X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2FText%2FTradition%2FAnalysis.pm;h=fda51376077c9e67781e1c5e134c203704fd706a;hb=f2fec47dc44816775c844e8b50cef03b12b69dae;hp=75897ca9f1f04d663053738009bac404f9dfbf38;hpb=a44aaf2a3c6e12fd2329a85718f2fc1fa077f9a4;p=scpubgit%2Fstemmatology.git diff --git a/lib/Text/Tradition/Analysis.pm b/lib/Text/Tradition/Analysis.pm index 75897ca..fda5137 100644 --- a/lib/Text/Tradition/Analysis.pm +++ b/lib/Text/Tradition/Analysis.pm @@ -5,6 +5,7 @@ use warnings; use Benchmark; use Encode qw/ encode_utf8 /; use Exporter 'import'; +use Graph; use JSON qw/ encode_json decode_json /; use LWP::UserAgent; use Text::Tradition; @@ -55,6 +56,8 @@ is 0 (i.e. the first). =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 @@ -109,8 +112,8 @@ foreach my $row ( @{$data->{'variants'}} ) { is( $row->{'genealogical'}, $expected_genealogical{$row->{'id'}}, "Got correct genealogical flag for row " . $row->{'id'} ); } -is( $data->{'conflict_count'}, 34, "Got right conflict count" ); is( $data->{'variant_count'}, 58, "Got right total variant number" ); +# TODO Make something meaningful of conflict count, maybe test other bits =end testing @@ -121,15 +124,16 @@ sub run_analysis { my $c = $tradition->collation; my $stemma_id = $opts{'stemma_id'} || 0; - my @ranks = @{$opts{'ranks'}} if ref( $opts{'ranks'} ) eq 'ARRAY'; - my @collapse = @{$opts{'merge_types'}} if ref( $opts{'merge_types'} ) eq 'ARRAY'; + my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); + my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : (); # Get the stemma my $stemma = $tradition->stemma( $stemma_id ); + # Figure out which witnesses we are working with my @lacunose = $stemma->hypotheticals; my @tradition_wits = map { $_->sigil } $tradition->witnesses; - map { push( @tradition_wits, $_->sigil."_ac" ) if $_->is_layered } + map { push( @tradition_wits, $_->sigil.$c->ac_label ) if $_->is_layered } $tradition->witnesses; push( @lacunose, _symmdiff( [ $stemma->witnesses ], \@tradition_wits ) ); @@ -148,12 +152,18 @@ sub run_analysis { my %lacunae; foreach my $rank ( @ranks ) { my $missing = [ @lacunose ]; - push( @groups, group_variants( $tradition, $rank, $missing, \@collapse ) ); + my $rankgroup = group_variants( $tradition, $rank, $missing, \@collapse ); + if( $opts{'exclude_type1'} ) { + # Check to see whether this is a "useful" group. + my( $rdgs, $grps ) = _useful_variant( $rankgroup ); + next unless @$rdgs; + } + push( @groups, $rankgroup ); $lacunae{$rank} = $missing; } - + $DB::single = 1; # Parse the answer - my $answer = solve_variants( $stemma->editable( ' ' ), @groups ); + my $answer = solve_variants( $stemma, @groups ); # Do further analysis on the answer my $conflict_count = 0; @@ -185,8 +195,8 @@ relationships in @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. -Returns two ordered lists $readings, $groups, where $readings->[$n] is attested -by the witnesses listed in $groups->[$n]. +Returns a hash $group_readings where $rdg is attested by the witnesses listed +in $group_readings->{$rdg}. =cut @@ -194,35 +204,33 @@ by the witnesses listed in $groups->[$n]. sub group_variants { my( $tradition, $rank, $lacunose, $collapse ) = @_; my $c = $tradition->collation; - my $aclabel = $c->ac_label; + my $aclabel = $c->ac_label; # Get the alignment table readings my %readings_at_rank; my @gap_wits; - foreach my $tablewit ( @{$tradition->collation->alignment_table->{'alignment'}} ) { + foreach my $tablewit ( @{$c->alignment_table->{'alignment'}} ) { my $rdg = $tablewit->{'tokens'}->[$rank-1]; my $wit = $tablewit->{'witness'}; - $wit =~ s/^(.*)\Q$aclabel\E$/${1}_ac/; if( $rdg && $rdg->{'t'}->is_lacuna ) { - _add_to_witlist( $wit, $lacunose, '_ac' ); + _add_to_witlist( $wit, $lacunose, $aclabel ); } elsif( $rdg ) { $readings_at_rank{$rdg->{'t'}->text} = $rdg->{'t'}; } else { - _add_to_witlist( $wit, \@gap_wits, '_ac' ); + _add_to_witlist( $wit, \@gap_wits, $aclabel ); } } # Group the readings, collapsing groups by relationship if needed my %grouped_readings; - foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } values %readings_at_rank ) { + foreach my $rdg ( sort { $b->witnesses <=> $a->witnesses } + values %readings_at_rank ) { # Skip readings that have been collapsed into others. next if exists $grouped_readings{$rdg->id} && !$grouped_readings{$rdg->id}; my @wits = $rdg->witnesses; - map { s/\Q$aclabel\E$/_ac/ } @wits; if( $collapse ) { my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; foreach my $other ( $rdg->related_readings( $filter ) ) { my @otherwits = $other->witnesses; - map { s/\Q$aclabel\E$/_ac/ } @otherwits; push( @wits, @otherwits ); $grouped_readings{$other->id} = 0; } @@ -256,18 +264,20 @@ The answer has the form =cut sub solve_variants { - my( $graph, @groups ) = @_; + my( $stemma, @groups ) = @_; # Make the json with stemma + groups - my $jsonstruct = { 'graph' => $graph, 'groupings' => [] }; + my $groupings = []; foreach my $ghash ( @groups ) { my @grouping; - foreach my $k ( sort keys %$ghash ) { + foreach my $k ( keys %$ghash ) { push( @grouping, $ghash->{$k} ); } - push( @{$jsonstruct->{'groupings'}}, \@grouping ); + push( @$groupings, \@grouping ); } - my $json = encode_json( $jsonstruct ); + ## Witness map is a HACK to get around limitations in node names from IDP + my $witness_map = {}; + my $json = encode_json( _safe_wit_strings( $stemma, $groupings, $witness_map ) ); # Send it off and get the result my $solver_url = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; @@ -276,13 +286,15 @@ sub solve_variants { 'Content' => $json ); my $answer; + my $used_idp; if( $resp->is_success ) { - $answer = decode_json( $resp->content ); + $answer = _desanitize_names( decode_json( $resp->content ), $witness_map ); + $used_idp = 1; } else { # Fall back to the old method. warn "IDP solver returned " . $resp->status_line . " / " . $resp->content . "; falling back to perl method"; - $answer = perl_solver( $graph, @groups ); + $answer = perl_solver( $stemma, @$groupings ); } # Fold the result back into what we know about the groups. @@ -290,7 +302,18 @@ sub solve_variants { my $genealogical = 0; foreach my $idx ( 0 .. $#groups ) { my( $calc_groups, $result ) = @{$answer->[$idx]}; - $genealogical++ if $result; + if( $result ) { + $genealogical++; + # Prune the calculated groups, in case the IDP solver failed to. + if( $used_idp ) { + my @pruned_groups; + foreach my $cg ( @$calc_groups ) { + my @pg = _prune_group( $cg, $stemma ); + push( @pruned_groups, \@pg ); + } + $calc_groups = \@pruned_groups; + } + } my $input_group = $groups[$idx]; foreach my $k ( sort keys %$input_group ) { my $cg = shift @$calc_groups; @@ -312,6 +335,88 @@ sub solve_variants { 'genealogical_count' => $genealogical }; } +#### HACKERY to cope with IDP's limited idea of what a node name looks like ### + +sub _safe_wit_strings { + my( $stemma, $groupings, $witness_map ) = @_; + my $safegraph = Graph->new(); + # Convert the graph to a safe representation and store the conversion. + foreach my $n ( $stemma->graph->vertices ) { + my $sn = _safe_witstr( $n ); + warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn} + if exists $witness_map->{$sn}; + $witness_map->{$sn} = $n; + $safegraph->add_vertex( $sn ); + $safegraph->set_vertex_attributes( $sn, + $stemma->graph->get_vertex_attributes( $n ) ); + } + foreach my $e ( $stemma->graph->edges ) { + my @safe_e = ( _safe_witstr( $e->[0] ), _safe_witstr( $e->[1] ) ); + $safegraph->add_edge( @safe_e ); + } + my $safe_stemma = Text::Tradition::Stemma->new( + 'collation' => $stemma->collation, 'graph' => $safegraph ); + + # Now convert the witness groupings to a safe representation. + my $safe_groupings = []; + foreach my $grouping ( @$groupings ) { + my $safe_grouping = []; + foreach my $group ( @$grouping ) { + my $safe_group = []; + foreach my $n ( @$group ) { + my $sn = _safe_witstr( $n ); + warn "Ambiguous stringification $sn for $n and " . $witness_map->{$sn} + if exists $witness_map->{$sn} && $witness_map->{$sn} ne $n; + $witness_map->{$sn} = $n; + push( @$safe_group, $sn ); + } + push( @$safe_grouping, $safe_group ); + } + push( @$safe_groupings, $safe_grouping ); + } + + # Return it all in the struct we expect. We have stored the reductions + # in the $witness_map that we were passed. + return { 'graph' => $safe_stemma->editable( ' ' ), 'groupings' => $safe_groupings }; +} + +sub _safe_witstr { + my $witstr = shift; + $witstr =~ s/\s+/_/g; + $witstr =~ s/[^\w\d-]//g; + return $witstr; +} + +sub _desanitize_names { + my( $jsonstruct, $witness_map ) = @_; + my $result = []; + foreach my $grouping ( @$jsonstruct ) { + my $real_grouping = []; + foreach my $element ( @$grouping ) { + if( ref( $element ) eq 'ARRAY' ) { + # it's the groupset. + my $real_groupset = []; + foreach my $group ( @$element ) { + my $real_group = []; + foreach my $n ( @$group ) { + my $rn = $witness_map->{$n}; + push( @$real_group, $rn ); + } + push( @$real_groupset, $real_group ); + } + push( @$real_grouping, $real_groupset ); + } else { + # It is the boolean, not actually a group. + push( @$real_grouping, $element ); + } + } + push( @$result, $real_grouping ); + } + return $result; +} + +### END HACKERY ### + =head2 analyze_location ( $tradition, $graph, $location_hash ) Given the tradition, its stemma graph, and the solution from the graph solver, @@ -425,189 +530,202 @@ possibly with the addition of hypothetical readings. =cut sub perl_solver { - my( $graph, @groups ) = @_; - - warn "Not implemented yet"; - return []; + my( $stemma, @groups ) = @_; + my $graph = $stemma->graph; + my @answer; + foreach my $g ( @groups ) { + push( @answer, _solve_variant_location( $graph, $g ) ); + } + return \@answer; } +sub _solve_variant_location { + my( $graph, $groups ) = @_; # Now do the work. -# my $contig = {}; -# my $subgraph = {}; -# my $is_conflicted; -# my $conflict = {}; -# my %reading_roots; -# my $variant_row = { 'id' => $rank, '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 -# # Copy the graph, and delete all non-members from the new graph. -# my $part = $graph->copy; -# my @group_roots; -# $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. -# my $reachable = {}; -# 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 ) { -# # We have to take directionality into account. -# # How many root nodes do we have? -# my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } -# $part->predecessorless_vertices; -# # Assuming that @$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. -# foreach my $root ( @roots ) { -# # Prune the tree to get rid of extraneous hypotheticals. -# $root = _prune_subtree( $part, $root, $contig ); -# next unless $root; -# # Save this root for our group. -# push( @group_roots, $root ); -# # Get all the successor nodes of our root. -# } -# } else { -# # Dispense with the trivial case of one reading. -# my $wit = pop @$g; -# @group_roots = ( $wit ); -# foreach my $v ( $part->vertices ) { -# $part->delete_vertex( $v ) unless $v eq $wit; -# } -# } -# } -# -# map { $reading_roots{$_} = 1 } @group_roots; -# if( @group_roots > 1 ) { -# $conflict->{$group_readings->{$gst}} = 1; -# $is_conflicted = 1; -# } -# # Paint the 'hypotheticals' with our group. -# foreach my $wit ( $part->vertices ) { -# if( ref( $contig->{$wit} ) ) { -# push( @{$contig->{$wit}}, $gst ); -# } elsif( $contig->{$wit} ne $gst ) { -# warn "How did we get here?"; -# } -# } -# -# -# # Start to write the reading, and save the group subgraph. -# my $reading = { 'readingid' => $group_readings->{$gst}, -# 'missing' => wit_stringify( \@lacunose ), -# 'group' => $gst }; # This will change if we find no conflict -# # Save the relevant subgraph. -# $subgraph->{$gst} = $part; -# push( @{$variant_row->{'readings'}}, $reading ); -# } -# -# # For each of our hypothetical readings, flatten its 'contig' array if -# # the array contains zero or one group. If we have any unflattened arrays, -# # we may need to run the resolution process. If the reading is already known -# # to have a conflict, flatten the 'contig' array to nothing; we won't resolve -# # it. -# my @resolve; -# foreach my $wit ( keys %$contig ) { -# next unless ref( $contig->{$wit} ); -# if( @{$contig->{$wit}} > 1 ) { -# if( $is_conflicted ) { -# $contig->{$wit} = ''; # We aren't going to decide. -# } else { -# push( @resolve, $wit ); -# } -# } else { -# my $gst = pop @{$contig->{$wit}}; -# $contig->{$wit} = $gst || ''; -# } -# } -# -# if( @resolve ) { -# 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}->copy(); -# # If we have come this far, there is only one root and everything -# # is reachable from it. -# my( $root ) = $gpart->predecessorless_vertices; -# my $reachable = {}; -# map { $reachable->{$_} = 1 } $gpart->vertices; -# -# # Try deleting the hypothetical node. -# $gpart->delete_vertex( $h ); -# if( $h eq $root ) { -# # See if we still have a single root. -# my @roots = $gpart->predecessorless_vertices; -# warn "This shouldn't have happened" unless @roots; -# if( @roots > 1 ) { -# # $h is needed by this group. -# if( exists( $still_contig->{$h} ) ) { -# # Conflict! -# $conflict->{$group_readings->{$gst}} = 1; -# $still_contig->{$h} = ''; -# } else { -# $still_contig->{$h} = $gst; -# } -# } -# } else { -# # $h is somewhere in the middle. See if everything -# # else can still be reached from the root. -# my %still_reachable = ( $root => 1 ); -# map { $still_reachable{$_} = 1 } -# $gpart->all_successors( $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}} = 1; -# $still_contig->{$h} = ''; -# } else { -# $still_contig->{$h} = $gst; -# } -# last; -# } # else we don't need $h in this group. -# } # end foreach $v -# } # endif $h eq $root -# } # end foreach $gst -# } # end foreach $h -# -# # Now we have some hypothetical vertices in $still_contig that are the -# # "real" group memberships. Replace these in $contig. -# foreach my $v ( keys %$contig ) { -# next unless ref $contig->{$v}; -# $contig->{$v} = $still_contig->{$v}; -# } -# } # end if @resolve -# -# -# $variant_row->{'genealogical'} = !( keys %$conflict ); -# return $variant_row; -# } + my $contig = {}; + my $subgraph = {}; + my $is_conflicted; + my $conflict = {}; + + # 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 + # Copy the graph, and delete all non-members from the new graph. + my $part = $graph->copy; + my @group_roots; + $part->delete_vertices( + grep { !ref( $contig->{$_} ) && $contig->{$_} ne $gst } $graph->vertices ); + + # Now look to see if our group is connected. + if( @$g > 1 ) { + # We have to take directionality into account. + # How many root nodes do we have? + my @roots = grep { ref( $contig->{$_} ) || $contig->{$_} eq $gst } + $part->predecessorless_vertices; + # Assuming that @$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. + foreach my $root ( @roots ) { + # Prune the tree to get rid of extraneous hypotheticals. + $root = _prune_subtree( $part, $root, $contig ); + next unless $root; + # Save this root for our group. + push( @group_roots, $root ); + # Get all the successor nodes of our root. + } + } else { + # Dispense with the trivial case of one reading. + my $wit = $g->[0]; + @group_roots = ( $wit ); + foreach my $v ( $part->vertices ) { + $part->delete_vertex( $v ) unless $v eq $wit; + } + } + + if( @group_roots > 1 ) { + $conflict->{$gst} = 1; + $is_conflicted = 1; + } + # Paint the 'hypotheticals' with our group. + foreach my $wit ( $part->vertices ) { + if( ref( $contig->{$wit} ) ) { + push( @{$contig->{$wit}}, $gst ); + } elsif( $contig->{$wit} ne $gst ) { + warn "How did we get here?"; + } + } + + + # Save the relevant subgraph. + $subgraph->{$gst} = $part; + } + + # For each of our hypothetical readings, flatten its 'contig' array if + # the array contains zero or one group. If we have any unflattened arrays, + # we may need to run the resolution process. If the reading is already known + # to have a conflict, flatten the 'contig' array to nothing; we won't resolve + # it. + my @resolve; + foreach my $wit ( keys %$contig ) { + next unless ref( $contig->{$wit} ); + if( @{$contig->{$wit}} > 1 ) { + if( $is_conflicted ) { + $contig->{$wit} = ''; # We aren't going to decide. + } else { + push( @resolve, $wit ); + } + } else { + my $gst = pop @{$contig->{$wit}}; + $contig->{$wit} = $gst || ''; + } + } + + if( @resolve ) { + 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}->copy(); + # If we have come this far, there is only one root and everything + # is reachable from it. + my( $root ) = $gpart->predecessorless_vertices; + my $reachable = {}; + map { $reachable->{$_} = 1 } $gpart->vertices; + + # Try deleting the hypothetical node. + $gpart->delete_vertex( $h ); + if( $h eq $root ) { + # See if we still have a single root. + my @roots = $gpart->predecessorless_vertices; + warn "This shouldn't have happened" unless @roots; + if( @roots > 1 ) { + # $h is needed by this group. + if( exists( $still_contig->{$h} ) ) { + # Conflict! + $conflict->{$gst} = 1; + $still_contig->{$h} = ''; + } else { + $still_contig->{$h} = $gst; + } + } + } else { + # $h is somewhere in the middle. See if everything + # else can still be reached from the root. + my %still_reachable = ( $root => 1 ); + map { $still_reachable{$_} = 1 } + $gpart->all_successors( $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! + $conflict->{$gst} = 1; + $still_contig->{$h} = ''; + } else { + $still_contig->{$h} = $gst; + } + last; + } # else we don't need $h in this group. + } # end foreach $v + } # endif $h eq $root + } # end foreach $gst + } # end foreach $h + + # Now we have some hypothetical vertices in $still_contig that are the + # "real" group memberships. Replace these in $contig. + foreach my $v ( keys %$contig ) { + next unless ref $contig->{$v}; + $contig->{$v} = $still_contig->{$v}; + } + } # end if @resolve + + my $is_genealogical = keys %$conflict ? JSON::false : JSON::true; + my $variant_row = [ [], $is_genealogical ]; + # Fill in the groupings from $contig. + foreach my $g ( @$groups ) { + my $gst = wit_stringify( $g ); + my @realgroup = grep { $contig->{$_} eq $gst } keys %$contig; + push( @{$variant_row->[0]}, \@realgroup ); + } + return $variant_row; +} + +sub _prune_group { + my( $group, $stemma ) = @_; + # Get these into a form prune_subtree will recognize. Make a "contighash" + my $hypohash = {}; + map { $hypohash->{$_} = 1 } @$group; + # ...with reference values for hypotheticals. + map { $hypohash->{$_} = [] } $stemma->hypotheticals; + # Make our subgraph + my $subgraph = $stemma->graph->copy; + map { $subgraph->delete_vertex( $_ ) unless exists $hypohash->{$_} } + $subgraph->vertices; + # ...and find the root. + my( $root ) = $subgraph->predecessorless_vertices; + # Now prune and return the remaining vertices. + _prune_subtree( $subgraph, $root, $hypohash ); + return $subgraph->vertices; +} sub _prune_subtree { my( $tree, $root, $contighash ) = @_;