = 0 } qw/ A B C D E F G H K P Q S T /;
	79	foreach my $wit ( $t->witnesses ) {
	80	$seen_wits{$wit->sigil} = 1;
	81	}
	82	is( scalar keys %seen_wits, 13, "No extra witnesses were made" );
	83	foreach my $k ( keys %seen_wits ) {
	84	ok( $seen_wits{$k}, "Witness $k still exists" );
	85	}
	86
	87	# Check that the witnesses have the right texts
	88	foreach my $wit ( $t->witnesses ) {
	89	my $origtext = join( ' ', @{$wit->text} );
	90	my $graphtext = $t->collation->path_text( $wit->sigil );
	91	is( $graphtext, $origtext, "Collation matches original for witness " . $wit->sigil );
	92	}
	93
	94	# Check that the a.c. witnesses have the right text
	95	map { $seen_wits{$_} = 0 } qw/ A B C D F G H K S /;
	96	foreach my $k ( keys %seen_wits ) {
	97	my $wit = $t->witness( $k );
	98	if( $seen_wits{$k} ) {
	99	ok( $wit->is_layered, "Witness $k got marked as layered" );
	100	ok( $wit->has_layertext, "Witness $k has an a.c. version" );
	101	my $origtext = join( ' ', @{$wit->layertext} );
	102	my $acsig = $wit->sigil . $t->collation->ac_label;
861c3e27	103	my $graphtext = $t->collation->path_text( $acsig );
b0b4421a	104	is( $graphtext, $origtext, "Collation matches original a.c. for witness $k" );
	105	} else {
	106	ok( !$wit->is_layered, "Witness $k not marked as layered" );
	107	ok( !$wit->has_layertext, "Witness $k has no a.c. version" );
	108	}
	109	}
	110
3b853983	111	=end testing
d9e873d0	112
	113	=cut
	114
	115	sub parse {
dfc37e38	116	my( $tradition, $opts ) = @_;
d9e873d0	117	my $c = $tradition->collation; # shorthand
97a52a67	118	my $csv_options = { 'binary' => 1 };
	119	$csv_options->{'sep_char'} = $opts->{'sep_char'} \|\| "\t";
	120	if( $csv_options->{'sep_char'} eq "\t" ) {
	121	# If it is really tab separated, nothing is an escape char.
	122	$csv_options->{'quote_char'} = undef;
bba696c6	123	$csv_options->{'escape_char'} = undef;
97a52a67	124	}
97a52a67	125	my $csv = Text::CSV_XS->new( $csv_options );
dfc37e38	126
d9e873d0	127	my $alignment_table;
dfc37e38	128	if( exists $opts->{'string' } ) {
	129	my @lines = split( "\n", $opts->{'string'} );
	130	foreach my $l ( @lines ) {
	131	my $status = $csv->parse( $l );
	132	if( $status ) {
	133	push( @$alignment_table, [ $csv->fields ] );
	134	} else {
	135	warn "Could not parse line $l: " . $csv->error_input;
	136	}
	137	}
	138	} elsif( exists $opts->{'file'} ) {
bb11025b	139	open( my $fh, $opts->{'file'} )
	140	or warn "Could not open input file " . $opts->{'file'};
	141	binmode( $fh, ':utf8' );
dfc37e38	142	while( my $row = $csv->getline( $fh ) ) {
dfc37e38	143	push( @$alignment_table, $row );
d9e873d0	144	}
dfc37e38	145	close $fh;
	146	} else {
	147	warn "Could not find string or file option to parse";
	148	return;
d9e873d0	149	}
dfc37e38	150
d9e873d0	151	# Set up the witnesses we find in the first line
d9e873d0	152	my @witnesses;
b0b4421a	153	my %ac_wits; # Track layered witness -> main witness mapping
d9e873d0	154	foreach my $sigil ( @{$alignment_table->[0]} ) {
	155	my $wit = $tradition->add_witness( 'sigil' => $sigil );
	156	$wit->path( [ $c->start ] );
	157	push( @witnesses, $wit );
3b853983	158	my $aclabel = $c->ac_label;
3b853983	159	if( $sigil =~ /^(.*)\Q$aclabel\E$/ ) {
b0b4421a	160	$ac_wits{$sigil} = $1;
3b853983	161	}
d9e873d0	162	}
d9e873d0	163
b0b4421a	164	# Save the original witness text sequences. Have to loop back through
	165	# the witness columns after we have identified all the a.c. witnesses.
	166	foreach my $idx ( 0 .. $#{$alignment_table->[0]} ) {
	167	my @sequence = map { $_->[$idx] } @{$alignment_table};
	168	my $sigil = shift @sequence;
	169	my $is_layer = exists( $ac_wits{$sigil} );
	170	my $wit = $tradition->witness( $is_layer ? $ac_wits{$sigil} : $sigil );
	171	# Now get rid of gaps and meta-readings like #LACUNA#
	172	my @words = grep { $_ && $_ !~ /^\#.*\#$/ } @sequence;
	173	$is_layer ? $wit->layertext( \@words ) : $wit->text( \@words );
	174	}
	175
d9e873d0	176	# Now for the next rows, make nodes as necessary, assign their ranks, and
d9e873d0	177	# add them to the witness paths.
d9e873d0	178	foreach my $idx ( 1 .. $#{$alignment_table} ) {
d9e873d0	179	my $row = $alignment_table->[$idx];
027d819c	180	my $nodes = _make_nodes( $c, $row, $idx );
d9e873d0	181	foreach my $w ( 0 .. $#{$row} ) {
	182	# push the appropriate node onto the appropriate witness path
	183	my $word = $row->[$w];
	184	if( $word ) {
	185	my $reading = $nodes->{$word};
	186	my $wit = $witnesses[$w];
	187	push( @{$wit->path}, $reading );
	188	} # else skip it for empty readings.
	189	}
	190	}
	191
eca16057	192	# Collapse our lacunae into a single node and
eca16057	193	# push the end node onto all paths.
d9e873d0	194	$c->end->rank( scalar @$alignment_table );
d9e873d0	195	foreach my $wit ( @witnesses ) {
eca16057	196	my $p = $wit->path;
	197	my $last_rdg = shift @$p;
	198	my $new_p = [ $last_rdg ];
	199	foreach my $rdg ( @$p ) {
83d5ac3a	200	# Omit the reading if we are in a lacuna already.
	201	next if $rdg->is_lacuna && $last_rdg->is_lacuna;
	202	# Save the reading otherwise.
	203	push( @$new_p, $rdg );
	204	$last_rdg = $rdg;
eca16057	205	}
	206	push( @$new_p, $c->end );
	207	$wit->path( $new_p );
d9e873d0	208	}
d9e873d0	209
3b853983	210	# Fold any a.c. witnesses into their main witness objects, and
	211	# delete the independent a.c. versions.
	212	foreach my $a ( keys %ac_wits ) {
b0b4421a	213	my $ac_wit = $tradition->witness( $a );
b0b4421a	214	my $main_wit = $tradition->witness( $ac_wits{$a} );
3b853983	215	next unless $main_wit;
861c3e27	216	$main_wit->is_layered(1);
3b853983	217	$main_wit->uncorrected_path( $ac_wit->path );
	218	$tradition->del_witness( $ac_wit );
	219	}
83d5ac3a	220
d9e873d0	221	# Join up the paths.
d9e873d0	222	$c->make_witness_paths;
83d5ac3a	223	# Delete our unused lacuna nodes.
	224	foreach my $rdg ( grep { $_->is_lacuna } $c->readings ) {
	225	$c->del_reading( $rdg ) unless $c->reading_witnesses( $rdg );
	226	}
861c3e27	227
	228	# Do a consistency check.
	229	foreach my $wit ( $tradition->witnesses ) {
	230	my $pathtext = $c->path_text( $wit->sigil );
	231	my $origtext = join( ' ', @{$wit->text} );
	232	warn "Text differs for witness " . $wit->sigil
	233	unless $pathtext eq $origtext;
	234	if( $wit->is_layered ) {
	235	$pathtext = $c->path_text( $wit->sigil.$c->ac_label );
	236	$origtext = join( ' ', @{$wit->layertext} );
	237	warn "Ante-corr text differs for witness " . $wit->sigil
	238	unless $pathtext eq $origtext;
	239	} else {
	240	warn "Text " . $wit->sigil . " has a layered text but is not marked as layered"
	241	if $wit->has_layertext;
	242	}
	243	}
202ccb18	244
	245	# Note that our ranks and common readings are set.
	246	$c->_graphcalc_done(1);
d9e873d0	247	}
d9e873d0	248
027d819c	249	sub _make_nodes {
d9e873d0	250	my( $collation, $row, $index ) = @_;
d9e873d0	251	my %unique;
15db7774	252	my $commonctr = 0; # Holds the number of unique readings + gaps, ex. lacunae.
d9e873d0	253	foreach my $w ( @$row ) {
d9e873d0	254	$unique{$w} = 1 if $w;
15db7774	255	$commonctr +=1 unless ( $w && $w eq '#LACUNA#' );
d9e873d0	256	}
	257	my $ctr = 1;
	258	foreach my $w ( keys %unique ) {
a753cc84	259	my $rargs = {
a753cc84	260	'id' => "$index,$ctr",
	261	'rank' => $index,
	262	'text' => $w,
	263	};
15db7774	264	if( $w eq '#LACUNA#' ) {
	265	$rargs->{'is_lacuna'} = 1;
	266	} elsif( $commonctr == 1 ) {
	267	$rargs->{'is_common'} = 1;
	268	}
a753cc84	269	my $r = $collation->add_reading( $rargs );
d9e873d0	270	$unique{$w} = $r;
a753cc84	271	$ctr++;
d9e873d0	272	}
	273	return \%unique;
	274	}
	275
3b853983	276	1;
	277
	278	=head1 LICENSE
	279
	280	This package is free software and is provided "as is" without express
	281	or implied warranty. You can redistribute it and/or modify it under
	282	the same terms as Perl itself.
	283
	284	=head1 AUTHOR
	285
	286	Tara L Andrews E<lt>aurum@cpan.orgE<gt>