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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'}} : (); |
e23225e7 |
151 | my $collapse = Set::Scalar->new(); |
152 | if( $opts{'merge_types'} && ref( $opts{'merge_types'} ) eq 'ARRAY' ) { |
153 | $collapse->insert( @{$opts{'merge_types'}} ); |
154 | } elsif( $opts{'merge_types'} ) { |
155 | $collapse->insert( $opts{'merge_types'} ); |
156 | } |
7e17346f |
157 | |
158 | # Make sure we have a lookup DB for graph calculation results; this will die |
159 | # if calcdir or calcdsn isn't passed. |
160 | my $dir = $opts{'calcdir'} ? delete $opts{'calcdir'} |
161 | : Text::Tradition::Directory->new( dsn => $opts{'calcdsn'} ); |
88a6bac5 |
162 | |
163 | # Get the stemma |
164 | my $stemma = $tradition->stemma( $stemma_id ); |
b4cb2d60 |
165 | |
4ce27d42 |
166 | # Figure out which witnesses we are working with - that is, the ones that |
167 | # appear both in the stemma and in the tradition. All others are 'lacunose' |
168 | # for our purposes. |
7e17346f |
169 | my $lacunose = Set::Scalar->new( $stemma->hypotheticals ); |
170 | my $stemma_wits = Set::Scalar->new( $stemma->witnesses ); |
171 | my $tradition_wits = Set::Scalar->new( map { $_->sigil } $tradition->witnesses ); |
172 | $lacunose->insert( $stemma_wits->symmetric_difference( $tradition_wits )->members ); |
88a6bac5 |
173 | |
174 | # Find and mark 'common' ranks for exclusion, unless they were |
175 | # explicitly specified. |
176 | unless( @ranks ) { |
177 | my %common_rank; |
a44aaf2a |
178 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
179 | $common_rank{$rdg->rank} = 1; |
180 | } |
181 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
182 | } |
7f52eac8 |
183 | |
88a6bac5 |
184 | # Group the variants to send to the solver |
185 | my @groups; |
f629cb3b |
186 | my @use_ranks; |
a44aaf2a |
187 | my %lacunae; |
94654e27 |
188 | my $moved = {}; |
88a6bac5 |
189 | foreach my $rank ( @ranks ) { |
7e17346f |
190 | my $missing = $lacunose->clone(); |
e23225e7 |
191 | my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, $collapse ); |
94654e27 |
192 | # Filter out any empty rankgroups |
193 | # (e.g. from the later rank for a transposition) |
194 | next unless keys %$rankgroup; |
7e17346f |
195 | # Get the graph for this rankgroup |
196 | my $rankgraph = _graph_for_grouping( $stemma, $rankgroup, $missing, $aclabel ); |
ffa22d6f |
197 | if( $opts{'exclude_type1'} ) { |
198 | # Check to see whether this is a "useful" group. |
7e17346f |
199 | next unless _useful_variant( $rankgroup, $rankgraph, $aclabel ); |
ffa22d6f |
200 | } |
f629cb3b |
201 | push( @use_ranks, $rank ); |
7e17346f |
202 | push( @groups, { grouping => $rankgroup, graph => $rankgraph } ); |
a44aaf2a |
203 | $lacunae{$rank} = $missing; |
d71100ed |
204 | } |
4ce27d42 |
205 | # Run the solver |
7e17346f |
206 | my $answer = solve_variants( $dir, @groups ); |
fae07016 |
207 | |
88a6bac5 |
208 | # Do further analysis on the answer |
a44aaf2a |
209 | my $conflict_count = 0; |
7e17346f |
210 | my $reversion_count = 0; |
f629cb3b |
211 | foreach my $idx ( 0 .. $#use_ranks ) { |
88a6bac5 |
212 | my $location = $answer->{'variants'}->[$idx]; |
213 | # Add the rank back in |
94654e27 |
214 | my $rank = $use_ranks[$idx]; |
215 | $location->{'id'} = $rank; |
7234b01d |
216 | # Note what our lacunae are |
f629cb3b |
217 | my %lmiss; |
7234b01d |
218 | map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}}; |
7234b01d |
219 | $location->{'missing'} = [ keys %lmiss ]; |
220 | |
88a6bac5 |
221 | # Run the extra analysis we need. |
428bcf0b |
222 | ## TODO We run through all the variants in this call, so |
223 | ## why not add the reading data there instead of here below? |
7e17346f |
224 | my $graph = $groups[$idx]->{graph}; |
225 | analyze_location( $tradition, $graph, $location, \%lmiss ); |
7234b01d |
226 | |
638e2a95 |
227 | my @layerwits; |
7234b01d |
228 | # Do the final post-analysis tidying up of the data. |
a44aaf2a |
229 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
e23225e7 |
230 | $conflict_count++ if $rdghash->{'is_conflict'}; |
231 | $reversion_count++ if $rdghash->{'is_reverted'}; |
94654e27 |
232 | # Add the reading text back in, setting display value as needed |
a44aaf2a |
233 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
94654e27 |
234 | if( $rdg ) { |
235 | $rdghash->{'text'} = $rdg->text . |
236 | ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' ); |
7b7abf10 |
237 | $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid; |
238 | $rdghash->{'is_nonsense'} = $rdg->is_nonsense; |
94654e27 |
239 | } |
f629cb3b |
240 | # Remove lacunose witnesses from this reading's list now that the |
7234b01d |
241 | # analysis is done |
f629cb3b |
242 | my @realgroup; |
7234b01d |
243 | map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}}; |
f629cb3b |
244 | $rdghash->{'group'} = \@realgroup; |
638e2a95 |
245 | # Note any layered witnesses that appear in this group |
246 | foreach( @realgroup ) { |
247 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
248 | push( @layerwits, $1 ); |
249 | } |
250 | } |
a44aaf2a |
251 | } |
638e2a95 |
252 | $location->{'layerwits'} = \@layerwits if @layerwits; |
88a6bac5 |
253 | } |
a44aaf2a |
254 | $answer->{'conflict_count'} = $conflict_count; |
7e17346f |
255 | $answer->{'reversion_count'} = $reversion_count; |
f00cefe8 |
256 | |
88a6bac5 |
257 | return $answer; |
d71100ed |
258 | } |
259 | |
e23225e7 |
260 | =head2 group_variants( $tradition, $rank, $lacunose, $transposed, $merge_relationship_types ) |
7f52eac8 |
261 | |
262 | Groups the variants at the given $rank of the collation, treating any |
e23225e7 |
263 | relationships in the set $merge_relationship_types as equivalent. |
264 | $lacunose should be a reference to an array, to which the sigla of lacunose |
265 | witnesses at this rank will be appended; $transposed should be a reference |
266 | to a hash, wherein the identities of transposed readings and their |
267 | relatives will be stored. |
7f52eac8 |
268 | |
ffa22d6f |
269 | Returns a hash $group_readings where $rdg is attested by the witnesses listed |
270 | in $group_readings->{$rdg}. |
7f52eac8 |
271 | |
272 | =cut |
273 | |
274 | # Return group_readings, groups, lacunose |
d1348d38 |
275 | sub group_variants { |
94654e27 |
276 | my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_; |
7f52eac8 |
277 | my $c = $tradition->collation; |
335a62ef |
278 | my $aclabel = $c->ac_label; |
d120c995 |
279 | my $table = $c->alignment_table; |
7f52eac8 |
280 | # Get the alignment table readings |
281 | my %readings_at_rank; |
7e17346f |
282 | my $check_for_gaps = Set::Scalar->new(); |
94654e27 |
283 | my %moved_wits; |
d120c995 |
284 | my $has_transposition; |
285 | foreach my $tablewit ( @{$table->{'alignment'}} ) { |
7f52eac8 |
286 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
287 | my $wit = $tablewit->{'witness'}; |
ffa22d6f |
288 | # Exclude the witness if it is "lacunose" which if we got here |
289 | # means "not in the stemma". |
7e17346f |
290 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
94654e27 |
291 | # Note if the witness is actually in a lacuna |
7f52eac8 |
292 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
335a62ef |
293 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
94654e27 |
294 | # Otherwise the witness either has a positive reading... |
7f52eac8 |
295 | } elsif( $rdg ) { |
94654e27 |
296 | # If the reading has been counted elsewhere as a transposition, ignore it. |
297 | if( $transposed->{$rdg->{'t'}->id} ) { |
d120c995 |
298 | # TODO Does this cope with three-way transpositions? |
94654e27 |
299 | map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}}; |
300 | next; |
301 | } |
302 | # Otherwise, record it... |
303 | $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'}; |
304 | # ...and grab any transpositions, and their relations. |
305 | my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings(); |
306 | foreach my $trdg ( @transp ) { |
d120c995 |
307 | next if exists $readings_at_rank{$trdg->id}; |
308 | $has_transposition = 1; |
309 | my @affected_wits = _table_witnesses( |
7e17346f |
310 | $table, $trdg, $lacunose, $aclabel ); |
d120c995 |
311 | next unless @affected_wits; |
312 | map { $moved_wits{$_} = 1 } @affected_wits; |
313 | $transposed->{$trdg->id} = |
7e17346f |
314 | [ _table_witnesses( $table, $rdg->{'t'}, $lacunose, $aclabel ) ]; |
94654e27 |
315 | $readings_at_rank{$trdg->id} = $trdg; |
316 | } |
317 | # ...or it is empty, ergo a gap. |
7f52eac8 |
318 | } else { |
7e17346f |
319 | _add_to_witlist( $wit, $check_for_gaps, $aclabel ); |
7f52eac8 |
320 | } |
321 | } |
7e17346f |
322 | my $gap_wits = Set::Scalar->new(); |
323 | map { _add_to_witlist( $_, $gap_wits, $aclabel ) |
324 | unless $moved_wits{$_} } $check_for_gaps->members; |
325 | |
326 | # Group the readings, collapsing groups by relationship if needed. |
d120c995 |
327 | my $grouped_readings = {}; |
4ce27d42 |
328 | foreach my $rdg ( values %readings_at_rank ) { |
7f52eac8 |
329 | # Skip readings that have been collapsed into others. |
d120c995 |
330 | next if exists $grouped_readings->{$rdg->id} |
331 | && $grouped_readings->{$rdg->id} eq 'COLLAPSE'; |
4ce27d42 |
332 | # Get the witness list, including from readings collapsed into this one. |
7e17346f |
333 | my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel ); |
e23225e7 |
334 | if( $collapse && $collapse->size ) { |
335 | my $filter = sub { $collapse->has( $_[0]->type ) }; |
7f52eac8 |
336 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
7e17346f |
337 | my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel ); |
fae07016 |
338 | push( @wits, @otherwits ); |
d120c995 |
339 | $grouped_readings->{$other->id} = 'COLLAPSE'; |
d1348d38 |
340 | } |
341 | } |
7e17346f |
342 | $grouped_readings->{$rdg->id} = Set::Scalar->new( @wits ); |
7f52eac8 |
343 | } |
7e17346f |
344 | if( $gap_wits->members ) { |
345 | $grouped_readings->{'(omitted)'} = $gap_wits; |
346 | } |
347 | |
7f52eac8 |
348 | # Get rid of our collapsed readings |
7e17346f |
349 | map { delete $grouped_readings->{$_} if( |
350 | $grouped_readings->{$_} eq 'COLLAPSE' |
351 | || $grouped_readings->{$_}->is_empty ) } |
352 | keys %$grouped_readings; |
d120c995 |
353 | |
354 | # If something was transposed, check the groups for doubled-up readings |
355 | if( $has_transposition ) { |
62a39b8f |
356 | # print STDERR "Group for rank $rank:\n"; |
357 | # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" } |
358 | # keys %$grouped_readings; |
d120c995 |
359 | _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings ); |
360 | } |
7f52eac8 |
361 | |
4ce27d42 |
362 | # Return the result |
d120c995 |
363 | return $grouped_readings; |
364 | } |
365 | |
366 | # Helper function to query the alignment table for all witnesses (a.c. included) |
367 | # that have a given reading at its rank. |
368 | sub _table_witnesses { |
369 | my( $table, $trdg, $lacunose, $aclabel ) = @_; |
370 | my $tableidx = $trdg->rank - 1; |
7e17346f |
371 | my $has_reading = Set::Scalar->new(); |
d120c995 |
372 | foreach my $row ( @{$table->{'alignment'}} ) { |
373 | my $wit = $row->{'witness'}; |
7e17346f |
374 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
d120c995 |
375 | my $rdg = $row->{'tokens'}->[$tableidx]; |
376 | next unless exists $rdg->{'t'} && defined $rdg->{'t'}; |
7e17346f |
377 | _add_to_witlist( $wit, $has_reading, $aclabel ) |
d120c995 |
378 | if $rdg->{'t'}->id eq $trdg->id; |
379 | } |
7e17346f |
380 | return $has_reading->members; |
381 | } |
382 | |
383 | # Helper function to see if a witness is lacunose even if we are asking about |
384 | # the a.c. version |
385 | sub _is_lacunose { |
386 | my ( $wit, $lac, $acstr ) = @_; |
387 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
388 | $wit = $1; |
389 | } |
390 | return $lac->has( $wit ); |
d1348d38 |
391 | } |
392 | |
335a62ef |
393 | # Helper function to ensure that X and X a.c. never appear in the same list. |
394 | sub _add_to_witlist { |
395 | my( $wit, $list, $acstr ) = @_; |
335a62ef |
396 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
7e17346f |
397 | # Don't add X a.c. if we already have X |
398 | return if $list->has( $1 ); |
335a62ef |
399 | } else { |
7e17346f |
400 | # Delete X a.c. if we are about to add X |
401 | $list->delete( $wit.$acstr ); |
335a62ef |
402 | } |
7e17346f |
403 | $list->insert( $wit ); |
335a62ef |
404 | } |
405 | |
d120c995 |
406 | sub _check_transposed_consistency { |
407 | my( $c, $rank, $transposed, $groupings ) = @_; |
408 | my %seen_wits; |
409 | my %thisrank; |
410 | # Note which readings are actually at this rank, and which witnesses |
411 | # belong to which reading. |
412 | foreach my $rdg ( keys %$groupings ) { |
413 | my $rdgobj = $c->reading( $rdg ); |
414 | # Count '(omitted)' as a reading at this rank |
415 | $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank; |
416 | map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}}; |
417 | } |
418 | # Our work is done if we have no witness belonging to more than one |
419 | # reading. |
420 | my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits; |
421 | return unless @doubled; |
422 | # If we have a symmetric related transposition, drop the non-rank readings. |
423 | if( @doubled == scalar keys %seen_wits ) { |
424 | foreach my $rdg ( keys %$groupings ) { |
425 | if( !$thisrank{$rdg} ) { |
426 | my $groupstr = wit_stringify( $groupings->{$rdg} ); |
427 | my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) } |
428 | keys %thisrank; |
429 | delete $groupings->{$rdg}; |
430 | # If we found a group match, assume there is a symmetry happening. |
431 | # TODO think more about this |
62a39b8f |
432 | # print STDERR "*** Deleting symmetric reading $rdg\n"; |
d120c995 |
433 | unless( $matched ) { |
434 | delete $transposed->{$rdg}; |
435 | warn "Found problem in evident symmetry with reading $rdg"; |
436 | } |
437 | } |
438 | } |
439 | # Otherwise 'unhook' the transposed reading(s) that have duplicates. |
440 | } else { |
441 | foreach my $dup ( @doubled ) { |
442 | foreach my $rdg ( @{$seen_wits{$dup}} ) { |
443 | next if $thisrank{$rdg}; |
444 | next unless exists $groupings->{$rdg}; |
62a39b8f |
445 | # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n"; |
d120c995 |
446 | delete $groupings->{$rdg}; |
447 | delete $transposed->{$rdg}; |
448 | } |
449 | } |
450 | # and put any now-orphaned readings into an 'omitted' reading. |
451 | foreach my $wit ( keys %seen_wits ) { |
452 | unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) { |
7e17346f |
453 | $groupings->{'(omitted)'} = Set::Scalar->new() |
454 | unless exists $groupings->{'(omitted)'}; |
d120c995 |
455 | _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label ); |
456 | } |
457 | } |
458 | } |
459 | } |
460 | |
7e17346f |
461 | # For the given grouping, return its situation graph based on the stemma. |
462 | sub _graph_for_grouping { |
463 | my( $stemma, $grouping, $lacunose, $aclabel ) = @_; |
464 | my $acwits = []; |
465 | my $extant = {}; |
466 | foreach my $gs ( values %$grouping ) { |
467 | map { |
468 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
469 | push( @$acwits, $1 ) unless $lacunose->has( $1 ); |
470 | } else { |
471 | $extant->{$_} = 1 unless $lacunose->has( $_ ); |
472 | } |
473 | } $gs->members; |
474 | } |
475 | my $graph; |
476 | try { |
477 | # contig contains all extant wits and all hypothetical wits |
478 | # needed to make up the groups. |
479 | $graph = $stemma->situation_graph( $extant, $acwits ); |
480 | } catch ( Text::Tradition::Error $e ) { |
481 | die "Could not extend graph with given extant and a.c. witnesses: " |
482 | . $e->message; |
483 | } catch { |
484 | die "Could not extend graph with a.c. witnesses @$acwits"; |
485 | } |
486 | return $graph; |
487 | } |
88a6bac5 |
488 | |
7e17346f |
489 | =head2 solve_variants( $calcdir, @groups ) |
490 | |
491 | Looks up the set of groups in the answers provided by the external graph solver |
492 | service and returns a cleaned-up answer, adding the rank IDs back where they belong. |
88a6bac5 |
493 | |
494 | The JSON has the form |
495 | { "graph": [ stemmagraph DOT string without newlines ], |
496 | "groupings": [ array of arrays of groups, one per rank ] } |
497 | |
498 | The answer has the form |
499 | { "variants" => [ array of variant location structures ], |
500 | "variant_count" => total, |
501 | "conflict_count" => number of conflicts detected, |
502 | "genealogical_count" => number of solutions found } |
503 | |
504 | =cut |
505 | |
506 | sub solve_variants { |
7e17346f |
507 | my( $dir, @groups ) = @_; |
335a62ef |
508 | |
7e17346f |
509 | ## For each graph/group combo, look it up in the DB. |
335a62ef |
510 | ## Witness map is a HACK to get around limitations in node names from IDP |
511 | my $witness_map = {}; |
512 | ## Variables to store answers as they come back |
7e17346f |
513 | my $variants = []; |
514 | my $genealogical = 0; # counter |
515 | foreach my $graphproblem ( @groups ) { |
516 | # Initialize the result structure for this graph problem |
517 | my $vstruct = { readings => [] }; |
518 | push( @$variants, $vstruct ); |
5c44c598 |
519 | |
7e17346f |
520 | # Construct the calc result key and look up its answer |
521 | my $reqkey = _get_calc_key( $graphproblem ); |
522 | my $scope = $dir->new_scope; |
523 | my $answer = $dir->lookup( $reqkey ); |
524 | unless( $answer ) { |
525 | #warn "No answer found for graph problem $reqkey, moving on"; |
526 | # Record the unsolved problem so that we can go get a solution |
527 | _save_problem( $graphproblem ); |
528 | # Put just the request, with no real result, into vstruct |
529 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
530 | push( @{$vstruct->{readings}}, { readingid => $rid, |
531 | group => [ $graphproblem->{grouping}->{$rid}->members ] } ); |
5c44c598 |
532 | } |
7e17346f |
533 | next; |
5c44c598 |
534 | } |
7e17346f |
535 | |
536 | ## The answer is a Text::Tradition::Analysis::Result containing a bunch |
537 | ## of information about this variant set. Record the information therein. |
5c44c598 |
538 | |
7e17346f |
539 | # 1. Did the group evaluate as genealogical? |
540 | $vstruct->{genealogical} = $answer->is_genealogical; |
541 | $genealogical++ if $answer->is_genealogical; |
542 | |
543 | # 2. What are the calculated minimum groupings for each variant loc? |
544 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
545 | my $inputset = $graphproblem->{grouping}->{$rid}; |
546 | my $minset = $answer->minimum_grouping_for( $inputset ); |
547 | push( @{$vstruct->{readings}}, { readingid => $rid, group => $minset } ); |
6d25a3a0 |
548 | } |
7e17346f |
549 | |
550 | # 3. What are the sources and classes calculated for each witness? |
551 | $vstruct->{witcopy_types} = { $answer->classes }; |
552 | $vstruct->{reading_roots} = {}; |
553 | map { $vstruct->{reading_roots}->{$_} = 1 } $answer->sources; |
554 | |
88a6bac5 |
555 | } |
556 | |
7e17346f |
557 | # Spit out any unsolved problems we encountered |
e23225e7 |
558 | # _list_unsolved(); |
7e17346f |
559 | |
88a6bac5 |
560 | return { 'variants' => $variants, |
561 | 'variant_count' => scalar @$variants, |
562 | 'genealogical_count' => $genealogical }; |
563 | } |
564 | |
7e17346f |
565 | sub _get_calc_key { |
566 | my( $graphproblem ) = @_; |
567 | my $graph = $graphproblem->{graph}; |
568 | my $grouping = [ values %{$graphproblem->{grouping}} ]; |
569 | my $key = Text::Tradition::Analysis::Result::string_from_graph_problem( |
570 | $graph, $grouping ); |
571 | return md5_hex( encode_utf8( $key ) ); |
5c44c598 |
572 | } |
573 | |
7e17346f |
574 | sub _save_problem { |
575 | my( $graphproblem ) = @_; |
e23225e7 |
576 | my $problem = Text::Tradition::Analysis::Result->new( |
577 | graph => $graphproblem->{graph}, |
578 | setlist => [ values %{$graphproblem->{grouping}} ] |
579 | ); |
580 | my $key = _get_calc_key( $graphproblem ); |
581 | my( $str ) = $problem->problem_json; |
582 | say STDERR "Stashing unsolved problem $str at key $key"; |
583 | $unsolved_problems->{$key} = $problem; |
b4cb2d60 |
584 | } |
585 | |
7e17346f |
586 | sub _list_unsolved { |
587 | #say STDERR "Problems needing a solution:"; |
e23225e7 |
588 | my @problems = values %$unsolved_problems; |
589 | return unless @problems; |
590 | my $first = shift @problems; |
591 | map { say STDERR $_ } $first->problem_json( @problems ); |
b4cb2d60 |
592 | } |
593 | |
fae07016 |
594 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
595 | |
fae07016 |
596 | Given the tradition, its stemma graph, and the solution from the graph solver, |
597 | work out the rest of the information we want. For each reading we need missing, |
5c44c598 |
598 | conflict, reading_parents, independent_occurrence, followed, not_followed, |
599 | and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
600 | |
601 | =cut |
732152b1 |
602 | |
fae07016 |
603 | sub analyze_location { |
7e17346f |
604 | my ( $tradition, $graph, $variant_row, $lacunose ) = @_; |
94654e27 |
605 | my $c = $tradition->collation; |
fae07016 |
606 | |
607 | # Make a hash of all known node memberships, and make the subgraphs. |
608 | my $contig = {}; |
609 | my $reading_roots = {}; |
610 | my $subgraph = {}; |
638e2a95 |
611 | my $acstr = $c->ac_label; |
612 | my @acwits; |
5c44c598 |
613 | |
614 | my $NO_IDP; |
615 | if( exists $variant_row->{'reading_roots'} ) { |
616 | $reading_roots = delete $variant_row->{'reading_roots'}; |
617 | } else { |
618 | warn "No reading source information from IDP - proceed at your own risk"; |
619 | $NO_IDP = 1; |
620 | } |
7e17346f |
621 | my $classinfo = delete $variant_row->{'witcopy_types'}; |
5c44c598 |
622 | |
623 | # Note which witnesses positively belong to which group. This information |
624 | # comes ultimately from the IDP solver. |
625 | # Also make a note of the reading's roots. |
fae07016 |
626 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
627 | my $rid = $rdghash->{'readingid'}; |
5c44c598 |
628 | my @roots; |
638e2a95 |
629 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
630 | $contig->{$wit} = $rid; |
631 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
632 | push( @acwits, $1 ); |
633 | } |
5c44c598 |
634 | if( exists $reading_roots->{$wit} && $reading_roots->{$wit} ) { |
635 | push( @roots, $wit ); |
636 | } |
638e2a95 |
637 | } |
5c44c598 |
638 | $rdghash->{'independent_occurrence'} = \@roots; |
94654e27 |
639 | } |
7e17346f |
640 | |
fae07016 |
641 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
642 | # non-followed/unknown values for each reading. Also figure out the |
643 | # reading's evident parent(s). |
644 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
645 | my $rid = $rdghash->{'readingid'}; |
428bcf0b |
646 | my $rdg = $c->reading( $rid ); |
5c44c598 |
647 | my @roots = @{$rdghash->{'independent_occurrence'}}; |
7e17346f |
648 | my @reversions; |
649 | if( $classinfo ) { |
650 | @reversions = grep { $classinfo->{$_} eq 'revert' } |
651 | $rdghash->{'group'}->members; |
652 | } |
5c44c598 |
653 | my @group = @{$rdghash->{'group'}}; |
fae07016 |
654 | |
655 | # Start figuring things out. |
7e17346f |
656 | $rdghash->{'followed'} = scalar( @group ) |
657 | - ( scalar( @roots ) + scalar( @reversions ) ); |
bebec0e9 |
658 | # Find the parent readings, if any, of this reading. |
7e17346f |
659 | my $sourceparents = _find_reading_parents( $rid, $graph, $contig, @roots ); |
7e17346f |
660 | # Work out relationships between readings and their non-followed parent. |
661 | _resolve_parent_relationships( $c, $rid, $rdg, $sourceparents ); |
7e17346f |
662 | $rdghash->{'reading_parents'} = $sourceparents; |
e23225e7 |
663 | |
664 | if( @reversions ) { |
665 | my $revparents = _find_reading_parents( $rid, $graph, $contig, @reversions ); |
666 | _resolve_parent_relationships( $c, $rid, $rdg, $revparents ); |
667 | $rdghash->{'reversion_parents'} = $revparents; |
668 | } |
bebec0e9 |
669 | |
670 | # Find the number of times this reading was altered, and the number of |
671 | # times we're not sure. |
672 | my( %nofollow, %unknownfollow ); |
5c44c598 |
673 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
bebec0e9 |
674 | foreach my $wchild ( $graph->successors( $wit ) ) { |
5c44c598 |
675 | if( $reading_roots->{$wchild} && $contig->{$wchild} |
676 | && $contig->{$wchild} ne $rid ) { |
bebec0e9 |
677 | # It definitely changed here. |
678 | $nofollow{$wchild} = 1; |
679 | } elsif( !($contig->{$wchild}) ) { |
680 | # The child is a hypothetical node not definitely in |
681 | # any group. Answer is unknown. |
682 | $unknownfollow{$wchild} = 1; |
5c44c598 |
683 | } # else it is either in our group, or it is a non-root node in a |
684 | # known group and therefore is presumed to have its reading from |
685 | # its group, not this link. |
bebec0e9 |
686 | } |
687 | } |
688 | $rdghash->{'not_followed'} = keys %nofollow; |
689 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
690 | |
691 | # Now say whether this reading represents a conflict. |
692 | unless( $variant_row->{'genealogical'} ) { |
7e17346f |
693 | $rdghash->{'is_conflict'} = @roots != 1; |
e23225e7 |
694 | $rdghash->{'is_reverted'} = scalar @reversions; |
7e17346f |
695 | } |
696 | } |
697 | } |
698 | |
699 | sub _find_reading_parents { |
700 | my( $rid, $graph, $contig, @list ) = @_; |
701 | my $parenthash = {}; |
702 | foreach my $wit ( @list ) { |
703 | # Look in the stemma graph to find this witness's extant or known-reading |
704 | # immediate ancestor(s), and look up the reading that each ancestor holds. |
705 | my @check = $graph->predecessors( $wit ); |
706 | while( @check ) { |
707 | my @next; |
708 | foreach my $wparent( @check ) { |
709 | my $preading = $contig->{$wparent}; |
710 | if( $preading && $preading ne $rid ) { |
711 | $parenthash->{$preading} = 1; |
712 | } else { |
713 | push( @next, $graph->predecessors( $wparent ) ); |
714 | } |
715 | } |
716 | @check = @next; |
717 | } |
718 | } |
719 | return $parenthash; |
720 | } |
721 | |
722 | sub _resolve_parent_relationships { |
723 | my( $c, $rid, $rdg, $rdgparents ) = @_; |
724 | foreach my $p ( keys %$rdgparents ) { |
725 | # Resolve the relationship of the parent to the reading, and |
726 | # save it in our hash. |
727 | my $pobj = $c->reading( $p ); |
728 | my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p; |
729 | my $phash = { 'label' => $prep }; |
730 | if( $pobj ) { |
731 | my $rel = $c->get_relationship( $p, $rid ); |
732 | if( $rel ) { |
733 | _add_to_hash( $rel, $phash ); |
734 | } elsif( $rdg ) { |
735 | # First check for a transposed relationship |
736 | if( $rdg->rank != $pobj->rank ) { |
737 | foreach my $ti ( $rdg->related_readings( 'transposition' ) ) { |
738 | next unless $ti->text eq $rdg->text; |
739 | $rel = $c->get_relationship( $ti, $pobj ); |
740 | if( $rel ) { |
741 | _add_to_hash( $rel, $phash, 1 ); |
742 | last; |
743 | } |
744 | } |
745 | unless( $rel ) { |
746 | foreach my $ti ( $pobj->related_readings( 'transposition' ) ) { |
747 | next unless $ti->text eq $pobj->text; |
748 | $rel = $c->get_relationship( $ti, $rdg ); |
749 | if( $rel ) { |
750 | _add_to_hash( $rel, $phash, 1 ); |
751 | last; |
752 | } |
753 | } |
5c44c598 |
754 | } |
755 | } |
7e17346f |
756 | unless( $rel ) { |
757 | # and then check for sheer word similarity. |
758 | my $rtext = $rdg->text; |
759 | my $ptext = $pobj->text; |
760 | if( similar( $rtext, $ptext ) ) { |
761 | # say STDERR "Words $rtext and $ptext judged similar"; |
762 | $phash->{relation} = { type => 'wordsimilar' }; |
763 | } |
764 | } |
5c44c598 |
765 | } else { |
7e17346f |
766 | $phash->{relation} = { type => 'deletion' }; |
5c44c598 |
767 | } |
7e17346f |
768 | # Get the attributes of the parent object while we are here |
769 | $phash->{'text'} = $pobj->text if $pobj; |
770 | $phash->{'is_nonsense'} = $pobj->is_nonsense; |
771 | $phash->{'is_ungrammatical'} = $pobj->grammar_invalid; |
772 | } elsif( $p eq '(omitted)' ) { |
773 | $phash->{relation} = { type => 'addition' }; |
774 | } |
775 | # Save it |
776 | $rdgparents->{$p} = $phash; |
777 | } |
d71100ed |
778 | } |
779 | |
428bcf0b |
780 | sub _add_to_hash { |
781 | my( $rel, $phash, $is_transposed ) = @_; |
782 | $phash->{relation} = { type => $rel->type }; |
783 | $phash->{relation}->{transposed} = 1 if $is_transposed; |
784 | $phash->{relation}->{annotation} = $rel->annotation |
785 | if $rel->has_annotation; |
786 | } |
787 | |
788 | =head2 similar( $word1, $word2 ) |
789 | |
790 | Use Algorithm::Diff to get a sense of how close the words are to each other. |
791 | This will hopefully handle substitutions a bit more nicely than Levenshtein. |
792 | |
793 | =cut |
794 | |
795 | #!/usr/bin/env perl |
796 | |
797 | sub similar { |
798 | my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_; |
799 | my @let1 = split( '', lc( $word1 ) ); |
800 | my @let2 = split( '', lc( $word2 ) ); |
801 | my $diff = Algorithm::Diff->new( \@let1, \@let2 ); |
802 | my $mag = 0; |
803 | while( $diff->Next ) { |
804 | if( $diff->Same ) { |
805 | # Take off points for longer strings |
806 | my $cs = $diff->Range(1) - 2; |
807 | $cs = 0 if $cs < 0; |
808 | $mag -= $cs; |
809 | } elsif( !$diff->Items(1) ) { |
810 | $mag += $diff->Range(2); |
811 | } elsif( !$diff->Items(2) ) { |
812 | $mag += $diff->Range(1); |
813 | } else { |
814 | # Split the difference for substitutions |
815 | my $c1 = $diff->Range(1) || 1; |
816 | my $c2 = $diff->Range(2) || 1; |
817 | my $cd = ( $c1 + $c2 ) / 2; |
818 | $mag += $cd; |
819 | } |
820 | } |
821 | return ( $mag <= length( $word1 ) / 2 ); |
822 | } |
823 | |
6d25a3a0 |
824 | sub _prune_group { |
5c44c598 |
825 | my( $group, $graph ) = @_; |
826 | my $relevant = {}; |
827 | # Record the existence of the vertices in the group |
828 | map { $relevant->{$_} = 1 } @$group; |
6d25a3a0 |
829 | # Make our subgraph |
5c44c598 |
830 | my $subgraph = $graph->deep_copy; |
831 | map { $subgraph->delete_vertex( $_ ) unless $relevant->{$_} } |
6d25a3a0 |
832 | $subgraph->vertices; |
6d25a3a0 |
833 | # Now prune and return the remaining vertices. |
5c44c598 |
834 | _prune_subtree( $subgraph ); |
835 | # Return the list of vertices and the list of roots. |
836 | my $pruned_group = [ sort $subgraph->vertices ]; |
837 | my $pruned_roots = [ $subgraph->predecessorless_vertices ]; |
838 | return( $pruned_group, $pruned_roots ); |
6d25a3a0 |
839 | } |
840 | |
7f52eac8 |
841 | sub _prune_subtree { |
5c44c598 |
842 | my( $tree ) = @_; |
94654e27 |
843 | |
844 | # Delete lacunose witnesses that have no successors |
5c44c598 |
845 | my @orphan_hypotheticals; |
846 | my $ctr = 0; |
847 | do { |
848 | die "Infinite loop on leaves" if $ctr > 100; |
849 | @orphan_hypotheticals = |
850 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
851 | $tree->successorless_vertices; |
852 | $tree->delete_vertices( @orphan_hypotheticals ); |
853 | $ctr++; |
854 | } while( @orphan_hypotheticals ); |
94654e27 |
855 | |
856 | # Delete lacunose roots that have a single successor |
857 | my @redundant_root; |
858 | $ctr = 0; |
859 | do { |
5c44c598 |
860 | die "Infinite loop on roots" if $ctr > 100; |
861 | @redundant_root = |
862 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' |
863 | && $tree->successors( $_ ) == 1 } |
864 | $tree->predecessorless_vertices; |
94654e27 |
865 | $tree->delete_vertices( @redundant_root ); |
866 | $ctr++; |
867 | } while( @redundant_root ); |
868 | } |
869 | |
5be0cdeb |
870 | sub _useful_variant { |
7e17346f |
871 | my( $rankgroup, $rankgraph, $acstr ) = @_; |
5be0cdeb |
872 | |
873 | # Sort by group size and return |
874 | my $is_useful = 0; |
7e17346f |
875 | foreach my $rdg ( keys %$rankgroup ) { |
876 | my @wits = $rankgroup->{$rdg}->members; |
877 | if( @wits > 1 ) { |
5be0cdeb |
878 | $is_useful++; |
879 | } else { |
7e17346f |
880 | $is_useful++ unless( $rankgraph->is_sink_vertex( $wits[0] ) |
881 | || $wits[0] =~ /\Q$acstr\E$/ ); |
5be0cdeb |
882 | } |
883 | } |
7e17346f |
884 | return $is_useful > 1; |
5be0cdeb |
885 | } |
886 | |
7f52eac8 |
887 | =head2 wit_stringify( $groups ) |
888 | |
889 | Takes an array of witness groupings and produces a string like |
890 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
891 | |
7f52eac8 |
892 | =cut |
d71100ed |
893 | |
894 | sub wit_stringify { |
895 | my $groups = shift; |
896 | my @gst; |
897 | # If we were passed an array of witnesses instead of an array of |
898 | # groupings, then "group" the witnesses first. |
899 | unless( ref( $groups->[0] ) ) { |
900 | my $mkgrp = [ $groups ]; |
901 | $groups = $mkgrp; |
902 | } |
903 | foreach my $g ( @$groups ) { |
904 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
905 | } |
906 | return join( ' / ', @gst ); |
907 | } |
7f52eac8 |
908 | |
7f52eac8 |
909 | 1; |
910 | |
911 | =head1 LICENSE |
912 | |
913 | This package is free software and is provided "as is" without express |
914 | or implied warranty. You can redistribute it and/or modify it under |
915 | the same terms as Perl itself. |
916 | |
917 | =head1 AUTHOR |
918 | |
919 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |