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d71100ed |
1 | package Text::Tradition::Analysis; |
2 | |
3 | use strict; |
4 | use warnings; |
428bcf0b |
5 | use Algorithm::Diff; # for word similarity measure |
e4386ba9 |
6 | use Benchmark; |
7e17346f |
7 | use Digest::MD5 qw/ md5_hex /; |
88a6bac5 |
8 | use Encode qw/ encode_utf8 /; |
d1348d38 |
9 | use Exporter 'import'; |
b4cb2d60 |
10 | use Graph; |
7e17346f |
11 | use JSON qw/ to_json /; |
12 | use Set::Scalar; |
d71100ed |
13 | use Text::Tradition; |
7e17346f |
14 | use Text::Tradition::Analysis::Result; |
15 | use Text::Tradition::Directory; |
d71100ed |
16 | use Text::Tradition::Stemma; |
d120c995 |
17 | use TryCatch; |
d71100ed |
18 | |
d1348d38 |
19 | use vars qw/ @EXPORT_OK /; |
a2cf85dd |
20 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
d1348d38 |
21 | |
7e17346f |
22 | my $unsolved_problems = {}; |
5c44c598 |
23 | |
7f52eac8 |
24 | =head1 NAME |
25 | |
26 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
27 | |
28 | =head1 SYNOPSIS |
29 | |
30 | use Text::Tradition; |
31 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
32 | my $t = Text::Tradition->new( |
33 | 'name' => 'this is a text', |
34 | 'input' => 'TEI', |
35 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
36 | $t->add_stemma( 'dotfile' => $stemmafile ); |
37 | |
38 | my $variant_data = run_analysis( $tradition ); |
39 | # Recalculate rank $n treating all orthographic variants as equivalent |
40 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
41 | |
42 | =head1 DESCRIPTION |
43 | |
44 | Text::Tradition is a library for representation and analysis of collated |
45 | texts, particularly medieval ones. The Collation is the central feature of |
46 | a Tradition, where the text, its sequence of readings, and its relationships |
47 | between readings are actually kept. |
48 | |
49 | =head1 SUBROUTINES |
50 | |
88a6bac5 |
51 | =head2 run_analysis( $tradition, %opts ) |
7f52eac8 |
52 | |
88a6bac5 |
53 | Runs the analysis described in analyze_variant_location on every location in the |
54 | collation of the given tradition, with the given options. These include: |
7f52eac8 |
55 | |
88a6bac5 |
56 | =over 4 |
57 | |
58 | =item * stemma_id - Specify which of the tradition's stemmata to use. Default |
59 | is 0 (i.e. the first). |
60 | |
61 | =item * ranks - Specify a list of location ranks to analyze; exclude the rest. |
62 | |
63 | =item * merge_types - Specify a list of relationship types, where related readings |
64 | should be treated as identical for the purposes of analysis. |
65 | |
ffa22d6f |
66 | =item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants. |
67 | |
88a6bac5 |
68 | =back |
7f52eac8 |
69 | |
70 | =begin testing |
71 | |
72 | use Text::Tradition; |
73 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
74 | |
75 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
76 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
77 | 'name' => 'test0', |
78 | 'file' => $datafile ); |
79 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
80 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
81 | |
f00cefe8 |
82 | my %expected_genealogical = ( |
a44aaf2a |
83 | 1 => 0, |
f00cefe8 |
84 | 2 => 1, |
a44aaf2a |
85 | 3 => 0, |
86 | 5 => 0, |
87 | 7 => 0, |
88 | 8 => 0, |
89 | 10 => 0, |
f00cefe8 |
90 | 13 => 1, |
a44aaf2a |
91 | 33 => 0, |
92 | 34 => 0, |
93 | 37 => 0, |
94 | 60 => 0, |
f00cefe8 |
95 | 81 => 1, |
a44aaf2a |
96 | 84 => 0, |
97 | 87 => 0, |
98 | 101 => 0, |
99 | 102 => 0, |
f00cefe8 |
100 | 122 => 1, |
a44aaf2a |
101 | 157 => 0, |
f00cefe8 |
102 | 166 => 1, |
103 | 169 => 1, |
a44aaf2a |
104 | 200 => 0, |
f00cefe8 |
105 | 216 => 1, |
106 | 217 => 1, |
107 | 219 => 1, |
108 | 241 => 1, |
109 | 242 => 1, |
110 | 243 => 1, |
111 | ); |
112 | |
7e17346f |
113 | my $data = run_analysis( $tradition, calcdsn => 'dbi:SQLite:dbname=t/data/analysis.db' ); |
7234b01d |
114 | my $c = $tradition->collation; |
f00cefe8 |
115 | foreach my $row ( @{$data->{'variants'}} ) { |
a44aaf2a |
116 | # Account for rows that used to be "not useful" |
117 | unless( exists $expected_genealogical{$row->{'id'}} ) { |
118 | $expected_genealogical{$row->{'id'}} = 1; |
119 | } |
18f48b82 |
120 | my $gen_bool = $row->{'genealogical'} ? 1 : 0; |
121 | is( $gen_bool, $expected_genealogical{$row->{'id'}}, |
f00cefe8 |
122 | "Got correct genealogical flag for row " . $row->{'id'} ); |
7234b01d |
123 | # Check that we have the right row with the right groups |
124 | my $rank = $row->{'id'}; |
125 | foreach my $rdghash ( @{$row->{'readings'}} ) { |
126 | # Skip 'readings' that aren't really |
127 | next unless $c->reading( $rdghash->{'readingid'} ); |
128 | # Check the rank |
129 | is( $c->reading( $rdghash->{'readingid'} )->rank, $rank, |
130 | "Got correct reading rank" ); |
131 | # Check the witnesses |
132 | my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} ); |
133 | my @sgrp = sort @{$rdghash->{'group'}}; |
134 | is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" ); |
135 | } |
f00cefe8 |
136 | } |
a44aaf2a |
137 | is( $data->{'variant_count'}, 58, "Got right total variant number" ); |
b4cb2d60 |
138 | # TODO Make something meaningful of conflict count, maybe test other bits |
7f52eac8 |
139 | |
140 | =end testing |
141 | |
142 | =cut |
143 | |
d71100ed |
144 | sub run_analysis { |
88a6bac5 |
145 | my( $tradition, %opts ) = @_; |
f00cefe8 |
146 | my $c = $tradition->collation; |
7e17346f |
147 | my $aclabel = $c->ac_label; |
88a6bac5 |
148 | |
149 | my $stemma_id = $opts{'stemma_id'} || 0; |
1d73ecad |
150 | my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); |
151 | my @collapse = ref( $opts{'merge_types'} ) eq 'ARRAY' ? @{$opts{'merge_types'}} : (); |
7e17346f |
152 | |
153 | # Make sure we have a lookup DB for graph calculation results; this will die |
154 | # if calcdir or calcdsn isn't passed. |
155 | my $dir = $opts{'calcdir'} ? delete $opts{'calcdir'} |
156 | : Text::Tradition::Directory->new( dsn => $opts{'calcdsn'} ); |
88a6bac5 |
157 | |
158 | # Get the stemma |
159 | my $stemma = $tradition->stemma( $stemma_id ); |
b4cb2d60 |
160 | |
4ce27d42 |
161 | # Figure out which witnesses we are working with - that is, the ones that |
162 | # appear both in the stemma and in the tradition. All others are 'lacunose' |
163 | # for our purposes. |
7e17346f |
164 | my $lacunose = Set::Scalar->new( $stemma->hypotheticals ); |
165 | my $stemma_wits = Set::Scalar->new( $stemma->witnesses ); |
166 | my $tradition_wits = Set::Scalar->new( map { $_->sigil } $tradition->witnesses ); |
167 | $lacunose->insert( $stemma_wits->symmetric_difference( $tradition_wits )->members ); |
88a6bac5 |
168 | |
169 | # Find and mark 'common' ranks for exclusion, unless they were |
170 | # explicitly specified. |
171 | unless( @ranks ) { |
172 | my %common_rank; |
a44aaf2a |
173 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
174 | $common_rank{$rdg->rank} = 1; |
175 | } |
176 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
177 | } |
7f52eac8 |
178 | |
88a6bac5 |
179 | # Group the variants to send to the solver |
180 | my @groups; |
f629cb3b |
181 | my @use_ranks; |
a44aaf2a |
182 | my %lacunae; |
94654e27 |
183 | my $moved = {}; |
88a6bac5 |
184 | foreach my $rank ( @ranks ) { |
7e17346f |
185 | my $missing = $lacunose->clone(); |
94654e27 |
186 | my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, \@collapse ); |
187 | # Filter out any empty rankgroups |
188 | # (e.g. from the later rank for a transposition) |
189 | next unless keys %$rankgroup; |
7e17346f |
190 | # Get the graph for this rankgroup |
191 | my $rankgraph = _graph_for_grouping( $stemma, $rankgroup, $missing, $aclabel ); |
ffa22d6f |
192 | if( $opts{'exclude_type1'} ) { |
193 | # Check to see whether this is a "useful" group. |
7e17346f |
194 | next unless _useful_variant( $rankgroup, $rankgraph, $aclabel ); |
ffa22d6f |
195 | } |
f629cb3b |
196 | push( @use_ranks, $rank ); |
7e17346f |
197 | push( @groups, { grouping => $rankgroup, graph => $rankgraph } ); |
a44aaf2a |
198 | $lacunae{$rank} = $missing; |
d71100ed |
199 | } |
4ce27d42 |
200 | # Run the solver |
7e17346f |
201 | my $answer = solve_variants( $dir, @groups ); |
fae07016 |
202 | |
88a6bac5 |
203 | # Do further analysis on the answer |
a44aaf2a |
204 | my $conflict_count = 0; |
7e17346f |
205 | my $reversion_count = 0; |
f629cb3b |
206 | foreach my $idx ( 0 .. $#use_ranks ) { |
88a6bac5 |
207 | my $location = $answer->{'variants'}->[$idx]; |
208 | # Add the rank back in |
94654e27 |
209 | my $rank = $use_ranks[$idx]; |
210 | $location->{'id'} = $rank; |
7234b01d |
211 | # Note what our lacunae are |
f629cb3b |
212 | my %lmiss; |
7234b01d |
213 | map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}}; |
7234b01d |
214 | $location->{'missing'} = [ keys %lmiss ]; |
215 | |
88a6bac5 |
216 | # Run the extra analysis we need. |
428bcf0b |
217 | ## TODO We run through all the variants in this call, so |
218 | ## why not add the reading data there instead of here below? |
7e17346f |
219 | my $graph = $groups[$idx]->{graph}; |
220 | analyze_location( $tradition, $graph, $location, \%lmiss ); |
7234b01d |
221 | |
638e2a95 |
222 | my @layerwits; |
7234b01d |
223 | # Do the final post-analysis tidying up of the data. |
a44aaf2a |
224 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
225 | $conflict_count++ |
226 | if exists $rdghash->{'conflict'} && $rdghash->{'conflict'}; |
7e17346f |
227 | $reversion_count++ if $rdghash->{'reverted'}; |
94654e27 |
228 | # Add the reading text back in, setting display value as needed |
a44aaf2a |
229 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
94654e27 |
230 | if( $rdg ) { |
231 | $rdghash->{'text'} = $rdg->text . |
232 | ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' ); |
7b7abf10 |
233 | $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid; |
234 | $rdghash->{'is_nonsense'} = $rdg->is_nonsense; |
94654e27 |
235 | } |
f629cb3b |
236 | # Remove lacunose witnesses from this reading's list now that the |
7234b01d |
237 | # analysis is done |
f629cb3b |
238 | my @realgroup; |
7234b01d |
239 | map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}}; |
f629cb3b |
240 | $rdghash->{'group'} = \@realgroup; |
638e2a95 |
241 | # Note any layered witnesses that appear in this group |
242 | foreach( @realgroup ) { |
243 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
244 | push( @layerwits, $1 ); |
245 | } |
246 | } |
a44aaf2a |
247 | } |
638e2a95 |
248 | $location->{'layerwits'} = \@layerwits if @layerwits; |
88a6bac5 |
249 | } |
a44aaf2a |
250 | $answer->{'conflict_count'} = $conflict_count; |
7e17346f |
251 | $answer->{'reversion_count'} = $reversion_count; |
f00cefe8 |
252 | |
88a6bac5 |
253 | return $answer; |
d71100ed |
254 | } |
255 | |
7f52eac8 |
256 | =head2 group_variants( $tradition, $rank, $lacunose, @merge_relationship_types ) |
257 | |
258 | Groups the variants at the given $rank of the collation, treating any |
259 | relationships in @merge_relationship_types as equivalent. $lacunose should |
260 | be a reference to an array, to which the sigla of lacunose witnesses at this |
94654e27 |
261 | rank will be appended; $transposed should be a reference to a hash, wherein |
262 | the identities of transposed readings and their relatives will be stored. |
7f52eac8 |
263 | |
ffa22d6f |
264 | Returns a hash $group_readings where $rdg is attested by the witnesses listed |
265 | in $group_readings->{$rdg}. |
7f52eac8 |
266 | |
267 | =cut |
268 | |
269 | # Return group_readings, groups, lacunose |
d1348d38 |
270 | sub group_variants { |
94654e27 |
271 | my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_; |
7f52eac8 |
272 | my $c = $tradition->collation; |
335a62ef |
273 | my $aclabel = $c->ac_label; |
d120c995 |
274 | my $table = $c->alignment_table; |
7f52eac8 |
275 | # Get the alignment table readings |
276 | my %readings_at_rank; |
7e17346f |
277 | my $check_for_gaps = Set::Scalar->new(); |
94654e27 |
278 | my %moved_wits; |
d120c995 |
279 | my $has_transposition; |
280 | foreach my $tablewit ( @{$table->{'alignment'}} ) { |
7f52eac8 |
281 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
282 | my $wit = $tablewit->{'witness'}; |
ffa22d6f |
283 | # Exclude the witness if it is "lacunose" which if we got here |
284 | # means "not in the stemma". |
7e17346f |
285 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
94654e27 |
286 | # Note if the witness is actually in a lacuna |
7f52eac8 |
287 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
335a62ef |
288 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
94654e27 |
289 | # Otherwise the witness either has a positive reading... |
7f52eac8 |
290 | } elsif( $rdg ) { |
94654e27 |
291 | # If the reading has been counted elsewhere as a transposition, ignore it. |
292 | if( $transposed->{$rdg->{'t'}->id} ) { |
d120c995 |
293 | # TODO Does this cope with three-way transpositions? |
94654e27 |
294 | map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}}; |
295 | next; |
296 | } |
297 | # Otherwise, record it... |
298 | $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'}; |
299 | # ...and grab any transpositions, and their relations. |
300 | my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings(); |
301 | foreach my $trdg ( @transp ) { |
d120c995 |
302 | next if exists $readings_at_rank{$trdg->id}; |
303 | $has_transposition = 1; |
304 | my @affected_wits = _table_witnesses( |
7e17346f |
305 | $table, $trdg, $lacunose, $aclabel ); |
d120c995 |
306 | next unless @affected_wits; |
307 | map { $moved_wits{$_} = 1 } @affected_wits; |
308 | $transposed->{$trdg->id} = |
7e17346f |
309 | [ _table_witnesses( $table, $rdg->{'t'}, $lacunose, $aclabel ) ]; |
94654e27 |
310 | $readings_at_rank{$trdg->id} = $trdg; |
311 | } |
312 | # ...or it is empty, ergo a gap. |
7f52eac8 |
313 | } else { |
7e17346f |
314 | _add_to_witlist( $wit, $check_for_gaps, $aclabel ); |
7f52eac8 |
315 | } |
316 | } |
7e17346f |
317 | my $gap_wits = Set::Scalar->new(); |
318 | map { _add_to_witlist( $_, $gap_wits, $aclabel ) |
319 | unless $moved_wits{$_} } $check_for_gaps->members; |
320 | |
321 | # Group the readings, collapsing groups by relationship if needed. |
d120c995 |
322 | my $grouped_readings = {}; |
4ce27d42 |
323 | foreach my $rdg ( values %readings_at_rank ) { |
7f52eac8 |
324 | # Skip readings that have been collapsed into others. |
d120c995 |
325 | next if exists $grouped_readings->{$rdg->id} |
326 | && $grouped_readings->{$rdg->id} eq 'COLLAPSE'; |
4ce27d42 |
327 | # Get the witness list, including from readings collapsed into this one. |
7e17346f |
328 | my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel ); |
d120c995 |
329 | if( $collapse && @$collapse ) { |
7f52eac8 |
330 | my $filter = sub { my $r = $_[0]; grep { $_ eq $r->type } @$collapse; }; |
331 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
7e17346f |
332 | my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel ); |
fae07016 |
333 | push( @wits, @otherwits ); |
d120c995 |
334 | $grouped_readings->{$other->id} = 'COLLAPSE'; |
d1348d38 |
335 | } |
336 | } |
7e17346f |
337 | $grouped_readings->{$rdg->id} = Set::Scalar->new( @wits ); |
7f52eac8 |
338 | } |
7e17346f |
339 | if( $gap_wits->members ) { |
340 | $grouped_readings->{'(omitted)'} = $gap_wits; |
341 | } |
342 | |
7f52eac8 |
343 | # Get rid of our collapsed readings |
7e17346f |
344 | map { delete $grouped_readings->{$_} if( |
345 | $grouped_readings->{$_} eq 'COLLAPSE' |
346 | || $grouped_readings->{$_}->is_empty ) } |
347 | keys %$grouped_readings; |
d120c995 |
348 | |
349 | # If something was transposed, check the groups for doubled-up readings |
350 | if( $has_transposition ) { |
62a39b8f |
351 | # print STDERR "Group for rank $rank:\n"; |
352 | # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" } |
353 | # keys %$grouped_readings; |
d120c995 |
354 | _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings ); |
355 | } |
7f52eac8 |
356 | |
4ce27d42 |
357 | # Return the result |
d120c995 |
358 | return $grouped_readings; |
359 | } |
360 | |
361 | # Helper function to query the alignment table for all witnesses (a.c. included) |
362 | # that have a given reading at its rank. |
363 | sub _table_witnesses { |
364 | my( $table, $trdg, $lacunose, $aclabel ) = @_; |
365 | my $tableidx = $trdg->rank - 1; |
7e17346f |
366 | my $has_reading = Set::Scalar->new(); |
d120c995 |
367 | foreach my $row ( @{$table->{'alignment'}} ) { |
368 | my $wit = $row->{'witness'}; |
7e17346f |
369 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
d120c995 |
370 | my $rdg = $row->{'tokens'}->[$tableidx]; |
371 | next unless exists $rdg->{'t'} && defined $rdg->{'t'}; |
7e17346f |
372 | _add_to_witlist( $wit, $has_reading, $aclabel ) |
d120c995 |
373 | if $rdg->{'t'}->id eq $trdg->id; |
374 | } |
7e17346f |
375 | return $has_reading->members; |
376 | } |
377 | |
378 | # Helper function to see if a witness is lacunose even if we are asking about |
379 | # the a.c. version |
380 | sub _is_lacunose { |
381 | my ( $wit, $lac, $acstr ) = @_; |
382 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
383 | $wit = $1; |
384 | } |
385 | return $lac->has( $wit ); |
d1348d38 |
386 | } |
387 | |
335a62ef |
388 | # Helper function to ensure that X and X a.c. never appear in the same list. |
389 | sub _add_to_witlist { |
390 | my( $wit, $list, $acstr ) = @_; |
335a62ef |
391 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
7e17346f |
392 | # Don't add X a.c. if we already have X |
393 | return if $list->has( $1 ); |
335a62ef |
394 | } else { |
7e17346f |
395 | # Delete X a.c. if we are about to add X |
396 | $list->delete( $wit.$acstr ); |
335a62ef |
397 | } |
7e17346f |
398 | $list->insert( $wit ); |
335a62ef |
399 | } |
400 | |
d120c995 |
401 | sub _check_transposed_consistency { |
402 | my( $c, $rank, $transposed, $groupings ) = @_; |
403 | my %seen_wits; |
404 | my %thisrank; |
405 | # Note which readings are actually at this rank, and which witnesses |
406 | # belong to which reading. |
407 | foreach my $rdg ( keys %$groupings ) { |
408 | my $rdgobj = $c->reading( $rdg ); |
409 | # Count '(omitted)' as a reading at this rank |
410 | $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank; |
411 | map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}}; |
412 | } |
413 | # Our work is done if we have no witness belonging to more than one |
414 | # reading. |
415 | my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits; |
416 | return unless @doubled; |
417 | # If we have a symmetric related transposition, drop the non-rank readings. |
418 | if( @doubled == scalar keys %seen_wits ) { |
419 | foreach my $rdg ( keys %$groupings ) { |
420 | if( !$thisrank{$rdg} ) { |
421 | my $groupstr = wit_stringify( $groupings->{$rdg} ); |
422 | my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) } |
423 | keys %thisrank; |
424 | delete $groupings->{$rdg}; |
425 | # If we found a group match, assume there is a symmetry happening. |
426 | # TODO think more about this |
62a39b8f |
427 | # print STDERR "*** Deleting symmetric reading $rdg\n"; |
d120c995 |
428 | unless( $matched ) { |
429 | delete $transposed->{$rdg}; |
430 | warn "Found problem in evident symmetry with reading $rdg"; |
431 | } |
432 | } |
433 | } |
434 | # Otherwise 'unhook' the transposed reading(s) that have duplicates. |
435 | } else { |
436 | foreach my $dup ( @doubled ) { |
437 | foreach my $rdg ( @{$seen_wits{$dup}} ) { |
438 | next if $thisrank{$rdg}; |
439 | next unless exists $groupings->{$rdg}; |
62a39b8f |
440 | # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n"; |
d120c995 |
441 | delete $groupings->{$rdg}; |
442 | delete $transposed->{$rdg}; |
443 | } |
444 | } |
445 | # and put any now-orphaned readings into an 'omitted' reading. |
446 | foreach my $wit ( keys %seen_wits ) { |
447 | unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) { |
7e17346f |
448 | $groupings->{'(omitted)'} = Set::Scalar->new() |
449 | unless exists $groupings->{'(omitted)'}; |
d120c995 |
450 | _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label ); |
451 | } |
452 | } |
453 | } |
454 | } |
455 | |
7e17346f |
456 | # For the given grouping, return its situation graph based on the stemma. |
457 | sub _graph_for_grouping { |
458 | my( $stemma, $grouping, $lacunose, $aclabel ) = @_; |
459 | my $acwits = []; |
460 | my $extant = {}; |
461 | foreach my $gs ( values %$grouping ) { |
462 | map { |
463 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
464 | push( @$acwits, $1 ) unless $lacunose->has( $1 ); |
465 | } else { |
466 | $extant->{$_} = 1 unless $lacunose->has( $_ ); |
467 | } |
468 | } $gs->members; |
469 | } |
470 | my $graph; |
471 | try { |
472 | # contig contains all extant wits and all hypothetical wits |
473 | # needed to make up the groups. |
474 | $graph = $stemma->situation_graph( $extant, $acwits ); |
475 | } catch ( Text::Tradition::Error $e ) { |
476 | die "Could not extend graph with given extant and a.c. witnesses: " |
477 | . $e->message; |
478 | } catch { |
479 | die "Could not extend graph with a.c. witnesses @$acwits"; |
480 | } |
481 | return $graph; |
482 | } |
88a6bac5 |
483 | |
7e17346f |
484 | =head2 solve_variants( $calcdir, @groups ) |
485 | |
486 | Looks up the set of groups in the answers provided by the external graph solver |
487 | service and returns a cleaned-up answer, adding the rank IDs back where they belong. |
88a6bac5 |
488 | |
489 | The JSON has the form |
490 | { "graph": [ stemmagraph DOT string without newlines ], |
491 | "groupings": [ array of arrays of groups, one per rank ] } |
492 | |
493 | The answer has the form |
494 | { "variants" => [ array of variant location structures ], |
495 | "variant_count" => total, |
496 | "conflict_count" => number of conflicts detected, |
497 | "genealogical_count" => number of solutions found } |
498 | |
499 | =cut |
500 | |
501 | sub solve_variants { |
7e17346f |
502 | my( $dir, @groups ) = @_; |
335a62ef |
503 | |
7e17346f |
504 | ## For each graph/group combo, look it up in the DB. |
335a62ef |
505 | ## Witness map is a HACK to get around limitations in node names from IDP |
506 | my $witness_map = {}; |
507 | ## Variables to store answers as they come back |
7e17346f |
508 | my $variants = []; |
509 | my $genealogical = 0; # counter |
510 | foreach my $graphproblem ( @groups ) { |
511 | # Initialize the result structure for this graph problem |
512 | my $vstruct = { readings => [] }; |
513 | push( @$variants, $vstruct ); |
5c44c598 |
514 | |
7e17346f |
515 | # Construct the calc result key and look up its answer |
516 | my $reqkey = _get_calc_key( $graphproblem ); |
517 | my $scope = $dir->new_scope; |
518 | my $answer = $dir->lookup( $reqkey ); |
519 | unless( $answer ) { |
520 | #warn "No answer found for graph problem $reqkey, moving on"; |
521 | # Record the unsolved problem so that we can go get a solution |
522 | _save_problem( $graphproblem ); |
523 | # Put just the request, with no real result, into vstruct |
524 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
525 | push( @{$vstruct->{readings}}, { readingid => $rid, |
526 | group => [ $graphproblem->{grouping}->{$rid}->members ] } ); |
5c44c598 |
527 | } |
7e17346f |
528 | next; |
5c44c598 |
529 | } |
7e17346f |
530 | |
531 | ## The answer is a Text::Tradition::Analysis::Result containing a bunch |
532 | ## of information about this variant set. Record the information therein. |
5c44c598 |
533 | |
7e17346f |
534 | # 1. Did the group evaluate as genealogical? |
535 | $vstruct->{genealogical} = $answer->is_genealogical; |
536 | $genealogical++ if $answer->is_genealogical; |
537 | |
538 | # 2. What are the calculated minimum groupings for each variant loc? |
539 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
540 | my $inputset = $graphproblem->{grouping}->{$rid}; |
541 | my $minset = $answer->minimum_grouping_for( $inputset ); |
542 | push( @{$vstruct->{readings}}, { readingid => $rid, group => $minset } ); |
6d25a3a0 |
543 | } |
7e17346f |
544 | |
545 | # 3. What are the sources and classes calculated for each witness? |
546 | $vstruct->{witcopy_types} = { $answer->classes }; |
547 | $vstruct->{reading_roots} = {}; |
548 | map { $vstruct->{reading_roots}->{$_} = 1 } $answer->sources; |
549 | |
88a6bac5 |
550 | } |
551 | |
7e17346f |
552 | # Spit out any unsolved problems we encountered |
553 | _list_unsolved(); |
554 | |
88a6bac5 |
555 | return { 'variants' => $variants, |
556 | 'variant_count' => scalar @$variants, |
557 | 'genealogical_count' => $genealogical }; |
558 | } |
559 | |
7e17346f |
560 | sub _get_calc_key { |
561 | my( $graphproblem ) = @_; |
562 | my $graph = $graphproblem->{graph}; |
563 | my $grouping = [ values %{$graphproblem->{grouping}} ]; |
564 | my $key = Text::Tradition::Analysis::Result::string_from_graph_problem( |
565 | $graph, $grouping ); |
566 | return md5_hex( encode_utf8( $key ) ); |
5c44c598 |
567 | } |
568 | |
7e17346f |
569 | sub _save_problem { |
570 | my( $graphproblem ) = @_; |
571 | my $graphstr = Text::Tradition::Stemma::editable_graph( |
572 | $graphproblem->{graph}, { 'linesep' => ' ' } ); |
573 | unless( exists $unsolved_problems->{$graphstr} ) { |
574 | $unsolved_problems->{$graphstr} = {}; |
b4cb2d60 |
575 | } |
7e17346f |
576 | my $grouping = []; |
577 | foreach my $set ( sort { Text::Tradition::Analysis::Result::by_size_and_alpha( $a, $b ) } values %{$graphproblem->{grouping}} ) { |
578 | push( @$grouping, [ sort $set->members ] ); |
b4cb2d60 |
579 | } |
7e17346f |
580 | $unsolved_problems->{$graphstr}->{wit_stringify( $grouping )} = $grouping; |
b4cb2d60 |
581 | } |
582 | |
7e17346f |
583 | sub _list_unsolved { |
584 | #say STDERR "Problems needing a solution:"; |
585 | foreach my $graphstr ( keys %$unsolved_problems ) { |
586 | my $struct = { graph => $graphstr, groupings => [] }; |
587 | foreach my $gp ( values %{$unsolved_problems->{$graphstr}} ) { |
588 | push( @{$struct->{groupings}}, $gp ); |
b4cb2d60 |
589 | } |
7e17346f |
590 | my $json = to_json( $struct ); |
591 | say STDERR "$json"; |
b4cb2d60 |
592 | } |
b4cb2d60 |
593 | } |
594 | |
fae07016 |
595 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
596 | |
fae07016 |
597 | Given the tradition, its stemma graph, and the solution from the graph solver, |
598 | work out the rest of the information we want. For each reading we need missing, |
5c44c598 |
599 | conflict, reading_parents, independent_occurrence, followed, not_followed, |
600 | and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
601 | |
602 | =cut |
732152b1 |
603 | |
fae07016 |
604 | sub analyze_location { |
7e17346f |
605 | my ( $tradition, $graph, $variant_row, $lacunose ) = @_; |
94654e27 |
606 | my $c = $tradition->collation; |
fae07016 |
607 | |
608 | # Make a hash of all known node memberships, and make the subgraphs. |
609 | my $contig = {}; |
610 | my $reading_roots = {}; |
611 | my $subgraph = {}; |
638e2a95 |
612 | my $acstr = $c->ac_label; |
613 | my @acwits; |
5c44c598 |
614 | |
615 | my $NO_IDP; |
616 | if( exists $variant_row->{'reading_roots'} ) { |
617 | $reading_roots = delete $variant_row->{'reading_roots'}; |
618 | } else { |
619 | warn "No reading source information from IDP - proceed at your own risk"; |
620 | $NO_IDP = 1; |
621 | } |
7e17346f |
622 | my $classinfo = delete $variant_row->{'witcopy_types'}; |
5c44c598 |
623 | |
624 | # Note which witnesses positively belong to which group. This information |
625 | # comes ultimately from the IDP solver. |
626 | # Also make a note of the reading's roots. |
fae07016 |
627 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
628 | my $rid = $rdghash->{'readingid'}; |
5c44c598 |
629 | my @roots; |
638e2a95 |
630 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
631 | $contig->{$wit} = $rid; |
632 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
633 | push( @acwits, $1 ); |
634 | } |
5c44c598 |
635 | if( exists $reading_roots->{$wit} && $reading_roots->{$wit} ) { |
636 | push( @roots, $wit ); |
637 | } |
638e2a95 |
638 | } |
5c44c598 |
639 | $rdghash->{'independent_occurrence'} = \@roots; |
94654e27 |
640 | } |
7e17346f |
641 | |
fae07016 |
642 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
643 | # non-followed/unknown values for each reading. Also figure out the |
644 | # reading's evident parent(s). |
645 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
646 | my $rid = $rdghash->{'readingid'}; |
428bcf0b |
647 | my $rdg = $c->reading( $rid ); |
5c44c598 |
648 | my @roots = @{$rdghash->{'independent_occurrence'}}; |
7e17346f |
649 | my @reversions; |
650 | if( $classinfo ) { |
651 | @reversions = grep { $classinfo->{$_} eq 'revert' } |
652 | $rdghash->{'group'}->members; |
653 | } |
5c44c598 |
654 | my @group = @{$rdghash->{'group'}}; |
fae07016 |
655 | |
656 | # Start figuring things out. |
7e17346f |
657 | $rdghash->{'followed'} = scalar( @group ) |
658 | - ( scalar( @roots ) + scalar( @reversions ) ); |
bebec0e9 |
659 | # Find the parent readings, if any, of this reading. |
7e17346f |
660 | my $sourceparents = _find_reading_parents( $rid, $graph, $contig, @roots ); |
661 | my $revertparents = _find_reading_parents( $rid, $graph, $contig, @reversions ); |
662 | # Work out relationships between readings and their non-followed parent. |
663 | _resolve_parent_relationships( $c, $rid, $rdg, $sourceparents ); |
664 | _resolve_parent_relationships( $c, $rid, $rdg, $revertparents ); |
94654e27 |
665 | |
7e17346f |
666 | $rdghash->{'reading_parents'} = $sourceparents; |
667 | $rdghash->{'reversion_parents'} = $revertparents; |
bebec0e9 |
668 | |
669 | # Find the number of times this reading was altered, and the number of |
670 | # times we're not sure. |
671 | my( %nofollow, %unknownfollow ); |
5c44c598 |
672 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
bebec0e9 |
673 | foreach my $wchild ( $graph->successors( $wit ) ) { |
5c44c598 |
674 | if( $reading_roots->{$wchild} && $contig->{$wchild} |
675 | && $contig->{$wchild} ne $rid ) { |
bebec0e9 |
676 | # It definitely changed here. |
677 | $nofollow{$wchild} = 1; |
678 | } elsif( !($contig->{$wchild}) ) { |
679 | # The child is a hypothetical node not definitely in |
680 | # any group. Answer is unknown. |
681 | $unknownfollow{$wchild} = 1; |
5c44c598 |
682 | } # else it is either in our group, or it is a non-root node in a |
683 | # known group and therefore is presumed to have its reading from |
684 | # its group, not this link. |
bebec0e9 |
685 | } |
686 | } |
687 | $rdghash->{'not_followed'} = keys %nofollow; |
688 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
689 | |
690 | # Now say whether this reading represents a conflict. |
691 | unless( $variant_row->{'genealogical'} ) { |
7e17346f |
692 | my @reversions; |
693 | if( $classinfo ) { |
5c44c598 |
694 | # We have tested for reversions. Use the information. |
7e17346f |
695 | @reversions = |
696 | $rdghash->{'reversions'} = \@reversions if @reversions; |
697 | } |
698 | $rdghash->{'is_conflict'} = @roots != 1; |
699 | $rdghash->{'is_reverted'} = !!@reversions; |
700 | } |
701 | } |
702 | } |
703 | |
704 | sub _find_reading_parents { |
705 | my( $rid, $graph, $contig, @list ) = @_; |
706 | my $parenthash = {}; |
707 | foreach my $wit ( @list ) { |
708 | # Look in the stemma graph to find this witness's extant or known-reading |
709 | # immediate ancestor(s), and look up the reading that each ancestor holds. |
710 | my @check = $graph->predecessors( $wit ); |
711 | while( @check ) { |
712 | my @next; |
713 | foreach my $wparent( @check ) { |
714 | my $preading = $contig->{$wparent}; |
715 | if( $preading && $preading ne $rid ) { |
716 | $parenthash->{$preading} = 1; |
717 | } else { |
718 | push( @next, $graph->predecessors( $wparent ) ); |
719 | } |
720 | } |
721 | @check = @next; |
722 | } |
723 | } |
724 | return $parenthash; |
725 | } |
726 | |
727 | sub _resolve_parent_relationships { |
728 | my( $c, $rid, $rdg, $rdgparents ) = @_; |
729 | foreach my $p ( keys %$rdgparents ) { |
730 | # Resolve the relationship of the parent to the reading, and |
731 | # save it in our hash. |
732 | my $pobj = $c->reading( $p ); |
733 | my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p; |
734 | my $phash = { 'label' => $prep }; |
735 | if( $pobj ) { |
736 | my $rel = $c->get_relationship( $p, $rid ); |
737 | if( $rel ) { |
738 | _add_to_hash( $rel, $phash ); |
739 | } elsif( $rdg ) { |
740 | # First check for a transposed relationship |
741 | if( $rdg->rank != $pobj->rank ) { |
742 | foreach my $ti ( $rdg->related_readings( 'transposition' ) ) { |
743 | next unless $ti->text eq $rdg->text; |
744 | $rel = $c->get_relationship( $ti, $pobj ); |
745 | if( $rel ) { |
746 | _add_to_hash( $rel, $phash, 1 ); |
747 | last; |
748 | } |
749 | } |
750 | unless( $rel ) { |
751 | foreach my $ti ( $pobj->related_readings( 'transposition' ) ) { |
752 | next unless $ti->text eq $pobj->text; |
753 | $rel = $c->get_relationship( $ti, $rdg ); |
754 | if( $rel ) { |
755 | _add_to_hash( $rel, $phash, 1 ); |
756 | last; |
757 | } |
758 | } |
5c44c598 |
759 | } |
760 | } |
7e17346f |
761 | unless( $rel ) { |
762 | # and then check for sheer word similarity. |
763 | my $rtext = $rdg->text; |
764 | my $ptext = $pobj->text; |
765 | if( similar( $rtext, $ptext ) ) { |
766 | # say STDERR "Words $rtext and $ptext judged similar"; |
767 | $phash->{relation} = { type => 'wordsimilar' }; |
768 | } |
769 | } |
5c44c598 |
770 | } else { |
7e17346f |
771 | $phash->{relation} = { type => 'deletion' }; |
5c44c598 |
772 | } |
7e17346f |
773 | # Get the attributes of the parent object while we are here |
774 | $phash->{'text'} = $pobj->text if $pobj; |
775 | $phash->{'is_nonsense'} = $pobj->is_nonsense; |
776 | $phash->{'is_ungrammatical'} = $pobj->grammar_invalid; |
777 | } elsif( $p eq '(omitted)' ) { |
778 | $phash->{relation} = { type => 'addition' }; |
779 | } |
780 | # Save it |
781 | $rdgparents->{$p} = $phash; |
782 | } |
d71100ed |
783 | } |
784 | |
428bcf0b |
785 | sub _add_to_hash { |
786 | my( $rel, $phash, $is_transposed ) = @_; |
787 | $phash->{relation} = { type => $rel->type }; |
788 | $phash->{relation}->{transposed} = 1 if $is_transposed; |
789 | $phash->{relation}->{annotation} = $rel->annotation |
790 | if $rel->has_annotation; |
791 | } |
792 | |
793 | =head2 similar( $word1, $word2 ) |
794 | |
795 | Use Algorithm::Diff to get a sense of how close the words are to each other. |
796 | This will hopefully handle substitutions a bit more nicely than Levenshtein. |
797 | |
798 | =cut |
799 | |
800 | #!/usr/bin/env perl |
801 | |
802 | sub similar { |
803 | my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_; |
804 | my @let1 = split( '', lc( $word1 ) ); |
805 | my @let2 = split( '', lc( $word2 ) ); |
806 | my $diff = Algorithm::Diff->new( \@let1, \@let2 ); |
807 | my $mag = 0; |
808 | while( $diff->Next ) { |
809 | if( $diff->Same ) { |
810 | # Take off points for longer strings |
811 | my $cs = $diff->Range(1) - 2; |
812 | $cs = 0 if $cs < 0; |
813 | $mag -= $cs; |
814 | } elsif( !$diff->Items(1) ) { |
815 | $mag += $diff->Range(2); |
816 | } elsif( !$diff->Items(2) ) { |
817 | $mag += $diff->Range(1); |
818 | } else { |
819 | # Split the difference for substitutions |
820 | my $c1 = $diff->Range(1) || 1; |
821 | my $c2 = $diff->Range(2) || 1; |
822 | my $cd = ( $c1 + $c2 ) / 2; |
823 | $mag += $cd; |
824 | } |
825 | } |
826 | return ( $mag <= length( $word1 ) / 2 ); |
827 | } |
828 | |
6d25a3a0 |
829 | sub _prune_group { |
5c44c598 |
830 | my( $group, $graph ) = @_; |
831 | my $relevant = {}; |
832 | # Record the existence of the vertices in the group |
833 | map { $relevant->{$_} = 1 } @$group; |
6d25a3a0 |
834 | # Make our subgraph |
5c44c598 |
835 | my $subgraph = $graph->deep_copy; |
836 | map { $subgraph->delete_vertex( $_ ) unless $relevant->{$_} } |
6d25a3a0 |
837 | $subgraph->vertices; |
6d25a3a0 |
838 | # Now prune and return the remaining vertices. |
5c44c598 |
839 | _prune_subtree( $subgraph ); |
840 | # Return the list of vertices and the list of roots. |
841 | my $pruned_group = [ sort $subgraph->vertices ]; |
842 | my $pruned_roots = [ $subgraph->predecessorless_vertices ]; |
843 | return( $pruned_group, $pruned_roots ); |
6d25a3a0 |
844 | } |
845 | |
7f52eac8 |
846 | sub _prune_subtree { |
5c44c598 |
847 | my( $tree ) = @_; |
94654e27 |
848 | |
849 | # Delete lacunose witnesses that have no successors |
5c44c598 |
850 | my @orphan_hypotheticals; |
851 | my $ctr = 0; |
852 | do { |
853 | die "Infinite loop on leaves" if $ctr > 100; |
854 | @orphan_hypotheticals = |
855 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
856 | $tree->successorless_vertices; |
857 | $tree->delete_vertices( @orphan_hypotheticals ); |
858 | $ctr++; |
859 | } while( @orphan_hypotheticals ); |
94654e27 |
860 | |
861 | # Delete lacunose roots that have a single successor |
862 | my @redundant_root; |
863 | $ctr = 0; |
864 | do { |
5c44c598 |
865 | die "Infinite loop on roots" if $ctr > 100; |
866 | @redundant_root = |
867 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' |
868 | && $tree->successors( $_ ) == 1 } |
869 | $tree->predecessorless_vertices; |
94654e27 |
870 | $tree->delete_vertices( @redundant_root ); |
871 | $ctr++; |
872 | } while( @redundant_root ); |
873 | } |
874 | |
5be0cdeb |
875 | sub _useful_variant { |
7e17346f |
876 | my( $rankgroup, $rankgraph, $acstr ) = @_; |
5be0cdeb |
877 | |
878 | # Sort by group size and return |
879 | my $is_useful = 0; |
7e17346f |
880 | foreach my $rdg ( keys %$rankgroup ) { |
881 | my @wits = $rankgroup->{$rdg}->members; |
882 | if( @wits > 1 ) { |
5be0cdeb |
883 | $is_useful++; |
884 | } else { |
7e17346f |
885 | $is_useful++ unless( $rankgraph->is_sink_vertex( $wits[0] ) |
886 | || $wits[0] =~ /\Q$acstr\E$/ ); |
5be0cdeb |
887 | } |
888 | } |
7e17346f |
889 | return $is_useful > 1; |
5be0cdeb |
890 | } |
891 | |
7f52eac8 |
892 | =head2 wit_stringify( $groups ) |
893 | |
894 | Takes an array of witness groupings and produces a string like |
895 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
896 | |
7f52eac8 |
897 | =cut |
d71100ed |
898 | |
899 | sub wit_stringify { |
900 | my $groups = shift; |
901 | my @gst; |
902 | # If we were passed an array of witnesses instead of an array of |
903 | # groupings, then "group" the witnesses first. |
904 | unless( ref( $groups->[0] ) ) { |
905 | my $mkgrp = [ $groups ]; |
906 | $groups = $mkgrp; |
907 | } |
908 | foreach my $g ( @$groups ) { |
909 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
910 | } |
911 | return join( ' / ', @gst ); |
912 | } |
7f52eac8 |
913 | |
7f52eac8 |
914 | 1; |
915 | |
916 | =head1 LICENSE |
917 | |
918 | This package is free software and is provided "as is" without express |
919 | or implied warranty. You can redistribute it and/or modify it under |
920 | the same terms as Perl itself. |
921 | |
922 | =head1 AUTHOR |
923 | |
924 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |