Commit | Line | Data |
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1 | package Text::Tradition::Collation; |
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2 | |
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3 | use feature 'say'; |
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4 | use Encode qw( decode_utf8 ); |
5 | use File::Temp; |
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6 | use File::Which; |
c9bf3dbf |
7 | use Graph; |
8e1394aa |
8 | use IPC::Run qw( run binary ); |
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9 | use Text::CSV; |
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10 | use Text::Tradition::Collation::Data; |
b15511bf |
11 | use Text::Tradition::Collation::Reading; |
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12 | use Text::Tradition::Collation::RelationshipStore; |
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13 | use Text::Tradition::Error; |
cc31ebaa |
14 | use XML::Easy::Syntax qw( $xml10_namestartchar_rx $xml10_namechar_rx ); |
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15 | use XML::LibXML; |
16 | use XML::LibXML::XPathContext; |
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17 | use Moose; |
18 | |
5c0072ef |
19 | has _data => ( |
20 | isa => 'Text::Tradition::Collation::Data', |
21 | is => 'ro', |
22 | required => 1, |
23 | handles => [ qw( |
24 | sequence |
25 | paths |
26 | _set_relations |
27 | relations |
28 | _set_start |
29 | _set_end |
30 | ac_label |
31 | has_cached_table |
32 | relationships |
33 | related_readings |
34 | get_relationship |
35 | del_relationship |
36 | equivalence |
37 | equivalence_graph |
38 | readings |
39 | reading |
40 | _add_reading |
41 | del_reading |
42 | has_reading |
43 | wit_list_separator |
44 | baselabel |
45 | linear |
46 | wordsep |
47 | start |
48 | end |
49 | cached_table |
50 | _graphcalc_done |
51 | has_cached_svg |
52 | wipe_table |
53 | )] |
54 | ); |
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55 | |
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56 | has 'tradition' => ( |
57 | is => 'ro', |
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58 | isa => 'Text::Tradition', |
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59 | writer => '_set_tradition', |
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60 | weak_ref => 1, |
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61 | ); |
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62 | |
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63 | =head1 NAME |
64 | |
65 | Text::Tradition::Collation - a software model for a text collation |
66 | |
67 | =head1 SYNOPSIS |
68 | |
69 | use Text::Tradition; |
70 | my $t = Text::Tradition->new( |
71 | 'name' => 'this is a text', |
72 | 'input' => 'TEI', |
73 | 'file' => '/path/to/tei_parallel_seg_file.xml' ); |
74 | |
75 | my $c = $t->collation; |
76 | my @readings = $c->readings; |
77 | my @paths = $c->paths; |
78 | my @relationships = $c->relationships; |
79 | |
80 | my $svg_variant_graph = $t->collation->as_svg(); |
81 | |
82 | =head1 DESCRIPTION |
83 | |
84 | Text::Tradition is a library for representation and analysis of collated |
85 | texts, particularly medieval ones. The Collation is the central feature of |
86 | a Tradition, where the text, its sequence of readings, and its relationships |
87 | between readings are actually kept. |
88 | |
89 | =head1 CONSTRUCTOR |
90 | |
91 | =head2 new |
92 | |
93 | The constructor. Takes a hash or hashref of the following arguments: |
94 | |
95 | =over |
96 | |
97 | =item * tradition - The Text::Tradition object to which the collation |
98 | belongs. Required. |
99 | |
100 | =item * linear - Whether the collation should be linear; that is, whether |
101 | transposed readings should be treated as two linked readings rather than one, |
102 | and therefore whether the collation graph is acyclic. Defaults to true. |
103 | |
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104 | =item * baselabel - The default label for the path taken by a base text |
105 | (if any). Defaults to 'base text'. |
106 | |
107 | =item * wit_list_separator - The string to join a list of witnesses for |
108 | purposes of making labels in display graphs. Defaults to ', '. |
109 | |
110 | =item * ac_label - The extra label to tack onto a witness sigil when |
111 | representing another layer of path for the given witness - that is, when |
112 | a text has more than one possible reading due to scribal corrections or |
113 | the like. Defaults to ' (a.c.)'. |
114 | |
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115 | =item * wordsep - The string used to separate words in the original text. |
116 | Defaults to ' '. |
117 | |
4e5a7b2c |
118 | =back |
119 | |
120 | =head1 ACCESSORS |
121 | |
122 | =head2 tradition |
123 | |
124 | =head2 linear |
125 | |
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126 | =head2 wit_list_separator |
127 | |
128 | =head2 baselabel |
129 | |
130 | =head2 ac_label |
131 | |
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132 | =head2 wordsep |
133 | |
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134 | Simple accessors for collation attributes. |
135 | |
136 | =head2 start |
137 | |
138 | The meta-reading at the start of every witness path. |
139 | |
140 | =head2 end |
141 | |
142 | The meta-reading at the end of every witness path. |
143 | |
144 | =head2 readings |
145 | |
146 | Returns all Reading objects in the graph. |
147 | |
148 | =head2 reading( $id ) |
149 | |
150 | Returns the Reading object corresponding to the given ID. |
151 | |
152 | =head2 add_reading( $reading_args ) |
153 | |
154 | Adds a new reading object to the collation. |
155 | See L<Text::Tradition::Collation::Reading> for the available arguments. |
156 | |
157 | =head2 del_reading( $object_or_id ) |
158 | |
159 | Removes the given reading from the collation, implicitly removing its |
160 | paths and relationships. |
161 | |
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162 | =head2 has_reading( $id ) |
163 | |
164 | Predicate to see whether a given reading ID is in the graph. |
165 | |
166 | =head2 reading_witnesses( $object_or_id ) |
167 | |
168 | Returns a list of sigils whose witnesses contain the reading. |
169 | |
170 | =head2 paths |
171 | |
172 | Returns all reading paths within the document - that is, all edges in the |
173 | collation graph. Each path is an arrayref of [ $source, $target ] reading IDs. |
174 | |
175 | =head2 add_path( $source, $target, $sigil ) |
176 | |
177 | Links the given readings in the collation in sequence, under the given witness |
178 | sigil. The readings may be specified by object or ID. |
179 | |
180 | =head2 del_path( $source, $target, $sigil ) |
181 | |
182 | Links the given readings in the collation in sequence, under the given witness |
183 | sigil. The readings may be specified by object or ID. |
184 | |
185 | =head2 has_path( $source, $target ); |
186 | |
187 | Returns true if the two readings are linked in sequence in any witness. |
188 | The readings may be specified by object or ID. |
189 | |
190 | =head2 relationships |
191 | |
192 | Returns all Relationship objects in the collation. |
193 | |
194 | =head2 add_relationship( $reading, $other_reading, $options ) |
195 | |
196 | Adds a new relationship of the type given in $options between the two readings, |
197 | which may be specified by object or ID. Returns a value of ( $status, @vectors) |
198 | where $status is true on success, and @vectors is a list of relationship edges |
199 | that were ultimately added. |
200 | See L<Text::Tradition::Collation::Relationship> for the available options. |
201 | |
202 | =cut |
dd3b58b0 |
203 | |
5c0072ef |
204 | sub BUILDARGS { |
205 | my ( $class, @args ) = @_; |
206 | my %args = @args == 1 ? %{ $args[0] } : @args; |
207 | # TODO determine these from the Moose::Meta object |
208 | my @delegate_attrs = qw(sequence relations readings wit_list_separator baselabel |
209 | linear wordsep start end cached_table _graphcalc_done); |
210 | my %data_args; |
211 | for my $attr (@delegate_attrs) { |
212 | $data_args{$attr} = delete $args{$attr} if exists $args{$attr}; |
213 | } |
214 | $args{_data} = Text::Tradition::Collation::Data->new(%data_args); |
215 | return \%args; |
216 | } |
217 | |
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218 | sub BUILD { |
3a2ebbf4 |
219 | my $self = shift; |
22222af9 |
220 | $self->_set_relations( Text::Tradition::Collation::RelationshipStore->new( 'collation' => $self ) ); |
e4b73942 |
221 | $self->_set_start( $self->add_reading( |
222 | { 'collation' => $self, 'is_start' => 1, 'init' => 1 } ) ); |
223 | $self->_set_end( $self->add_reading( |
224 | { 'collation' => $self, 'is_end' => 1, 'init' => 1 } ) ); |
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225 | } |
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226 | |
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227 | sub register_relationship_type { |
228 | my $self = shift; |
229 | my %args = @_ == 1 ? %{$_[0]} : @_; |
230 | if( $self->relations->has_type( $args{name} ) ) { |
231 | throw( 'Relationship type ' . $args{name} . ' already registered' ); |
232 | } |
233 | $self->relations->add_type( %args ); |
234 | } |
235 | |
39d1ddc7 |
236 | sub get_relationship_type { |
237 | my( $self, $name ) = @_; |
238 | return $self->relations->has_type( $name ) |
239 | ? $self->relations->type( $name ) : undef; |
240 | } |
241 | |
3a2ebbf4 |
242 | ### Reading construct/destruct functions |
243 | |
244 | sub add_reading { |
245 | my( $self, $reading ) = @_; |
246 | unless( ref( $reading ) eq 'Text::Tradition::Collation::Reading' ) { |
247 | my %args = %$reading; |
e4b73942 |
248 | if( $args{'init'} ) { |
249 | # If we are initializing an empty collation, don't assume that we |
250 | # have set a tradition. |
251 | delete $args{'init'}; |
8943ff68 |
252 | } elsif( $self->tradition->can('language') && $self->tradition->has_language |
253 | && !exists $args{'language'} ) { |
6ad2ce78 |
254 | $args{'language'} = $self->tradition->language; |
255 | } |
3a2ebbf4 |
256 | $reading = Text::Tradition::Collation::Reading->new( |
257 | 'collation' => $self, |
258 | %args ); |
259 | } |
260 | # First check to see if a reading with this ID exists. |
261 | if( $self->reading( $reading->id ) ) { |
63778331 |
262 | throw( "Collation already has a reading with id " . $reading->id ); |
3a2ebbf4 |
263 | } |
c1915ab9 |
264 | $self->_graphcalc_done(0); |
3a2ebbf4 |
265 | $self->_add_reading( $reading->id => $reading ); |
266 | # Once the reading has been added, put it in both graphs. |
267 | $self->sequence->add_vertex( $reading->id ); |
cecbe56d |
268 | $self->relations->add_reading( $reading->id ); |
3a2ebbf4 |
269 | return $reading; |
eca16057 |
270 | }; |
271 | |
3a2ebbf4 |
272 | around del_reading => sub { |
273 | my $orig = shift; |
274 | my $self = shift; |
275 | my $arg = shift; |
276 | |
cecbe56d |
277 | if( ref( $arg ) eq 'Text::Tradition::Collation::Reading' ) { |
278 | $arg = $arg->id; |
3a2ebbf4 |
279 | } |
3a2ebbf4 |
280 | # Remove the reading from the graphs. |
c1915ab9 |
281 | $self->_graphcalc_done(0); |
4e483aa5 |
282 | $self->_clear_cache; # Explicitly clear caches to GC the reading |
cecbe56d |
283 | $self->sequence->delete_vertex( $arg ); |
284 | $self->relations->delete_reading( $arg ); |
3a2ebbf4 |
285 | |
286 | # Carry on. |
cecbe56d |
287 | $self->$orig( $arg ); |
3a2ebbf4 |
288 | }; |
7854e12e |
289 | |
3c234eb6 |
290 | =head2 merge_readings( $main, $second, $concatenate, $with_str ) |
291 | |
292 | Merges the $second reading into the $main one. If $concatenate is true, then |
293 | the merged node will carry the text of both readings, concatenated with either |
294 | $with_str (if specified) or a sensible default (the empty string if the |
295 | appropriate 'join_*' flag is set on either reading, or else $self->wordsep.) |
296 | |
297 | The first two arguments may be either readings or reading IDs. |
298 | |
4e483aa5 |
299 | =begin testing |
300 | |
301 | use Text::Tradition; |
58568d5c |
302 | use TryCatch; |
4e483aa5 |
303 | |
304 | my $cxfile = 't/data/Collatex-16.xml'; |
305 | my $t = Text::Tradition->new( |
306 | 'name' => 'inline', |
307 | 'input' => 'CollateX', |
308 | 'file' => $cxfile, |
309 | ); |
310 | my $c = $t->collation; |
311 | |
312 | my $rno = scalar $c->readings; |
4ef65ab4 |
313 | # Split n21 ('unto') for testing purposes |
4e483aa5 |
314 | my $new_r = $c->add_reading( { 'id' => 'n21p0', 'text' => 'un', 'join_next' => 1 } ); |
315 | my $old_r = $c->reading( 'n21' ); |
316 | $old_r->alter_text( 'to' ); |
317 | $c->del_path( 'n20', 'n21', 'A' ); |
318 | $c->add_path( 'n20', 'n21p0', 'A' ); |
319 | $c->add_path( 'n21p0', 'n21', 'A' ); |
7a0956c1 |
320 | $c->add_relationship( 'n21', 'n22', { type => 'collated', scope => 'local' } ); |
4e483aa5 |
321 | $c->flatten_ranks(); |
322 | ok( $c->reading( 'n21p0' ), "New reading exists" ); |
323 | is( scalar $c->readings, $rno, "Reading add offset by flatten_ranks" ); |
324 | |
679f17e1 |
325 | # Combine n3 and n4 ( with his ) |
4e483aa5 |
326 | $c->merge_readings( 'n3', 'n4', 1 ); |
327 | ok( !$c->reading('n4'), "Reading n4 is gone" ); |
328 | is( $c->reading('n3')->text, 'with his', "Reading n3 has both words" ); |
329 | |
679f17e1 |
330 | # Collapse n9 and n10 ( rood / root ) |
331 | $c->merge_readings( 'n9', 'n10' ); |
332 | ok( !$c->reading('n10'), "Reading n10 is gone" ); |
333 | is( $c->reading('n9')->text, 'rood', "Reading n9 has an unchanged word" ); |
4e483aa5 |
334 | |
58568d5c |
335 | # Try to combine n21 and n21p0. This should break. |
4e483aa5 |
336 | my $remaining = $c->reading('n21'); |
337 | $remaining ||= $c->reading('n22'); # one of these should still exist |
58568d5c |
338 | try { |
339 | $c->merge_readings( 'n21p0', $remaining, 1 ); |
340 | ok( 0, "Bad reading merge changed the graph" ); |
341 | } catch( Text::Tradition::Error $e ) { |
342 | like( $e->message, qr/neither concatenated nor collated/, "Expected exception from bad concatenation" ); |
343 | } catch { |
344 | ok( 0, "Unexpected error on bad reading merge: $@" ); |
345 | } |
346 | |
347 | try { |
348 | $c->calculate_ranks(); |
349 | ok( 1, "Graph is still evidently whole" ); |
350 | } catch( Text::Tradition::Error $e ) { |
351 | ok( 0, "Caught a rank exception: " . $e->message ); |
352 | } |
4e483aa5 |
353 | |
354 | =end testing |
355 | |
356 | =cut |
7854e12e |
357 | |
3a2ebbf4 |
358 | sub merge_readings { |
359 | my $self = shift; |
360 | |
56772e8c |
361 | # Sanity check |
362 | my( $kept_obj, $del_obj, $combine, $combine_char ) = $self->_objectify_args( @_ ); |
363 | my $mergemeta = $kept_obj->is_meta; |
364 | throw( "Cannot merge meta and non-meta reading" ) |
365 | unless ( $mergemeta && $del_obj->is_meta ) |
366 | || ( !$mergemeta && !$del_obj->is_meta ); |
367 | if( $mergemeta ) { |
368 | throw( "Cannot merge with start or end node" ) |
369 | if( $kept_obj eq $self->start || $kept_obj eq $self->end |
370 | || $del_obj eq $self->start || $del_obj eq $self->end ); |
a445ce40 |
371 | throw( "Cannot combine text of meta readings" ) if $combine; |
56772e8c |
372 | } |
e4f00901 |
373 | # We can only merge readings in a linear graph if: |
374 | # - they are contiguous with only one edge between them, OR |
375 | # - they are at equivalent ranks in the graph. |
376 | if( $self->linear ) { |
377 | my @delpred = $del_obj->predecessors; |
378 | my @keptsuc = $kept_obj->successors; |
379 | unless ( @delpred == 1 && $delpred[0] eq $kept_obj |
380 | && @keptsuc == 1 && $keptsuc[0] eq $del_obj ) { |
381 | my( $is_ok, $msg ) = $self->relations->relationship_valid( |
382 | $kept_obj, $del_obj, 'collated' ); |
383 | unless( $is_ok ) { |
384 | throw( "Readings $kept_obj and $del_obj can be neither concatenated nor collated" ); |
385 | } |
386 | } |
387 | } |
388 | |
3a2ebbf4 |
389 | # We only need the IDs for adding paths to the graph, not the reading |
390 | # objects themselves. |
56772e8c |
391 | my $kept = $kept_obj->id; |
392 | my $deleted = $del_obj->id; |
c1915ab9 |
393 | $self->_graphcalc_done(0); |
10943ab0 |
394 | |
3a2ebbf4 |
395 | # The kept reading should inherit the paths and the relationships |
396 | # of the deleted reading. |
397 | foreach my $path ( $self->sequence->edges_at( $deleted ) ) { |
398 | my @vector = ( $kept ); |
399 | push( @vector, $path->[1] ) if $path->[0] eq $deleted; |
400 | unshift( @vector, $path->[0] ) if $path->[1] eq $deleted; |
49d4f2ac |
401 | next if $vector[0] eq $vector[1]; # Don't add a self loop |
3a2ebbf4 |
402 | my %wits = %{$self->sequence->get_edge_attributes( @$path )}; |
403 | $self->sequence->add_edge( @vector ); |
404 | my $fwits = $self->sequence->get_edge_attributes( @vector ); |
405 | @wits{keys %$fwits} = values %$fwits; |
406 | $self->sequence->set_edge_attributes( @vector, \%wits ); |
407 | } |
cecbe56d |
408 | $self->relations->merge_readings( $kept, $deleted, $combine ); |
3a2ebbf4 |
409 | |
410 | # Do the deletion deed. |
4e483aa5 |
411 | if( $combine ) { |
869a1ada |
412 | # Combine the text of the readings |
4e483aa5 |
413 | my $joinstr = $combine_char; |
414 | unless( defined $joinstr ) { |
415 | $joinstr = '' if $kept_obj->join_next || $del_obj->join_prior; |
416 | $joinstr = $self->wordsep unless defined $joinstr; |
417 | } |
a445ce40 |
418 | $kept_obj->_combine( $del_obj, $joinstr ); |
49d4f2ac |
419 | } |
3a2ebbf4 |
420 | $self->del_reading( $deleted ); |
421 | } |
7854e12e |
422 | |
8d9494a8 |
423 | =head2 merge_related( @relationship_types ) |
424 | |
425 | Merge all readings linked with the relationship types given. If any of the selected type(s) is not a colocation, the graph will no longer be linear. The majority/plurality reading in each case will be the one kept. |
426 | |
427 | WARNING: This operation cannot be undone. |
428 | |
429 | =cut |
430 | |
431 | =begin testing |
432 | |
58568d5c |
433 | use Test::Warn; |
8d9494a8 |
434 | use Text::Tradition; |
435 | use TryCatch; |
436 | |
58568d5c |
437 | my $t; |
438 | warnings_exist { |
439 | $t = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/legendfrag.xml' ); |
440 | } [qr/Cannot set relationship on a meta reading/], |
441 | "Got expected relationship drop warning on parse"; |
442 | |
8d9494a8 |
443 | my $c = $t->collation; |
444 | |
445 | my %rdg_ids; |
446 | map { $rdg_ids{$_} = 1 } $c->readings; |
447 | $c->merge_related( 'orthographic' ); |
448 | is( scalar( $c->readings ), keys( %rdg_ids ) - 8, |
449 | "Successfully collapsed orthographic variation" ); |
450 | map { $rdg_ids{$_} = undef } qw/ r13.3 r11.4 r8.5 r8.2 r7.7 r7.5 r7.4 r7.1 /; |
451 | foreach my $rid ( keys %rdg_ids ) { |
452 | my $exp = $rdg_ids{$rid}; |
453 | is( !$c->reading( $rid ), !$exp, "Reading $rid correctly " . |
454 | ( $exp ? "retained" : "removed" ) ); |
455 | } |
456 | ok( $c->linear, "Graph is still linear" ); |
457 | try { |
458 | $c->calculate_ranks; # This should succeed |
459 | ok( 1, "Can still calculate ranks on the new graph" ); |
460 | } catch { |
461 | ok( 0, "Rank calculation on merged graph failed: $@" ); |
462 | } |
463 | |
464 | # Now add some transpositions |
465 | $c->add_relationship( 'r8.4', 'r10.4', { type => 'transposition' } ); |
466 | $c->merge_related( 'transposition' ); |
467 | is( scalar( $c->readings ), keys( %rdg_ids ) - 9, |
468 | "Transposed relationship is merged away" ); |
469 | ok( !$c->reading('r8.4'), "Correct transposed reading removed" ); |
470 | ok( !$c->linear, "Graph is no longer linear" ); |
471 | try { |
472 | $c->calculate_ranks; # This should fail |
473 | ok( 0, "Rank calculation happened on nonlinear graph?!" ); |
474 | } catch ( Text::Tradition::Error $e ) { |
475 | is( $e->message, 'Cannot calculate ranks on a non-linear graph', |
476 | "Rank calculation on merged graph threw an error" ); |
477 | } |
478 | |
8d9494a8 |
479 | =end testing |
480 | |
481 | =cut |
482 | |
483 | # TODO: there should be a way to display merged without affecting the underlying data! |
484 | |
485 | sub merge_related { |
486 | my $self = shift; |
487 | my %reltypehash; |
488 | map { $reltypehash{$_} = 1 } @_; |
489 | |
490 | # Set up the filter for finding related readings |
491 | my $filter = sub { |
492 | exists $reltypehash{$_[0]->type}; |
493 | }; |
494 | |
8d9494a8 |
495 | # Go through all readings looking for related ones |
496 | foreach my $r ( $self->readings ) { |
497 | next unless $self->reading( "$r" ); # might have been deleted meanwhile |
498 | my @related = $self->related_readings( $r, $filter ); |
499 | if( @related ) { |
500 | push( @related, $r ); |
501 | @related = sort { |
502 | scalar $b->witnesses <=> scalar $a->witnesses |
503 | } @related; |
504 | my $keep = shift @related; |
505 | foreach my $delr ( @related ) { |
58568d5c |
506 | $self->linear( 0 ) |
8d9494a8 |
507 | unless( $self->get_relationship( $keep, $delr )->colocated ); |
508 | $self->merge_readings( $keep, $delr ); |
509 | } |
510 | } |
511 | } |
8d9494a8 |
512 | } |
513 | |
6771a1b1 |
514 | =head2 compress_readings |
515 | |
516 | Where possible in the graph, compresses plain sequences of readings into a |
517 | single reading. The sequences must consist of readings with no |
518 | relationships to other readings, with only a single witness path between |
519 | them and no other witness paths from either that would skip the other. The |
520 | readings must also not be marked as nonsense or bad grammar. |
521 | |
522 | WARNING: This operation cannot be undone. |
523 | |
524 | =cut |
525 | |
526 | sub compress_readings { |
527 | my $self = shift; |
528 | # Anywhere in the graph that there is a reading that joins only to a single |
529 | # successor, and neither of these have any relationships, just join the two |
530 | # readings. |
6771a1b1 |
531 | foreach my $rdg ( sort { $a->rank <=> $b->rank } $self->readings ) { |
428bcf0b |
532 | # Now look for readings that can be joined to their successors. |
a445ce40 |
533 | next unless $rdg->is_combinable; |
6771a1b1 |
534 | my %seen; |
535 | while( $self->sequence->successors( $rdg ) == 1 ) { |
536 | my( $next ) = $self->reading( $self->sequence->successors( $rdg ) ); |
537 | throw( "Infinite loop" ) if $seen{$next->id}; |
538 | $seen{$next->id} = 1; |
539 | last if $self->sequence->predecessors( $next ) > 1; |
a445ce40 |
540 | last unless $next->is_combinable; |
6771a1b1 |
541 | say "Joining readings $rdg and $next"; |
542 | $self->merge_readings( $rdg, $next, 1 ); |
543 | } |
544 | } |
545 | # Make sure we haven't screwed anything up |
546 | foreach my $wit ( $self->tradition->witnesses ) { |
547 | my $pathtext = $self->path_text( $wit->sigil ); |
548 | my $origtext = join( ' ', @{$wit->text} ); |
549 | throw( "Text differs for witness " . $wit->sigil ) |
550 | unless $pathtext eq $origtext; |
551 | if( $wit->is_layered ) { |
552 | $pathtext = $self->path_text( $wit->sigil.$self->ac_label ); |
553 | $origtext = join( ' ', @{$wit->layertext} ); |
554 | throw( "Ante-corr text differs for witness " . $wit->sigil ) |
555 | unless $pathtext eq $origtext; |
556 | } |
557 | } |
558 | |
559 | $self->relations->rebuild_equivalence(); |
560 | $self->calculate_ranks(); |
561 | } |
3265b0ce |
562 | |
3a2ebbf4 |
563 | # Helper function for manipulating the graph. |
564 | sub _stringify_args { |
4e483aa5 |
565 | my( $self, $first, $second, @args ) = @_; |
3a2ebbf4 |
566 | $first = $first->id |
567 | if ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
568 | $second = $second->id |
569 | if ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
4e483aa5 |
570 | return( $first, $second, @args ); |
3a2ebbf4 |
571 | } |
df6d9812 |
572 | |
4e5a7b2c |
573 | # Helper function for manipulating the graph. |
574 | sub _objectify_args { |
575 | my( $self, $first, $second, $arg ) = @_; |
576 | $first = $self->reading( $first ) |
577 | unless ref( $first ) eq 'Text::Tradition::Collation::Reading'; |
578 | $second = $self->reading( $second ) |
579 | unless ref( $second ) eq 'Text::Tradition::Collation::Reading'; |
580 | return( $first, $second, $arg ); |
581 | } |
f97ef19e |
582 | |
583 | =head2 duplicate_reading( $reading, @witlist ) |
584 | |
585 | Split the given reading into two, so that the new reading is in the path for |
ef73c20a |
586 | the witnesses given in @witlist. If the result is that certain non-colocated |
587 | relationships (e.g. transpositions) are no longer valid, these will be removed. |
588 | Returns the newly-created reading. |
f97ef19e |
589 | |
590 | =begin testing |
591 | |
68e48c06 |
592 | use Test::More::UTF8; |
f97ef19e |
593 | use Text::Tradition; |
68e48c06 |
594 | use TryCatch; |
f97ef19e |
595 | |
596 | my $st = Text::Tradition->new( 'input' => 'Self', 'file' => 't/data/collatecorr.xml' ); |
597 | is( ref( $st ), 'Text::Tradition', "Got a tradition from test file" ); |
598 | ok( $st->has_witness('Ba96'), "Tradition has the affected witness" ); |
599 | |
600 | my $sc = $st->collation; |
601 | my $numr = 17; |
602 | ok( $sc->reading('n131'), "Tradition has the affected reading" ); |
603 | is( scalar( $sc->readings ), $numr, "There are $numr readings in the graph" ); |
604 | is( $sc->end->rank, 14, "There are fourteen ranks in the graph" ); |
605 | |
606 | # Detach the erroneously collated reading |
2dcb5d11 |
607 | my( $newr, @del_rdgs ) = $sc->duplicate_reading( 'n131', 'Ba96' ); |
ef73c20a |
608 | ok( $newr, "New reading was created" ); |
f97ef19e |
609 | ok( $sc->reading('n131_0'), "Detached the bad collation with a new reading" ); |
610 | is( scalar( $sc->readings ), $numr + 1, "A reading was added to the graph" ); |
611 | is( $sc->end->rank, 10, "There are now only ten ranks in the graph" ); |
3c234eb6 |
612 | my $csucc = $sc->common_successor( 'n131', 'n131_0' ); |
613 | is( $csucc->id, 'n136', "Found correct common successor to duped reading" ); |
f97ef19e |
614 | |
615 | # Check that the bad transposition is gone |
2dcb5d11 |
616 | is( scalar @del_rdgs, 1, "Deleted reading was returned by API call" ); |
f97ef19e |
617 | is( $sc->get_relationship( 'n130', 'n135' ), undef, "Bad transposition relationship is gone" ); |
618 | |
e19635f8 |
619 | # The collation should not be fixed |
620 | my @pairs = $sc->identical_readings(); |
621 | is( scalar @pairs, 0, "Not re-collated yet" ); |
f97ef19e |
622 | # Fix the collation |
3c234eb6 |
623 | ok( $sc->merge_readings( 'n124', 'n131_0' ), "Collated the readings correctly" ); |
e19635f8 |
624 | @pairs = $sc->identical_readings( start => 'n124', end => $csucc->id ); |
3c234eb6 |
625 | is( scalar @pairs, 3, "Found three more identical readings" ); |
e19635f8 |
626 | is( $sc->end->rank, 11, "The ranks shifted appropriately" ); |
3c234eb6 |
627 | $sc->flatten_ranks(); |
f97ef19e |
628 | is( scalar( $sc->readings ), $numr - 3, "Now we are collated correctly" ); |
629 | |
68e48c06 |
630 | # Check that we can't "duplicate" a reading with no wits or with all wits |
631 | try { |
632 | my( $badr, @del_rdgs ) = $sc->duplicate_reading( 'n124' ); |
633 | ok( 0, "Reading duplication without witnesses throws an error" ); |
634 | } catch( Text::Tradition::Error $e ) { |
635 | like( $e->message, qr/Must specify one or more witnesses/, |
636 | "Reading duplication without witnesses throws the expected error" ); |
637 | } catch { |
638 | ok( 0, "Reading duplication without witnesses threw the wrong error" ); |
639 | } |
640 | |
641 | try { |
642 | my( $badr, @del_rdgs ) = $sc->duplicate_reading( 'n124', 'Ba96', 'Mü11475' ); |
643 | ok( 0, "Reading duplication with all witnesses throws an error" ); |
644 | } catch( Text::Tradition::Error $e ) { |
645 | like( $e->message, qr/Cannot join all witnesses/, |
646 | "Reading duplication with all witnesses throws the expected error" ); |
647 | } catch { |
648 | ok( 0, "Reading duplication with all witnesses threw the wrong error" ); |
649 | } |
650 | |
58568d5c |
651 | try { |
652 | $sc->calculate_ranks(); |
653 | ok( 1, "Graph is still evidently whole" ); |
654 | } catch( Text::Tradition::Error $e ) { |
655 | ok( 0, "Caught a rank exception: " . $e->message ); |
656 | } |
657 | |
f97ef19e |
658 | =end testing |
659 | |
660 | =cut |
661 | |
662 | sub duplicate_reading { |
663 | my( $self, $r, @wits ) = @_; |
68e48c06 |
664 | # Check that we are not doing anything unwise. |
665 | throw( "Must specify one or more witnesses for the duplicated reading" ) |
666 | unless @wits; |
f97ef19e |
667 | unless( ref( $r ) eq 'Text::Tradition::Collation::Reading' ) { |
668 | $r = $self->reading( $r ); |
669 | } |
670 | throw( "Cannot duplicate a meta-reading" ) |
671 | if $r->is_meta; |
68e48c06 |
672 | throw( "Cannot join all witnesses to the new reading" ) |
47cd4d16 |
673 | if scalar( @wits ) == scalar( $r->witnesses ); |
68e48c06 |
674 | |
f97ef19e |
675 | # Get all the reading attributes and duplicate them. |
676 | my $rmeta = Text::Tradition::Collation::Reading->meta; |
677 | my %args; |
678 | foreach my $attr( $rmeta->get_all_attributes ) { |
679 | next if $attr->name =~ /^_/; |
680 | my $acc = $attr->get_read_method; |
681 | if( !$acc && $attr->has_applied_traits ) { |
682 | my $tr = $attr->applied_traits; |
683 | if( $tr->[0] =~ /::(Array|Hash)$/ ) { |
684 | my $which = $1; |
685 | my %methods = reverse %{$attr->handles}; |
686 | $acc = $methods{elements}; |
687 | $args{$attr->name} = $which eq 'Array' |
688 | ? [ $r->$acc ] : { $r->$acc }; |
689 | } |
690 | } else { |
691 | $args{$attr->name} = $r->$acc if $acc; |
692 | } |
693 | } |
694 | # By definition the new reading will no longer be common. |
695 | $args{is_common} = 0; |
696 | # The new reading also needs its own ID. |
697 | $args{id} = $self->_generate_dup_id( $r->id ); |
698 | |
699 | # Try to make the new reading. |
700 | my $newr = $self->add_reading( \%args ); |
701 | # The old reading is also no longer common. |
702 | $r->is_common( 0 ); |
703 | |
704 | # For each of the witnesses, dissociate from the old reading and |
705 | # associate with the new. |
706 | foreach my $wit ( @wits ) { |
707 | my $prior = $self->prior_reading( $r, $wit ); |
708 | my $next = $self->next_reading( $r, $wit ); |
709 | $self->del_path( $prior, $r, $wit ); |
710 | $self->add_path( $prior, $newr, $wit ); |
711 | $self->del_path( $r, $next, $wit ); |
712 | $self->add_path( $newr, $next, $wit ); |
713 | } |
714 | |
3c234eb6 |
715 | # If the graph is ranked, we need to look for relationships that are now |
716 | # invalid (i.e. 'non-colocation' types that might now be colocated) and |
717 | # remove them. If not, we can skip it. |
f97ef19e |
718 | my $succ; |
3c234eb6 |
719 | my %rrk; |
2dcb5d11 |
720 | my @deleted_relations; |
f97ef19e |
721 | if( $self->end->has_rank ) { |
3c234eb6 |
722 | # Find the point where we can stop checking |
f97ef19e |
723 | $succ = $self->common_successor( $r, $newr ); |
3c234eb6 |
724 | |
725 | # Hash the existing ranks |
f97ef19e |
726 | foreach my $rdg ( $self->readings ) { |
727 | $rrk{$rdg->id} = $rdg->rank; |
728 | } |
3c234eb6 |
729 | # Calculate the new ranks |
730 | $self->calculate_ranks(); |
f97ef19e |
731 | |
3c234eb6 |
732 | # Check for invalid non-colocated relationships among changed-rank readings |
733 | # from where the ranks start changing up to $succ |
f97ef19e |
734 | my $lastrank = $succ->rank; |
735 | foreach my $rdg ( $self->readings ) { |
736 | next if $rdg->rank > $lastrank; |
737 | next if $rdg->rank == $rrk{$rdg->id}; |
738 | my @noncolo = $rdg->related_readings( sub { !$_[0]->colocated } ); |
739 | next unless @noncolo; |
740 | foreach my $nc ( @noncolo ) { |
2dcb5d11 |
741 | unless( $self->relations->verify_or_delete( $rdg, $nc ) ) { |
f6a1d5f0 |
742 | push( @deleted_relations, [ $rdg->id, $nc->id ] ); |
2dcb5d11 |
743 | } |
f97ef19e |
744 | } |
745 | } |
ef73c20a |
746 | } |
2dcb5d11 |
747 | return ( $newr, @deleted_relations ); |
f97ef19e |
748 | } |
749 | |
750 | sub _generate_dup_id { |
751 | my( $self, $rid ) = @_; |
752 | my $newid; |
753 | my $i = 0; |
754 | while( !$newid ) { |
755 | $newid = $rid."_$i"; |
756 | if( $self->has_reading( $newid ) ) { |
757 | $newid = ''; |
758 | $i++; |
759 | } |
760 | } |
761 | return $newid; |
762 | } |
763 | |
3a2ebbf4 |
764 | ### Path logic |
765 | |
766 | sub add_path { |
767 | my $self = shift; |
768 | |
769 | # We only need the IDs for adding paths to the graph, not the reading |
770 | # objects themselves. |
cecbe56d |
771 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
3a2ebbf4 |
772 | |
c1915ab9 |
773 | $self->_graphcalc_done(0); |
3a2ebbf4 |
774 | # Connect the readings |
359944f7 |
775 | unless( $self->sequence->has_edge( $source, $target ) ) { |
776 | $self->sequence->add_edge( $source, $target ); |
777 | $self->relations->add_equivalence_edge( $source, $target ); |
778 | } |
3a2ebbf4 |
779 | # Note the witness in question |
780 | $self->sequence->set_edge_attribute( $source, $target, $wit, 1 ); |
359944f7 |
781 | } |
b15511bf |
782 | |
3a2ebbf4 |
783 | sub del_path { |
784 | my $self = shift; |
49d4f2ac |
785 | my @args; |
786 | if( ref( $_[0] ) eq 'ARRAY' ) { |
787 | my $e = shift @_; |
788 | @args = ( @$e, @_ ); |
789 | } else { |
790 | @args = @_; |
791 | } |
3a2ebbf4 |
792 | |
f97ef19e |
793 | # We only need the IDs for removing paths from the graph, not the reading |
3a2ebbf4 |
794 | # objects themselves. |
49d4f2ac |
795 | my( $source, $target, $wit ) = $self->_stringify_args( @args ); |
3a2ebbf4 |
796 | |
c1915ab9 |
797 | $self->_graphcalc_done(0); |
3a2ebbf4 |
798 | if( $self->sequence->has_edge_attribute( $source, $target, $wit ) ) { |
49d4f2ac |
799 | $self->sequence->delete_edge_attribute( $source, $target, $wit ); |
3a2ebbf4 |
800 | } |
30897024 |
801 | unless( $self->sequence->has_edge_attributes( $source, $target ) ) { |
3a2ebbf4 |
802 | $self->sequence->delete_edge( $source, $target ); |
359944f7 |
803 | $self->relations->delete_equivalence_edge( $source, $target ); |
3a2ebbf4 |
804 | } |
784877d9 |
805 | } |
806 | |
3a2ebbf4 |
807 | |
15d2d3df |
808 | # Extra graph-alike utility |
809 | sub has_path { |
3a2ebbf4 |
810 | my $self = shift; |
811 | my( $source, $target, $wit ) = $self->_stringify_args( @_ ); |
812 | return undef unless $self->sequence->has_edge( $source, $target ); |
813 | return $self->sequence->has_edge_attribute( $source, $target, $wit ); |
b15511bf |
814 | } |
815 | |
4e5a7b2c |
816 | =head2 clear_witness( @sigil_list ) |
3a2ebbf4 |
817 | |
4e5a7b2c |
818 | Clear the given witnesses out of the collation entirely, removing references |
819 | to them in paths, and removing readings that belong only to them. Should only |
820 | be called via $tradition->del_witness. |
3a2ebbf4 |
821 | |
822 | =cut |
823 | |
4e5a7b2c |
824 | sub clear_witness { |
825 | my( $self, @sigils ) = @_; |
826 | |
c1915ab9 |
827 | $self->_graphcalc_done(0); |
4e5a7b2c |
828 | # Clear the witness(es) out of the paths |
829 | foreach my $e ( $self->paths ) { |
830 | foreach my $sig ( @sigils ) { |
831 | $self->del_path( $e, $sig ); |
832 | } |
833 | } |
834 | |
835 | # Clear out the newly unused readings |
836 | foreach my $r ( $self->readings ) { |
837 | unless( $self->reading_witnesses( $r ) ) { |
838 | $self->del_reading( $r ); |
839 | } |
840 | } |
841 | } |
3a2ebbf4 |
842 | |
843 | sub add_relationship { |
844 | my $self = shift; |
22222af9 |
845 | my( $source, $target, $opts ) = $self->_stringify_args( @_ ); |
414cc046 |
846 | my( @vectors ) = $self->relations->add_relationship( $source, $target, $opts ); |
864ee4bf |
847 | foreach my $v ( @vectors ) { |
848 | next unless $self->get_relationship( $v )->colocated; |
849 | if( $self->reading( $v->[0] )->has_rank && $self->reading( $v->[1] )->has_rank |
850 | && $self->reading( $v->[0] )->rank ne $self->reading( $v->[1] )->rank ) { |
851 | $self->_graphcalc_done(0); |
852 | $self->_clear_cache; |
853 | last; |
854 | } |
855 | } |
63778331 |
856 | return @vectors; |
22222af9 |
857 | } |
ef9d481f |
858 | |
ca6e6095 |
859 | around qw/ get_relationship del_relationship / => sub { |
860 | my $orig = shift; |
861 | my $self = shift; |
862 | my @args = @_; |
863 | if( @args == 1 && ref( $args[0] ) eq 'ARRAY' ) { |
864 | @args = @{$_[0]}; |
865 | } |
e19635f8 |
866 | my @stringargs = $self->_stringify_args( @args ); |
867 | $self->$orig( @stringargs ); |
ca6e6095 |
868 | }; |
869 | |
22222af9 |
870 | =head2 reading_witnesses( $reading ) |
910a0a6d |
871 | |
22222af9 |
872 | Return a list of sigils corresponding to the witnesses in which the reading appears. |
3265b0ce |
873 | |
22222af9 |
874 | =cut |
1d310495 |
875 | |
1d310495 |
876 | sub reading_witnesses { |
877 | my( $self, $reading ) = @_; |
878 | # We need only check either the incoming or the outgoing edges; I have |
96dc90ec |
879 | # arbitrarily chosen "incoming". Thus, special-case the start node. |
880 | if( $reading eq $self->start ) { |
bed6ce83 |
881 | return map { $_->sigil } grep { $_->is_collated } $self->tradition->witnesses; |
96dc90ec |
882 | } |
1d310495 |
883 | my %all_witnesses; |
884 | foreach my $e ( $self->sequence->edges_to( $reading ) ) { |
885 | my $wits = $self->sequence->get_edge_attributes( @$e ); |
886 | @all_witnesses{ keys %$wits } = 1; |
887 | } |
c12bb878 |
888 | my $acstr = $self->ac_label; |
889 | foreach my $acwit ( grep { $_ =~ s/^(.*)\Q$acstr\E$/$1/ } keys %all_witnesses ) { |
890 | delete $all_witnesses{$acwit.$acstr} if exists $all_witnesses{$acwit}; |
891 | } |
1d310495 |
892 | return keys %all_witnesses; |
910a0a6d |
893 | } |
894 | |
4e5a7b2c |
895 | =head1 OUTPUT METHODS |
8e1394aa |
896 | |
0ecb975c |
897 | =head2 as_svg( \%options ) |
8e1394aa |
898 | |
0068967c |
899 | Returns an SVG string that represents the graph, via as_dot and graphviz. |
bfcbcecb |
900 | See as_dot for a list of options. Must have GraphViz (dot) installed to run. |
8e1394aa |
901 | |
902 | =cut |
903 | |
904 | sub as_svg { |
0ecb975c |
905 | my( $self, $opts ) = @_; |
bfcbcecb |
906 | throw( "Need GraphViz installed to output SVG" ) |
907 | unless File::Which::which( 'dot' ); |
e247aad1 |
908 | my $want_subgraph = exists $opts->{'from'} || exists $opts->{'to'}; |
1ff82d4f |
909 | $self->calculate_ranks() |
910 | unless( $self->_graphcalc_done || $opts->{'nocalc'} || !$self->linear ); |
be3af600 |
911 | my @cmd = qw/dot -Tsvg/; |
912 | my( $svg, $err ); |
913 | my $dotfile = File::Temp->new(); |
914 | ## USE FOR DEBUGGING |
915 | # $dotfile->unlink_on_destroy(0); |
916 | binmode $dotfile, ':utf8'; |
917 | print $dotfile $self->as_dot( $opts ); |
918 | push( @cmd, $dotfile->filename ); |
919 | run( \@cmd, ">", binary(), \$svg ); |
920 | $svg = decode_utf8( $svg ); |
921 | return $svg; |
8e1394aa |
922 | } |
923 | |
b22576c6 |
924 | |
0ecb975c |
925 | =head2 as_dot( \%options ) |
b22576c6 |
926 | |
0ecb975c |
927 | Returns a string that is the collation graph expressed in dot |
928 | (i.e. GraphViz) format. Options include: |
b22576c6 |
929 | |
0ecb975c |
930 | =over 4 |
b22576c6 |
931 | |
0ecb975c |
932 | =item * from |
b22576c6 |
933 | |
0ecb975c |
934 | =item * to |
df6d9812 |
935 | |
0ecb975c |
936 | =item * color_common |
937 | |
938 | =back |
df6d9812 |
939 | |
940 | =cut |
941 | |
942 | sub as_dot { |
0ecb975c |
943 | my( $self, $opts ) = @_; |
944 | my $startrank = $opts->{'from'} if $opts; |
945 | my $endrank = $opts->{'to'} if $opts; |
946 | my $color_common = $opts->{'color_common'} if $opts; |
b365fbae |
947 | my $STRAIGHTENHACK = !$startrank && !$endrank && $self->end->rank |
948 | && $self->end->rank > 100; |
6648ee3d |
949 | $STRAIGHTENHACK = 1 if $opts->{'straight'}; # even for subgraphs or small graphs |
b365fbae |
950 | |
b22576c6 |
951 | # Check the arguments |
952 | if( $startrank ) { |
953 | return if $endrank && $startrank > $endrank; |
954 | return if $startrank > $self->end->rank; |
955 | } |
956 | if( defined $endrank ) { |
957 | return if $endrank < 0; |
f1b3b33a |
958 | $endrank = undef if $endrank == $self->end->rank; |
b22576c6 |
959 | } |
960 | |
67da8d6c |
961 | my $graph_name = $self->tradition->name; |
962 | $graph_name =~ s/[^\w\s]//g; |
963 | $graph_name = join( '_', split( /\s+/, $graph_name ) ); |
f13b5582 |
964 | |
965 | my %graph_attrs = ( |
966 | 'rankdir' => 'LR', |
967 | 'bgcolor' => 'none', |
968 | ); |
969 | my %node_attrs = ( |
b8990398 |
970 | 'fontsize' => 14, |
f13b5582 |
971 | 'fillcolor' => 'white', |
972 | 'style' => 'filled', |
973 | 'shape' => 'ellipse' |
974 | ); |
975 | my %edge_attrs = ( |
976 | 'arrowhead' => 'open', |
977 | 'color' => '#000000', |
978 | 'fontcolor' => '#000000', |
979 | ); |
980 | |
67da8d6c |
981 | my $dot = sprintf( "digraph %s {\n", $graph_name ); |
f13b5582 |
982 | $dot .= "\tgraph " . _dot_attr_string( \%graph_attrs ) . ";\n"; |
983 | $dot .= "\tnode " . _dot_attr_string( \%node_attrs ) . ";\n"; |
df6d9812 |
984 | |
b22576c6 |
985 | # Output substitute start/end readings if necessary |
986 | if( $startrank ) { |
43c94341 |
987 | $dot .= "\t\"__SUBSTART__\" [ label=\"...\",id=\"__START__\" ];\n"; |
b22576c6 |
988 | } |
989 | if( $endrank ) { |
43c94341 |
990 | $dot .= "\t\"__SUBEND__\" [ label=\"...\",id=\"__END__\" ];\n"; |
b22576c6 |
991 | } |
b365fbae |
992 | if( $STRAIGHTENHACK ) { |
993 | ## HACK part 1 |
43c94341 |
994 | my $startlabel = $startrank ? '__SUBSTART__' : '__START__'; |
995 | $dot .= "\tsubgraph { rank=same \"$startlabel\" \"#SILENT#\" }\n"; |
b365fbae |
996 | $dot .= "\t\"#SILENT#\" [ shape=diamond,color=white,penwidth=0,label=\"\" ];" |
997 | } |
b22576c6 |
998 | my %used; # Keep track of the readings that actually appear in the graph |
30ddc24c |
999 | # Sort the readings by rank if we have ranks; this speeds layout. |
1000 | my @all_readings = $self->end->has_rank |
1001 | ? sort { $a->rank <=> $b->rank } $self->readings |
1002 | : $self->readings; |
4633f9e4 |
1003 | # TODO Refrain from outputting lacuna nodes - just grey out the edges. |
30ddc24c |
1004 | foreach my $reading ( @all_readings ) { |
b22576c6 |
1005 | # Only output readings within our rank range. |
1006 | next if $startrank && $reading->rank < $startrank; |
1007 | next if $endrank && $reading->rank > $endrank; |
1008 | $used{$reading->id} = 1; |
910a0a6d |
1009 | # Need not output nodes without separate labels |
3a2ebbf4 |
1010 | next if $reading->id eq $reading->text; |
d4b75f44 |
1011 | my $rattrs; |
30f0df34 |
1012 | my $label = $reading->text; |
629e27b0 |
1013 | $label .= '-' if $reading->join_next; |
1014 | $label = "-$label" if $reading->join_prior; |
8f9cab7b |
1015 | $label =~ s/\"/\\\"/g; |
d4b75f44 |
1016 | $rattrs->{'label'} = $label; |
10e4b1ac |
1017 | $rattrs->{'id'} = $reading->id; |
0ecb975c |
1018 | $rattrs->{'fillcolor'} = '#b3f36d' if $reading->is_common && $color_common; |
d4b75f44 |
1019 | $dot .= sprintf( "\t\"%s\" %s;\n", $reading->id, _dot_attr_string( $rattrs ) ); |
df6d9812 |
1020 | } |
3a2ebbf4 |
1021 | |
30ddc24c |
1022 | # Add the real edges. Need to weight one edge per rank jump, in a |
1023 | # continuous line. |
b365fbae |
1024 | # my $weighted = $self->_add_edge_weights; |
b22576c6 |
1025 | my @edges = $self->paths; |
3bdec618 |
1026 | my( %substart, %subend ); |
b22576c6 |
1027 | foreach my $edge ( @edges ) { |
1028 | # Do we need to output this edge? |
508fd430 |
1029 | if( $used{$edge->[0]} && $used{$edge->[1]} ) { |
57560672 |
1030 | my $label = $self->_path_display_label( $opts, |
1031 | $self->path_witnesses( $edge ) ); |
f13b5582 |
1032 | my $variables = { %edge_attrs, 'label' => $label }; |
30ddc24c |
1033 | |
b22576c6 |
1034 | # Account for the rank gap if necessary |
30ddc24c |
1035 | my $rank0 = $self->reading( $edge->[0] )->rank |
1036 | if $self->reading( $edge->[0] )->has_rank; |
1037 | my $rank1 = $self->reading( $edge->[1] )->rank |
1038 | if $self->reading( $edge->[1] )->has_rank; |
1039 | if( defined $rank0 && defined $rank1 && $rank1 - $rank0 > 1 ) { |
1040 | $variables->{'minlen'} = $rank1 - $rank0; |
1041 | } |
1042 | |
1043 | # Add the calculated edge weights |
b365fbae |
1044 | # if( exists $weighted->{$edge->[0]} |
e247aad1 |
1045 | # && $weighted->{$edge->[0]} eq $edge->[1] ) { |
1046 | # # $variables->{'color'} = 'red'; |
1047 | # $variables->{'weight'} = 3.0; |
1048 | # } |
30ddc24c |
1049 | |
508fd430 |
1050 | # EXPERIMENTAL: make edge width reflect no. of witnesses |
1051 | my $extrawidth = scalar( $self->path_witnesses( $edge ) ) * 0.2; |
1052 | $variables->{'penwidth'} = $extrawidth + 0.8; # gives 1 for a single wit |
1053 | |
f13b5582 |
1054 | my $varopts = _dot_attr_string( $variables ); |
1055 | $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n", |
1056 | $edge->[0], $edge->[1], $varopts ); |
3bdec618 |
1057 | } elsif( $used{$edge->[0]} ) { |
96ba0418 |
1058 | $subend{$edge->[0]} = $edge->[1]; |
3bdec618 |
1059 | } elsif( $used{$edge->[1]} ) { |
96ba0418 |
1060 | $substart{$edge->[1]} = $edge->[0]; |
b22576c6 |
1061 | } |
df6d9812 |
1062 | } |
bed6ce83 |
1063 | |
1064 | # If we are asked to, add relationship links |
1065 | if( exists $opts->{show_relations} ) { |
1066 | my $filter = $opts->{show_relations}; # can be 'transposition' or 'all' |
1067 | if( $filter eq 'transposition' ) { |
1068 | $filter =~ qr/^transposition$/; |
1069 | } |
9e54e11b |
1070 | my %typecolors; |
1071 | my @types = sort( map { $_->name } $self->relations->types ); |
1072 | if( exists $opts->{graphcolors} ) { |
1073 | foreach my $tdx ( 0 .. $#types ) { |
1074 | $typecolors{$types[$tdx]} = $opts->{graphcolors}->[$tdx]; |
1075 | } |
1076 | } else { |
1077 | map { $typecolors{$_} = '#FFA14F' } @types; |
1078 | } |
bed6ce83 |
1079 | foreach my $redge ( $self->relationships ) { |
1080 | if( $used{$redge->[0]} && $used{$redge->[1]} ) { |
9e54e11b |
1081 | my $rel = $self->get_relationship( $redge ); |
1082 | next unless $filter eq 'all' || $rel->type =~ /$filter/; |
1083 | my $variables = { |
1084 | arrowhead => 'none', |
1085 | color => $typecolors{$rel->type}, |
1086 | constraint => 'false', |
1087 | penwidth => '3', |
1088 | }; |
1089 | unless( exists $opts->{graphcolors} ) { |
1090 | $variables->{label} = uc( substr( $rel->type, 0, 4 ) ), |
bed6ce83 |
1091 | } |
9e54e11b |
1092 | $dot .= sprintf( "\t\"%s\" -> \"%s\" %s;\n", |
1093 | $redge->[0], $redge->[1], _dot_attr_string( $variables ) ); |
bed6ce83 |
1094 | } |
1095 | } |
1096 | } |
1097 | |
3bdec618 |
1098 | # Add substitute start and end edges if necessary |
1099 | foreach my $node ( keys %substart ) { |
57560672 |
1100 | my $witstr = $self->_path_display_label( $opts, |
1101 | $self->path_witnesses( $substart{$node}, $node ) ); |
f13b5582 |
1102 | my $variables = { %edge_attrs, 'label' => $witstr }; |
96ba0418 |
1103 | my $nrdg = $self->reading( $node ); |
1104 | if( $nrdg->has_rank && $nrdg->rank > $startrank ) { |
1105 | # Substart is actually one lower than $startrank |
1106 | $variables->{'minlen'} = $nrdg->rank - ( $startrank - 1 ); |
1107 | } |
f13b5582 |
1108 | my $varopts = _dot_attr_string( $variables ); |
96ba0418 |
1109 | $dot .= "\t\"__SUBSTART__\" -> \"$node\" $varopts;\n"; |
3bdec618 |
1110 | } |
1111 | foreach my $node ( keys %subend ) { |
57560672 |
1112 | my $witstr = $self->_path_display_label( $opts, |
1113 | $self->path_witnesses( $node, $subend{$node} ) ); |
f13b5582 |
1114 | my $variables = { %edge_attrs, 'label' => $witstr }; |
1115 | my $varopts = _dot_attr_string( $variables ); |
96ba0418 |
1116 | $dot .= "\t\"$node\" -> \"__SUBEND__\" $varopts;\n"; |
3bdec618 |
1117 | } |
b365fbae |
1118 | # HACK part 2 |
1119 | if( $STRAIGHTENHACK ) { |
43c94341 |
1120 | my $endlabel = $endrank ? '__SUBEND__' : '__END__'; |
1121 | $dot .= "\t\"$endlabel\" -> \"#SILENT#\" [ color=white,penwidth=0 ];\n"; |
b365fbae |
1122 | } |
30ddc24c |
1123 | |
df6d9812 |
1124 | $dot .= "}\n"; |
1125 | return $dot; |
1126 | } |
1127 | |
f13b5582 |
1128 | sub _dot_attr_string { |
1129 | my( $hash ) = @_; |
1130 | my @attrs; |
1131 | foreach my $k ( sort keys %$hash ) { |
1132 | my $v = $hash->{$k}; |
1133 | push( @attrs, $k.'="'.$v.'"' ); |
1134 | } |
1135 | return( '[ ' . join( ', ', @attrs ) . ' ]' ); |
1136 | } |
1137 | |
30ddc24c |
1138 | sub _add_edge_weights { |
1139 | my $self = shift; |
1140 | # Walk the graph from START to END, choosing the successor node with |
1141 | # the largest number of witness paths each time. |
1142 | my $weighted = {}; |
1143 | my $curr = $self->start->id; |
008fc8a6 |
1144 | my $ranked = $self->end->has_rank; |
30ddc24c |
1145 | while( $curr ne $self->end->id ) { |
008fc8a6 |
1146 | my $rank = $ranked ? $self->reading( $curr )->rank : 0; |
30ddc24c |
1147 | my @succ = sort { $self->path_witnesses( $curr, $a ) |
1148 | <=> $self->path_witnesses( $curr, $b ) } |
1149 | $self->sequence->successors( $curr ); |
1150 | my $next = pop @succ; |
008fc8a6 |
1151 | my $nextrank = $ranked ? $self->reading( $next )->rank : 0; |
30ddc24c |
1152 | # Try to avoid lacunae in the weighted path. |
008fc8a6 |
1153 | while( @succ && |
1154 | ( $self->reading( $next )->is_lacuna || |
1155 | $nextrank - $rank > 1 ) ){ |
30ddc24c |
1156 | $next = pop @succ; |
1157 | } |
1158 | $weighted->{$curr} = $next; |
1159 | $curr = $next; |
1160 | } |
1161 | return $weighted; |
1162 | } |
1163 | |
027d819c |
1164 | =head2 path_witnesses( $edge ) |
1165 | |
1166 | Returns the list of sigils whose witnesses are associated with the given edge. |
1167 | The edge can be passed as either an array or an arrayref of ( $source, $target ). |
1168 | |
1169 | =cut |
1170 | |
3a2ebbf4 |
1171 | sub path_witnesses { |
1172 | my( $self, @edge ) = @_; |
1173 | # If edge is an arrayref, cope. |
1174 | if( @edge == 1 && ref( $edge[0] ) eq 'ARRAY' ) { |
1175 | my $e = shift @edge; |
1176 | @edge = @$e; |
1177 | } |
1178 | my @wits = keys %{$self->sequence->get_edge_attributes( @edge )}; |
508fd430 |
1179 | return @wits; |
3a2ebbf4 |
1180 | } |
1181 | |
7f9f05e8 |
1182 | # Helper function. Make a display label for the given witnesses, showing a.c. |
1183 | # witnesses only where the main witness is not also in the list. |
027d819c |
1184 | sub _path_display_label { |
508fd430 |
1185 | my $self = shift; |
57560672 |
1186 | my $opts = shift; |
7f9f05e8 |
1187 | my %wits; |
1188 | map { $wits{$_} = 1 } @_; |
1189 | |
1190 | # If an a.c. wit is listed, remove it if the main wit is also listed. |
1191 | # Otherwise keep it for explicit listing. |
1192 | my $aclabel = $self->ac_label; |
1193 | my @disp_ac; |
1194 | foreach my $w ( sort keys %wits ) { |
1195 | if( $w =~ /^(.*)\Q$aclabel\E$/ ) { |
1196 | if( exists $wits{$1} ) { |
1197 | delete $wits{$w}; |
1198 | } else { |
1199 | push( @disp_ac, $w ); |
1200 | } |
1201 | } |
1202 | } |
1203 | |
57560672 |
1204 | if( $opts->{'explicit_wits'} ) { |
7f9f05e8 |
1205 | return join( ', ', sort keys %wits ); |
57560672 |
1206 | } else { |
1207 | # See if we are in a majority situation. |
1208 | my $maj = scalar( $self->tradition->witnesses ) * 0.6; |
1209 | $maj = $maj > 5 ? $maj : 5; |
1210 | if( scalar keys %wits > $maj ) { |
1211 | unshift( @disp_ac, 'majority' ); |
1212 | return join( ', ', @disp_ac ); |
1213 | } else { |
1214 | return join( ', ', sort keys %wits ); |
1215 | } |
8f9cab7b |
1216 | } |
1217 | } |
1dd07bda |
1218 | |
bf6e338d |
1219 | =head2 readings_at_rank( $rank ) |
1dd07bda |
1220 | |
bf6e338d |
1221 | Returns a list of readings at a given rank, taken from the alignment table. |
1dd07bda |
1222 | |
1223 | =cut |
1224 | |
bf6e338d |
1225 | sub readings_at_rank { |
1dd07bda |
1226 | my( $self, $rank ) = @_; |
bf6e338d |
1227 | my $table = $self->alignment_table; |
1228 | # Table rank is real rank - 1. |
1229 | my @elements = map { $_->{'tokens'}->[$rank-1] } @{$table->{'alignment'}}; |
1230 | my %readings; |
1231 | foreach my $e ( @elements ) { |
1232 | next unless ref( $e ) eq 'HASH'; |
1233 | next unless exists $e->{'t'}; |
1234 | $readings{$e->{'t'}->id} = $e->{'t'}; |
1235 | } |
1236 | return values %readings; |
1dd07bda |
1237 | } |
8f9cab7b |
1238 | |
4e5a7b2c |
1239 | =head2 as_graphml |
8e1394aa |
1240 | |
4e5a7b2c |
1241 | Returns a GraphML representation of the collation. The GraphML will contain |
1242 | two graphs. The first expresses the attributes of the readings and the witness |
1243 | paths that link them; the second expresses the relationships that link the |
1244 | readings. This is the native transfer format for a tradition. |
8e1394aa |
1245 | |
56eefa04 |
1246 | =begin testing |
1247 | |
1248 | use Text::Tradition; |
951ddfe8 |
1249 | use TryCatch; |
56eefa04 |
1250 | |
1251 | my $READINGS = 311; |
1252 | my $PATHS = 361; |
1253 | |
1254 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
1255 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
1256 | 'name' => 'test0', |
1257 | 'file' => $datafile, |
1258 | 'linear' => 1 ); |
1259 | |
1260 | ok( $tradition, "Got a tradition object" ); |
1261 | is( scalar $tradition->witnesses, 13, "Found all witnesses" ); |
1262 | ok( $tradition->collation, "Tradition has a collation" ); |
1263 | |
1264 | my $c = $tradition->collation; |
1265 | is( scalar $c->readings, $READINGS, "Collation has all readings" ); |
1266 | is( scalar $c->paths, $PATHS, "Collation has all paths" ); |
1267 | is( scalar $c->relationships, 0, "Collation has all relationships" ); |
1268 | |
1269 | # Add a few relationships |
1270 | $c->add_relationship( 'w123', 'w125', { 'type' => 'collated' } ); |
1271 | $c->add_relationship( 'w193', 'w196', { 'type' => 'collated' } ); |
b71e7ea8 |
1272 | $c->add_relationship( 'w257', 'w262', { 'type' => 'transposition', |
1273 | 'is_significant' => 'yes' } ); |
56eefa04 |
1274 | |
1275 | # Now write it to GraphML and parse it again. |
1276 | |
1277 | my $graphml = $c->as_graphml; |
1278 | my $st = Text::Tradition->new( 'input' => 'Self', 'string' => $graphml ); |
1279 | is( scalar $st->collation->readings, $READINGS, "Reparsed collation has all readings" ); |
1280 | is( scalar $st->collation->paths, $PATHS, "Reparsed collation has all paths" ); |
1281 | is( scalar $st->collation->relationships, 3, "Reparsed collation has new relationships" ); |
b71e7ea8 |
1282 | my $sigrel = $st->collation->get_relationship( 'w257', 'w262' ); |
1283 | is( $sigrel->is_significant, 'yes', "Ternary attribute value was restored" ); |
56eefa04 |
1284 | |
9fef629b |
1285 | # Now add a stemma, write to GraphML, and look at the output. |
951ddfe8 |
1286 | SKIP: { |
37bf09f4 |
1287 | skip "Analysis module not present", 3 unless $tradition->can( 'add_stemma' ); |
951ddfe8 |
1288 | my $stemma = $tradition->add_stemma( 'dotfile' => 't/data/florilegium.dot' ); |
1289 | is( ref( $stemma ), 'Text::Tradition::Stemma', "Parsed dotfile into stemma" ); |
1290 | is( $tradition->stemmata, 1, "Tradition now has the stemma" ); |
1291 | $graphml = $c->as_graphml; |
1292 | like( $graphml, qr/digraph/, "Digraph declaration exists in GraphML" ); |
1293 | } |
2a812726 |
1294 | |
56eefa04 |
1295 | =end testing |
1296 | |
8e1394aa |
1297 | =cut |
1298 | |
a445ce40 |
1299 | ## TODO MOVE this to Tradition.pm and modularize it better |
8e1394aa |
1300 | sub as_graphml { |
a30ca502 |
1301 | my( $self, $options ) = @_; |
3d14b48e |
1302 | $self->calculate_ranks unless $self->_graphcalc_done; |
1303 | |
a30ca502 |
1304 | my $start = $options->{'from'} |
1305 | ? $self->reading( $options->{'from'} ) : $self->start; |
1306 | my $end = $options->{'to'} |
1307 | ? $self->reading( $options->{'to'} ) : $self->end; |
1308 | if( $start->has_rank && $end->has_rank && $end->rank < $start->rank ) { |
1309 | throw( 'Start node must be before end node' ); |
1310 | } |
1311 | # The readings need to be ranked for this to work. |
1312 | $start = $self->start unless $start->has_rank; |
1313 | $end = $self->end unless $end->has_rank; |
414cc046 |
1314 | my $rankoffset = 0; |
1315 | unless( $start eq $self->start ) { |
1316 | $rankoffset = $start->rank - 1; |
1317 | } |
a30ca502 |
1318 | my %use_readings; |
1319 | |
8e1394aa |
1320 | # Some namespaces |
1321 | my $graphml_ns = 'http://graphml.graphdrawing.org/xmlns'; |
1322 | my $xsi_ns = 'http://www.w3.org/2001/XMLSchema-instance'; |
1323 | my $graphml_schema = 'http://graphml.graphdrawing.org/xmlns ' . |
910a0a6d |
1324 | 'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd'; |
8e1394aa |
1325 | |
1326 | # Create the document and root node |
428bcf0b |
1327 | require XML::LibXML; |
8e1394aa |
1328 | my $graphml = XML::LibXML->createDocument( "1.0", "UTF-8" ); |
1329 | my $root = $graphml->createElementNS( $graphml_ns, 'graphml' ); |
1330 | $graphml->setDocumentElement( $root ); |
1331 | $root->setNamespace( $xsi_ns, 'xsi', 0 ); |
1332 | $root->setAttributeNS( $xsi_ns, 'schemaLocation', $graphml_schema ); |
bbd064a9 |
1333 | |
1334 | # List of attribute types to save on our objects and their corresponding |
1335 | # GraphML types |
1336 | my %save_types = ( |
1337 | 'Str' => 'string', |
1338 | 'Int' => 'int', |
1339 | 'Bool' => 'boolean', |
10e4b1ac |
1340 | 'ReadingID' => 'string', |
bbd064a9 |
1341 | 'RelationshipType' => 'string', |
1342 | 'RelationshipScope' => 'string', |
b71e7ea8 |
1343 | 'Ternary' => 'string', |
bbd064a9 |
1344 | ); |
1345 | |
bbd064a9 |
1346 | # Add the data keys for the graph. Include an extra key 'version' for the |
1347 | # GraphML output version. |
e309421a |
1348 | my %graph_data_keys; |
1349 | my $gdi = 0; |
bbd064a9 |
1350 | my %graph_attributes = ( 'version' => 'string' ); |
1351 | # Graph attributes include those of Tradition and those of Collation. |
1352 | my %gattr_from; |
f97ef19e |
1353 | # TODO Use meta introspection method from duplicate_reading to do this |
1354 | # instead of naming custom keys. |
bbd064a9 |
1355 | my $tmeta = $self->tradition->meta; |
1356 | my $cmeta = $self->meta; |
1357 | map { $gattr_from{$_->name} = 'Tradition' } $tmeta->get_all_attributes; |
1358 | map { $gattr_from{$_->name} = 'Collation' } $cmeta->get_all_attributes; |
1359 | foreach my $attr ( ( $tmeta->get_all_attributes, $cmeta->get_all_attributes ) ) { |
1360 | next if $attr->name =~ /^_/; |
bbd064a9 |
1361 | next unless $save_types{$attr->type_constraint->name}; |
1362 | $graph_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
1363 | } |
9fef629b |
1364 | # Extra custom keys for complex objects that should be saved in some form. |
1365 | # The subroutine should return a string, or undef/empty. |
951ddfe8 |
1366 | if( $tmeta->has_method('stemmata') ) { |
1367 | $graph_attributes{'stemmata'} = sub { |
1368 | my @stemstrs; |
1369 | map { push( @stemstrs, $_->editable( {linesep => ''} ) ) } |
1370 | $self->tradition->stemmata; |
1371 | join( "\n", @stemstrs ); |
1372 | }; |
1373 | } |
1374 | |
8943ff68 |
1375 | if( $tmeta->has_method('user') ) { |
1376 | $graph_attributes{'user'} = sub { |
1377 | $self->tradition->user ? $self->tradition->user->id : undef |
1378 | }; |
1379 | } |
bbd064a9 |
1380 | |
1381 | foreach my $datum ( sort keys %graph_attributes ) { |
e309421a |
1382 | $graph_data_keys{$datum} = 'dg'.$gdi++; |
1383 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
9fef629b |
1384 | my $dtype = ref( $graph_attributes{$datum} ) ? 'string' |
1385 | : $graph_attributes{$datum}; |
e309421a |
1386 | $key->setAttribute( 'attr.name', $datum ); |
9fef629b |
1387 | $key->setAttribute( 'attr.type', $dtype ); |
e309421a |
1388 | $key->setAttribute( 'for', 'graph' ); |
1389 | $key->setAttribute( 'id', $graph_data_keys{$datum} ); |
1390 | } |
f6066bac |
1391 | |
bbd064a9 |
1392 | # Add the data keys for reading nodes |
1393 | my %reading_attributes; |
1394 | my $rmeta = Text::Tradition::Collation::Reading->meta; |
1395 | foreach my $attr( $rmeta->get_all_attributes ) { |
1396 | next if $attr->name =~ /^_/; |
bbd064a9 |
1397 | next unless $save_types{$attr->type_constraint->name}; |
1398 | $reading_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
1399 | } |
a445ce40 |
1400 | if( $self->start->does('Text::Tradition::Morphology' ) ) { |
1401 | # Extra custom key for the reading morphology |
1402 | $reading_attributes{'lexemes'} = 'string'; |
1403 | } |
7cd9f181 |
1404 | |
ef9d481f |
1405 | my %node_data_keys; |
1406 | my $ndi = 0; |
bbd064a9 |
1407 | foreach my $datum ( sort keys %reading_attributes ) { |
910a0a6d |
1408 | $node_data_keys{$datum} = 'dn'.$ndi++; |
1409 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
1410 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
1411 | $key->setAttribute( 'attr.type', $reading_attributes{$datum} ); |
910a0a6d |
1412 | $key->setAttribute( 'for', 'node' ); |
1413 | $key->setAttribute( 'id', $node_data_keys{$datum} ); |
8e1394aa |
1414 | } |
1415 | |
bbd064a9 |
1416 | # Add the data keys for edges, that is, paths and relationships. Path |
1417 | # data does not come from a Moose class so is here manually. |
ef9d481f |
1418 | my $edi = 0; |
1419 | my %edge_data_keys; |
bbd064a9 |
1420 | my %edge_attributes = ( |
3a2ebbf4 |
1421 | witness => 'string', # ID/label for a path |
3a2ebbf4 |
1422 | extra => 'boolean', # Path key |
3a2ebbf4 |
1423 | ); |
bbd064a9 |
1424 | my @path_attributes = keys %edge_attributes; # track our manual additions |
1425 | my $pmeta = Text::Tradition::Collation::Relationship->meta; |
1426 | foreach my $attr( $pmeta->get_all_attributes ) { |
1427 | next if $attr->name =~ /^_/; |
bbd064a9 |
1428 | next unless $save_types{$attr->type_constraint->name}; |
1429 | $edge_attributes{$attr->name} = $save_types{$attr->type_constraint->name}; |
1430 | } |
1431 | foreach my $datum ( sort keys %edge_attributes ) { |
3a2ebbf4 |
1432 | $edge_data_keys{$datum} = 'de'.$edi++; |
910a0a6d |
1433 | my $key = $root->addNewChild( $graphml_ns, 'key' ); |
3a2ebbf4 |
1434 | $key->setAttribute( 'attr.name', $datum ); |
bbd064a9 |
1435 | $key->setAttribute( 'attr.type', $edge_attributes{$datum} ); |
910a0a6d |
1436 | $key->setAttribute( 'for', 'edge' ); |
3a2ebbf4 |
1437 | $key->setAttribute( 'id', $edge_data_keys{$datum} ); |
8e1394aa |
1438 | } |
3a2ebbf4 |
1439 | |
cc31ebaa |
1440 | # Add the collation graph itself. First, sanitize the name to a valid XML ID. |
1441 | my $xmlidname = $self->tradition->name; |
1442 | $xmlidname =~ s/(?!$xml10_namechar_rx)./_/g; |
1443 | if( $xmlidname !~ /^$xml10_namestartchar_rx/ ) { |
1444 | $xmlidname = '_'.$xmlidname; |
1445 | } |
2c669bca |
1446 | my $sgraph = $root->addNewChild( $graphml_ns, 'graph' ); |
1447 | $sgraph->setAttribute( 'edgedefault', 'directed' ); |
cc31ebaa |
1448 | $sgraph->setAttribute( 'id', $xmlidname ); |
2c669bca |
1449 | $sgraph->setAttribute( 'parse.edgeids', 'canonical' ); |
cc31ebaa |
1450 | $sgraph->setAttribute( 'parse.edges', 0 ); # fill in later |
2c669bca |
1451 | $sgraph->setAttribute( 'parse.nodeids', 'canonical' ); |
cc31ebaa |
1452 | $sgraph->setAttribute( 'parse.nodes', 0 ); # fill in later |
2c669bca |
1453 | $sgraph->setAttribute( 'parse.order', 'nodesfirst' ); |
22222af9 |
1454 | |
2a812726 |
1455 | # Tradition/collation attribute data |
bbd064a9 |
1456 | foreach my $datum ( keys %graph_attributes ) { |
1457 | my $value; |
1458 | if( $datum eq 'version' ) { |
2a812726 |
1459 | $value = '3.2'; |
9fef629b |
1460 | } elsif( ref( $graph_attributes{$datum} ) ) { |
1461 | my $sub = $graph_attributes{$datum}; |
1462 | $value = &$sub(); |
bbd064a9 |
1463 | } elsif( $gattr_from{$datum} eq 'Tradition' ) { |
1464 | $value = $self->tradition->$datum; |
1465 | } else { |
1466 | $value = $self->$datum; |
1467 | } |
2c669bca |
1468 | _add_graphml_data( $sgraph, $graph_data_keys{$datum}, $value ); |
e309421a |
1469 | } |
8e1394aa |
1470 | |
1471 | my $node_ctr = 0; |
1472 | my %node_hash; |
22222af9 |
1473 | # Add our readings to the graph |
3a2ebbf4 |
1474 | foreach my $n ( sort { $a->id cmp $b->id } $self->readings ) { |
a30ca502 |
1475 | next if $n->has_rank && $n ne $self->start && $n ne $self->end && |
1476 | ( $n->rank < $start->rank || $n->rank > $end->rank ); |
1477 | $use_readings{$n->id} = 1; |
2c669bca |
1478 | # Add to the main graph |
1479 | my $node_el = $sgraph->addNewChild( $graphml_ns, 'node' ); |
910a0a6d |
1480 | my $node_xmlid = 'n' . $node_ctr++; |
3a2ebbf4 |
1481 | $node_hash{ $n->id } = $node_xmlid; |
910a0a6d |
1482 | $node_el->setAttribute( 'id', $node_xmlid ); |
bbd064a9 |
1483 | foreach my $d ( keys %reading_attributes ) { |
255875b8 |
1484 | my $nval = $n->$d; |
7cd9f181 |
1485 | # Custom serialization |
1486 | if( $d eq 'lexemes' ) { |
1487 | # If nval is a true value, we have lexemes so we need to |
1488 | # serialize them. Otherwise set nval to undef so that the |
1489 | # key is excluded from this reading. |
1490 | $nval = $nval ? $n->_serialize_lexemes : undef; |
18c64d55 |
1491 | } elsif( $d eq 'normal_form' && $n->normal_form eq $n->text ) { |
1492 | $nval = undef; |
7cd9f181 |
1493 | } |
cc31ebaa |
1494 | if( $rankoffset && $d eq 'rank' && $n ne $self->start ) { |
414cc046 |
1495 | # Adjust the ranks within the subgraph. |
cc31ebaa |
1496 | $nval = $n eq $self->end ? $end->rank - $rankoffset + 1 |
1497 | : $nval - $rankoffset; |
414cc046 |
1498 | } |
255875b8 |
1499 | _add_graphml_data( $node_el, $node_data_keys{$d}, $nval ) |
1500 | if defined $nval; |
1501 | } |
b15511bf |
1502 | } |
1503 | |
2c669bca |
1504 | # Add the path edges to the sequence graph |
df6d9812 |
1505 | my $edge_ctr = 0; |
3a2ebbf4 |
1506 | foreach my $e ( sort { $a->[0] cmp $b->[0] } $self->sequence->edges() ) { |
1507 | # We add an edge in the graphml for every witness in $e. |
a30ca502 |
1508 | next unless( $use_readings{$e->[0]} || $use_readings{$e->[1]} ); |
1509 | my @edge_wits = sort $self->path_witnesses( $e ); |
cc31ebaa |
1510 | $e->[0] = $self->start->id unless $use_readings{$e->[0]}; |
1511 | $e->[1] = $self->end->id unless $use_readings{$e->[1]}; |
1512 | # Skip any path from start to end; that witness is not in the subgraph. |
1513 | next if ( $e->[0] eq $self->start->id && $e->[1] eq $self->end->id ); |
a30ca502 |
1514 | foreach my $wit ( @edge_wits ) { |
3a2ebbf4 |
1515 | my( $id, $from, $to ) = ( 'e'.$edge_ctr++, |
1516 | $node_hash{ $e->[0] }, |
1517 | $node_hash{ $e->[1] } ); |
2c669bca |
1518 | my $edge_el = $sgraph->addNewChild( $graphml_ns, 'edge' ); |
3a2ebbf4 |
1519 | $edge_el->setAttribute( 'source', $from ); |
1520 | $edge_el->setAttribute( 'target', $to ); |
1521 | $edge_el->setAttribute( 'id', $id ); |
3a2ebbf4 |
1522 | |
1523 | # It's a witness path, so add the witness |
1524 | my $base = $wit; |
1525 | my $key = $edge_data_keys{'witness'}; |
1526 | # Is this an ante-corr witness? |
1527 | my $aclabel = $self->ac_label; |
1528 | if( $wit =~ /^(.*)\Q$aclabel\E$/ ) { |
1529 | # Keep the base witness |
1530 | $base = $1; |
1531 | # ...and record that this is an 'extra' reading path |
1532 | _add_graphml_data( $edge_el, $edge_data_keys{'extra'}, $aclabel ); |
1533 | } |
1534 | _add_graphml_data( $edge_el, $edge_data_keys{'witness'}, $base ); |
1535 | } |
1536 | } |
1537 | |
cc31ebaa |
1538 | # Report the actual number of nodes and edges that went in |
1539 | $sgraph->setAttribute( 'parse.edges', $edge_ctr ); |
1540 | $sgraph->setAttribute( 'parse.nodes', $node_ctr ); |
1541 | |
22222af9 |
1542 | # Add the relationship graph to the XML |
bbd064a9 |
1543 | map { delete $edge_data_keys{$_} } @path_attributes; |
826d8773 |
1544 | $self->relations->_as_graphml( $graphml_ns, $root, \%node_hash, |
1545 | $node_data_keys{'id'}, \%edge_data_keys ); |
8e1394aa |
1546 | |
94c00c71 |
1547 | # Save and return the thing |
1548 | my $result = decode_utf8( $graphml->toString(1) ); |
94c00c71 |
1549 | return $result; |
df6d9812 |
1550 | } |
1551 | |
b15511bf |
1552 | sub _add_graphml_data { |
1553 | my( $el, $key, $value ) = @_; |
b15511bf |
1554 | return unless defined $value; |
c9bf3dbf |
1555 | my $data_el = $el->addNewChild( $el->namespaceURI, 'data' ); |
b15511bf |
1556 | $data_el->setAttribute( 'key', $key ); |
1557 | $data_el->appendText( $value ); |
8e1394aa |
1558 | } |
1559 | |
4e5a7b2c |
1560 | =head2 as_csv |
910a0a6d |
1561 | |
1562 | Returns a CSV alignment table representation of the collation graph, one |
2c669bca |
1563 | row per witness (or witness uncorrected.) |
910a0a6d |
1564 | |
ce5966fb |
1565 | =head2 as_tsv |
1566 | |
1567 | Returns a tab-separated alignment table representation of the collation graph, |
1568 | one row per witness (or witness uncorrected.) |
1569 | |
16203db5 |
1570 | =begin testing |
1571 | |
1572 | use Text::Tradition; |
34ca808b |
1573 | use Text::CSV; |
16203db5 |
1574 | |
1575 | my $READINGS = 311; |
1576 | my $PATHS = 361; |
34ca808b |
1577 | my $WITS = 13; |
1578 | my $WITAC = 4; |
16203db5 |
1579 | |
1580 | my $datafile = 't/data/florilegium_tei_ps.xml'; |
1581 | my $tradition = Text::Tradition->new( 'input' => 'TEI', |
1582 | 'name' => 'test0', |
1583 | 'file' => $datafile, |
1584 | 'linear' => 1 ); |
1585 | |
1586 | my $c = $tradition->collation; |
1587 | # Export the thing to CSV |
1588 | my $csvstr = $c->as_csv(); |
34ca808b |
1589 | # Count the columns |
1590 | my $csv = Text::CSV->new({ sep_char => ',', binary => 1 }); |
1591 | my @lines = split(/\n/, $csvstr ); |
1592 | ok( $csv->parse( $lines[0] ), "Successfully parsed first line of CSV" ); |
1593 | is( scalar( $csv->fields ), $WITS + $WITAC, "CSV has correct number of witness columns" ); |
cbc8e08f |
1594 | my @q_ac = grep { $_ eq 'Q'.$c->ac_label } $csv->fields; |
1595 | ok( @q_ac, "Found a layered witness" ); |
1596 | |
16203db5 |
1597 | my $t2 = Text::Tradition->new( input => 'Tabular', |
1598 | name => 'test2', |
1599 | string => $csvstr, |
1600 | sep_char => ',' ); |
1601 | is( scalar $t2->collation->readings, $READINGS, "Reparsed CSV collation has all readings" ); |
1602 | is( scalar $t2->collation->paths, $PATHS, "Reparsed CSV collation has all paths" ); |
1603 | |
1604 | # Now do it with TSV |
1605 | my $tsvstr = $c->as_tsv(); |
1606 | my $t3 = Text::Tradition->new( input => 'Tabular', |
1607 | name => 'test3', |
1608 | string => $tsvstr, |
1609 | sep_char => "\t" ); |
1610 | is( scalar $t3->collation->readings, $READINGS, "Reparsed TSV collation has all readings" ); |
1611 | is( scalar $t3->collation->paths, $PATHS, "Reparsed TSV collation has all paths" ); |
1612 | |
4e64b669 |
1613 | my $table = $c->alignment_table; |
34ca808b |
1614 | my $noaccsv = $c->as_csv({ noac => 1 }); |
1615 | my @noaclines = split(/\n/, $noaccsv ); |
1616 | ok( $csv->parse( $noaclines[0] ), "Successfully parsed first line of no-ac CSV" ); |
1617 | is( scalar( $csv->fields ), $WITS, "CSV has correct number of witness columns" ); |
4e64b669 |
1618 | is( $c->alignment_table, $table, "Request for CSV did not alter the alignment table" ); |
34ca808b |
1619 | |
cbc8e08f |
1620 | my $safecsv = $c->as_csv({ safe_ac => 1}); |
1621 | my @safelines = split(/\n/, $safecsv ); |
1622 | ok( $csv->parse( $safelines[0] ), "Successfully parsed first line of safe CSV" ); |
1623 | is( scalar( $csv->fields ), $WITS + $WITAC, "CSV has correct number of witness columns" ); |
1624 | @q_ac = grep { $_ eq 'Q__L' } $csv->fields; |
1625 | ok( @q_ac, "Found a sanitized layered witness" ); |
1626 | is( $c->alignment_table, $table, "Request for CSV did not alter the alignment table" ); |
16203db5 |
1627 | |
1628 | =end testing |
1629 | |
910a0a6d |
1630 | =cut |
1631 | |
ce5966fb |
1632 | sub _tabular { |
34ca808b |
1633 | my( $self, $opts ) = @_; |
1634 | my $table = $self->alignment_table( $opts ); |
16203db5 |
1635 | my $csv_options = { binary => 1, quote_null => 0 }; |
34ca808b |
1636 | $csv_options->{'sep_char'} = $opts->{fieldsep}; |
1637 | if( $opts->{fieldsep} eq "\t" ) { |
16203db5 |
1638 | # If it is really tab separated, nothing is an escape char. |
1639 | $csv_options->{'quote_char'} = undef; |
1640 | $csv_options->{'escape_char'} = ''; |
1641 | } |
1642 | my $csv = Text::CSV->new( $csv_options ); |
910a0a6d |
1643 | my @result; |
2c669bca |
1644 | # Make the header row |
1645 | $csv->combine( map { $_->{'witness'} } @{$table->{'alignment'}} ); |
43800a64 |
1646 | push( @result, $csv->string ); |
2c669bca |
1647 | # Make the rest of the rows |
1648 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
566f4595 |
1649 | my @rowobjs = map { $_->{'tokens'}->[$idx] } @{$table->{'alignment'}}; |
1dd07bda |
1650 | my @row = map { $_ ? $_->{'t'}->text : $_ } @rowobjs; |
2c669bca |
1651 | $csv->combine( @row ); |
43800a64 |
1652 | push( @result, $csv->string ); |
910a0a6d |
1653 | } |
3a2ebbf4 |
1654 | return join( "\n", @result ); |
910a0a6d |
1655 | } |
1656 | |
ce5966fb |
1657 | sub as_csv { |
1658 | my $self = shift; |
34ca808b |
1659 | my $opts = shift || {}; |
1660 | $opts->{fieldsep} = ','; |
1661 | return $self->_tabular( $opts ); |
ce5966fb |
1662 | } |
1663 | |
1664 | sub as_tsv { |
1665 | my $self = shift; |
34ca808b |
1666 | my $opts = shift || {}; |
1667 | $opts->{fieldsep} = "\t"; |
1668 | return $self->_tabular( $opts ); |
ce5966fb |
1669 | } |
1670 | |
248276a2 |
1671 | =head2 alignment_table |
2c669bca |
1672 | |
566f4595 |
1673 | Return a reference to an alignment table, in a slightly enhanced CollateX |
1674 | format which looks like this: |
1675 | |
1676 | $table = { alignment => [ { witness => "SIGIL", |
4e5a7b2c |
1677 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1678 | { witness => "SIG2", |
4e5a7b2c |
1679 | tokens => [ { t => "TEXT" }, ... ] }, |
566f4595 |
1680 | ... ], |
1681 | length => TEXTLEN }; |
1682 | |
2c669bca |
1683 | =cut |
9f3ba6f7 |
1684 | |
1dd07bda |
1685 | sub alignment_table { |
34ca808b |
1686 | my( $self, $opts ) = @_; |
4e64b669 |
1687 | if( $self->has_cached_table ) { |
cbc8e08f |
1688 | return $self->cached_table |
1689 | unless $opts->{noac} || $opts->{safe_ac}; |
4e64b669 |
1690 | } |
1dd07bda |
1691 | |
0ecb975c |
1692 | # Make sure we can do this |
1693 | throw( "Need a linear graph in order to make an alignment table" ) |
1694 | unless $self->linear; |
b39e7cb5 |
1695 | $self->calculate_ranks() |
1696 | unless $self->_graphcalc_done && $self->end->has_rank; |
1697 | |
2c669bca |
1698 | my $table = { 'alignment' => [], 'length' => $self->end->rank - 1 }; |
3a2ebbf4 |
1699 | my @all_pos = ( 1 .. $self->end->rank - 1 ); |
68454b71 |
1700 | foreach my $wit ( sort { $a->sigil cmp $b->sigil } $self->tradition->witnesses ) { |
6771a1b1 |
1701 | # say STDERR "Making witness row(s) for " . $wit->sigil; |
1f7aa795 |
1702 | my @wit_path = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
1dd07bda |
1703 | my @row = _make_witness_row( \@wit_path, \@all_pos ); |
bed6ce83 |
1704 | my $witobj = { 'witness' => $wit->sigil, 'tokens' => \@row }; |
1705 | $witobj->{'identifier'} = $wit->identifier if $wit->identifier; |
1706 | push( @{$table->{'alignment'}}, $witobj ); |
34ca808b |
1707 | if( $wit->is_layered && !$opts->{noac} ) { |
1f7aa795 |
1708 | my @wit_ac_path = $self->reading_sequence( $self->start, $self->end, |
861c3e27 |
1709 | $wit->sigil.$self->ac_label ); |
1dd07bda |
1710 | my @ac_row = _make_witness_row( \@wit_ac_path, \@all_pos ); |
cbc8e08f |
1711 | my $witlabel = $opts->{safe_ac} |
1712 | ? $wit->sigil . '__L' : $wit->sigil.$self->ac_label; |
1713 | my $witacobj = { 'witness' => $witlabel, |
bed6ce83 |
1714 | 'tokens' => \@ac_row }; |
1715 | $witacobj->{'identifier'} = $wit->identifier if $wit->identifier; |
1716 | push( @{$table->{'alignment'}}, $witacobj ); |
910a0a6d |
1717 | } |
1718 | } |
cbc8e08f |
1719 | unless( $opts->{noac} || $opts->{safe_ac} ) { |
4e64b669 |
1720 | $self->cached_table( $table ); |
1721 | } |
1dd07bda |
1722 | return $table; |
910a0a6d |
1723 | } |
1724 | |
1725 | sub _make_witness_row { |
1dd07bda |
1726 | my( $path, $positions ) = @_; |
910a0a6d |
1727 | my %char_hash; |
1728 | map { $char_hash{$_} = undef } @$positions; |
2c669bca |
1729 | my $debug = 0; |
910a0a6d |
1730 | foreach my $rdg ( @$path ) { |
6771a1b1 |
1731 | say STDERR "rank " . $rdg->rank if $debug; |
1732 | # say STDERR "No rank for " . $rdg->id unless defined $rdg->rank; |
1dd07bda |
1733 | $char_hash{$rdg->rank} = { 't' => $rdg }; |
910a0a6d |
1734 | } |
1735 | my @row = map { $char_hash{$_} } @$positions; |
eca16057 |
1736 | # Fill in lacuna markers for undef spots in the row |
1737 | my $last_el = shift @row; |
1738 | my @filled_row = ( $last_el ); |
1739 | foreach my $el ( @row ) { |
0e476982 |
1740 | # If we are using node reference, make the lacuna node appear many times |
1741 | # in the table. If not, use the lacuna tag. |
1dd07bda |
1742 | if( $last_el && $last_el->{'t'}->is_lacuna && !defined $el ) { |
1743 | $el = $last_el; |
eca16057 |
1744 | } |
1745 | push( @filled_row, $el ); |
1746 | $last_el = $el; |
1747 | } |
1748 | return @filled_row; |
910a0a6d |
1749 | } |
1750 | |
248276a2 |
1751 | |
4e5a7b2c |
1752 | =head1 NAVIGATION METHODS |
910a0a6d |
1753 | |
4e5a7b2c |
1754 | =head2 reading_sequence( $first, $last, $sigil, $backup ) |
e2902068 |
1755 | |
1756 | Returns the ordered list of readings, starting with $first and ending |
4e5a7b2c |
1757 | with $last, for the witness given in $sigil. If a $backup sigil is |
1758 | specified (e.g. when walking a layered witness), it will be used wherever |
1759 | no $sigil path exists. If there is a base text reading, that will be |
1760 | used wherever no path exists for $sigil or $backup. |
e2902068 |
1761 | |
1762 | =cut |
1763 | |
910a0a6d |
1764 | # TODO Think about returning some lazy-eval iterator. |
b0b4421a |
1765 | # TODO Get rid of backup; we should know from what witness is whether we need it. |
910a0a6d |
1766 | |
e2902068 |
1767 | sub reading_sequence { |
861c3e27 |
1768 | my( $self, $start, $end, $witness ) = @_; |
e2902068 |
1769 | |
930ff666 |
1770 | $witness = $self->baselabel unless $witness; |
e2902068 |
1771 | my @readings = ( $start ); |
1772 | my %seen; |
1773 | my $n = $start; |
3a2ebbf4 |
1774 | while( $n && $n->id ne $end->id ) { |
1775 | if( exists( $seen{$n->id} ) ) { |
63778331 |
1776 | throw( "Detected loop for $witness at " . $n->id ); |
910a0a6d |
1777 | } |
3a2ebbf4 |
1778 | $seen{$n->id} = 1; |
910a0a6d |
1779 | |
861c3e27 |
1780 | my $next = $self->next_reading( $n, $witness ); |
44771cf2 |
1781 | unless( $next ) { |
63778331 |
1782 | throw( "Did not find any path for $witness from reading " . $n->id ); |
44771cf2 |
1783 | } |
910a0a6d |
1784 | push( @readings, $next ); |
1785 | $n = $next; |
e2902068 |
1786 | } |
1787 | # Check that the last reading is our end reading. |
1788 | my $last = $readings[$#readings]; |
63778331 |
1789 | throw( "Last reading found from " . $start->text . |
1790 | " for witness $witness is not the end!" ) # TODO do we get this far? |
3a2ebbf4 |
1791 | unless $last->id eq $end->id; |
e2902068 |
1792 | |
1793 | return @readings; |
1794 | } |
1795 | |
4e5a7b2c |
1796 | =head2 next_reading( $reading, $sigil ); |
8e1394aa |
1797 | |
4a8828f0 |
1798 | Returns the reading that follows the given reading along the given witness |
930ff666 |
1799 | path. |
8e1394aa |
1800 | |
1801 | =cut |
1802 | |
4a8828f0 |
1803 | sub next_reading { |
e2902068 |
1804 | # Return the successor via the corresponding path. |
8e1394aa |
1805 | my $self = shift; |
3a2ebbf4 |
1806 | my $answer = $self->_find_linked_reading( 'next', @_ ); |
2c669bca |
1807 | return undef unless $answer; |
3a2ebbf4 |
1808 | return $self->reading( $answer ); |
8e1394aa |
1809 | } |
1810 | |
4e5a7b2c |
1811 | =head2 prior_reading( $reading, $sigil ) |
8e1394aa |
1812 | |
4a8828f0 |
1813 | Returns the reading that precedes the given reading along the given witness |
930ff666 |
1814 | path. |
8e1394aa |
1815 | |
1816 | =cut |
1817 | |
4a8828f0 |
1818 | sub prior_reading { |
e2902068 |
1819 | # Return the predecessor via the corresponding path. |
8e1394aa |
1820 | my $self = shift; |
3a2ebbf4 |
1821 | my $answer = $self->_find_linked_reading( 'prior', @_ ); |
1822 | return $self->reading( $answer ); |
8e1394aa |
1823 | } |
1824 | |
4a8828f0 |
1825 | sub _find_linked_reading { |
861c3e27 |
1826 | my( $self, $direction, $node, $path ) = @_; |
1827 | |
1828 | # Get a backup if we are dealing with a layered witness |
1829 | my $alt_path; |
1830 | my $aclabel = $self->ac_label; |
1831 | if( $path && $path =~ /^(.*)\Q$aclabel\E$/ ) { |
1832 | $alt_path = $1; |
1833 | } |
1834 | |
e2902068 |
1835 | my @linked_paths = $direction eq 'next' |
3a2ebbf4 |
1836 | ? $self->sequence->edges_from( $node ) |
1837 | : $self->sequence->edges_to( $node ); |
e2902068 |
1838 | return undef unless scalar( @linked_paths ); |
8e1394aa |
1839 | |
e2902068 |
1840 | # We have to find the linked path that contains all of the |
1841 | # witnesses supplied in $path. |
1842 | my( @path_wits, @alt_path_wits ); |
4e5a7b2c |
1843 | @path_wits = sort( $self->_witnesses_of_label( $path ) ) if $path; |
1844 | @alt_path_wits = sort( $self->_witnesses_of_label( $alt_path ) ) if $alt_path; |
e2902068 |
1845 | my $base_le; |
1846 | my $alt_le; |
1847 | foreach my $le ( @linked_paths ) { |
3a2ebbf4 |
1848 | if( $self->sequence->has_edge_attribute( @$le, $self->baselabel ) ) { |
910a0a6d |
1849 | $base_le = $le; |
910a0a6d |
1850 | } |
508fd430 |
1851 | my @le_wits = sort $self->path_witnesses( $le ); |
3a2ebbf4 |
1852 | if( _is_within( \@path_wits, \@le_wits ) ) { |
1853 | # This is the right path. |
1854 | return $direction eq 'next' ? $le->[1] : $le->[0]; |
1855 | } elsif( _is_within( \@alt_path_wits, \@le_wits ) ) { |
1856 | $alt_le = $le; |
1857 | } |
8e1394aa |
1858 | } |
e2902068 |
1859 | # Got this far? Return the alternate path if it exists. |
3a2ebbf4 |
1860 | return $direction eq 'next' ? $alt_le->[1] : $alt_le->[0] |
910a0a6d |
1861 | if $alt_le; |
e2902068 |
1862 | |
1863 | # Got this far? Return the base path if it exists. |
3a2ebbf4 |
1864 | return $direction eq 'next' ? $base_le->[1] : $base_le->[0] |
910a0a6d |
1865 | if $base_le; |
e2902068 |
1866 | |
1867 | # Got this far? We have no appropriate path. |
2c669bca |
1868 | warn "Could not find $direction node from " . $node->id |
910a0a6d |
1869 | . " along path $path"; |
8e1394aa |
1870 | return undef; |
1871 | } |
1872 | |
4a8828f0 |
1873 | # Some set logic. |
1874 | sub _is_within { |
1875 | my( $set1, $set2 ) = @_; |
7854e12e |
1876 | my $ret = @$set1; # will be 0, i.e. false, if set1 is empty |
4a8828f0 |
1877 | foreach my $el ( @$set1 ) { |
910a0a6d |
1878 | $ret = 0 unless grep { /^\Q$el\E$/ } @$set2; |
4a8828f0 |
1879 | } |
1880 | return $ret; |
1881 | } |
1882 | |
4e5a7b2c |
1883 | # Return the string that joins together a list of witnesses for |
1884 | # display on a single path. |
1885 | sub _witnesses_of_label { |
1886 | my( $self, $label ) = @_; |
1887 | my $regex = $self->wit_list_separator; |
1888 | my @answer = split( /\Q$regex\E/, $label ); |
1889 | return @answer; |
b0b4421a |
1890 | } |
1891 | |
d4b75f44 |
1892 | =head2 common_readings |
1893 | |
1894 | Returns the list of common readings in the graph (i.e. those readings that are |
1895 | shared by all non-lacunose witnesses.) |
1896 | |
1897 | =cut |
1898 | |
1899 | sub common_readings { |
1900 | my $self = shift; |
1901 | my @common = grep { $_->is_common } $self->readings; |
1902 | return @common; |
1903 | } |
1904 | |
fae52efd |
1905 | =head2 path_text( $sigil, [, $start, $end ] ) |
b0b4421a |
1906 | |
1907 | Returns the text of a witness (plus its backup, if we are using a layer) |
1908 | as stored in the collation. The text is returned as a string, where the |
1909 | individual readings are joined with spaces and the meta-readings (e.g. |
1910 | lacunae) are omitted. Optional specification of $start and $end allows |
1911 | the generation of a subset of the witness text. |
4e5a7b2c |
1912 | |
b0b4421a |
1913 | =cut |
1914 | |
1915 | sub path_text { |
861c3e27 |
1916 | my( $self, $wit, $start, $end ) = @_; |
b0b4421a |
1917 | $start = $self->start unless $start; |
1918 | $end = $self->end unless $end; |
861c3e27 |
1919 | my @path = grep { !$_->is_meta } $self->reading_sequence( $start, $end, $wit ); |
629e27b0 |
1920 | my $pathtext = ''; |
1921 | my $last; |
1922 | foreach my $r ( @path ) { |
6ad2ce78 |
1923 | unless ( $r->join_prior || !$last || $last->join_next ) { |
1924 | $pathtext .= ' '; |
1925 | } |
1926 | $pathtext .= $r->text; |
629e27b0 |
1927 | $last = $r; |
1928 | } |
1929 | return $pathtext; |
b0b4421a |
1930 | } |
4e5a7b2c |
1931 | |
1932 | =head1 INITIALIZATION METHODS |
1933 | |
1934 | These are mostly for use by parsers. |
1935 | |
1936 | =head2 make_witness_path( $witness ) |
1937 | |
1938 | Link the array of readings contained in $witness->path (and in |
1939 | $witness->uncorrected_path if it exists) into collation paths. |
1940 | Clear out the arrays when finished. |
de51424a |
1941 | |
4e5a7b2c |
1942 | =head2 make_witness_paths |
1943 | |
1944 | Call make_witness_path for all witnesses in the tradition. |
1945 | |
1946 | =cut |
930ff666 |
1947 | |
7e450e44 |
1948 | # For use when a collation is constructed from a base text and an apparatus. |
1949 | # We have the sequences of readings and just need to add path edges. |
1f7aa795 |
1950 | # When we are done, clear out the witness path attributes, as they are no |
1951 | # longer needed. |
1952 | # TODO Find a way to replace the witness path attributes with encapsulated functions? |
e2902068 |
1953 | |
6a222840 |
1954 | sub make_witness_paths { |
1955 | my( $self ) = @_; |
910a0a6d |
1956 | foreach my $wit ( $self->tradition->witnesses ) { |
6771a1b1 |
1957 | # say STDERR "Making path for " . $wit->sigil; |
910a0a6d |
1958 | $self->make_witness_path( $wit ); |
7854e12e |
1959 | } |
7854e12e |
1960 | } |
1961 | |
6a222840 |
1962 | sub make_witness_path { |
7854e12e |
1963 | my( $self, $wit ) = @_; |
1964 | my @chain = @{$wit->path}; |
15d2d3df |
1965 | my $sig = $wit->sigil; |
fae52efd |
1966 | # Add start and end if necessary |
1967 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1968 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
7854e12e |
1969 | foreach my $idx ( 0 .. $#chain-1 ) { |
910a0a6d |
1970 | $self->add_path( $chain[$idx], $chain[$idx+1], $sig ); |
7854e12e |
1971 | } |
1f7aa795 |
1972 | if( $wit->is_layered ) { |
d9e873d0 |
1973 | @chain = @{$wit->uncorrected_path}; |
fae52efd |
1974 | unshift( @chain, $self->start ) unless $chain[0] eq $self->start; |
1975 | push( @chain, $self->end ) unless $chain[-1] eq $self->end; |
d9e873d0 |
1976 | foreach my $idx( 0 .. $#chain-1 ) { |
1977 | my $source = $chain[$idx]; |
1978 | my $target = $chain[$idx+1]; |
1979 | $self->add_path( $source, $target, $sig.$self->ac_label ) |
1980 | unless $self->has_path( $source, $target, $sig ); |
1981 | } |
15d2d3df |
1982 | } |
1f7aa795 |
1983 | $wit->clear_path; |
1984 | $wit->clear_uncorrected_path; |
e2902068 |
1985 | } |
1986 | |
4e5a7b2c |
1987 | =head2 calculate_ranks |
1988 | |
1989 | Calculate the reading ranks (that is, their aligned positions relative |
1990 | to each other) for the graph. This can only be called on linear collations. |
1991 | |
b365fbae |
1992 | =begin testing |
1993 | |
1994 | use Text::Tradition; |
1995 | |
1996 | my $cxfile = 't/data/Collatex-16.xml'; |
1997 | my $t = Text::Tradition->new( |
1998 | 'name' => 'inline', |
1999 | 'input' => 'CollateX', |
2000 | 'file' => $cxfile, |
2001 | ); |
2002 | my $c = $t->collation; |
2003 | |
2004 | # Make an svg |
bfcbcecb |
2005 | my $table = $c->alignment_table; |
2006 | ok( $c->has_cached_table, "Alignment table was cached" ); |
2007 | is( $c->alignment_table, $table, "Cached table returned upon second call" ); |
b365fbae |
2008 | $c->calculate_ranks; |
bfcbcecb |
2009 | is( $c->alignment_table, $table, "Cached table retained with no rank change" ); |
864ee4bf |
2010 | $c->add_relationship( 'n13', 'n23', { type => 'repetition' } ); |
2011 | is( $c->alignment_table, $table, "Alignment table unchanged after non-colo relationship add" ); |
2012 | $c->add_relationship( 'n24', 'n23', { type => 'spelling' } ); |
2013 | isnt( $c->alignment_table, $table, "Alignment table changed after colo relationship add" ); |
b365fbae |
2014 | |
2015 | =end testing |
2016 | |
4e5a7b2c |
2017 | =cut |
2018 | |
910a0a6d |
2019 | sub calculate_ranks { |
2020 | my $self = shift; |
b365fbae |
2021 | # Save the existing ranks, in case we need to invalidate the cached SVG. |
8d9494a8 |
2022 | throw( "Cannot calculate ranks on a non-linear graph" ) |
2023 | unless $self->linear; |
b365fbae |
2024 | my %existing_ranks; |
ac4d7ac2 |
2025 | map { $existing_ranks{$_} = $_->rank } $self->readings; |
359944f7 |
2026 | |
2027 | # Do the rankings based on the relationship equivalence graph, starting |
2028 | # with the start node. |
56772e8c |
2029 | my ( $node_ranks, $rank_nodes ) = $self->relations->equivalence_ranks(); |
2030 | |
910a0a6d |
2031 | # Transfer our rankings from the topological graph to the real one. |
2032 | foreach my $r ( $self->readings ) { |
cecbe56d |
2033 | if( defined $node_ranks->{$self->equivalence( $r->id )} ) { |
359944f7 |
2034 | $r->rank( $node_ranks->{$self->equivalence( $r->id )} ); |
67da8d6c |
2035 | } else { |
63778331 |
2036 | # Die. Find the last rank we calculated. |
359944f7 |
2037 | my @all_defined = sort { ( $node_ranks->{$self->equivalence( $a->id )}||-1 ) |
2038 | <=> ( $node_ranks->{$self->equivalence( $b->id )}||-1 ) } |
63778331 |
2039 | $self->readings; |
2040 | my $last = pop @all_defined; |
2041 | throw( "Ranks not calculated after $last - do you have a cycle in the graph?" ); |
67da8d6c |
2042 | } |
de51424a |
2043 | } |
bfcbcecb |
2044 | # Do we need to invalidate the cached data? |
be3af600 |
2045 | if( $self->has_cached_table ) { |
b365fbae |
2046 | foreach my $r ( $self->readings ) { |
7c293912 |
2047 | next if defined( $existing_ranks{$r} ) |
2048 | && $existing_ranks{$r} == $r->rank; |
c1915ab9 |
2049 | # Something has changed, so clear the cache |
bfcbcecb |
2050 | $self->_clear_cache; |
c1915ab9 |
2051 | # ...and recalculate the common readings. |
2052 | $self->calculate_common_readings(); |
b365fbae |
2053 | last; |
2054 | } |
2055 | } |
c1915ab9 |
2056 | # The graph calculation information is now up to date. |
2057 | $self->_graphcalc_done(1); |
8e1394aa |
2058 | } |
3a1f2523 |
2059 | |
c1915ab9 |
2060 | sub _clear_cache { |
2061 | my $self = shift; |
c1915ab9 |
2062 | $self->wipe_table if $self->has_cached_table; |
2063 | } |
2064 | |
2065 | |
4e5a7b2c |
2066 | =head2 flatten_ranks |
2067 | |
2068 | A convenience method for parsing collation data. Searches the graph for readings |
2069 | with the same text at the same rank, and merges any that are found. |
2070 | |
2071 | =cut |
2072 | |
0e476982 |
2073 | sub flatten_ranks { |
4ef65ab4 |
2074 | my ( $self, %args ) = shift; |
0e476982 |
2075 | my %unique_rank_rdg; |
bf6e338d |
2076 | my $changed; |
4ef65ab4 |
2077 | foreach my $p ( $self->identical_readings( %args ) ) { |
2078 | # say STDERR "Combining readings at same rank: @$p"; |
2079 | $changed = 1; |
2080 | $self->merge_readings( @$p ); |
2081 | # TODO see if this now makes a common point. |
7a0956c1 |
2082 | } |
2083 | # If we merged readings, the ranks are still fine but the alignment |
2084 | # table is wrong. Wipe it. |
2085 | $self->wipe_table() if $changed; |
2086 | } |
2087 | |
2088 | =head2 identical_readings |
2089 | =head2 identical_readings( start => $startnode, end => $endnode ) |
2090 | =head2 identical_readings( startrank => $startrank, endrank => $endrank ) |
2091 | |
2092 | Goes through the graph identifying all pairs of readings that appear to be |
2093 | identical, and therefore able to be merged into a single reading. Returns the |
2094 | relevant identical pairs. Can be restricted to run over only a part of the |
2095 | graph, specified either by node or by rank. |
2096 | |
2097 | =cut |
2098 | |
2099 | sub identical_readings { |
2100 | my ( $self, %args ) = @_; |
2101 | # Find where we should start and end. |
2102 | my $startrank = $args{startrank} || 0; |
2103 | if( $args{start} ) { |
2104 | throw( "Starting reading has no rank" ) unless $self->reading( $args{start} ) |
2105 | && $self->reading( $args{start} )->has_rank; |
2106 | $startrank = $self->reading( $args{start} )->rank; |
2107 | } |
2108 | my $endrank = $args{endrank} || $self->end->rank; |
2109 | if( $args{end} ) { |
2110 | throw( "Ending reading has no rank" ) unless $self->reading( $args{end} ) |
2111 | && $self->reading( $args{end} )->has_rank; |
3c234eb6 |
2112 | $endrank = $self->reading( $args{end} )->rank; |
7a0956c1 |
2113 | } |
2114 | |
2115 | # Make sure the ranks are correct. |
2116 | unless( $self->_graphcalc_done ) { |
2117 | $self->calculate_ranks; |
2118 | } |
2119 | # Go through the readings looking for duplicates. |
2120 | my %unique_rank_rdg; |
2121 | my @pairs; |
0e476982 |
2122 | foreach my $rdg ( $self->readings ) { |
2123 | next unless $rdg->has_rank; |
7a0956c1 |
2124 | my $rk = $rdg->rank; |
2125 | next if $rk > $endrank || $rk < $startrank; |
2126 | my $key = $rk . "||" . $rdg->text; |
0e476982 |
2127 | if( exists $unique_rank_rdg{$key} ) { |
07e6765f |
2128 | # Make sure they don't have different grammatical forms |
2129 | my $ur = $unique_rank_rdg{$key}; |
a445ce40 |
2130 | if( $rdg->is_identical( $ur ) ) { |
7a0956c1 |
2131 | push( @pairs, [ $ur, $rdg ] ); |
07e6765f |
2132 | } |
0e476982 |
2133 | } else { |
2134 | $unique_rank_rdg{$key} = $rdg; |
2135 | } |
7a0956c1 |
2136 | } |
2137 | |
2138 | return @pairs; |
0e476982 |
2139 | } |
4633f9e4 |
2140 | |
2141 | |
d4b75f44 |
2142 | =head2 calculate_common_readings |
2143 | |
2144 | Goes through the graph identifying the readings that appear in every witness |
2145 | (apart from those with lacunae at that spot.) Marks them as common and returns |
2146 | the list. |
2147 | |
2148 | =begin testing |
2149 | |
2150 | use Text::Tradition; |
2151 | |
2152 | my $cxfile = 't/data/Collatex-16.xml'; |
2153 | my $t = Text::Tradition->new( |
2154 | 'name' => 'inline', |
2155 | 'input' => 'CollateX', |
2156 | 'file' => $cxfile, |
2157 | ); |
2158 | my $c = $t->collation; |
2159 | |
2160 | my @common = $c->calculate_common_readings(); |
2161 | is( scalar @common, 8, "Found correct number of common readings" ); |
2162 | my @marked = sort $c->common_readings(); |
2163 | is( scalar @common, 8, "All common readings got marked as such" ); |
679f17e1 |
2164 | my @expected = qw/ n1 n11 n16 n19 n20 n5 n6 n7 /; |
d4b75f44 |
2165 | is_deeply( \@marked, \@expected, "Found correct list of common readings" ); |
2166 | |
2167 | =end testing |
2168 | |
2169 | =cut |
2170 | |
2171 | sub calculate_common_readings { |
2172 | my $self = shift; |
2173 | my @common; |
c1915ab9 |
2174 | map { $_->is_common( 0 ) } $self->readings; |
2175 | # Implicitly calls calculate_ranks |
1dd07bda |
2176 | my $table = $self->alignment_table; |
d4b75f44 |
2177 | foreach my $idx ( 0 .. $table->{'length'} - 1 ) { |
7f52eac8 |
2178 | my @row = map { $_->{'tokens'}->[$idx] |
2179 | ? $_->{'tokens'}->[$idx]->{'t'} : '' } |
2180 | @{$table->{'alignment'}}; |
d4b75f44 |
2181 | my %hash; |
2182 | foreach my $r ( @row ) { |
2183 | if( $r ) { |
2184 | $hash{$r->id} = $r unless $r->is_meta; |
2185 | } else { |
2186 | $hash{'UNDEF'} = $r; |
2187 | } |
2188 | } |
2189 | if( keys %hash == 1 && !exists $hash{'UNDEF'} ) { |
2190 | my( $r ) = values %hash; |
2191 | $r->is_common( 1 ); |
2192 | push( @common, $r ); |
2193 | } |
2194 | } |
2195 | return @common; |
2196 | } |
2197 | |
861c3e27 |
2198 | =head2 text_from_paths |
2199 | |
2200 | Calculate the text array for all witnesses from the path, for later consistency |
2201 | checking. Only to be used if there is no non-graph-based way to know the |
2202 | original texts. |
2203 | |
2204 | =cut |
2205 | |
2206 | sub text_from_paths { |
2207 | my $self = shift; |
2208 | foreach my $wit ( $self->tradition->witnesses ) { |
5164a6f0 |
2209 | my @readings = $self->reading_sequence( $self->start, $self->end, $wit->sigil ); |
2210 | my @text; |
2211 | foreach my $r ( @readings ) { |
2212 | next if $r->is_meta; |
2213 | push( @text, $r->text ); |
2214 | } |
861c3e27 |
2215 | $wit->text( \@text ); |
2216 | if( $wit->is_layered ) { |
5164a6f0 |
2217 | my @ucrdgs = $self->reading_sequence( $self->start, $self->end, |
2218 | $wit->sigil.$self->ac_label ); |
2219 | my @uctext; |
2220 | foreach my $r ( @ucrdgs ) { |
2221 | next if $r->is_meta; |
2222 | push( @uctext, $r->text ); |
2223 | } |
2224 | $wit->layertext( \@uctext ); |
861c3e27 |
2225 | } |
2226 | } |
2227 | } |
0e476982 |
2228 | |
4e5a7b2c |
2229 | =head1 UTILITY FUNCTIONS |
2230 | |
2231 | =head2 common_predecessor( $reading_a, $reading_b ) |
8e1394aa |
2232 | |
4e5a7b2c |
2233 | Find the last reading that occurs in sequence before both the given readings. |
414cc046 |
2234 | At the very least this should be $self->start. |
4e5a7b2c |
2235 | |
2236 | =head2 common_successor( $reading_a, $reading_b ) |
2237 | |
2238 | Find the first reading that occurs in sequence after both the given readings. |
414cc046 |
2239 | At the very least this should be $self->end. |
4e5a7b2c |
2240 | |
22222af9 |
2241 | =begin testing |
2242 | |
2243 | use Text::Tradition; |
2244 | |
2245 | my $cxfile = 't/data/Collatex-16.xml'; |
2246 | my $t = Text::Tradition->new( |
2247 | 'name' => 'inline', |
2248 | 'input' => 'CollateX', |
2249 | 'file' => $cxfile, |
2250 | ); |
2251 | my $c = $t->collation; |
2252 | |
679f17e1 |
2253 | is( $c->common_predecessor( 'n24', 'n23' )->id, |
22222af9 |
2254 | 'n20', "Found correct common predecessor" ); |
679f17e1 |
2255 | is( $c->common_successor( 'n24', 'n23' )->id, |
10e4b1ac |
2256 | '__END__', "Found correct common successor" ); |
22222af9 |
2257 | |
4e5a7b2c |
2258 | is( $c->common_predecessor( 'n19', 'n17' )->id, |
22222af9 |
2259 | 'n16', "Found correct common predecessor for readings on same path" ); |
679f17e1 |
2260 | is( $c->common_successor( 'n21', 'n10' )->id, |
10e4b1ac |
2261 | '__END__', "Found correct common successor for readings on same path" ); |
22222af9 |
2262 | |
2263 | =end testing |
2264 | |
2265 | =cut |
2266 | |
2267 | ## Return the closest reading that is a predecessor of both the given readings. |
2268 | sub common_predecessor { |
2269 | my $self = shift; |
4e5a7b2c |
2270 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
2271 | return $self->_common_in_path( $r1, $r2, 'predecessors' ); |
22222af9 |
2272 | } |
2273 | |
2274 | sub common_successor { |
2275 | my $self = shift; |
4e5a7b2c |
2276 | my( $r1, $r2 ) = $self->_objectify_args( @_ ); |
027d819c |
2277 | return $self->_common_in_path( $r1, $r2, 'successors' ); |
22222af9 |
2278 | } |
2279 | |
414cc046 |
2280 | |
2281 | # TODO think about how to do this without ranks... |
027d819c |
2282 | sub _common_in_path { |
22222af9 |
2283 | my( $self, $r1, $r2, $dir ) = @_; |
414cc046 |
2284 | my $iter = $self->end->rank; |
22222af9 |
2285 | my @candidates; |
414cc046 |
2286 | my @last_r1 = ( $r1 ); |
2287 | my @last_r2 = ( $r2 ); |
2288 | # my %all_seen = ( $r1 => 'r1', $r2 => 'r2' ); |
22222af9 |
2289 | my %all_seen; |
6771a1b1 |
2290 | # say STDERR "Finding common $dir for $r1, $r2"; |
22222af9 |
2291 | while( !@candidates ) { |
414cc046 |
2292 | last unless $iter--; # Avoid looping infinitely |
2293 | # Iterate separately down the graph from r1 and r2 |
2294 | my( @new_lc1, @new_lc2 ); |
2295 | foreach my $lc ( @last_r1 ) { |
2296 | foreach my $p ( $lc->$dir ) { |
2297 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r1' ) { |
6771a1b1 |
2298 | # say STDERR "Path candidate $p from $lc"; |
414cc046 |
2299 | push( @candidates, $p ); |
002e3600 |
2300 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
2301 | $all_seen{$p->id} = 'r1'; |
2302 | push( @new_lc1, $p ); |
2303 | } |
2304 | } |
2305 | } |
2306 | foreach my $lc ( @last_r2 ) { |
22222af9 |
2307 | foreach my $p ( $lc->$dir ) { |
414cc046 |
2308 | if( $all_seen{$p->id} && $all_seen{$p->id} ne 'r2' ) { |
6771a1b1 |
2309 | # say STDERR "Path candidate $p from $lc"; |
22222af9 |
2310 | push( @candidates, $p ); |
002e3600 |
2311 | } elsif( !$all_seen{$p->id} ) { |
414cc046 |
2312 | $all_seen{$p->id} = 'r2'; |
2313 | push( @new_lc2, $p ); |
22222af9 |
2314 | } |
2315 | } |
2316 | } |
414cc046 |
2317 | @last_r1 = @new_lc1; |
2318 | @last_r2 = @new_lc2; |
22222af9 |
2319 | } |
2320 | my @answer = sort { $a->rank <=> $b->rank } @candidates; |
2321 | return $dir eq 'predecessors' ? pop( @answer ) : shift ( @answer ); |
2322 | } |
2323 | |
63778331 |
2324 | sub throw { |
2325 | Text::Tradition::Error->throw( |
2326 | 'ident' => 'Collation error', |
2327 | 'message' => $_[0], |
2328 | ); |
2329 | } |
2330 | |
dd3b58b0 |
2331 | no Moose; |
2332 | __PACKAGE__->meta->make_immutable; |
e867486f |
2333 | |
a445ce40 |
2334 | =head1 BUGS/TODO |
2335 | |
2336 | =over |
2337 | |
2338 | =item * Rework XML serialization in a more modular way |
2339 | |
2340 | =back |
2341 | |
027d819c |
2342 | =head1 LICENSE |
e867486f |
2343 | |
027d819c |
2344 | This package is free software and is provided "as is" without express |
2345 | or implied warranty. You can redistribute it and/or modify it under |
2346 | the same terms as Perl itself. |
e867486f |
2347 | |
027d819c |
2348 | =head1 AUTHOR |
e867486f |
2349 | |
027d819c |
2350 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |