use strict;
use warnings;
-use Text::Tradition;
+use Algorithm::Diff; # for word similarity measure
+use Encode qw/ decode_utf8 encode_utf8 /;
+use Exporter 'import';
+use Graph;
+use JSON qw/ to_json decode_json /;
+use LWP::UserAgent;
+use Set::Scalar;
+use Text::Tradition::Analysis::Result;
+use Text::Tradition::Directory;
use Text::Tradition::Stemma;
+use TryCatch;
+
+use vars qw/ @EXPORT_OK /;
+@EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /;
+
+my $SOLVER_URL = 'http://byzantini.st/cgi-bin/graphcalc.cgi';
+my $unsolved_problems = {};
+
+=head1 NAME
+
+Text::Tradition::Analysis - functions for stemma analysis of a tradition
+
+=head1 SYNOPSIS
+
+ use Text::Tradition;
+ use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+ my $t = Text::Tradition->new(
+ 'name' => 'this is a text',
+ 'input' => 'TEI',
+ 'file' => '/path/to/tei_parallel_seg_file.xml' );
+ $t->add_stemma( 'dotfile' => $stemmafile );
+
+ my $variant_data = run_analysis( $tradition );
+ # Recalculate rank $n treating all orthographic variants as equivalent
+ my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' );
+
+=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 SUBROUTINES
+
+=head2 run_analysis( $tradition, %opts )
+
+Runs the analysis described in analyze_variant_location on every location in the
+collation of the given tradition, with the given options. These include:
+
+=over 4
+
+=item * stemma_id - Specify which of the tradition's stemmata to use. Default
+is 0 (i.e. the first).
+
+=item * ranks - Specify a list of location ranks to analyze; exclude the rest.
+
+=item * merge_types - Specify a list of relationship types, where related readings
+should be treated as identical for the purposes of analysis.
+
+=item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants.
+
+=back
+
+=begin testing
+
+use Text::Tradition;
+use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /;
+
+my $datafile = 't/data/florilegium_tei_ps.xml';
+my $tradition = Text::Tradition->new( 'input' => 'TEI',
+ 'name' => 'test0',
+ 'file' => $datafile );
+my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' );
+is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" );
-sub new {
- my( $class, $args ) = @_;
- my $self = {};
- bless( $self, $class );
- $self->{'data'} = [];
- foreach my $t ( @{$args->{'traditions'}} ) {
- $self->run_analysis( $t->{'file'}, $t->{'stemmadot'} );
+my %expected_genealogical = (
+ 1 => 0,
+ 2 => 1,
+ 3 => 0,
+ 5 => 0,
+ 7 => 0,
+ 8 => 0,
+ 10 => 0,
+ 13 => 1,
+ 33 => 0,
+ 34 => 0,
+ 37 => 0,
+ 60 => 0,
+ 81 => 1,
+ 84 => 0,
+ 87 => 0,
+ 101 => 0,
+ 102 => 0,
+ 122 => 1,
+ 157 => 0,
+ 166 => 1,
+ 169 => 1,
+ 200 => 0,
+ 216 => 1,
+ 217 => 1,
+ 219 => 1,
+ 241 => 1,
+ 242 => 1,
+ 243 => 1,
+);
+
+my $data = run_analysis( $tradition, calcdsn => 'dbi:SQLite:dbname=t/data/analysis.db' );
+my $c = $tradition->collation;
+foreach my $row ( @{$data->{'variants'}} ) {
+ # Account for rows that used to be "not useful"
+ unless( exists $expected_genealogical{$row->{'id'}} ) {
+ $expected_genealogical{$row->{'id'}} = 1;
+ }
+ my $gen_bool = $row->{'genealogical'} ? 1 : 0;
+ is( $gen_bool, $expected_genealogical{$row->{'id'}},
+ "Got correct genealogical flag for row " . $row->{'id'} );
+ # Check that we have the right row with the right groups
+ my $rank = $row->{'id'};
+ foreach my $rdghash ( @{$row->{'readings'}} ) {
+ # Skip 'readings' that aren't really
+ next unless $c->reading( $rdghash->{'readingid'} );
+ # Check the rank
+ is( $c->reading( $rdghash->{'readingid'} )->rank, $rank,
+ "Got correct reading rank" );
+ # Check the witnesses
+ my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} );
+ my @sgrp = sort @{$rdghash->{'group'}};
+ is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" );
}
- return $self;
}
+is( $data->{'variant_count'}, 58, "Got right total variant number" );
+# TODO Make something meaningful of conflict count, maybe test other bits
+
+=end testing
+
+=cut
sub run_analysis {
- my( $self, $file, $stemmadot ) = @_;
- # What we will return
- my $svg;
- my $variants = [];
- my $data = {};
-
- # Read in the file and stemma
- my $tradition = Text::Tradition->new(
- 'input' => 'Self',
- 'file' => $file,
- 'linear' => 1,
- );
- $data->{'title'} = $tradition->name;
+ my( $tradition, %opts ) = @_;
+ my $c = $tradition->collation;
+ my $aclabel = $c->ac_label;
+
+ my $stemma_id = $opts{'stemma_id'} || 0;
+ my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : ();
+ my $collapse = Set::Scalar->new();
+ if( $opts{'merge_types'} && ref( $opts{'merge_types'} ) eq 'ARRAY' ) {
+ $collapse->insert( @{$opts{'merge_types'}} );
+ } elsif( $opts{'merge_types'} ) {
+ $collapse->insert( $opts{'merge_types'} );
+ }
- my $stemma = Text::Tradition::Stemma->new(
- 'collation' => $tradition->collation,
- 'dot' => $stemmadot,
- );
- # We will return the stemma picture
- $svg = $stemma->as_svg( { size => "8,7.5" } );;
- $data->{'svg'} = $svg;
+ # Make sure we have a lookup DB for graph calculation results; this will die
+ # if calcdir or calcdsn isn't passed.
+ my $dir;
+ if( exists $opts{'calcdir'} ) {
+ $dir = delete $opts{'calcdir'}
+ } elsif ( exists $opts{'calcdsn'} ) {
+ $dir = Text::Tradition::Directory->new( dsn => $opts{'calcdsn'} );
+ }
+
+ # Get the stemma
+ my $stemma = $tradition->stemma( $stemma_id );
+
+ # Figure out which witnesses we are working with - that is, the ones that
+ # appear both in the stemma and in the tradition. All others are 'lacunose'
+ # for our purposes.
+ my $lacunose = Set::Scalar->new( $stemma->hypotheticals );
+ my $stemma_wits = Set::Scalar->new( $stemma->witnesses );
+ my $tradition_wits = Set::Scalar->new( map { $_->sigil } $tradition->witnesses );
+ $lacunose->insert( $stemma_wits->symmetric_difference( $tradition_wits )->members );
+
+ # Find and mark 'common' ranks for exclusion, unless they were
+ # explicitly specified.
+ unless( @ranks ) {
+ my %common_rank;
+ foreach my $rdg ( $c->common_readings ) {
+ $common_rank{$rdg->rank} = 1;
+ }
+ @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 );
+ }
- # We have the collation, so get the alignment table with witnesses in rows.
- # Also return the reading objects in the table, rather than just the words.
- my $wits = {};
- map { $wits->{$_} = 1 } $stemma->witnesses;
- my $all_wits_table = $tradition->collation->make_alignment_table( 'refs', $wits );
+ # Group the variants to send to the solver
+ my @groups;
+ my @use_ranks;
+ my %lacunae;
+ my $moved = {};
+ foreach my $rank ( @ranks ) {
+ my $missing = $lacunose->clone();
+ my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, $collapse );
+ # Filter out any empty rankgroups
+ # (e.g. from the later rank for a transposition)
+ next unless keys %$rankgroup;
+ # Get the graph for this rankgroup
+ my $rankgraph = _graph_for_grouping( $stemma, $rankgroup, $missing, $aclabel );
+ if( $opts{'exclude_type1'} ) {
+ # Check to see whether this is a "useful" group.
+ next unless _useful_variant( $rankgroup, $rankgraph, $aclabel );
+ }
+ push( @use_ranks, $rank );
+ push( @groups, { grouping => $rankgroup, graph => $rankgraph } );
+ $lacunae{$rank} = $missing;
+ }
+ # Run the solver
+ my $answer;
+ try {
+ $answer = solve_variants( $dir, @groups );
+ } catch ( Text::Tradition::Error $e ) {
+ if( $e->message =~ /IDP/ ) {
+ # Something is wrong with the solver; make the variants table anyway
+ $answer->{'variants'} = [];
+ map { push( @{$answer->{'variants'}}, _init_unsolved( $_, 'IDP error' ) ) }
+ @groups;
+ } else {
+ # Something else is wrong; error out.
+ $e->throw;
+ }
+ }
+
+ # Do further analysis on the answer
+ my $conflict_count = 0;
+ my $reversion_count = 0;
+ foreach my $idx ( 0 .. $#use_ranks ) {
+ my $location = $answer->{'variants'}->[$idx];
+ # Add the rank back in
+ my $rank = $use_ranks[$idx];
+ $location->{'id'} = $rank;
+ # Note what our lacunae are
+ my %lmiss;
+ map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}};
+ $location->{'missing'} = [ keys %lmiss ];
+
+ # Run the extra analysis we need.
+ ## TODO We run through all the variants in this call, so
+ ## why not add the reading data there instead of here below?
+ my $graph = $groups[$idx]->{graph};
+ analyze_location( $tradition, $graph, $location, \%lmiss );
+
+ my @layerwits;
+ # Do the final post-analysis tidying up of the data.
+ foreach my $rdghash ( @{$location->{'readings'}} ) {
+ $conflict_count++ if $rdghash->{'is_conflict'};
+ $reversion_count++ if $rdghash->{'is_reverted'};
+ # Add the reading text back in, setting display value as needed
+ my $rdg = $c->reading( $rdghash->{'readingid'} );
+ if( $rdg ) {
+ $rdghash->{'text'} = $rdg->text .
+ ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' );
+ $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid;
+ $rdghash->{'is_nonsense'} = $rdg->is_nonsense;
+ }
+ # Remove lacunose witnesses from this reading's list now that the
+ # analysis is done
+ my @realgroup;
+ map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}};
+ $rdghash->{'group'} = \@realgroup;
+ # Note any layered witnesses that appear in this group
+ foreach( @realgroup ) {
+ if( $_ =~ /^(.*)\Q$aclabel\E$/ ) {
+ push( @layerwits, $1 );
+ }
+ }
+ }
+ $location->{'layerwits'} = \@layerwits if @layerwits;
+ }
+ $answer->{'conflict_count'} = $conflict_count;
+ $answer->{'reversion_count'} = $reversion_count;
- # For each column in the alignment table, we want to see if the existing
- # groupings of witnesses match our stemma hypothesis. We also want, at the
- # end, to produce an HTML table with all the variants.
- my $html_columns = 0;
- my ( $total, $genealogical, $conflicts ) = ( 0, 0, 0 );
+ return $answer;
+}
+
+=head2 group_variants( $tradition, $rank, $lacunose, $transposed, $merge_relationship_types )
+
+Groups the variants at the given $rank of the collation, treating any
+relationships in the set $merge_relationship_types as equivalent.
+$lacunose should be a reference to an array, to which the sigla of lacunose
+witnesses at this rank will be appended; $transposed should be a reference
+to a hash, wherein the identities of transposed readings and their
+relatives will be stored.
+
+Returns a hash $group_readings where $rdg is attested by the witnesses listed
+in $group_readings->{$rdg}.
+
+=cut
+
+# Return group_readings, groups, lacunose
+sub group_variants {
+ my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_;
+ my $c = $tradition->collation;
+ my $aclabel = $c->ac_label;
+ my $table = $c->alignment_table;
+ # Get the alignment table readings
+ my %readings_at_rank;
+ my $check_for_gaps = Set::Scalar->new();
+ my %moved_wits;
+ my $has_transposition;
+ foreach my $tablewit ( @{$table->{'alignment'}} ) {
+ my $rdg = $tablewit->{'tokens'}->[$rank-1];
+ my $wit = $tablewit->{'witness'};
+ # Exclude the witness if it is "lacunose" which if we got here
+ # means "not in the stemma".
+ next if _is_lacunose( $wit, $lacunose, $aclabel );
+ # Note if the witness is actually in a lacuna
+ if( $rdg && $rdg->{'t'}->is_lacuna ) {
+ _add_to_witlist( $wit, $lacunose, $aclabel );
+ # Otherwise the witness either has a positive reading...
+ } elsif( $rdg ) {
+ # If the reading has been counted elsewhere as a transposition, ignore it.
+ if( $transposed->{$rdg->{'t'}->id} ) {
+ # TODO Does this cope with three-way transpositions?
+ map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}};
+ next;
+ }
+ # Otherwise, record it...
+ $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'};
+ # ...and grab any transpositions, and their relations.
+ my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings();
+ foreach my $trdg ( @transp ) {
+ next if exists $readings_at_rank{$trdg->id};
+ $has_transposition = 1;
+ my @affected_wits = _table_witnesses(
+ $table, $trdg, $lacunose, $aclabel );
+ next unless @affected_wits;
+ map { $moved_wits{$_} = 1 } @affected_wits;
+ $transposed->{$trdg->id} =
+ [ _table_witnesses( $table, $rdg->{'t'}, $lacunose, $aclabel ) ];
+ $readings_at_rank{$trdg->id} = $trdg;
+ }
+ # ...or it is empty, ergo a gap.
+ } else {
+ _add_to_witlist( $wit, $check_for_gaps, $aclabel );
+ }
+ }
+ my $gap_wits = Set::Scalar->new();
+ map { _add_to_witlist( $_, $gap_wits, $aclabel )
+ unless $moved_wits{$_} } $check_for_gaps->members;
+
+ # Group the readings, collapsing groups by relationship if needed.
+ my $grouped_readings = {};
+ foreach my $rdg ( values %readings_at_rank ) {
+ # Skip readings that have been collapsed into others.
+ next if exists $grouped_readings->{$rdg->id}
+ && $grouped_readings->{$rdg->id} eq 'COLLAPSE';
+ # Get the witness list, including from readings collapsed into this one.
+ my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel );
+ if( $collapse && $collapse->size ) {
+ my $filter = sub { $collapse->has( $_[0]->type ) };
+ foreach my $other ( $rdg->related_readings( $filter ) ) {
+ my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel );
+ push( @wits, @otherwits );
+ $grouped_readings->{$other->id} = 'COLLAPSE';
+ }
+ }
+ $grouped_readings->{$rdg->id} = Set::Scalar->new( @wits );
+ }
+ if( $gap_wits->members ) {
+ $grouped_readings->{'(omitted)'} = $gap_wits;
+ }
- # Strip the list of sigla and save it for correlation to the readings.
- my $col_wits = shift @$all_wits_table;
+ # Get rid of our collapsed readings
+ map { delete $grouped_readings->{$_} if(
+ $grouped_readings->{$_} eq 'COLLAPSE'
+ || $grouped_readings->{$_}->is_empty ) }
+ keys %$grouped_readings;
+
+ # If something was transposed, check the groups for doubled-up readings
+ if( $has_transposition ) {
+ # print STDERR "Group for rank $rank:\n";
+ # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" }
+ # keys %$grouped_readings;
+ _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings );
+ }
- # We will return a data structure, an array for each row that looks like:
- # { id = X, genealogical = Y, readings = [ text = X, group = Y], empty = N }
- foreach my $i ( 0 .. $#$all_wits_table ) {
- # For each column in the table, group the readings by witness.
- my $rdg_wits = {};
- my $col_rdgs = shift @$all_wits_table;
- my $rank;
- my $lacunose = [];
- foreach my $j ( 0 .. $#{$col_rdgs} ) {
- my $rdg = $col_rdgs->[$j];
- my $rdg_text = '(omitted)'; # Initialize in case of empty reading
- if( $rdg ) {
- if( $rdg->is_lacuna ) {
- $rdg_text = undef; # Don't count lacunae
- push( @$lacunose, $col_wits->[$j] );
- } else {
- $rdg_text = $rdg->text;
- # Get the rank from any real reading; they should be identical.
- $rank = $rdg->rank;
+ # Return the result
+ return $grouped_readings;
+}
+
+# Helper function to query the alignment table for all witnesses (a.c. included)
+# that have a given reading at its rank.
+sub _table_witnesses {
+ my( $table, $trdg, $lacunose, $aclabel ) = @_;
+ my $tableidx = $trdg->rank - 1;
+ my $has_reading = Set::Scalar->new();
+ foreach my $row ( @{$table->{'alignment'}} ) {
+ my $wit = $row->{'witness'};
+ next if _is_lacunose( $wit, $lacunose, $aclabel );
+ my $rdg = $row->{'tokens'}->[$tableidx];
+ next unless exists $rdg->{'t'} && defined $rdg->{'t'};
+ _add_to_witlist( $wit, $has_reading, $aclabel )
+ if $rdg->{'t'}->id eq $trdg->id;
+ }
+ return $has_reading->members;
+}
+
+# Helper function to see if a witness is lacunose even if we are asking about
+# the a.c. version
+sub _is_lacunose {
+ my ( $wit, $lac, $acstr ) = @_;
+ if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
+ $wit = $1;
+ }
+ return $lac->has( $wit );
+}
+
+# Helper function to ensure that X and X a.c. never appear in the same list.
+sub _add_to_witlist {
+ my( $wit, $list, $acstr ) = @_;
+ if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
+ # Don't add X a.c. if we already have X
+ return if $list->has( $1 );
+ } else {
+ # Delete X a.c. if we are about to add X
+ $list->delete( $wit.$acstr );
+ }
+ $list->insert( $wit );
+}
+
+sub _check_transposed_consistency {
+ my( $c, $rank, $transposed, $groupings ) = @_;
+ my %seen_wits;
+ my %thisrank;
+ # Note which readings are actually at this rank, and which witnesses
+ # belong to which reading.
+ foreach my $rdg ( keys %$groupings ) {
+ my $rdgobj = $c->reading( $rdg );
+ # Count '(omitted)' as a reading at this rank
+ $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank;
+ map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}};
+ }
+ # Our work is done if we have no witness belonging to more than one
+ # reading.
+ my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits;
+ return unless @doubled;
+ # If we have a symmetric related transposition, drop the non-rank readings.
+ if( @doubled == scalar keys %seen_wits ) {
+ foreach my $rdg ( keys %$groupings ) {
+ if( !$thisrank{$rdg} ) {
+ my $groupstr = wit_stringify( $groupings->{$rdg} );
+ my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) }
+ keys %thisrank;
+ delete $groupings->{$rdg};
+ # If we found a group match, assume there is a symmetry happening.
+ # TODO think more about this
+ # print STDERR "*** Deleting symmetric reading $rdg\n";
+ unless( $matched ) {
+ delete $transposed->{$rdg};
+ warn "Found problem in evident symmetry with reading $rdg";
}
}
- if( defined $rdg_text ) {
- # Initialize the witness array if we haven't got one yet
- $rdg_wits->{$rdg_text} = [] unless $rdg_wits->{$rdg_text};
- # Add the relevant witness, subject to a.c. logic
- add_variant_wit( $rdg_wits->{$rdg_text}, $col_wits->[$j],
- $tradition->collation->ac_label );
+ }
+ # Otherwise 'unhook' the transposed reading(s) that have duplicates.
+ } else {
+ foreach my $dup ( @doubled ) {
+ foreach my $rdg ( @{$seen_wits{$dup}} ) {
+ next if $thisrank{$rdg};
+ next unless exists $groupings->{$rdg};
+ # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n";
+ delete $groupings->{$rdg};
+ delete $transposed->{$rdg};
+ }
+ }
+ # and put any now-orphaned readings into an 'omitted' reading.
+ foreach my $wit ( keys %seen_wits ) {
+ unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) {
+ $groupings->{'(omitted)'} = Set::Scalar->new()
+ unless exists $groupings->{'(omitted)'};
+ _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label );
}
}
+ }
+}
+
+# For the given grouping, return its situation graph based on the stemma.
+sub _graph_for_grouping {
+ my( $stemma, $grouping, $lacunose, $aclabel ) = @_;
+ my $acwits = [];
+ my $extant = {};
+ foreach my $gs ( values %$grouping ) {
+ map {
+ if( $_ =~ /^(.*)\Q$aclabel\E$/ ) {
+ push( @$acwits, $1 ) unless $lacunose->has( $1 );
+ } else {
+ $extant->{$_} = 1 unless $lacunose->has( $_ );
+ }
+ } $gs->members;
+ }
+ my $graph;
+ try {
+ # contig contains all extant wits and all hypothetical wits
+ # needed to make up the groups.
+ $graph = $stemma->situation_graph( $extant, $acwits );
+ } catch ( Text::Tradition::Error $e ) {
+ throw( "Could not extend graph with given extant and a.c. witnesses: "
+ . $e->message );
+ } catch {
+ throw( "Could not extend graph with a.c. witnesses @$acwits" );
+ }
+ return $graph;
+}
+
+=head2 solve_variants( $calcdir, @groups )
+
+Looks up the set of groups in the answers provided by the external graph solver
+service and returns a cleaned-up answer, adding the rank IDs back where they belong.
+
+The answer has the form
+ { "variants" => [ array of variant location structures ],
+ "variant_count" => total,
+ "conflict_count" => number of conflicts detected,
+ "genealogical_count" => number of solutions found }
+
+=cut
+
+sub solve_variants {
+ my( @groups ) = @_;
+
+ # Are we using a local result directory, or did we pass an empty value
+ # for the directory?
+ my $dir;
+ unless( ref( $groups[0] ) eq 'HASH' ) {
+ $dir = shift @groups;
+ }
+
+ ## For each graph/group combo, make a Text::Tradition::Analysis::Result
+ ## object so that we can send it off for IDP lookup.
+ my $variants = [];
+ my $genealogical = 0; # counter
+ # TODO Optimize for unique graph problems
+ my %problems;
+ foreach my $graphproblem ( @groups ) {
+ # Construct the calc result key and look up its answer
+ my $problem = Text::Tradition::Analysis::Result->new(
+ graph => $graphproblem->{'graph'},
+ setlist => [ values %{$graphproblem->{'grouping'}} ] );
+ if( exists $problems{$problem->object_key} ) {
+ $problem = $problems{$problem->object_key};
+ } else {
+ $problems{$problem->object_key} = $problem;
+ }
+ $graphproblem->{'object'} = $problem;
+ }
+
+ my %results;
+ if( $dir ) {
+ my $scope = $dir->new_scope;
+ map { $results{$_} = $dir->lookup( $_ ) || $problems{$_} } keys %problems;
+ } else {
+ my $json = JSON->new->allow_blessed->convert_blessed->utf8->encode(
+ [ values %problems ] );
+ # Send it off and get the result
+ # print STDERR "Sending request: " . decode_utf8( $json ) . "\n";
+ my $ua = LWP::UserAgent->new();
+ my $resp = $ua->post( $SOLVER_URL, 'Content-Type' => 'application/json',
+ 'Content' => $json );
+ my $answer;
+ if( $resp->is_success ) {
+ $answer = decode_json( $resp->content );
+ throw( "Unexpected answer from IDP: $answer" ) unless ref( $answer ) eq 'ARRAY';
+ } else {
+ throw( "IDP solver returned " . $resp->status_line . " / " . $resp->content
+ . "; cannot run graph analysis" );
+ }
+ # One more sanity check
+ throw( "Something went wrong with answer symmetricity" )
+ unless keys( %problems ) == @$answer;
+ # Convert the results
+ foreach my $a ( @$answer ) {
+ my $r = Text::Tradition::Analysis::Result->new( $a );
+ $results{$r->object_key} = $r;
+ }
+ }
+
+ # We now have a single JSON-encoded Result object per problem sent. Fold its
+ # answers into our variant info structure.
+ foreach my $graphproblem ( @groups ) {
+ my $result = $results{$graphproblem->{'object'}->object_key}
+ || $graphproblem->{'object'};
- # See if this column has any potentially genealogical variants.
- # If not, skip to the next.
- $total++ unless scalar keys %$rdg_wits == 1;
- my( $groups, $readings ) = useful_variant( $rdg_wits );
- next unless $groups && $readings;
-
- # Keep track of our widest row
- $html_columns = scalar @$groups if scalar @$groups > $html_columns;
+ # Initialize the result structure for this graph problem
+ my $vstruct;
+ if( $result->status eq 'OK' ) {
+ $vstruct = { readings => [] };
+ push( @$variants, $vstruct );
+ } else {
+ push( @$variants, _init_unsolved( $graphproblem, $result->status ) );
+ next;
+ }
+
+ # 1. Did the group evaluate as genealogical?
+ $vstruct->{genealogical} = $result->is_genealogical;
+ $genealogical++ if $result->is_genealogical;
- # We can already look up witnesses for a reading; we also want to look
- # up readings for a given witness.
- my $group_readings = {};
- foreach my $x ( 0 .. $#$groups ) {
- $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
+ # 2. What are the calculated minimum groupings for each variant loc?
+ foreach my $rid ( keys %{$graphproblem->{grouping}} ) {
+ my $inputset = $graphproblem->{grouping}->{$rid};
+ my $minset = $result->minimum_grouping_for( $inputset );
+ push( @{$vstruct->{readings}}, { readingid => $rid, group => $minset } );
}
- # For all the groups with more than one member, collect the list of all
- # contiguous vertices needed to connect them.
- $DB::single = 1;
- my $variant_row = analyze_variant_location( $group_readings, $groups,
- $stemma->graph, $lacunose );
- $variant_row->{'id'} = $rank;
- $genealogical++ if $variant_row->{'genealogical'};
- $conflicts += grep { $_->{'conflict'} } @{$variant_row->{'readings'}};
-
- # Now run the same analysis given the calculated distance tree(s).
-# my @trees = @{$stemma->distance_trees};
-# if( @trees ) {
-# foreach my $tree ( 0 .. $#trees ) {
-# my $dc = analyze_variant_location( $group_readings, $groups, $tree, $lacunose, 'undirected' );
-# foreach my $rdg ( keys %$dc ) {
-# my $var = $dc->{$rdg};
-# # TODO Do something with this
-# }
-# }
-# }
-
- # Record that we used this variant in an analysis
- push( @$variants, $variant_row );
+ # 3. What are the sources and classes calculated for each witness?
+ $vstruct->{witcopy_types} = { $result->classes };
+ $vstruct->{reading_roots} = {};
+ map { $vstruct->{reading_roots}->{$_} = 1 } $result->sources;
+
}
- # Go through our variant rows, after we have seen all of them once,
- # and add the number of empty columns needed by each.
- foreach my $row ( @$variants ) {
- my $empty = $html_columns - scalar @{$row->{'readings'}};
- $row->{'empty'} = $empty;
+ return { 'variants' => $variants,
+ 'variant_count' => scalar @$variants,
+ 'genealogical_count' => $genealogical };
+}
+
+sub _init_unsolved {
+ my( $graphproblem, $status ) = @_;
+ my $vstruct = { 'readings' => [] };
+ $vstruct->{'unsolved'} = $status;
+ foreach my $rid ( keys %{$graphproblem->{grouping}} ) {
+ push( @{$vstruct->{readings}}, { readingid => $rid,
+ group => [ $graphproblem->{grouping}->{$rid}->members ] } );
}
-
- # Populate self with our analysis data.
- $data->{'variants'} = $variants;
- $data->{'variant_count'} = $total;
- $data->{'conflict_count'} = $conflicts;
- $data->{'genealogical_count'} = $genealogical;
- push( @{$self->{'data'}}, $data );
+ return $vstruct;
}
-# variant_row -> genealogical
-# -> readings [ { text, group, conflict, missing } ]
-
-sub analyze_variant_location {
- my( $group_readings, $groups, $graph, $lacunose, $undirected ) = @_;
- my $contig = {};
- my $subgraph = {};
- my $is_conflicted;
- my $conflict = {};
- my $missing = {};
- map { $missing->{$_} = 1 } @$lacunose;
- my $variant_row = { 'readings' => [] };
- # Mark each ms as in its own group, first.
- foreach my $g ( @$groups ) {
- my $gst = wit_stringify( $g );
- map { $contig->{$_} = $gst } @$g;
- }
- # Now for each unmarked node in the graph, initialize an array
- # for possible group memberships. We will use this later to
- # resolve potential conflicts.
- map { $contig->{$_} = [] unless $contig->{$_} } $graph->vertices;
- foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
- my $gst = wit_stringify( $g ); # This is the group name
- my $reachable = { $g->[0] => 1 };
- # Copy the graph, and delete all non-members from the new graph.
- my $part = $graph->copy;
- my $group_root;
- $part->delete_vertices(
- grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices );
-
- # Now look to see if our group is connected.
- if( $undirected ) { # For use with distance trees etc.
- # Find all vertices reachable from the first (arbitrary) group
- # member. If we are genealogical this should include them all.
- map { $reachable->{$_} = 1 } $part->all_reachable( $g->[0] );
- # TODO This is a terrible way to do distance trees, since all
- # non-leaf nodes are included in every graph part now. We may
- # have to go back to SPDP.
- } else {
- if( @$g > 1 ) {
- # Dispense with the trivial case of one reading.
- # We have to take directionality into account.
- # How many root nodes do we have?
- my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst }
- $part->source_vertices;
- # Assuming that @$g > 1, find the first root node that has at
- # least one successor belonging to our group. If this reading
- # is genealogical, there should be only one, but we will check
- # that implicitly later.
- my $nodes_in_subtree = 0;
- foreach my $root ( @roots ) {
- # Prune the tree to get rid of extraneous hypotheticals.
- $root = prune_subtree( $part, $root, $contig );
- # Get all the successor nodes of our root.
- my $tmp_reach = { $root => 1 };
- map { $tmp_reach->{$_} = 1 } $part->all_successors( $root );
- # Skip this root if none of our successors are in our group
- # (e.g. isolated 'hypothetical' witnesses with no group)
- next unless grep { $contig->{$_} } keys %$tmp_reach;
- if( keys %$tmp_reach > $nodes_in_subtree ) {
- $nodes_in_subtree = keys %$tmp_reach;
- $reachable = $tmp_reach;
- $group_root = $root;
- }
- }
- } # else it is a single-node group, nothing to calculate.
- }
-
- # None of the 'reachable' nodes should be marked as being in another
- # group. Paint the 'hypotheticals' with our group while we are at it,
- # unless there is a conflict present.
- foreach ( keys %$reachable ) {
- if( ref $contig->{$_} ) {
- push( @{$contig->{$_}}, $gst );
- } elsif( $contig->{$_} ne $gst ) {
- $conflict->{$group_readings->{$gst}} = $group_readings->{$contig->{$_}};
- } # else it is an 'extant' node marked with our group already.
- }
- # None of the unreachable nodes should be in our group either.
- foreach ( $part->vertices ) {
- next if $reachable->{$_};
- if( $contig->{$_} eq $gst ) {
- $conflict->{$group_readings->{$gst}} = $group_readings->{$gst};
- last;
- }
- }
-
- # Now, if we have a conflict, we can write the reading in full. If not,
- # we have to save the subgraph so that we can resolve possible conflicts
- # on hypothetical nodes.
- $is_conflicted = 1 if exists $conflict->{$group_readings->{$gst}};
-
- # Write the reading.
- my $reading = { 'text' => $group_readings->{$gst},
- 'missing' => wit_stringify( $lacunose ),
- 'group' => $gst }; # This will change if we find no conflict
- if( $is_conflicted ) {
- $reading->{'conflict'} = $conflict->{$group_readings->{$gst}}
- } else {
- # Save the relevant subgraph.
- $subgraph->{$gst} = { 'graph' => $part,
- 'root' => $group_root,
- 'reachable' => $reachable };
- }
- push( @{$variant_row->{'readings'}}, $reading );
- }
-
- # Now that we have gone through all the rows, check the hypothetical
- # readings for conflict if we haven't found one yet.
- if( keys %$subgraph && !keys %$conflict ) {
- my @resolve;
- foreach ( keys %$contig ) {
- next unless ref $contig->{$_};
- if( scalar @{$contig->{$_}} > 1 ) {
- push( @resolve, $_ );
- } else {
- $contig->{$_} = scalar @{$contig->{$_}} ? $contig->{$_}->[0] : '';
- }
- }
- # Do we still have a possible conflict?
- my $still_contig = {};
- foreach my $h ( @resolve ) {
- # For each of the hypothetical readings with more than one possibility,
- # try deleting it from each of its member subgraphs in turn, and see
- # if that breaks the contiguous grouping.
- # TODO This can still break in a corner case where group A can use
- # either vertex 1 or 2, and group B can use either vertex 2 or 1.
- # Revisit this if necessary; it could get brute-force nasty.
- foreach my $gst ( @{$contig->{$h}} ) {
- my $gpart = $subgraph->{$gst}->{'graph'}->copy;
- my $reachable = $subgraph->{$gst}->{'reachable'};
- $gpart->delete_vertex( $h );
- # Is everything else still reachable from the root?
- # TODO If $h was the root, see if we still have a single root.
- my %still_reachable = ( $subgraph->{$gst}->{'root'} => 1 );
- map { $still_reachable{$_} = 1 }
- $gpart->all_successors( $subgraph->{$gst}->{'root'} );
- foreach my $v ( keys %$reachable ) {
- next if $v eq $h;
- if( !$still_reachable{$v}
- && ( $contig->{$v} eq $gst
- || ( exists $still_contig->{$v}
- && $still_contig->{$v} eq $gst ) ) ) {
- # We need $h.
- if( exists $still_contig->{$h} ) {
- # Conflict!
- $conflict->{$group_readings->{$gst}} =
- $group_readings->{$still_contig->{$h}};
- } else {
- $still_contig->{$h} = $gst;
- }
- last;
- } # else we don't need $h in this group.
- }
- }
+=head2 analyze_location ( $tradition, $graph, $location_hash )
+
+Given the tradition, its stemma graph, and the solution from the graph solver,
+work out the rest of the information we want. For each reading we need missing,
+conflict, reading_parents, independent_occurrence, followed, not_followed,
+and follow_unknown. Alters the location_hash in place.
+
+=cut
+
+sub analyze_location {
+ my ( $tradition, $graph, $variant_row, $lacunose ) = @_;
+ my $c = $tradition->collation;
+
+ if( exists $variant_row->{'unsolved'} ) {
+ return;
+ }
+ my $reading_roots = delete $variant_row->{'reading_roots'};
+ my $classinfo = delete $variant_row->{'witcopy_types'};
+
+ # Make a hash of all known node memberships, and make the subgraphs.
+ my $contig = {};
+ my $subgraph = {};
+ my $acstr = $c->ac_label;
+ my @acwits;
+
+ # Note which witnesses positively belong to which group. This information
+ # comes ultimately from the IDP solver.
+ # Also make a note of the reading's roots.
+ foreach my $rdghash ( @{$variant_row->{'readings'}} ) {
+ my $rid = $rdghash->{'readingid'};
+ my @roots;
+ foreach my $wit ( @{$rdghash->{'group'}} ) {
+ $contig->{$wit} = $rid;
+ if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
+ push( @acwits, $1 );
+ }
+ if( exists $reading_roots->{$wit} && $reading_roots->{$wit} ) {
+ push( @roots, $wit );
+ }
+ }
+ $rdghash->{'independent_occurrence'} = \@roots;
+ }
+
+ # Now that we have all the node group memberships, calculate followed/
+ # non-followed/unknown values for each reading. Also figure out the
+ # reading's evident parent(s).
+ foreach my $rdghash ( @{$variant_row->{'readings'}} ) {
+ my $rid = $rdghash->{'readingid'};
+ my $rdg = $c->reading( $rid );
+ my @roots = @{$rdghash->{'independent_occurrence'}};
+ my @reversions;
+ if( $classinfo ) {
+ @reversions = grep { $classinfo->{$_} eq 'revert' }
+ $rdghash->{'group'}->members;
+ $rdghash->{'reversions'} = \@reversions;
}
+ my @group = @{$rdghash->{'group'}};
- # Now, assuming no conflict, we have some hypothetical vertices in
- # $still_contig that are the "real" group memberships. Replace these
- # in $contig.
- unless ( keys %$conflict ) {
- foreach my $v ( keys %$contig ) {
- next unless ref $contig->{$v};
- $contig->{$v} = $still_contig->{$v};
- }
- }
- }
-
- # Now write the group and conflict information into the respective rows.
- foreach my $rdg ( @{$variant_row->{'readings'}} ) {
- $rdg->{'conflict'} = $conflict->{$rdg->{'text'}};
- next if $rdg->{'conflict'};
- my @members = grep { $contig->{$_} eq $rdg->{'group'} && !$missing->{$_} }
- keys %$contig;
- $rdg->{'group'} = wit_stringify( \@members );
+ # Start figuring things out.
+ $rdghash->{'followed'} = scalar( @group )
+ - ( scalar( @roots ) + scalar( @reversions ) );
+ # Find the parent readings, if any, of this reading.
+ my $sourceparents = _find_reading_parents( $rid, $graph, $contig, @roots );
+ # Work out relationships between readings and their non-followed parent.
+ _resolve_parent_relationships( $c, $rid, $rdg, $sourceparents );
+ $rdghash->{'source_parents'} = $sourceparents;
+
+ if( @reversions ) {
+ my $revparents = _find_reading_parents( $rid, $graph, $contig, @reversions );
+ _resolve_parent_relationships( $c, $rid, $rdg, $revparents );
+ $rdghash->{'reversion_parents'} = $revparents;
+ }
+
+ # Find the number of times this reading was altered, and the number of
+ # times we're not sure.
+ my( %nofollow, %unknownfollow );
+ foreach my $wit ( @{$rdghash->{'group'}} ) {
+ foreach my $wchild ( $graph->successors( $wit ) ) {
+ if( $reading_roots->{$wchild} && $contig->{$wchild}
+ && $contig->{$wchild} ne $rid ) {
+ # It definitely changed here.
+ $nofollow{$wchild} = 1;
+ } elsif( !($contig->{$wchild}) ) {
+ # The child is a hypothetical node not definitely in
+ # any group. Answer is unknown.
+ $unknownfollow{$wchild} = 1;
+ } # else it is either in our group, or it is a non-root node in a
+ # known group and therefore is presumed to have its reading from
+ # its group, not this link.
+ }
+ }
+ $rdghash->{'not_followed'} = keys %nofollow;
+ $rdghash->{'follow_unknown'} = keys %unknownfollow;
+
+ # Now say whether this reading represents a conflict.
+ unless( $variant_row->{'genealogical'} ) {
+ $rdghash->{'is_conflict'} = @roots != 1;
+ $rdghash->{'is_reverted'} = scalar @reversions;
+ }
}
-
- $variant_row->{'genealogical'} = !( keys %$conflict );
- return $variant_row;
}
-sub prune_subtree {
- my( $tree, $root, $contighash ) = @_;
- # First, delete hypothetical leaves / orphans until there are none left.
- my @orphan_hypotheticals = grep { ref( $contighash->{$_} ) }
- $tree->successorless_vertices;
- while( @orphan_hypotheticals ) {
- $tree->delete_vertices( @orphan_hypotheticals );
- @orphan_hypotheticals = grep { ref( $contighash->{$_} ) }
- $tree->successorless_vertices;
- }
- # Then delete a hypothetical root with only one successor, moving the
- # root to the child.
- while( $tree->successors( $root ) == 1 && ref $contighash->{$root} ) {
- my @nextroot = $tree->successors( $root );
- $tree->delete_vertex( $root );
- $root = $nextroot[0];
- }
- # The tree has been modified in place, but we need to know the new root.
- return $root;
+sub _find_reading_parents {
+ my( $rid, $graph, $contig, @list ) = @_;
+ my $parenthash = {};
+ foreach my $wit ( @list ) {
+ # Look in the stemma graph to find this witness's extant or known-reading
+ # immediate ancestor(s), and look up the reading that each ancestor holds.
+ my @check = $graph->predecessors( $wit );
+ while( @check ) {
+ my @next;
+ foreach my $wparent( @check ) {
+ my $preading = $contig->{$wparent};
+ if( $preading && $preading ne $rid ) {
+ $parenthash->{$preading} = 1;
+ } else {
+ push( @next, $graph->predecessors( $wparent ) );
+ }
+ }
+ @check = @next;
+ }
+ }
+ return $parenthash;
}
-# Add the variant, subject to a.c. representation logic.
-# This assumes that we will see the 'main' version before the a.c. version.
-sub add_variant_wit {
- my( $arr, $wit, $acstr ) = @_;
- my $skip;
- if( $wit =~ /^(.*)\Q$acstr\E$/ ) {
- my $real = $1;
- $skip = grep { $_ =~ /^\Q$real\E$/ } @$arr;
- }
- push( @$arr, $wit ) unless $skip;
+
+sub _resolve_parent_relationships {
+ my( $c, $rid, $rdg, $rdgparents ) = @_;
+ foreach my $p ( keys %$rdgparents ) {
+ # Resolve the relationship of the parent to the reading, and
+ # save it in our hash.
+ my $pobj = $c->reading( $p );
+ my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p;
+ my $phash = { 'label' => $prep };
+ if( $pobj ) {
+ my $rel = $c->get_relationship( $p, $rid );
+ if( $rel ) {
+ _add_to_hash( $rel, $phash );
+ } elsif( $rdg ) {
+ # First check for a transposed relationship
+ if( $rdg->rank != $pobj->rank ) {
+ foreach my $ti ( $rdg->related_readings( 'transposition' ) ) {
+ next unless $ti->text eq $rdg->text;
+ $rel = $c->get_relationship( $ti, $pobj );
+ if( $rel ) {
+ _add_to_hash( $rel, $phash, 1 );
+ last;
+ }
+ }
+ unless( $rel ) {
+ foreach my $ti ( $pobj->related_readings( 'transposition' ) ) {
+ next unless $ti->text eq $pobj->text;
+ $rel = $c->get_relationship( $ti, $rdg );
+ if( $rel ) {
+ _add_to_hash( $rel, $phash, 1 );
+ last;
+ }
+ }
+ }
+ }
+ unless( $rel ) {
+ # and then check for sheer word similarity.
+ my $rtext = $rdg->text;
+ my $ptext = $pobj->text;
+ if( similar( $rtext, $ptext ) ) {
+ # say STDERR "Words $rtext and $ptext judged similar";
+ $phash->{relation} = { type => 'wordsimilar' };
+ }
+ }
+ } else {
+ $phash->{relation} = { type => 'deletion' };
+ }
+ # Get the attributes of the parent object while we are here
+ $phash->{'text'} = $pobj->text if $pobj;
+ $phash->{'is_nonsense'} = $pobj->is_nonsense;
+ $phash->{'is_ungrammatical'} = $pobj->grammar_invalid;
+ } elsif( $p eq '(omitted)' ) {
+ $phash->{relation} = { type => 'addition' };
+ }
+ # Save it
+ $rdgparents->{$p} = $phash;
+ }
}
-# Return an answer if the variant is useful, i.e. if there are at least 2 variants
-# with at least 2 witnesses each.
-sub useful_variant {
- my( $readings ) = @_;
- my $total = keys %$readings;
- foreach my $var ( keys %$readings ) {
- $total-- if @{$readings->{$var}} == 1;
- }
- return( undef, undef ) if $total <= 1;
- my( $groups, $text );
- foreach my $var ( keys %$readings ) {
- push( @$groups, $readings->{$var} );
- push( @$text, $var );
- }
- return( $groups, $text );
+sub _add_to_hash {
+ my( $rel, $phash, $is_transposed ) = @_;
+ $phash->{relation} = { type => $rel->type };
+ $phash->{relation}->{transposed} = 1 if $is_transposed;
+ $phash->{relation}->{annotation} = $rel->annotation
+ if $rel->has_annotation;
+}
+
+=head2 similar( $word1, $word2 )
+
+Use Algorithm::Diff to get a sense of how close the words are to each other.
+This will hopefully handle substitutions a bit more nicely than Levenshtein.
+
+=cut
+
+#!/usr/bin/env perl
+
+sub similar {
+ my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_;
+ my @let1 = split( '', lc( $word1 ) );
+ my @let2 = split( '', lc( $word2 ) );
+ my $diff = Algorithm::Diff->new( \@let1, \@let2 );
+ my $mag = 0;
+ while( $diff->Next ) {
+ if( $diff->Same ) {
+ # Take off points for longer strings
+ my $cs = $diff->Range(1) - 2;
+ $cs = 0 if $cs < 0;
+ $mag -= $cs;
+ } elsif( !$diff->Items(1) ) {
+ $mag += $diff->Range(2);
+ } elsif( !$diff->Items(2) ) {
+ $mag += $diff->Range(1);
+ } else {
+ # Split the difference for substitutions
+ my $c1 = $diff->Range(1) || 1;
+ my $c2 = $diff->Range(2) || 1;
+ my $cd = ( $c1 + $c2 ) / 2;
+ $mag += $cd;
+ }
+ }
+ return ( $mag <= length( $word1 ) / 2 );
+}
+
+sub _useful_variant {
+ my( $rankgroup, $rankgraph, $acstr ) = @_;
+
+ # Sort by group size and return
+ my $is_useful = 0;
+ foreach my $rdg ( keys %$rankgroup ) {
+ my @wits = $rankgroup->{$rdg}->members;
+ if( @wits > 1 ) {
+ $is_useful++;
+ } else {
+ $is_useful++ unless( $rankgraph->is_sink_vertex( $wits[0] )
+ || $wits[0] =~ /\Q$acstr\E$/ );
+ }
+ }
+ return $is_useful > 1;
}
-# Take an array of witness groupings and produce a string like
-# ['A','B'] / ['C','D','E'] / ['F']
+=head2 wit_stringify( $groups )
+
+Takes an array of witness groupings and produces a string like
+['A','B'] / ['C','D','E'] / ['F']
+
+=cut
sub wit_stringify {
my $groups = shift;
}
return join( ' / ', @gst );
}
-
-1;
\ No newline at end of file
+
+1;
+
+sub throw {
+ Text::Tradition::Error->throw(
+ 'ident' => 'Analysis error',
+ 'message' => $_[0],
+ );
+}
+
+=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