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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 | |
951ddfe8 |
17 | use vars qw/ @EXPORT_OK $VERSION /; |
a2cf85dd |
18 | @EXPORT_OK = qw/ run_analysis group_variants analyze_variant_location wit_stringify /; |
37bf09f4 |
19 | $VERSION = "1.1"; |
951ddfe8 |
20 | |
d1348d38 |
21 | |
03c0a7d7 |
22 | my $SOLVER_URL = 'http://byzantini.st/cgi-bin/graphcalc.cgi'; |
7e17346f |
23 | my $unsolved_problems = {}; |
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24 | |
7f52eac8 |
25 | =head1 NAME |
26 | |
27 | Text::Tradition::Analysis - functions for stemma analysis of a tradition |
28 | |
29 | =head1 SYNOPSIS |
30 | |
31 | use Text::Tradition; |
32 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
33 | my $t = Text::Tradition->new( |
34 | 'name' => 'this is a text', |
35 | 'input' => 'TEI', |
36 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
37 | $t->add_stemma( 'dotfile' => $stemmafile ); |
38 | |
39 | my $variant_data = run_analysis( $tradition ); |
40 | # Recalculate rank $n treating all orthographic variants as equivalent |
41 | my $reanalyze = analyze_variant_location( $tradition, $n, 0, 'orthographic' ); |
42 | |
43 | =head1 DESCRIPTION |
44 | |
45 | Text::Tradition is a library for representation and analysis of collated |
951ddfe8 |
46 | texts, particularly medieval ones. Where the Collation is the central feature of |
47 | a Tradition, it may also have one or more temmata associated with it, and these stemmata may be analyzed. This package provides the following modules: |
48 | |
49 | =over 4 |
50 | |
51 | =item * L<Text::Tradition::HasStemma> - a role that can be composed into Text::Tradition objects, providing the ability for Text::Tradition::Stemma objects to be associated with them. |
52 | |
53 | =item * L<Text::Tradition::Stemma> - an object class that represents stemma hypotheses, both rooted (with a single archetype) and unrooted (e.g. phylogenetic trees). |
54 | |
55 | =item * Text::Tradition::Analysis (this package). Provides functions for the analysis of a given stemma against the collation within a given Tradition. |
56 | |
57 | =back |
7f52eac8 |
58 | |
59 | =head1 SUBROUTINES |
60 | |
88a6bac5 |
61 | =head2 run_analysis( $tradition, %opts ) |
7f52eac8 |
62 | |
88a6bac5 |
63 | Runs the analysis described in analyze_variant_location on every location in the |
64 | collation of the given tradition, with the given options. These include: |
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65 | |
88a6bac5 |
66 | =over 4 |
67 | |
68 | =item * stemma_id - Specify which of the tradition's stemmata to use. Default |
69 | is 0 (i.e. the first). |
70 | |
71 | =item * ranks - Specify a list of location ranks to analyze; exclude the rest. |
72 | |
73 | =item * merge_types - Specify a list of relationship types, where related readings |
74 | should be treated as identical for the purposes of analysis. |
75 | |
ffa22d6f |
76 | =item * exclude_type1 - Exclude those ranks whose groupings have only type-1 variants. |
77 | |
88a6bac5 |
78 | =back |
7f52eac8 |
79 | |
80 | =begin testing |
81 | |
82 | use Text::Tradition; |
83 | use Text::Tradition::Analysis qw/ run_analysis analyze_variant_location /; |
84 | |
85 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
86 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
87 | 'name' => 'test0', |
88 | 'file' => $datafile ); |
89 | my $s = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
90 | is( ref( $s ), 'Text::Tradition::Stemma', "Added stemma to tradition" ); |
91 | |
f00cefe8 |
92 | my %expected_genealogical = ( |
a44aaf2a |
93 | 1 => 0, |
f00cefe8 |
94 | 2 => 1, |
a44aaf2a |
95 | 3 => 0, |
96 | 5 => 0, |
97 | 7 => 0, |
98 | 8 => 0, |
99 | 10 => 0, |
f00cefe8 |
100 | 13 => 1, |
a44aaf2a |
101 | 33 => 0, |
102 | 34 => 0, |
103 | 37 => 0, |
104 | 60 => 0, |
f00cefe8 |
105 | 81 => 1, |
a44aaf2a |
106 | 84 => 0, |
107 | 87 => 0, |
108 | 101 => 0, |
109 | 102 => 0, |
f00cefe8 |
110 | 122 => 1, |
a44aaf2a |
111 | 157 => 0, |
f00cefe8 |
112 | 166 => 1, |
113 | 169 => 1, |
a44aaf2a |
114 | 200 => 0, |
f00cefe8 |
115 | 216 => 1, |
116 | 217 => 1, |
117 | 219 => 1, |
118 | 241 => 1, |
119 | 242 => 1, |
120 | 243 => 1, |
121 | ); |
122 | |
7e17346f |
123 | my $data = run_analysis( $tradition, calcdsn => 'dbi:SQLite:dbname=t/data/analysis.db' ); |
7234b01d |
124 | my $c = $tradition->collation; |
f00cefe8 |
125 | foreach my $row ( @{$data->{'variants'}} ) { |
a44aaf2a |
126 | # Account for rows that used to be "not useful" |
127 | unless( exists $expected_genealogical{$row->{'id'}} ) { |
128 | $expected_genealogical{$row->{'id'}} = 1; |
129 | } |
18f48b82 |
130 | my $gen_bool = $row->{'genealogical'} ? 1 : 0; |
131 | is( $gen_bool, $expected_genealogical{$row->{'id'}}, |
f00cefe8 |
132 | "Got correct genealogical flag for row " . $row->{'id'} ); |
7234b01d |
133 | # Check that we have the right row with the right groups |
134 | my $rank = $row->{'id'}; |
135 | foreach my $rdghash ( @{$row->{'readings'}} ) { |
136 | # Skip 'readings' that aren't really |
137 | next unless $c->reading( $rdghash->{'readingid'} ); |
138 | # Check the rank |
139 | is( $c->reading( $rdghash->{'readingid'} )->rank, $rank, |
140 | "Got correct reading rank" ); |
141 | # Check the witnesses |
142 | my @realwits = sort $c->reading_witnesses( $rdghash->{'readingid'} ); |
143 | my @sgrp = sort @{$rdghash->{'group'}}; |
144 | is_deeply( \@sgrp, \@realwits, "Reading analyzed with correct groups" ); |
145 | } |
f00cefe8 |
146 | } |
a44aaf2a |
147 | is( $data->{'variant_count'}, 58, "Got right total variant number" ); |
b4cb2d60 |
148 | # TODO Make something meaningful of conflict count, maybe test other bits |
7f52eac8 |
149 | |
150 | =end testing |
151 | |
152 | =cut |
153 | |
d71100ed |
154 | sub run_analysis { |
88a6bac5 |
155 | my( $tradition, %opts ) = @_; |
f00cefe8 |
156 | my $c = $tradition->collation; |
7e17346f |
157 | my $aclabel = $c->ac_label; |
88a6bac5 |
158 | |
159 | my $stemma_id = $opts{'stemma_id'} || 0; |
1d73ecad |
160 | my @ranks = ref( $opts{'ranks'} ) eq 'ARRAY' ? @{$opts{'ranks'}} : (); |
e23225e7 |
161 | my $collapse = Set::Scalar->new(); |
162 | if( $opts{'merge_types'} && ref( $opts{'merge_types'} ) eq 'ARRAY' ) { |
163 | $collapse->insert( @{$opts{'merge_types'}} ); |
164 | } elsif( $opts{'merge_types'} ) { |
165 | $collapse->insert( $opts{'merge_types'} ); |
166 | } |
7e17346f |
167 | |
168 | # Make sure we have a lookup DB for graph calculation results; this will die |
169 | # if calcdir or calcdsn isn't passed. |
03c0a7d7 |
170 | my $dir; |
171 | if( exists $opts{'calcdir'} ) { |
172 | $dir = delete $opts{'calcdir'} |
173 | } elsif ( exists $opts{'calcdsn'} ) { |
174 | $dir = Text::Tradition::Directory->new( dsn => $opts{'calcdsn'} ); |
175 | } |
88a6bac5 |
176 | |
177 | # Get the stemma |
178 | my $stemma = $tradition->stemma( $stemma_id ); |
b4cb2d60 |
179 | |
4ce27d42 |
180 | # Figure out which witnesses we are working with - that is, the ones that |
181 | # appear both in the stemma and in the tradition. All others are 'lacunose' |
182 | # for our purposes. |
7e17346f |
183 | my $lacunose = Set::Scalar->new( $stemma->hypotheticals ); |
184 | my $stemma_wits = Set::Scalar->new( $stemma->witnesses ); |
185 | my $tradition_wits = Set::Scalar->new( map { $_->sigil } $tradition->witnesses ); |
186 | $lacunose->insert( $stemma_wits->symmetric_difference( $tradition_wits )->members ); |
88a6bac5 |
187 | |
188 | # Find and mark 'common' ranks for exclusion, unless they were |
189 | # explicitly specified. |
190 | unless( @ranks ) { |
191 | my %common_rank; |
a44aaf2a |
192 | foreach my $rdg ( $c->common_readings ) { |
88a6bac5 |
193 | $common_rank{$rdg->rank} = 1; |
194 | } |
195 | @ranks = grep { !$common_rank{$_} } ( 1 .. $c->end->rank-1 ); |
d71100ed |
196 | } |
7f52eac8 |
197 | |
88a6bac5 |
198 | # Group the variants to send to the solver |
199 | my @groups; |
f629cb3b |
200 | my @use_ranks; |
a44aaf2a |
201 | my %lacunae; |
94654e27 |
202 | my $moved = {}; |
88a6bac5 |
203 | foreach my $rank ( @ranks ) { |
7e17346f |
204 | my $missing = $lacunose->clone(); |
e23225e7 |
205 | my $rankgroup = group_variants( $tradition, $rank, $missing, $moved, $collapse ); |
94654e27 |
206 | # Filter out any empty rankgroups |
207 | # (e.g. from the later rank for a transposition) |
208 | next unless keys %$rankgroup; |
7e17346f |
209 | # Get the graph for this rankgroup |
210 | my $rankgraph = _graph_for_grouping( $stemma, $rankgroup, $missing, $aclabel ); |
ffa22d6f |
211 | if( $opts{'exclude_type1'} ) { |
212 | # Check to see whether this is a "useful" group. |
7e17346f |
213 | next unless _useful_variant( $rankgroup, $rankgraph, $aclabel ); |
ffa22d6f |
214 | } |
f629cb3b |
215 | push( @use_ranks, $rank ); |
7e17346f |
216 | push( @groups, { grouping => $rankgroup, graph => $rankgraph } ); |
a44aaf2a |
217 | $lacunae{$rank} = $missing; |
d71100ed |
218 | } |
4ce27d42 |
219 | # Run the solver |
b7bd7aa5 |
220 | my $answer; |
221 | try { |
222 | $answer = solve_variants( $dir, @groups ); |
223 | } catch ( Text::Tradition::Error $e ) { |
224 | if( $e->message =~ /IDP/ ) { |
225 | # Something is wrong with the solver; make the variants table anyway |
226 | $answer->{'variants'} = []; |
227 | map { push( @{$answer->{'variants'}}, _init_unsolved( $_, 'IDP error' ) ) } |
228 | @groups; |
229 | } else { |
230 | # Something else is wrong; error out. |
231 | $e->throw; |
232 | } |
233 | } |
fae07016 |
234 | |
88a6bac5 |
235 | # Do further analysis on the answer |
a44aaf2a |
236 | my $conflict_count = 0; |
7e17346f |
237 | my $reversion_count = 0; |
f629cb3b |
238 | foreach my $idx ( 0 .. $#use_ranks ) { |
88a6bac5 |
239 | my $location = $answer->{'variants'}->[$idx]; |
240 | # Add the rank back in |
94654e27 |
241 | my $rank = $use_ranks[$idx]; |
242 | $location->{'id'} = $rank; |
7234b01d |
243 | # Note what our lacunae are |
f629cb3b |
244 | my %lmiss; |
7234b01d |
245 | map { $lmiss{$_} = 1 } @{$lacunae{$use_ranks[$idx]}}; |
7234b01d |
246 | $location->{'missing'} = [ keys %lmiss ]; |
247 | |
88a6bac5 |
248 | # Run the extra analysis we need. |
428bcf0b |
249 | ## TODO We run through all the variants in this call, so |
250 | ## why not add the reading data there instead of here below? |
7e17346f |
251 | my $graph = $groups[$idx]->{graph}; |
252 | analyze_location( $tradition, $graph, $location, \%lmiss ); |
7234b01d |
253 | |
638e2a95 |
254 | my @layerwits; |
7234b01d |
255 | # Do the final post-analysis tidying up of the data. |
a44aaf2a |
256 | foreach my $rdghash ( @{$location->{'readings'}} ) { |
e23225e7 |
257 | $conflict_count++ if $rdghash->{'is_conflict'}; |
258 | $reversion_count++ if $rdghash->{'is_reverted'}; |
94654e27 |
259 | # Add the reading text back in, setting display value as needed |
a44aaf2a |
260 | my $rdg = $c->reading( $rdghash->{'readingid'} ); |
94654e27 |
261 | if( $rdg ) { |
262 | $rdghash->{'text'} = $rdg->text . |
263 | ( $rdg->rank == $rank ? '' : ' [' . $rdg->rank . ']' ); |
a445ce40 |
264 | if( $rdg->does( 'Text::Tradition::Morphology' ) ) { |
265 | $rdghash->{'is_ungrammatical'} = $rdg->grammar_invalid; |
266 | $rdghash->{'is_nonsense'} = $rdg->is_nonsense; |
267 | } |
94654e27 |
268 | } |
f629cb3b |
269 | # Remove lacunose witnesses from this reading's list now that the |
7234b01d |
270 | # analysis is done |
f629cb3b |
271 | my @realgroup; |
7234b01d |
272 | map { push( @realgroup, $_ ) unless $lmiss{$_} } @{$rdghash->{'group'}}; |
f629cb3b |
273 | $rdghash->{'group'} = \@realgroup; |
638e2a95 |
274 | # Note any layered witnesses that appear in this group |
275 | foreach( @realgroup ) { |
276 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
277 | push( @layerwits, $1 ); |
278 | } |
279 | } |
a44aaf2a |
280 | } |
638e2a95 |
281 | $location->{'layerwits'} = \@layerwits if @layerwits; |
88a6bac5 |
282 | } |
a44aaf2a |
283 | $answer->{'conflict_count'} = $conflict_count; |
7e17346f |
284 | $answer->{'reversion_count'} = $reversion_count; |
f00cefe8 |
285 | |
88a6bac5 |
286 | return $answer; |
d71100ed |
287 | } |
288 | |
e23225e7 |
289 | =head2 group_variants( $tradition, $rank, $lacunose, $transposed, $merge_relationship_types ) |
7f52eac8 |
290 | |
291 | Groups the variants at the given $rank of the collation, treating any |
e23225e7 |
292 | relationships in the set $merge_relationship_types as equivalent. |
293 | $lacunose should be a reference to an array, to which the sigla of lacunose |
294 | witnesses at this rank will be appended; $transposed should be a reference |
295 | to a hash, wherein the identities of transposed readings and their |
296 | relatives will be stored. |
7f52eac8 |
297 | |
ffa22d6f |
298 | Returns a hash $group_readings where $rdg is attested by the witnesses listed |
299 | in $group_readings->{$rdg}. |
7f52eac8 |
300 | |
301 | =cut |
302 | |
303 | # Return group_readings, groups, lacunose |
d1348d38 |
304 | sub group_variants { |
94654e27 |
305 | my( $tradition, $rank, $lacunose, $transposed, $collapse ) = @_; |
7f52eac8 |
306 | my $c = $tradition->collation; |
335a62ef |
307 | my $aclabel = $c->ac_label; |
d120c995 |
308 | my $table = $c->alignment_table; |
7f52eac8 |
309 | # Get the alignment table readings |
310 | my %readings_at_rank; |
7e17346f |
311 | my $check_for_gaps = Set::Scalar->new(); |
94654e27 |
312 | my %moved_wits; |
d120c995 |
313 | my $has_transposition; |
314 | foreach my $tablewit ( @{$table->{'alignment'}} ) { |
7f52eac8 |
315 | my $rdg = $tablewit->{'tokens'}->[$rank-1]; |
fae07016 |
316 | my $wit = $tablewit->{'witness'}; |
ffa22d6f |
317 | # Exclude the witness if it is "lacunose" which if we got here |
318 | # means "not in the stemma". |
7e17346f |
319 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
94654e27 |
320 | # Note if the witness is actually in a lacuna |
7f52eac8 |
321 | if( $rdg && $rdg->{'t'}->is_lacuna ) { |
335a62ef |
322 | _add_to_witlist( $wit, $lacunose, $aclabel ); |
94654e27 |
323 | # Otherwise the witness either has a positive reading... |
7f52eac8 |
324 | } elsif( $rdg ) { |
94654e27 |
325 | # If the reading has been counted elsewhere as a transposition, ignore it. |
326 | if( $transposed->{$rdg->{'t'}->id} ) { |
d120c995 |
327 | # TODO Does this cope with three-way transpositions? |
94654e27 |
328 | map { $moved_wits{$_} = 1 } @{$transposed->{$rdg->{'t'}->id}}; |
329 | next; |
330 | } |
331 | # Otherwise, record it... |
332 | $readings_at_rank{$rdg->{'t'}->id} = $rdg->{'t'}; |
333 | # ...and grab any transpositions, and their relations. |
334 | my @transp = grep { $_->rank != $rank } $rdg->{'t'}->related_readings(); |
335 | foreach my $trdg ( @transp ) { |
d120c995 |
336 | next if exists $readings_at_rank{$trdg->id}; |
337 | $has_transposition = 1; |
338 | my @affected_wits = _table_witnesses( |
7e17346f |
339 | $table, $trdg, $lacunose, $aclabel ); |
d120c995 |
340 | next unless @affected_wits; |
341 | map { $moved_wits{$_} = 1 } @affected_wits; |
342 | $transposed->{$trdg->id} = |
7e17346f |
343 | [ _table_witnesses( $table, $rdg->{'t'}, $lacunose, $aclabel ) ]; |
94654e27 |
344 | $readings_at_rank{$trdg->id} = $trdg; |
345 | } |
346 | # ...or it is empty, ergo a gap. |
7f52eac8 |
347 | } else { |
7e17346f |
348 | _add_to_witlist( $wit, $check_for_gaps, $aclabel ); |
7f52eac8 |
349 | } |
350 | } |
7e17346f |
351 | my $gap_wits = Set::Scalar->new(); |
352 | map { _add_to_witlist( $_, $gap_wits, $aclabel ) |
353 | unless $moved_wits{$_} } $check_for_gaps->members; |
354 | |
355 | # Group the readings, collapsing groups by relationship if needed. |
d120c995 |
356 | my $grouped_readings = {}; |
4ce27d42 |
357 | foreach my $rdg ( values %readings_at_rank ) { |
7f52eac8 |
358 | # Skip readings that have been collapsed into others. |
d120c995 |
359 | next if exists $grouped_readings->{$rdg->id} |
360 | && $grouped_readings->{$rdg->id} eq 'COLLAPSE'; |
4ce27d42 |
361 | # Get the witness list, including from readings collapsed into this one. |
7e17346f |
362 | my @wits = _table_witnesses( $table, $rdg, $lacunose, $aclabel ); |
e23225e7 |
363 | if( $collapse && $collapse->size ) { |
364 | my $filter = sub { $collapse->has( $_[0]->type ) }; |
7f52eac8 |
365 | foreach my $other ( $rdg->related_readings( $filter ) ) { |
7e17346f |
366 | my @otherwits = _table_witnesses( $table, $other, $lacunose, $aclabel ); |
fae07016 |
367 | push( @wits, @otherwits ); |
d120c995 |
368 | $grouped_readings->{$other->id} = 'COLLAPSE'; |
d1348d38 |
369 | } |
370 | } |
7e17346f |
371 | $grouped_readings->{$rdg->id} = Set::Scalar->new( @wits ); |
7f52eac8 |
372 | } |
7e17346f |
373 | if( $gap_wits->members ) { |
374 | $grouped_readings->{'(omitted)'} = $gap_wits; |
375 | } |
376 | |
7f52eac8 |
377 | # Get rid of our collapsed readings |
7e17346f |
378 | map { delete $grouped_readings->{$_} if( |
379 | $grouped_readings->{$_} eq 'COLLAPSE' |
380 | || $grouped_readings->{$_}->is_empty ) } |
381 | keys %$grouped_readings; |
d120c995 |
382 | |
383 | # If something was transposed, check the groups for doubled-up readings |
384 | if( $has_transposition ) { |
62a39b8f |
385 | # print STDERR "Group for rank $rank:\n"; |
386 | # map { print STDERR "\t$_: " . join( ' ' , @{$grouped_readings->{$_}} ) . "\n" } |
387 | # keys %$grouped_readings; |
d120c995 |
388 | _check_transposed_consistency( $c, $rank, $transposed, $grouped_readings ); |
389 | } |
7f52eac8 |
390 | |
4ce27d42 |
391 | # Return the result |
d120c995 |
392 | return $grouped_readings; |
393 | } |
394 | |
395 | # Helper function to query the alignment table for all witnesses (a.c. included) |
396 | # that have a given reading at its rank. |
397 | sub _table_witnesses { |
398 | my( $table, $trdg, $lacunose, $aclabel ) = @_; |
399 | my $tableidx = $trdg->rank - 1; |
7e17346f |
400 | my $has_reading = Set::Scalar->new(); |
d120c995 |
401 | foreach my $row ( @{$table->{'alignment'}} ) { |
402 | my $wit = $row->{'witness'}; |
7e17346f |
403 | next if _is_lacunose( $wit, $lacunose, $aclabel ); |
d120c995 |
404 | my $rdg = $row->{'tokens'}->[$tableidx]; |
405 | next unless exists $rdg->{'t'} && defined $rdg->{'t'}; |
7e17346f |
406 | _add_to_witlist( $wit, $has_reading, $aclabel ) |
d120c995 |
407 | if $rdg->{'t'}->id eq $trdg->id; |
408 | } |
7e17346f |
409 | return $has_reading->members; |
410 | } |
411 | |
412 | # Helper function to see if a witness is lacunose even if we are asking about |
413 | # the a.c. version |
414 | sub _is_lacunose { |
415 | my ( $wit, $lac, $acstr ) = @_; |
416 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
417 | $wit = $1; |
418 | } |
419 | return $lac->has( $wit ); |
d1348d38 |
420 | } |
421 | |
335a62ef |
422 | # Helper function to ensure that X and X a.c. never appear in the same list. |
423 | sub _add_to_witlist { |
424 | my( $wit, $list, $acstr ) = @_; |
335a62ef |
425 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
7e17346f |
426 | # Don't add X a.c. if we already have X |
427 | return if $list->has( $1 ); |
335a62ef |
428 | } else { |
7e17346f |
429 | # Delete X a.c. if we are about to add X |
430 | $list->delete( $wit.$acstr ); |
335a62ef |
431 | } |
7e17346f |
432 | $list->insert( $wit ); |
335a62ef |
433 | } |
434 | |
d120c995 |
435 | sub _check_transposed_consistency { |
436 | my( $c, $rank, $transposed, $groupings ) = @_; |
437 | my %seen_wits; |
438 | my %thisrank; |
439 | # Note which readings are actually at this rank, and which witnesses |
440 | # belong to which reading. |
441 | foreach my $rdg ( keys %$groupings ) { |
442 | my $rdgobj = $c->reading( $rdg ); |
443 | # Count '(omitted)' as a reading at this rank |
444 | $thisrank{$rdg} = 1 if !$rdgobj || $rdgobj->rank == $rank; |
445 | map { push( @{$seen_wits{$_}}, $rdg ) } @{$groupings->{$rdg}}; |
446 | } |
447 | # Our work is done if we have no witness belonging to more than one |
448 | # reading. |
449 | my @doubled = grep { scalar @{$seen_wits{$_}} > 1 } keys %seen_wits; |
450 | return unless @doubled; |
451 | # If we have a symmetric related transposition, drop the non-rank readings. |
452 | if( @doubled == scalar keys %seen_wits ) { |
453 | foreach my $rdg ( keys %$groupings ) { |
454 | if( !$thisrank{$rdg} ) { |
455 | my $groupstr = wit_stringify( $groupings->{$rdg} ); |
456 | my ( $matched ) = grep { $groupstr eq wit_stringify( $groupings->{$_} ) } |
457 | keys %thisrank; |
458 | delete $groupings->{$rdg}; |
459 | # If we found a group match, assume there is a symmetry happening. |
460 | # TODO think more about this |
62a39b8f |
461 | # print STDERR "*** Deleting symmetric reading $rdg\n"; |
d120c995 |
462 | unless( $matched ) { |
463 | delete $transposed->{$rdg}; |
464 | warn "Found problem in evident symmetry with reading $rdg"; |
465 | } |
466 | } |
467 | } |
468 | # Otherwise 'unhook' the transposed reading(s) that have duplicates. |
469 | } else { |
470 | foreach my $dup ( @doubled ) { |
471 | foreach my $rdg ( @{$seen_wits{$dup}} ) { |
472 | next if $thisrank{$rdg}; |
473 | next unless exists $groupings->{$rdg}; |
62a39b8f |
474 | # print STDERR "*** Deleting asymmetric doubled-up reading $rdg\n"; |
d120c995 |
475 | delete $groupings->{$rdg}; |
476 | delete $transposed->{$rdg}; |
477 | } |
478 | } |
479 | # and put any now-orphaned readings into an 'omitted' reading. |
480 | foreach my $wit ( keys %seen_wits ) { |
481 | unless( grep { exists $groupings->{$_} } @{$seen_wits{$wit}} ) { |
7e17346f |
482 | $groupings->{'(omitted)'} = Set::Scalar->new() |
483 | unless exists $groupings->{'(omitted)'}; |
d120c995 |
484 | _add_to_witlist( $wit, $groupings->{'(omitted)'}, $c->ac_label ); |
485 | } |
486 | } |
487 | } |
488 | } |
489 | |
7e17346f |
490 | # For the given grouping, return its situation graph based on the stemma. |
491 | sub _graph_for_grouping { |
492 | my( $stemma, $grouping, $lacunose, $aclabel ) = @_; |
493 | my $acwits = []; |
494 | my $extant = {}; |
495 | foreach my $gs ( values %$grouping ) { |
496 | map { |
497 | if( $_ =~ /^(.*)\Q$aclabel\E$/ ) { |
498 | push( @$acwits, $1 ) unless $lacunose->has( $1 ); |
499 | } else { |
500 | $extant->{$_} = 1 unless $lacunose->has( $_ ); |
501 | } |
502 | } $gs->members; |
503 | } |
504 | my $graph; |
505 | try { |
506 | # contig contains all extant wits and all hypothetical wits |
507 | # needed to make up the groups. |
ace5fce5 |
508 | $graph = $stemma->situation_graph( $extant, $acwits, $aclabel ); |
7e17346f |
509 | } catch ( Text::Tradition::Error $e ) { |
03c0a7d7 |
510 | throw( "Could not extend graph with given extant and a.c. witnesses: " |
511 | . $e->message ); |
7e17346f |
512 | } catch { |
03c0a7d7 |
513 | throw( "Could not extend graph with a.c. witnesses @$acwits" ); |
7e17346f |
514 | } |
515 | return $graph; |
516 | } |
88a6bac5 |
517 | |
7e17346f |
518 | =head2 solve_variants( $calcdir, @groups ) |
519 | |
520 | Looks up the set of groups in the answers provided by the external graph solver |
521 | service and returns a cleaned-up answer, adding the rank IDs back where they belong. |
88a6bac5 |
522 | |
88a6bac5 |
523 | The answer has the form |
524 | { "variants" => [ array of variant location structures ], |
525 | "variant_count" => total, |
526 | "conflict_count" => number of conflicts detected, |
527 | "genealogical_count" => number of solutions found } |
528 | |
529 | =cut |
530 | |
531 | sub solve_variants { |
03c0a7d7 |
532 | my( @groups ) = @_; |
533 | |
a745c3d9 |
534 | # Are we using a local result directory, or did we pass an empty value |
535 | # for the directory? |
03c0a7d7 |
536 | my $dir; |
a745c3d9 |
537 | unless( ref( $groups[0] ) eq 'HASH' ) { |
03c0a7d7 |
538 | $dir = shift @groups; |
539 | } |
335a62ef |
540 | |
03c0a7d7 |
541 | ## For each graph/group combo, make a Text::Tradition::Analysis::Result |
542 | ## object so that we can send it off for IDP lookup. |
7e17346f |
543 | my $variants = []; |
544 | my $genealogical = 0; # counter |
03c0a7d7 |
545 | # TODO Optimize for unique graph problems |
554e2e7d |
546 | my %problems; |
7e17346f |
547 | foreach my $graphproblem ( @groups ) { |
03c0a7d7 |
548 | # Construct the calc result key and look up its answer |
549 | my $problem = Text::Tradition::Analysis::Result->new( |
550 | graph => $graphproblem->{'graph'}, |
551 | setlist => [ values %{$graphproblem->{'grouping'}} ] ); |
554e2e7d |
552 | if( exists $problems{$problem->object_key} ) { |
553 | $problem = $problems{$problem->object_key}; |
554 | } else { |
555 | $problems{$problem->object_key} = $problem; |
556 | } |
557 | $graphproblem->{'object'} = $problem; |
03c0a7d7 |
558 | } |
559 | |
554e2e7d |
560 | my %results; |
03c0a7d7 |
561 | if( $dir ) { |
562 | my $scope = $dir->new_scope; |
554e2e7d |
563 | map { $results{$_} = $dir->lookup( $_ ) || $problems{$_} } keys %problems; |
564 | } else { |
565 | my $json = JSON->new->allow_blessed->convert_blessed->utf8->encode( |
566 | [ values %problems ] ); |
03c0a7d7 |
567 | # Send it off and get the result |
568 | # print STDERR "Sending request: " . decode_utf8( $json ) . "\n"; |
569 | my $ua = LWP::UserAgent->new(); |
570 | my $resp = $ua->post( $SOLVER_URL, 'Content-Type' => 'application/json', |
571 | 'Content' => $json ); |
a745c3d9 |
572 | my $answer; |
03c0a7d7 |
573 | if( $resp->is_success ) { |
a745c3d9 |
574 | $answer = decode_json( $resp->content ); |
03c0a7d7 |
575 | throw( "Unexpected answer from IDP: $answer" ) unless ref( $answer ) eq 'ARRAY'; |
576 | } else { |
577 | throw( "IDP solver returned " . $resp->status_line . " / " . $resp->content |
578 | . "; cannot run graph analysis" ); |
579 | } |
580 | # One more sanity check |
581 | throw( "Something went wrong with answer symmetricity" ) |
554e2e7d |
582 | unless keys( %problems ) == @$answer; |
03c0a7d7 |
583 | # Convert the results |
554e2e7d |
584 | foreach my $a ( @$answer ) { |
585 | my $r = Text::Tradition::Analysis::Result->new( $a ); |
586 | $results{$r->object_key} = $r; |
587 | } |
03c0a7d7 |
588 | } |
589 | |
590 | # We now have a single JSON-encoded Result object per problem sent. Fold its |
591 | # answers into our variant info structure. |
554e2e7d |
592 | foreach my $graphproblem ( @groups ) { |
593 | my $result = $results{$graphproblem->{'object'}->object_key} |
594 | || $graphproblem->{'object'}; |
03c0a7d7 |
595 | |
7e17346f |
596 | # Initialize the result structure for this graph problem |
b7bd7aa5 |
597 | my $vstruct; |
598 | if( $result->status eq 'OK' ) { |
599 | $vstruct = { readings => [] }; |
600 | push( @$variants, $vstruct ); |
601 | } else { |
602 | push( @$variants, _init_unsolved( $graphproblem, $result->status ) ); |
7e17346f |
603 | next; |
5c44c598 |
604 | } |
b7bd7aa5 |
605 | |
7e17346f |
606 | # 1. Did the group evaluate as genealogical? |
03c0a7d7 |
607 | $vstruct->{genealogical} = $result->is_genealogical; |
608 | $genealogical++ if $result->is_genealogical; |
7e17346f |
609 | |
610 | # 2. What are the calculated minimum groupings for each variant loc? |
611 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
612 | my $inputset = $graphproblem->{grouping}->{$rid}; |
03c0a7d7 |
613 | my $minset = $result->minimum_grouping_for( $inputset ); |
7e17346f |
614 | push( @{$vstruct->{readings}}, { readingid => $rid, group => $minset } ); |
6d25a3a0 |
615 | } |
7e17346f |
616 | |
617 | # 3. What are the sources and classes calculated for each witness? |
03c0a7d7 |
618 | $vstruct->{witcopy_types} = { $result->classes }; |
7e17346f |
619 | $vstruct->{reading_roots} = {}; |
03c0a7d7 |
620 | map { $vstruct->{reading_roots}->{$_} = 1 } $result->sources; |
7e17346f |
621 | |
88a6bac5 |
622 | } |
623 | |
624 | return { 'variants' => $variants, |
625 | 'variant_count' => scalar @$variants, |
626 | 'genealogical_count' => $genealogical }; |
627 | } |
628 | |
b7bd7aa5 |
629 | sub _init_unsolved { |
630 | my( $graphproblem, $status ) = @_; |
631 | my $vstruct = { 'readings' => [] }; |
632 | $vstruct->{'unsolved'} = $status; |
633 | foreach my $rid ( keys %{$graphproblem->{grouping}} ) { |
634 | push( @{$vstruct->{readings}}, { readingid => $rid, |
635 | group => [ $graphproblem->{grouping}->{$rid}->members ] } ); |
636 | } |
637 | return $vstruct; |
638 | } |
639 | |
fae07016 |
640 | =head2 analyze_location ( $tradition, $graph, $location_hash ) |
7f52eac8 |
641 | |
fae07016 |
642 | Given the tradition, its stemma graph, and the solution from the graph solver, |
643 | work out the rest of the information we want. For each reading we need missing, |
5c44c598 |
644 | conflict, reading_parents, independent_occurrence, followed, not_followed, |
645 | and follow_unknown. Alters the location_hash in place. |
7f52eac8 |
646 | |
647 | =cut |
732152b1 |
648 | |
fae07016 |
649 | sub analyze_location { |
7e17346f |
650 | my ( $tradition, $graph, $variant_row, $lacunose ) = @_; |
94654e27 |
651 | my $c = $tradition->collation; |
fae07016 |
652 | |
03c0a7d7 |
653 | if( exists $variant_row->{'unsolved'} ) { |
654 | return; |
655 | } |
656 | my $reading_roots = delete $variant_row->{'reading_roots'}; |
657 | my $classinfo = delete $variant_row->{'witcopy_types'}; |
658 | |
fae07016 |
659 | # Make a hash of all known node memberships, and make the subgraphs. |
660 | my $contig = {}; |
fae07016 |
661 | my $subgraph = {}; |
638e2a95 |
662 | my $acstr = $c->ac_label; |
663 | my @acwits; |
5c44c598 |
664 | |
5c44c598 |
665 | # Note which witnesses positively belong to which group. This information |
666 | # comes ultimately from the IDP solver. |
667 | # Also make a note of the reading's roots. |
fae07016 |
668 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
669 | my $rid = $rdghash->{'readingid'}; |
5c44c598 |
670 | my @roots; |
638e2a95 |
671 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
672 | $contig->{$wit} = $rid; |
673 | if( $wit =~ /^(.*)\Q$acstr\E$/ ) { |
674 | push( @acwits, $1 ); |
675 | } |
5c44c598 |
676 | if( exists $reading_roots->{$wit} && $reading_roots->{$wit} ) { |
677 | push( @roots, $wit ); |
678 | } |
638e2a95 |
679 | } |
5c44c598 |
680 | $rdghash->{'independent_occurrence'} = \@roots; |
94654e27 |
681 | } |
7e17346f |
682 | |
fae07016 |
683 | # Now that we have all the node group memberships, calculate followed/ |
bebec0e9 |
684 | # non-followed/unknown values for each reading. Also figure out the |
685 | # reading's evident parent(s). |
686 | foreach my $rdghash ( @{$variant_row->{'readings'}} ) { |
fae07016 |
687 | my $rid = $rdghash->{'readingid'}; |
428bcf0b |
688 | my $rdg = $c->reading( $rid ); |
5c44c598 |
689 | my @roots = @{$rdghash->{'independent_occurrence'}}; |
7e17346f |
690 | my @reversions; |
691 | if( $classinfo ) { |
692 | @reversions = grep { $classinfo->{$_} eq 'revert' } |
693 | $rdghash->{'group'}->members; |
be590045 |
694 | $rdghash->{'reversions'} = \@reversions; |
7e17346f |
695 | } |
5c44c598 |
696 | my @group = @{$rdghash->{'group'}}; |
fae07016 |
697 | |
698 | # Start figuring things out. |
7e17346f |
699 | $rdghash->{'followed'} = scalar( @group ) |
700 | - ( scalar( @roots ) + scalar( @reversions ) ); |
bebec0e9 |
701 | # Find the parent readings, if any, of this reading. |
7e17346f |
702 | my $sourceparents = _find_reading_parents( $rid, $graph, $contig, @roots ); |
7e17346f |
703 | # Work out relationships between readings and their non-followed parent. |
704 | _resolve_parent_relationships( $c, $rid, $rdg, $sourceparents ); |
be590045 |
705 | $rdghash->{'source_parents'} = $sourceparents; |
e23225e7 |
706 | |
707 | if( @reversions ) { |
708 | my $revparents = _find_reading_parents( $rid, $graph, $contig, @reversions ); |
709 | _resolve_parent_relationships( $c, $rid, $rdg, $revparents ); |
710 | $rdghash->{'reversion_parents'} = $revparents; |
711 | } |
bebec0e9 |
712 | |
713 | # Find the number of times this reading was altered, and the number of |
714 | # times we're not sure. |
715 | my( %nofollow, %unknownfollow ); |
5c44c598 |
716 | foreach my $wit ( @{$rdghash->{'group'}} ) { |
bebec0e9 |
717 | foreach my $wchild ( $graph->successors( $wit ) ) { |
5c44c598 |
718 | if( $reading_roots->{$wchild} && $contig->{$wchild} |
719 | && $contig->{$wchild} ne $rid ) { |
bebec0e9 |
720 | # It definitely changed here. |
721 | $nofollow{$wchild} = 1; |
722 | } elsif( !($contig->{$wchild}) ) { |
723 | # The child is a hypothetical node not definitely in |
724 | # any group. Answer is unknown. |
725 | $unknownfollow{$wchild} = 1; |
5c44c598 |
726 | } # else it is either in our group, or it is a non-root node in a |
727 | # known group and therefore is presumed to have its reading from |
728 | # its group, not this link. |
bebec0e9 |
729 | } |
730 | } |
731 | $rdghash->{'not_followed'} = keys %nofollow; |
732 | $rdghash->{'follow_unknown'} = keys %unknownfollow; |
fae07016 |
733 | |
734 | # Now say whether this reading represents a conflict. |
735 | unless( $variant_row->{'genealogical'} ) { |
7e17346f |
736 | $rdghash->{'is_conflict'} = @roots != 1; |
e23225e7 |
737 | $rdghash->{'is_reverted'} = scalar @reversions; |
7e17346f |
738 | } |
739 | } |
740 | } |
741 | |
742 | sub _find_reading_parents { |
743 | my( $rid, $graph, $contig, @list ) = @_; |
744 | my $parenthash = {}; |
745 | foreach my $wit ( @list ) { |
746 | # Look in the stemma graph to find this witness's extant or known-reading |
747 | # immediate ancestor(s), and look up the reading that each ancestor holds. |
748 | my @check = $graph->predecessors( $wit ); |
749 | while( @check ) { |
750 | my @next; |
751 | foreach my $wparent( @check ) { |
752 | my $preading = $contig->{$wparent}; |
753 | if( $preading && $preading ne $rid ) { |
754 | $parenthash->{$preading} = 1; |
755 | } else { |
756 | push( @next, $graph->predecessors( $wparent ) ); |
757 | } |
758 | } |
759 | @check = @next; |
760 | } |
761 | } |
762 | return $parenthash; |
763 | } |
764 | |
765 | sub _resolve_parent_relationships { |
766 | my( $c, $rid, $rdg, $rdgparents ) = @_; |
767 | foreach my $p ( keys %$rdgparents ) { |
768 | # Resolve the relationship of the parent to the reading, and |
769 | # save it in our hash. |
770 | my $pobj = $c->reading( $p ); |
771 | my $prep = $pobj ? $pobj->id . ' (' . $pobj->text . ')' : $p; |
772 | my $phash = { 'label' => $prep }; |
773 | if( $pobj ) { |
774 | my $rel = $c->get_relationship( $p, $rid ); |
775 | if( $rel ) { |
776 | _add_to_hash( $rel, $phash ); |
777 | } elsif( $rdg ) { |
778 | # First check for a transposed relationship |
779 | if( $rdg->rank != $pobj->rank ) { |
780 | foreach my $ti ( $rdg->related_readings( 'transposition' ) ) { |
781 | next unless $ti->text eq $rdg->text; |
782 | $rel = $c->get_relationship( $ti, $pobj ); |
783 | if( $rel ) { |
784 | _add_to_hash( $rel, $phash, 1 ); |
785 | last; |
786 | } |
787 | } |
788 | unless( $rel ) { |
789 | foreach my $ti ( $pobj->related_readings( 'transposition' ) ) { |
790 | next unless $ti->text eq $pobj->text; |
791 | $rel = $c->get_relationship( $ti, $rdg ); |
792 | if( $rel ) { |
793 | _add_to_hash( $rel, $phash, 1 ); |
794 | last; |
795 | } |
796 | } |
5c44c598 |
797 | } |
798 | } |
7e17346f |
799 | unless( $rel ) { |
800 | # and then check for sheer word similarity. |
801 | my $rtext = $rdg->text; |
802 | my $ptext = $pobj->text; |
803 | if( similar( $rtext, $ptext ) ) { |
804 | # say STDERR "Words $rtext and $ptext judged similar"; |
805 | $phash->{relation} = { type => 'wordsimilar' }; |
806 | } |
807 | } |
5c44c598 |
808 | } else { |
7e17346f |
809 | $phash->{relation} = { type => 'deletion' }; |
5c44c598 |
810 | } |
7e17346f |
811 | # Get the attributes of the parent object while we are here |
812 | $phash->{'text'} = $pobj->text if $pobj; |
a445ce40 |
813 | if( $pobj && $pobj->does('Text::Tradition::Morphology') ) { |
814 | $phash->{'is_nonsense'} = $pobj->is_nonsense; |
815 | $phash->{'is_ungrammatical'} = $pobj->grammar_invalid; |
816 | } |
7e17346f |
817 | } elsif( $p eq '(omitted)' ) { |
818 | $phash->{relation} = { type => 'addition' }; |
819 | } |
820 | # Save it |
821 | $rdgparents->{$p} = $phash; |
822 | } |
d71100ed |
823 | } |
824 | |
428bcf0b |
825 | sub _add_to_hash { |
826 | my( $rel, $phash, $is_transposed ) = @_; |
827 | $phash->{relation} = { type => $rel->type }; |
828 | $phash->{relation}->{transposed} = 1 if $is_transposed; |
829 | $phash->{relation}->{annotation} = $rel->annotation |
830 | if $rel->has_annotation; |
831 | } |
832 | |
833 | =head2 similar( $word1, $word2 ) |
834 | |
835 | Use Algorithm::Diff to get a sense of how close the words are to each other. |
836 | This will hopefully handle substitutions a bit more nicely than Levenshtein. |
837 | |
838 | =cut |
839 | |
840 | #!/usr/bin/env perl |
841 | |
842 | sub similar { |
843 | my( $word1, $word2 ) = sort { length($a) <=> length($b) } @_; |
844 | my @let1 = split( '', lc( $word1 ) ); |
845 | my @let2 = split( '', lc( $word2 ) ); |
846 | my $diff = Algorithm::Diff->new( \@let1, \@let2 ); |
847 | my $mag = 0; |
848 | while( $diff->Next ) { |
849 | if( $diff->Same ) { |
850 | # Take off points for longer strings |
851 | my $cs = $diff->Range(1) - 2; |
852 | $cs = 0 if $cs < 0; |
853 | $mag -= $cs; |
854 | } elsif( !$diff->Items(1) ) { |
855 | $mag += $diff->Range(2); |
856 | } elsif( !$diff->Items(2) ) { |
857 | $mag += $diff->Range(1); |
858 | } else { |
859 | # Split the difference for substitutions |
860 | my $c1 = $diff->Range(1) || 1; |
861 | my $c2 = $diff->Range(2) || 1; |
862 | my $cd = ( $c1 + $c2 ) / 2; |
863 | $mag += $cd; |
864 | } |
865 | } |
866 | return ( $mag <= length( $word1 ) / 2 ); |
867 | } |
868 | |
5be0cdeb |
869 | sub _useful_variant { |
7e17346f |
870 | my( $rankgroup, $rankgraph, $acstr ) = @_; |
5be0cdeb |
871 | |
872 | # Sort by group size and return |
873 | my $is_useful = 0; |
7e17346f |
874 | foreach my $rdg ( keys %$rankgroup ) { |
875 | my @wits = $rankgroup->{$rdg}->members; |
876 | if( @wits > 1 ) { |
5be0cdeb |
877 | $is_useful++; |
878 | } else { |
7e17346f |
879 | $is_useful++ unless( $rankgraph->is_sink_vertex( $wits[0] ) |
880 | || $wits[0] =~ /\Q$acstr\E$/ ); |
5be0cdeb |
881 | } |
882 | } |
7e17346f |
883 | return $is_useful > 1; |
5be0cdeb |
884 | } |
885 | |
7f52eac8 |
886 | =head2 wit_stringify( $groups ) |
887 | |
888 | Takes an array of witness groupings and produces a string like |
889 | ['A','B'] / ['C','D','E'] / ['F'] |
d71100ed |
890 | |
7f52eac8 |
891 | =cut |
d71100ed |
892 | |
893 | sub wit_stringify { |
894 | my $groups = shift; |
895 | my @gst; |
896 | # If we were passed an array of witnesses instead of an array of |
897 | # groupings, then "group" the witnesses first. |
898 | unless( ref( $groups->[0] ) ) { |
899 | my $mkgrp = [ $groups ]; |
900 | $groups = $mkgrp; |
901 | } |
902 | foreach my $g ( @$groups ) { |
903 | push( @gst, '[' . join( ',', map { "'$_'" } @$g ) . ']' ); |
904 | } |
905 | return join( ' / ', @gst ); |
906 | } |
7f52eac8 |
907 | |
7f52eac8 |
908 | 1; |
909 | |
a745c3d9 |
910 | sub throw { |
911 | Text::Tradition::Error->throw( |
912 | 'ident' => 'Analysis error', |
913 | 'message' => $_[0], |
914 | ); |
915 | } |
916 | |
7f52eac8 |
917 | =head1 LICENSE |
918 | |
919 | This package is free software and is provided "as is" without express |
920 | or implied warranty. You can redistribute it and/or modify it under |
921 | the same terms as Perl itself. |
922 | |
923 | =head1 AUTHOR |
924 | |
925 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |