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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 |
03c0a7d7 |
6 | use Encode qw/ decode_utf8 encode_utf8 /; |
d1348d38 |
7 | use Exporter 'import'; |
b4cb2d60 |
8 | use Graph; |
a745c3d9 |
9 | use JSON qw/ to_json decode_json /; |
03c0a7d7 |
10 | use LWP::UserAgent; |
7e17346f |
11 | use Set::Scalar; |
7e17346f |
12 | use Text::Tradition::Analysis::Result; |
13 | use Text::Tradition::Directory; |
d71100ed |
14 | use Text::Tradition::Stemma; |
d120c995 |
15 | use TryCatch; |
d71100ed |
16 | |
d1348d38 |
17 | use vars qw/ @EXPORT_OK /; |
a2cf85dd |
18 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
d1348d38 |
19 | |
03c0a7d7 |
20 | my $SOLVER_URL = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
7e17346f |
21 | my $unsolved_problems = {}; |
5c44c598 |
22 | |
7f52eac8 |
23 | =head1 NAME |
24 | |
25 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
26 | |
27 | =head1 SYNOPSIS |
28 | |
29 | use Text::Tradition; |
30 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
31 | my $t = Text::Tradition->new( |
32 | 'name' => 'this is a text', |
33 | 'input' => 'TEI', |
34 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
35 | $t->add_stemma( 'dotfile' => $stemmafile ); |
36 | |
37 | my $variant_data = run_analysis( $tradition ); |
38 | # Recalculate rank $n treating all orthographic variants as equivalent |
39 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
40 | |
41 | =head1 DESCRIPTION |
42 | |
43 | Text::Tradition is a library for representation and analysis of collated |
44 | texts, particularly medieval ones. The Collation is the central feature of |
45 | a Tradition, where the text, its sequence of readings, and its relationships |
46 | between readings are actually kept. |
47 | |
48 | =head1 SUBROUTINES |
49 | |
88a6bac5 |
50 | =head2 run_analysis( $tradition, %opts ) |
7f52eac8 |
51 | |
88a6bac5 |
52 | Runs the analysis described in analyze_variant_location on every location in the |
53 | collation of the given tradition, with the given options. These include: |
7f52eac8 |
54 | |
88a6bac5 |
55 | =over 4 |
56 | |
57 | =item * stemma_id - Specify which of the tradition's stemmata to use. Default |
58 | is 0 (i.e. the first). |
59 | |
60 | =item * ranks - Specify a list of location ranks to analyze; exclude the rest. |
61 | |
62 | =item * merge_types - Specify a list of relationship types, where related readings |
63 | should be treated as identical for the purposes of analysis. |
64 | |
ffa22d6f |
65 | =item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants. |
66 | |
88a6bac5 |
67 | =back |
7f52eac8 |
68 | |
69 | =begin testing |
70 | |
71 | use Text::Tradition; |
72 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
73 | |
74 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
75 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
76 | 'name' => 'test0', |
77 | 'file' => $datafile ); |
78 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
79 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
80 | |
f00cefe8 |
81 | my %expected_genealogical = ( |
a44aaf2a |
82 | 1 => 0, |
f00cefe8 |
83 | 2 => 1, |
a44aaf2a |
84 | 3 => 0, |
85 | 5 => 0, |
86 | 7 => 0, |
87 | 8 => 0, |
88 | 10 => 0, |
f00cefe8 |
89 | 13 => 1, |
a44aaf2a |
90 | 33 => 0, |
91 | 34 => 0, |
92 | 37 => 0, |
93 | 60 => 0, |
f00cefe8 |
94 | 81 => 1, |
a44aaf2a |
95 | 84 => 0, |
96 | 87 => 0, |
97 | 101 => 0, |
98 | 102 => 0, |
f00cefe8 |
99 | 122 => 1, |
a44aaf2a |
100 | 157 => 0, |
f00cefe8 |
101 | 166 => 1, |
102 | 169 => 1, |
a44aaf2a |
103 | 200 => 0, |
f00cefe8 |
104 | 216 => 1, |
105 | 217 => 1, |
106 | 219 => 1, |
107 | 241 => 1, |
108 | 242 => 1, |
109 | 243 => 1, |
110 | ); |
111 | |
7e17346f |
112 | my $data = run_analysis( $tradition, calcdsn => 'dbi:SQLite:dbname=t/data/analysis.db' ); |
7234b01d |
113 | my $c = $tradition->collation; |
f00cefe8 |
114 | foreach my $row ( @{$data->{'variants'}} ) { |
a44aaf2a |
115 | # Account for rows that used to be "not useful" |
116 | unless( exists $expected_genealogical{$row->{'id'}} ) { |
117 | $expected_genealogical{$row->{'id'}} = 1; |
118 | } |
18f48b82 |
119 | my $gen_bool = $row->{'genealogical'} ? 1 : 0; |
120 | is( $gen_bool, $expected_genealogical{$row->{'id'}}, |
f00cefe8 |
121 | "Got correct genealogical flag for row " . $row->{'id'} ); |
7234b01d |
122 | # Check that we have the right row with the right groups |
123 | my $rank = $row->{'id'}; |
124 | foreach my $rdghash ( @{$row->{'readings'}} ) { |
125 | # Skip 'readings' that aren't really |
126 | next unless $c->reading( $rdghash->{'readingid'} ); |
127 | # Check the rank |
128 | is( $c->reading( $rdghash->{'readingid'} )->rank, $rank, |
129 | "Got correct reading rank" ); |
130 | # Check the witnesses |
131 | my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} ); |
132 | my @sgrp = sort @{$rdghash->{'group'}}; |
133 | is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" ); |
134 | } |
f00cefe8 |
135 | } |
a44aaf2a |
136 | is( $data->{'variant_count'}, 58, "Got right total variant number" ); |
b4cb2d60 |
137 | # TODO Make something meaningful of conflict count, maybe test other bits |
7f52eac8 |
138 | |
139 | =end testing |
140 | |
141 | =cut |
142 | |
d71100ed |
143 | sub run_analysis { |
88a6bac5 |
144 | my( $tradition, %opts ) = @_; |
f00cefe8 |
145 | my $c = $tradition->collation; |
7e17346f |
146 | my $aclabel = $c->ac_label; |
88a6bac5 |
147 | |
148 | my $stemma_id = $opts{'stemma_id'} || 0; |
1d73ecad |
149 | my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); |
e23225e7 |
150 | my $collapse = Set::Scalar->new(); |
151 | if( $opts{'merge_types'} && ref( $opts{'merge_types'} ) eq 'ARRAY' ) { |
152 | $collapse->insert( @{$opts{'merge_types'}} ); |
153 | } elsif( $opts{'merge_types'} ) { |
154 | $collapse->insert( $opts{'merge_types'} ); |
155 | } |
7e17346f |
156 | |
157 | # Make sure we have a lookup DB for graph calculation results; this will die |
158 | # if calcdir or calcdsn isn't passed. |
03c0a7d7 |
159 | my $dir; |
160 | if( exists $opts{'calcdir'} ) { |
161 | $dir = delete $opts{'calcdir'} |
162 | } elsif ( exists $opts{'calcdsn'} ) { |
163 | $dir = Text::Tradition::Directory->new( dsn => $opts{'calcdsn'} ); |
164 | } |
88a6bac5 |
165 | |
166 | # Get the stemma |
167 | my $stemma = $tradition->stemma( $stemma_id ); |
b4cb2d60 |
168 | |
4ce27d42 |
169 | # Figure out which witnesses we are working with - that is, the ones that |
170 | # appear both in the stemma and in the tradition. All others are 'lacunose' |
171 | # for our purposes. |
7e17346f |
172 | my $lacunose = Set::Scalar->new( $stemma->hypotheticals ); |
173 | my $stemma_wits = Set::Scalar->new( $stemma->witnesses ); |
174 | my $tradition_wits = Set::Scalar->new( map { $_->sigil } $tradition->witnesses ); |
175 | $lacunose->insert( $stemma_wits->symmetric_difference( $tradition_wits )->members ); |
88a6bac5 |
176 | |
177 | # Find and mark 'common' ranks for exclusion, unless they were |
178 | # explicitly specified. |
179 | unless( @ranks ) { |
180 | my %common_rank; |
a44aaf2a |
181 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
182 | $common_rank{$rdg->rank} = 1; |
183 | } |
184 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
185 | } |
7f52eac8 |
186 | |
88a6bac5 |
187 | # Group the variants to send to the solver |
188 | my @groups; |
f629cb3b |
189 | my @use_ranks; |
a44aaf2a |
190 | my %lacunae; |
94654e27 |
191 | my $moved = {}; |
88a6bac5 |
192 | foreach my $rank ( @ranks ) { |
7e17346f |
193 | my $missing = $lacunose->clone(); |
e23225e7 |
194 | my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, $collapse ); |
94654e27 |
195 | # Filter out any empty rankgroups |
196 | # (e.g. from the later rank for a transposition) |
197 | next unless keys %$rankgroup; |
7e17346f |
198 | # Get the graph for this rankgroup |
199 | my $rankgraph = _graph_for_grouping( $stemma, $rankgroup, $missing, $aclabel ); |
ffa22d6f |
200 | if( $opts{'exclude_type1'} ) { |
201 | # Check to see whether this is a "useful" group. |
7e17346f |
202 | next unless _useful_variant( $rankgroup, $rankgraph, $aclabel ); |
ffa22d6f |
203 | } |
f629cb3b |
204 | push( @use_ranks, $rank ); |
7e17346f |
205 | push( @groups, { grouping => $rankgroup, graph => $rankgraph } ); |
a44aaf2a |
206 | $lacunae{$rank} = $missing; |
d71100ed |
207 | } |
4ce27d42 |
208 | # Run the solver |
7e17346f |
209 | my $answer = solve_variants( $dir, @groups ); |
fae07016 |
210 | |
88a6bac5 |
211 | # Do further analysis on the answer |
a44aaf2a |
212 | my $conflict_count = 0; |
7e17346f |
213 | my $reversion_count = 0; |
f629cb3b |
214 | foreach my $idx ( 0 .. $#use_ranks ) { |
88a6bac5 |
215 | my $location = $answer->{'variants'}->[$idx]; |
216 | # Add the rank back in |
94654e27 |
217 | my $rank = $use_ranks[$idx]; |
218 | $location->{'id'} = $rank; |
7234b01d |
219 | # Note what our lacunae are |
f629cb3b |
220 | my %lmiss; |
7234b01d |
221 | map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}}; |
7234b01d |
222 | $location->{'missing'} = [ keys %lmiss ]; |
223 | |
88a6bac5 |
224 | # Run the extra analysis we need. |
428bcf0b |
225 | ## TODO We run through all the variants in this call, so |
226 | ## why not add the reading data there instead of here below? |
7e17346f |
227 | my $graph = $groups[$idx]->{graph}; |
228 | analyze_location( $tradition, $graph, $location, \%lmiss ); |
7234b01d |
229 | |
638e2a95 |
230 | my @layerwits; |
7234b01d |
231 | # Do the final post-analysis tidying up of the data. |
a44aaf2a |
232 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
e23225e7 |
233 | $conflict_count++ if $rdghash->{'is_conflict'}; |
234 | $reversion_count++ if $rdghash->{'is_reverted'}; |
94654e27 |
235 | # Add the reading text back in, setting display value as needed |
a44aaf2a |
236 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
94654e27 |
237 | if( $rdg ) { |
238 | $rdghash->{'text'} = $rdg->text . |
239 | ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' ); |
7b7abf10 |
240 | $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid; |
241 | $rdghash->{'is_nonsense'} = $rdg->is_nonsense; |
94654e27 |
242 | } |
f629cb3b |
243 | # Remove lacunose witnesses from this reading's list now that the |
7234b01d |
244 | # analysis is done |
f629cb3b |
245 | my @realgroup; |
7234b01d |
246 | map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}}; |
f629cb3b |
247 | $rdghash->{'group'} = \@realgroup; |
638e2a95 |
248 | # Note any layered witnesses that appear in this group |
249 | foreach( @realgroup ) { |
250 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
251 | push( @layerwits, $1 ); |
252 | } |
253 | } |
a44aaf2a |
254 | } |
638e2a95 |
255 | $location->{'layerwits'} = \@layerwits if @layerwits; |
88a6bac5 |
256 | } |
a44aaf2a |
257 | $answer->{'conflict_count'} = $conflict_count; |
7e17346f |
258 | $answer->{'reversion_count'} = $reversion_count; |
f00cefe8 |
259 | |
88a6bac5 |
260 | return $answer; |
d71100ed |
261 | } |
262 | |
e23225e7 |
263 | =head2 group_variants( $tradition, $rank, $lacunose, $transposed, $merge_relationship_types ) |
7f52eac8 |
264 | |
265 | Groups the variants at the given $rank of the collation, treating any |
e23225e7 |
266 | relationships in the set $merge_relationship_types as equivalent. |
267 | $lacunose should be a reference to an array, to which the sigla of lacunose |
268 | witnesses at this rank will be appended; $transposed should be a reference |
269 | to a hash, wherein the identities of transposed readings and their |
270 | relatives will be stored. |
7f52eac8 |
271 | |
ffa22d6f |
272 | Returns a hash $group_readings where $rdg is attested by the witnesses listed |
273 | in $group_readings->{$rdg}. |
7f52eac8 |
274 | |
275 | =cut |
276 | |
277 | # Return group_readings, groups, lacunose |
d1348d38 |
278 | sub group_variants { |
94654e27 |
279 | my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_; |
7f52eac8 |
280 | my $c = $tradition->collation; |
335a62ef |
281 | my $aclabel = $c->ac_label; |
d120c995 |
282 | my $table = $c->alignment_table; |
7f52eac8 |
283 | # Get the alignment table readings |
284 | my %readings_at_rank; |
7e17346f |
285 | my $check_for_gaps = Set::Scalar->new(); |
94654e27 |
286 | my %moved_wits; |
d120c995 |
287 | my $has_transposition; |
288 | foreach my $tablewit ( @{$table->{'alignment'}} ) { |
7f52eac8 |
289 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
290 | my $wit = $tablewit->{'witness'}; |
ffa22d6f |
291 | # Exclude the witness if it is "lacunose" which if we got here |
292 | # means "not in the stemma". |
7e17346f |
293 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
94654e27 |
294 | # Note if the witness is actually in a lacuna |
7f52eac8 |
295 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
335a62ef |
296 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
94654e27 |
297 | # Otherwise the witness either has a positive reading... |
7f52eac8 |
298 | } elsif( $rdg ) { |
94654e27 |
299 | # If the reading has been counted elsewhere as a transposition, ignore it. |
300 | if( $transposed->{$rdg->{'t'}->id} ) { |
d120c995 |
301 | # TODO Does this cope with three-way transpositions? |
94654e27 |
302 | map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}}; |
303 | next; |
304 | } |
305 | # Otherwise, record it... |
306 | $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'}; |
307 | # ...and grab any transpositions, and their relations. |
308 | my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings(); |
309 | foreach my $trdg ( @transp ) { |
d120c995 |
310 | next if exists $readings_at_rank{$trdg->id}; |
311 | $has_transposition = 1; |
312 | my @affected_wits = _table_witnesses( |
7e17346f |
313 | $table, $trdg, $lacunose, $aclabel ); |
d120c995 |
314 | next unless @affected_wits; |
315 | map { $moved_wits{$_} = 1 } @affected_wits; |
316 | $transposed->{$trdg->id} = |
7e17346f |
317 | [ _table_witnesses( $table, $rdg->{'t'}, $lacunose, $aclabel ) ]; |
94654e27 |
318 | $readings_at_rank{$trdg->id} = $trdg; |
319 | } |
320 | # ...or it is empty, ergo a gap. |
7f52eac8 |
321 | } else { |
7e17346f |
322 | _add_to_witlist( $wit, $check_for_gaps, $aclabel ); |
7f52eac8 |
323 | } |
324 | } |
7e17346f |
325 | my $gap_wits = Set::Scalar->new(); |
326 | map { _add_to_witlist( $_, $gap_wits, $aclabel ) |
327 | unless $moved_wits{$_} } $check_for_gaps->members; |
328 | |
329 | # Group the readings, collapsing groups by relationship if needed. |
d120c995 |
330 | my $grouped_readings = {}; |
4ce27d42 |
331 | foreach my $rdg ( values %readings_at_rank ) { |
7f52eac8 |
332 | # Skip readings that have been collapsed into others. |
d120c995 |
333 | next if exists $grouped_readings->{$rdg->id} |
334 | && $grouped_readings->{$rdg->id} eq 'COLLAPSE'; |
4ce27d42 |
335 | # Get the witness list, including from readings collapsed into this one. |
7e17346f |
336 | my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel ); |
e23225e7 |
337 | if( $collapse && $collapse->size ) { |
338 | my $filter = sub { $collapse->has( $_[0]->type ) }; |
7f52eac8 |
339 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
7e17346f |
340 | my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel ); |
fae07016 |
341 | push( @wits, @otherwits ); |
d120c995 |
342 | $grouped_readings->{$other->id} = 'COLLAPSE'; |
d1348d38 |
343 | } |
344 | } |
7e17346f |
345 | $grouped_readings->{$rdg->id} = Set::Scalar->new( @wits ); |
7f52eac8 |
346 | } |
7e17346f |
347 | if( $gap_wits->members ) { |
348 | $grouped_readings->{'(omitted)'} = $gap_wits; |
349 | } |
350 | |
7f52eac8 |
351 | # Get rid of our collapsed readings |
7e17346f |
352 | map { delete $grouped_readings->{$_} if( |
353 | $grouped_readings->{$_} eq 'COLLAPSE' |
354 | || $grouped_readings->{$_}->is_empty ) } |
355 | keys %$grouped_readings; |
d120c995 |
356 | |
357 | # If something was transposed, check the groups for doubled-up readings |
358 | if( $has_transposition ) { |
62a39b8f |
359 | # print STDERR "Group for rank $rank:\n"; |
360 | # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" } |
361 | # keys %$grouped_readings; |
d120c995 |
362 | _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings ); |
363 | } |
7f52eac8 |
364 | |
4ce27d42 |
365 | # Return the result |
d120c995 |
366 | return $grouped_readings; |
367 | } |
368 | |
369 | # Helper function to query the alignment table for all witnesses (a.c. included) |
370 | # that have a given reading at its rank. |
371 | sub _table_witnesses { |
372 | my( $table, $trdg, $lacunose, $aclabel ) = @_; |
373 | my $tableidx = $trdg->rank - 1; |
7e17346f |
374 | my $has_reading = Set::Scalar->new(); |
d120c995 |
375 | foreach my $row ( @{$table->{'alignment'}} ) { |
376 | my $wit = $row->{'witness'}; |
7e17346f |
377 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
d120c995 |
378 | my $rdg = $row->{'tokens'}->[$tableidx]; |
379 | next unless exists $rdg->{'t'} && defined $rdg->{'t'}; |
7e17346f |
380 | _add_to_witlist( $wit, $has_reading, $aclabel ) |
d120c995 |
381 | if $rdg->{'t'}->id eq $trdg->id; |
382 | } |
7e17346f |
383 | return $has_reading->members; |
384 | } |
385 | |
386 | # Helper function to see if a witness is lacunose even if we are asking about |
387 | # the a.c. version |
388 | sub _is_lacunose { |
389 | my ( $wit, $lac, $acstr ) = @_; |
390 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
391 | $wit = $1; |
392 | } |
393 | return $lac->has( $wit ); |
d1348d38 |
394 | } |
395 | |
335a62ef |
396 | # Helper function to ensure that X and X a.c. never appear in the same list. |
397 | sub _add_to_witlist { |
398 | my( $wit, $list, $acstr ) = @_; |
335a62ef |
399 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
7e17346f |
400 | # Don't add X a.c. if we already have X |
401 | return if $list->has( $1 ); |
335a62ef |
402 | } else { |
7e17346f |
403 | # Delete X a.c. if we are about to add X |
404 | $list->delete( $wit.$acstr ); |
335a62ef |
405 | } |
7e17346f |
406 | $list->insert( $wit ); |
335a62ef |
407 | } |
408 | |
d120c995 |
409 | sub _check_transposed_consistency { |
410 | my( $c, $rank, $transposed, $groupings ) = @_; |
411 | my %seen_wits; |
412 | my %thisrank; |
413 | # Note which readings are actually at this rank, and which witnesses |
414 | # belong to which reading. |
415 | foreach my $rdg ( keys %$groupings ) { |
416 | my $rdgobj = $c->reading( $rdg ); |
417 | # Count '(omitted)' as a reading at this rank |
418 | $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank; |
419 | map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}}; |
420 | } |
421 | # Our work is done if we have no witness belonging to more than one |
422 | # reading. |
423 | my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits; |
424 | return unless @doubled; |
425 | # If we have a symmetric related transposition, drop the non-rank readings. |
426 | if( @doubled == scalar keys %seen_wits ) { |
427 | foreach my $rdg ( keys %$groupings ) { |
428 | if( !$thisrank{$rdg} ) { |
429 | my $groupstr = wit_stringify( $groupings->{$rdg} ); |
430 | my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) } |
431 | keys %thisrank; |
432 | delete $groupings->{$rdg}; |
433 | # If we found a group match, assume there is a symmetry happening. |
434 | # TODO think more about this |
62a39b8f |
435 | # print STDERR "*** Deleting symmetric reading $rdg\n"; |
d120c995 |
436 | unless( $matched ) { |
437 | delete $transposed->{$rdg}; |
438 | warn "Found problem in evident symmetry with reading $rdg"; |
439 | } |
440 | } |
441 | } |
442 | # Otherwise 'unhook' the transposed reading(s) that have duplicates. |
443 | } else { |
444 | foreach my $dup ( @doubled ) { |
445 | foreach my $rdg ( @{$seen_wits{$dup}} ) { |
446 | next if $thisrank{$rdg}; |
447 | next unless exists $groupings->{$rdg}; |
62a39b8f |
448 | # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n"; |
d120c995 |
449 | delete $groupings->{$rdg}; |
450 | delete $transposed->{$rdg}; |
451 | } |
452 | } |
453 | # and put any now-orphaned readings into an 'omitted' reading. |
454 | foreach my $wit ( keys %seen_wits ) { |
455 | unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) { |
7e17346f |
456 | $groupings->{'(omitted)'} = Set::Scalar->new() |
457 | unless exists $groupings->{'(omitted)'}; |
d120c995 |
458 | _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label ); |
459 | } |
460 | } |
461 | } |
462 | } |
463 | |
7e17346f |
464 | # For the given grouping, return its situation graph based on the stemma. |
465 | sub _graph_for_grouping { |
466 | my( $stemma, $grouping, $lacunose, $aclabel ) = @_; |
467 | my $acwits = []; |
468 | my $extant = {}; |
469 | foreach my $gs ( values %$grouping ) { |
470 | map { |
471 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
472 | push( @$acwits, $1 ) unless $lacunose->has( $1 ); |
473 | } else { |
474 | $extant->{$_} = 1 unless $lacunose->has( $_ ); |
475 | } |
476 | } $gs->members; |
477 | } |
478 | my $graph; |
479 | try { |
480 | # contig contains all extant wits and all hypothetical wits |
481 | # needed to make up the groups. |
482 | $graph = $stemma->situation_graph( $extant, $acwits ); |
483 | } catch ( Text::Tradition::Error $e ) { |
03c0a7d7 |
484 | throw( "Could not extend graph with given extant and a.c. witnesses: " |
485 | . $e->message ); |
7e17346f |
486 | } catch { |
03c0a7d7 |
487 | throw( "Could not extend graph with a.c. witnesses @$acwits" ); |
7e17346f |
488 | } |
489 | return $graph; |
490 | } |
88a6bac5 |
491 | |
7e17346f |
492 | =head2 solve_variants( $calcdir, @groups ) |
493 | |
494 | Looks up the set of groups in the answers provided by the external graph solver |
495 | service and returns a cleaned-up answer, adding the rank IDs back where they belong. |
88a6bac5 |
496 | |
88a6bac5 |
497 | The answer has the form |
498 | { "variants" => [ array of variant location structures ], |
499 | "variant_count" => total, |
500 | "conflict_count" => number of conflicts detected, |
501 | "genealogical_count" => number of solutions found } |
502 | |
503 | =cut |
504 | |
505 | sub solve_variants { |
03c0a7d7 |
506 | my( @groups ) = @_; |
507 | |
a745c3d9 |
508 | # Are we using a local result directory, or did we pass an empty value |
509 | # for the directory? |
03c0a7d7 |
510 | my $dir; |
a745c3d9 |
511 | unless( ref( $groups[0] ) eq 'HASH' ) { |
03c0a7d7 |
512 | $dir = shift @groups; |
513 | } |
335a62ef |
514 | |
03c0a7d7 |
515 | ## For each graph/group combo, make a Text::Tradition::Analysis::Result |
516 | ## object so that we can send it off for IDP lookup. |
7e17346f |
517 | my $variants = []; |
518 | my $genealogical = 0; # counter |
03c0a7d7 |
519 | # TODO Optimize for unique graph problems |
520 | my @problems; |
7e17346f |
521 | foreach my $graphproblem ( @groups ) { |
03c0a7d7 |
522 | # Construct the calc result key and look up its answer |
523 | my $problem = Text::Tradition::Analysis::Result->new( |
524 | graph => $graphproblem->{'graph'}, |
525 | setlist => [ values %{$graphproblem->{'grouping'}} ] ); |
526 | push( @problems, $problem ); |
527 | } |
528 | |
529 | my @results; |
530 | if( $dir ) { |
531 | my $scope = $dir->new_scope; |
532 | @results = map { $dir->lookup( $_->object_key ) || $_ } @problems; |
533 | } else { |
534 | my $json = JSON->new->allow_blessed->convert_blessed->utf8->encode( \@problems ); |
535 | # Send it off and get the result |
536 | # print STDERR "Sending request: " . decode_utf8( $json ) . "\n"; |
537 | my $ua = LWP::UserAgent->new(); |
538 | my $resp = $ua->post( $SOLVER_URL, 'Content-Type' => 'application/json', |
539 | 'Content' => $json ); |
a745c3d9 |
540 | my $answer; |
03c0a7d7 |
541 | if( $resp->is_success ) { |
a745c3d9 |
542 | $answer = decode_json( $resp->content ); |
03c0a7d7 |
543 | throw( "Unexpected answer from IDP: $answer" ) unless ref( $answer ) eq 'ARRAY'; |
544 | } else { |
545 | throw( "IDP solver returned " . $resp->status_line . " / " . $resp->content |
546 | . "; cannot run graph analysis" ); |
547 | } |
548 | # One more sanity check |
549 | throw( "Something went wrong with answer symmetricity" ) |
550 | unless @groups == @$answer; |
551 | # Convert the results |
552 | @results = map { Text::Tradition::Analysis::Result->new( $_ ) } @$answer; |
553 | } |
554 | |
555 | # We now have a single JSON-encoded Result object per problem sent. Fold its |
556 | # answers into our variant info structure. |
557 | foreach my $idx ( 0 .. $#groups ) { |
558 | my $graphproblem = $groups[$idx]; |
559 | my $result = $results[$idx]; |
560 | |
7e17346f |
561 | # Initialize the result structure for this graph problem |
562 | my $vstruct = { readings => [] }; |
563 | push( @$variants, $vstruct ); |
5c44c598 |
564 | |
03c0a7d7 |
565 | # 0. Do we have a calculated result at all? |
566 | unless( $result->status eq 'OK' ) { |
567 | $vstruct->{'unsolved'} = $result->status; |
7e17346f |
568 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
569 | push( @{$vstruct->{readings}}, { readingid => $rid, |
570 | group => [ $graphproblem->{grouping}->{$rid}->members ] } ); |
5c44c598 |
571 | } |
7e17346f |
572 | next; |
5c44c598 |
573 | } |
574 | |
7e17346f |
575 | # 1. Did the group evaluate as genealogical? |
03c0a7d7 |
576 | $vstruct->{genealogical} = $result->is_genealogical; |
577 | $genealogical++ if $result->is_genealogical; |
7e17346f |
578 | |
579 | # 2. What are the calculated minimum groupings for each variant loc? |
580 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
581 | my $inputset = $graphproblem->{grouping}->{$rid}; |
03c0a7d7 |
582 | my $minset = $result->minimum_grouping_for( $inputset ); |
7e17346f |
583 | push( @{$vstruct->{readings}}, { readingid => $rid, group => $minset } ); |
6d25a3a0 |
584 | } |
7e17346f |
585 | |
586 | # 3. What are the sources and classes calculated for each witness? |
03c0a7d7 |
587 | $vstruct->{witcopy_types} = { $result->classes }; |
7e17346f |
588 | $vstruct->{reading_roots} = {}; |
03c0a7d7 |
589 | map { $vstruct->{reading_roots}->{$_} = 1 } $result->sources; |
7e17346f |
590 | |
88a6bac5 |
591 | } |
592 | |
593 | return { 'variants' => $variants, |
594 | 'variant_count' => scalar @$variants, |
595 | 'genealogical_count' => $genealogical }; |
596 | } |
597 | |
fae07016 |
598 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
599 | |
fae07016 |
600 | Given the tradition, its stemma graph, and the solution from the graph solver, |
601 | work out the rest of the information we want. For each reading we need missing, |
5c44c598 |
602 | conflict, reading_parents, independent_occurrence, followed, not_followed, |
603 | and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
604 | |
605 | =cut |
732152b1 |
606 | |
fae07016 |
607 | sub analyze_location { |
7e17346f |
608 | my ( $tradition, $graph, $variant_row, $lacunose ) = @_; |
94654e27 |
609 | my $c = $tradition->collation; |
fae07016 |
610 | |
03c0a7d7 |
611 | if( exists $variant_row->{'unsolved'} ) { |
612 | return; |
613 | } |
614 | my $reading_roots = delete $variant_row->{'reading_roots'}; |
615 | my $classinfo = delete $variant_row->{'witcopy_types'}; |
616 | |
fae07016 |
617 | # Make a hash of all known node memberships, and make the subgraphs. |
618 | my $contig = {}; |
fae07016 |
619 | my $subgraph = {}; |
638e2a95 |
620 | my $acstr = $c->ac_label; |
621 | my @acwits; |
5c44c598 |
622 | |
5c44c598 |
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; |
be590045 |
652 | $rdghash->{'reversions'} = \@reversions; |
7e17346f |
653 | } |
5c44c598 |
654 | my @group = @{$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 ); |
7e17346f |
661 | # Work out relationships between readings and their non-followed parent. |
662 | _resolve_parent_relationships( $c, $rid, $rdg, $sourceparents ); |
be590045 |
663 | $rdghash->{'source_parents'} = $sourceparents; |
e23225e7 |
664 | |
665 | if( @reversions ) { |
666 | my $revparents = _find_reading_parents( $rid, $graph, $contig, @reversions ); |
667 | _resolve_parent_relationships( $c, $rid, $rdg, $revparents ); |
668 | $rdghash->{'reversion_parents'} = $revparents; |
669 | } |
bebec0e9 |
670 | |
671 | # Find the number of times this reading was altered, and the number of |
672 | # times we're not sure. |
673 | my( %nofollow, %unknownfollow ); |
5c44c598 |
674 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
bebec0e9 |
675 | foreach my $wchild ( $graph->successors( $wit ) ) { |
5c44c598 |
676 | if( $reading_roots->{$wchild} && $contig->{$wchild} |
677 | && $contig->{$wchild} ne $rid ) { |
bebec0e9 |
678 | # It definitely changed here. |
679 | $nofollow{$wchild} = 1; |
680 | } elsif( !($contig->{$wchild}) ) { |
681 | # The child is a hypothetical node not definitely in |
682 | # any group. Answer is unknown. |
683 | $unknownfollow{$wchild} = 1; |
5c44c598 |
684 | } # else it is either in our group, or it is a non-root node in a |
685 | # known group and therefore is presumed to have its reading from |
686 | # its group, not this link. |
bebec0e9 |
687 | } |
688 | } |
689 | $rdghash->{'not_followed'} = keys %nofollow; |
690 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
691 | |
692 | # Now say whether this reading represents a conflict. |
693 | unless( $variant_row->{'genealogical'} ) { |
7e17346f |
694 | $rdghash->{'is_conflict'} = @roots != 1; |
e23225e7 |
695 | $rdghash->{'is_reverted'} = scalar @reversions; |
7e17346f |
696 | } |
697 | } |
698 | } |
699 | |
700 | sub _find_reading_parents { |
701 | my( $rid, $graph, $contig, @list ) = @_; |
702 | my $parenthash = {}; |
703 | foreach my $wit ( @list ) { |
704 | # Look in the stemma graph to find this witness's extant or known-reading |
705 | # immediate ancestor(s), and look up the reading that each ancestor holds. |
706 | my @check = $graph->predecessors( $wit ); |
707 | while( @check ) { |
708 | my @next; |
709 | foreach my $wparent( @check ) { |
710 | my $preading = $contig->{$wparent}; |
711 | if( $preading && $preading ne $rid ) { |
712 | $parenthash->{$preading} = 1; |
713 | } else { |
714 | push( @next, $graph->predecessors( $wparent ) ); |
715 | } |
716 | } |
717 | @check = @next; |
718 | } |
719 | } |
720 | return $parenthash; |
721 | } |
722 | |
723 | sub _resolve_parent_relationships { |
724 | my( $c, $rid, $rdg, $rdgparents ) = @_; |
725 | foreach my $p ( keys %$rdgparents ) { |
726 | # Resolve the relationship of the parent to the reading, and |
727 | # save it in our hash. |
728 | my $pobj = $c->reading( $p ); |
729 | my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p; |
730 | my $phash = { 'label' => $prep }; |
731 | if( $pobj ) { |
732 | my $rel = $c->get_relationship( $p, $rid ); |
733 | if( $rel ) { |
734 | _add_to_hash( $rel, $phash ); |
735 | } elsif( $rdg ) { |
736 | # First check for a transposed relationship |
737 | if( $rdg->rank != $pobj->rank ) { |
738 | foreach my $ti ( $rdg->related_readings( 'transposition' ) ) { |
739 | next unless $ti->text eq $rdg->text; |
740 | $rel = $c->get_relationship( $ti, $pobj ); |
741 | if( $rel ) { |
742 | _add_to_hash( $rel, $phash, 1 ); |
743 | last; |
744 | } |
745 | } |
746 | unless( $rel ) { |
747 | foreach my $ti ( $pobj->related_readings( 'transposition' ) ) { |
748 | next unless $ti->text eq $pobj->text; |
749 | $rel = $c->get_relationship( $ti, $rdg ); |
750 | if( $rel ) { |
751 | _add_to_hash( $rel, $phash, 1 ); |
752 | last; |
753 | } |
754 | } |
5c44c598 |
755 | } |
756 | } |
7e17346f |
757 | unless( $rel ) { |
758 | # and then check for sheer word similarity. |
759 | my $rtext = $rdg->text; |
760 | my $ptext = $pobj->text; |
761 | if( similar( $rtext, $ptext ) ) { |
762 | # say STDERR "Words $rtext and $ptext judged similar"; |
763 | $phash->{relation} = { type => 'wordsimilar' }; |
764 | } |
765 | } |
5c44c598 |
766 | } else { |
7e17346f |
767 | $phash->{relation} = { type => 'deletion' }; |
5c44c598 |
768 | } |
7e17346f |
769 | # Get the attributes of the parent object while we are here |
770 | $phash->{'text'} = $pobj->text if $pobj; |
771 | $phash->{'is_nonsense'} = $pobj->is_nonsense; |
772 | $phash->{'is_ungrammatical'} = $pobj->grammar_invalid; |
773 | } elsif( $p eq '(omitted)' ) { |
774 | $phash->{relation} = { type => 'addition' }; |
775 | } |
776 | # Save it |
777 | $rdgparents->{$p} = $phash; |
778 | } |
d71100ed |
779 | } |
780 | |
428bcf0b |
781 | sub _add_to_hash { |
782 | my( $rel, $phash, $is_transposed ) = @_; |
783 | $phash->{relation} = { type => $rel->type }; |
784 | $phash->{relation}->{transposed} = 1 if $is_transposed; |
785 | $phash->{relation}->{annotation} = $rel->annotation |
786 | if $rel->has_annotation; |
787 | } |
788 | |
789 | =head2 similar( $word1, $word2 ) |
790 | |
791 | Use Algorithm::Diff to get a sense of how close the words are to each other. |
792 | This will hopefully handle substitutions a bit more nicely than Levenshtein. |
793 | |
794 | =cut |
795 | |
796 | #!/usr/bin/env perl |
797 | |
798 | sub similar { |
799 | my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_; |
800 | my @let1 = split( '', lc( $word1 ) ); |
801 | my @let2 = split( '', lc( $word2 ) ); |
802 | my $diff = Algorithm::Diff->new( \@let1, \@let2 ); |
803 | my $mag = 0; |
804 | while( $diff->Next ) { |
805 | if( $diff->Same ) { |
806 | # Take off points for longer strings |
807 | my $cs = $diff->Range(1) - 2; |
808 | $cs = 0 if $cs < 0; |
809 | $mag -= $cs; |
810 | } elsif( !$diff->Items(1) ) { |
811 | $mag += $diff->Range(2); |
812 | } elsif( !$diff->Items(2) ) { |
813 | $mag += $diff->Range(1); |
814 | } else { |
815 | # Split the difference for substitutions |
816 | my $c1 = $diff->Range(1) || 1; |
817 | my $c2 = $diff->Range(2) || 1; |
818 | my $cd = ( $c1 + $c2 ) / 2; |
819 | $mag += $cd; |
820 | } |
821 | } |
822 | return ( $mag <= length( $word1 ) / 2 ); |
823 | } |
824 | |
6d25a3a0 |
825 | sub _prune_group { |
5c44c598 |
826 | my( $group, $graph ) = @_; |
827 | my $relevant = {}; |
828 | # Record the existence of the vertices in the group |
829 | map { $relevant->{$_} = 1 } @$group; |
6d25a3a0 |
830 | # Make our subgraph |
5c44c598 |
831 | my $subgraph = $graph->deep_copy; |
832 | map { $subgraph->delete_vertex( $_ ) unless $relevant->{$_} } |
6d25a3a0 |
833 | $subgraph->vertices; |
6d25a3a0 |
834 | # Now prune and return the remaining vertices. |
5c44c598 |
835 | _prune_subtree( $subgraph ); |
836 | # Return the list of vertices and the list of roots. |
837 | my $pruned_group = [ sort $subgraph->vertices ]; |
838 | my $pruned_roots = [ $subgraph->predecessorless_vertices ]; |
839 | return( $pruned_group, $pruned_roots ); |
6d25a3a0 |
840 | } |
841 | |
7f52eac8 |
842 | sub _prune_subtree { |
5c44c598 |
843 | my( $tree ) = @_; |
94654e27 |
844 | |
845 | # Delete lacunose witnesses that have no successors |
5c44c598 |
846 | my @orphan_hypotheticals; |
847 | my $ctr = 0; |
848 | do { |
03c0a7d7 |
849 | throw( "Infinite loop on leaves" ) if $ctr > 100; |
5c44c598 |
850 | @orphan_hypotheticals = |
851 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' } |
852 | $tree->successorless_vertices; |
853 | $tree->delete_vertices( @orphan_hypotheticals ); |
854 | $ctr++; |
855 | } while( @orphan_hypotheticals ); |
94654e27 |
856 | |
857 | # Delete lacunose roots that have a single successor |
858 | my @redundant_root; |
859 | $ctr = 0; |
860 | do { |
03c0a7d7 |
861 | throw( "Infinite loop on roots" ) if $ctr > 100; |
5c44c598 |
862 | @redundant_root = |
863 | grep { $tree->get_vertex_attribute( $_, 'class' ) eq 'hypothetical' |
864 | && $tree->successors( $_ ) == 1 } |
865 | $tree->predecessorless_vertices; |
94654e27 |
866 | $tree->delete_vertices( @redundant_root ); |
867 | $ctr++; |
868 | } while( @redundant_root ); |
869 | } |
870 | |
5be0cdeb |
871 | sub _useful_variant { |
7e17346f |
872 | my( $rankgroup, $rankgraph, $acstr ) = @_; |
5be0cdeb |
873 | |
874 | # Sort by group size and return |
875 | my $is_useful = 0; |
7e17346f |
876 | foreach my $rdg ( keys %$rankgroup ) { |
877 | my @wits = $rankgroup->{$rdg}->members; |
878 | if( @wits > 1 ) { |
5be0cdeb |
879 | $is_useful++; |
880 | } else { |
7e17346f |
881 | $is_useful++ unless( $rankgraph->is_sink_vertex( $wits[0] ) |
882 | || $wits[0] =~ /\Q$acstr\E$/ ); |
5be0cdeb |
883 | } |
884 | } |
7e17346f |
885 | return $is_useful > 1; |
5be0cdeb |
886 | } |
887 | |
7f52eac8 |
888 | =head2 wit_stringify( $groups ) |
889 | |
890 | Takes an array of witness groupings and produces a string like |
891 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
892 | |
7f52eac8 |
893 | =cut |
d71100ed |
894 | |
895 | sub wit_stringify { |
896 | my $groups = shift; |
897 | my @gst; |
898 | # If we were passed an array of witnesses instead of an array of |
899 | # groupings, then "group" the witnesses first. |
900 | unless( ref( $groups->[0] ) ) { |
901 | my $mkgrp = [ $groups ]; |
902 | $groups = $mkgrp; |
903 | } |
904 | foreach my $g ( @$groups ) { |
905 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
906 | } |
907 | return join( ' / ', @gst ); |
908 | } |
7f52eac8 |
909 | |
7f52eac8 |
910 | 1; |
911 | |
a745c3d9 |
912 | sub throw { |
913 | Text::Tradition::Error->throw( |
914 | 'ident' => 'Analysis error', |
915 | 'message' => $_[0], |
916 | ); |
917 | } |
918 | |
7f52eac8 |
919 | =head1 LICENSE |
920 | |
921 | This package is free software and is provided "as is" without express |
922 | or implied warranty. You can redistribute it and/or modify it under |
923 | the same terms as Perl itself. |
924 | |
925 | =head1 AUTHOR |
926 | |
927 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |