| line |
true |
false |
branch |
|
54
|
9 |
0 |
if (defined $_[0]) { } |
|
60
|
0 |
9 |
unless open OBO_FILE, $$self{'OBO_FILE'} |
|
71
|
9 |
0 |
if (defined $chunks[0] and $chunks[0] =~ /^format-version:\s*(.*)/) { } |
|
81
|
9 |
0 |
if ($chunks[0] =~ /(^format-version:\s*(.*)\n?)/m) |
|
90
|
1 |
8 |
if ($chunks[0] =~ /(^data-version:\s*(.*)\n?)/m) |
|
99
|
1 |
8 |
if ($chunks[0] =~ /(^ontology:\s*(.*)\n?)/m) |
|
108
|
9 |
0 |
if ($chunks[0] =~ /(^date:\s*(.*)\n?)/m) |
|
117
|
7 |
2 |
if ($chunks[0] =~ /(^saved-by:\s*(.*)\n?)/m) |
|
126
|
8 |
1 |
if ($chunks[0] =~ /(^auto-generated-by:\s*(.*)\n?)/m) |
|
163
|
4 |
1 |
if defined $sc and $sc =~ s/\s// |
|
178
|
3 |
0 |
if defined $dc |
|
188
|
1 |
8 |
if ($chunks[0] =~ /(^default_relationship_id_prefix:\s*(.*)\n?)/m) |
|
197
|
9 |
0 |
if ($chunks[0] =~ /(^default-namespace:\s*(.*)\n?)/m) |
|
212
|
0 |
9 |
unless (defined $format_version) |
|
239
|
1 |
8 |
if $data_version |
|
240
|
1 |
8 |
if $ontology_id_space |
|
241
|
9 |
0 |
if $date |
|
242
|
7 |
2 |
if $saved_by |
|
248
|
1 |
8 |
if $default_relationship_id_prefix |
|
249
|
9 |
0 |
if $default_namespace |
|
254
|
0 |
9 |
if ($chunks[0]) |
|
294
|
2025 |
126 |
if ($stanza and $stanza =~ /\[Term\]/) { } |
|
|
112 |
14 |
elsif ($stanza and $stanza =~ /\[Typedef\]/) { } |
|
|
5 |
9 |
elsif ($stanza and $stanza =~ /\[Instance\]/) { } |
|
|
0 |
18 |
elsif ($stanza and $stanza =~ /\[Annotation\]/) { } |
|
310
|
2025 |
9979 |
if ($line =~ /^id:\s*(\S+)/) { } |
|
|
2 |
9977 |
elsif ($line =~ /^is_anonymous:$r_true_false/) { } |
|
|
2023 |
7954 |
elsif ($line =~ /^name:\s*(.*)/) { } |
|
|
13 |
7941 |
elsif ($line =~ /^namespace:\s*(.*)/) { } |
|
|
9 |
7932 |
elsif ($line =~ /^alt_id:$r_db_acc/) { } |
|
|
1337 |
6595 |
elsif ($line =~ /^def:\s*\"(.*)\"$r_dbxref/) { } |
|
|
193 |
6402 |
elsif ($line =~ /^comment:\s*(.*)/) { } |
|
|
34 |
6368 |
elsif ($line =~ /^subset:\s*(\S+)/) { } |
|
|
573 |
5795 |
elsif ($line =~ /^(exact|narrow|broad|related)_synonym:\s*\"(.*)\"$r_dbxref/) { } |
|
|
1535 |
4260 |
elsif ($line =~ /^synonym:\s*\"(.*)\"$syn_scope(\s+([-\w]+))?$r_dbxref/) { } |
|
|
1161 |
3099 |
elsif ($line =~ /^xref:\s*(.*)/ or $line =~ /^xref_analog:\s*(.*)/ or $line =~ /^xref_unknown:\s*(.*)/) { } |
|
|
2149 |
950 |
elsif ($line =~ /^is_a:$r_db_acc$r_comments/) { } |
|
|
2 |
948 |
elsif ($line =~ m[^intersection_of:\s*([\w/]+)?$r_db_acc$r_comments]) { } |
|
|
0 |
948 |
elsif ($line =~ /^union_of:$r_db_acc$r_comments/) { } |
|
|
15 |
933 |
elsif ($line =~ /^disjoint_from:$r_db_acc$r_comments/) { } |
|
|
898 |
35 |
elsif ($line =~ m[^relationship:\s*([\w/]+)$r_db_acc$r_comments] or $line =~ /^relationship:\s*$r_db_acc$r_db_acc$r_comments/) { } |
|
|
4 |
31 |
elsif ($line =~ /^created_by:\s*(.*)/) { } |
|
|
4 |
27 |
elsif ($line =~ /^creation_date:\s*(.*)/) { } |
|
|
0 |
27 |
elsif ($line =~ /^modified_by:\s*(.*)/) { } |
|
|
0 |
27 |
elsif ($line =~ /^modification_date:\s*(.*)/) { } |
|
|
20 |
7 |
elsif ($line =~ /^is_obsolete:$r_true_false/) { } |
|
|
0 |
7 |
elsif ($line =~ /^replaced_by:\s*(.*)/) { } |
|
|
0 |
7 |
elsif ($line =~ /^consider:\s*(.*)/) { } |
|
|
0 |
7 |
elsif ($line =~ /^builtin:$r_true_false/) { } |
|
|
6 |
1 |
elsif ($line =~ /^property_value:\s*(\w+)$r_db_acc/ or $line =~ m<^property_value:\s*(\w+)\s+"([ '\#~\w:\\\+\?\{\}\$/\(\)\[\]\.=&!%_,-]+)"$r_db_acc>) { } |
|
|
1 |
0 |
elsif ($line =~ /^!/) { } |
|
311
|
2025 |
0 |
if ($line =~ /^id:$r_db_acc/) { } |
|
312
|
0 |
2025 |
if $only_one_id_tag_per_entry |
|
314
|
1621 |
404 |
if (not defined $term) { } |
|
|
0 |
808 |
elsif (defined $term->def->text and $term->def->text ne '') { } |
|
327
|
2 |
0 |
$1 eq 'true' ? : |
|
329
|
0 |
2023 |
if $only_one_name_tag_per_entry |
|
330
|
0 |
2023 |
if (not defined $1) { } |
|
349
|
34 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
359
|
1531 |
4 |
defined $3 ? : |
|
362
|
5 |
1530 |
if (defined $5) |
|
365
|
5 |
2 |
if ($st->name eq $5) |
|
366
|
1 |
4 |
unless (defined $3) |
|
368
|
1 |
0 |
if defined $default_scope |
|
374
|
0 |
5 |
unless $found |
|
383
|
0 |
2149 |
if ($t_id eq $1) |
|
391
|
264 |
1885 |
unless (defined $target) |
|
407
|
1 |
1 |
unless (defined $target) |
|
418
|
0 |
0 |
unless (defined $target) |
|
435
|
144 |
754 |
unless (defined $target) |
|
447
|
0 |
4 |
unless ($pd) |
|
459
|
0 |
0 |
unless ($pd) |
|
464
|
20 |
0 |
$1 eq 'true' ? : |
|
470
|
0 |
0 |
$1 eq 'true' ? : |
|
474
|
6 |
0 |
unless (defined $r2_type) |
|
489
|
1 |
5 |
if (not defined $3) { } |
|
|
5 |
0 |
elsif (defined $3) { } |
|
495
|
0 |
1 |
if (defined $target) { } |
|
500
|
1 |
0 |
unless (defined $target) |
|
517
|
5 |
0 |
unless (defined $target) |
|
522
|
0 |
5 |
unless exists $allowed_data_types{$3} |
|
543
|
0 |
2025 |
if (defined $term and not defined $term->id) |
|
546
|
0 |
2025 |
if ($intersection_of_counter == 1) |
|
549
|
0 |
2025 |
if ($union_of_counter == 1) |
|
566
|
112 |
490 |
if ($line =~ /^id:\s*(.*)/) { } |
|
|
0 |
490 |
elsif ($line =~ /^is_anonymous:$r_true_false/) { } |
|
|
112 |
378 |
elsif ($line =~ /^name:\s*(.*)/) { } |
|
|
0 |
378 |
elsif ($line =~ /^namespace:\s*(.*)/) { } |
|
|
0 |
378 |
elsif ($line =~ /^alt_id:\s*([:\w]+)/) { } |
|
|
59 |
319 |
elsif ($line =~ /^def:\s*\"(.*)\"$r_dbxref/) { } |
|
|
36 |
283 |
elsif ($line =~ /^comment:\s*(.*)/) { } |
|
|
1 |
282 |
elsif ($line =~ /^subset:\s*(\S+)/) { } |
|
|
0 |
282 |
elsif ($line =~ /^domain:\s*(.*)/) { } |
|
|
0 |
282 |
elsif ($line =~ /^range:\s*(.*)/) { } |
|
|
13 |
269 |
elsif ($line =~ /^is_anti_symmetric:$r_true_false/) { } |
|
|
0 |
269 |
elsif ($line =~ /^is_cyclic:$r_true_false/) { } |
|
|
24 |
245 |
elsif ($line =~ /^is_reflexive:$r_true_false/) { } |
|
|
2 |
243 |
elsif ($line =~ /^is_symmetric:$r_true_false/) { } |
|
|
47 |
196 |
elsif ($line =~ /^is_transitive:$r_true_false/) { } |
|
|
62 |
134 |
elsif ($line =~ /^is_a:\s*([:\w]+)$r_comments/) { } |
|
|
0 |
134 |
elsif ($line =~ /^is_metadata_tag:$r_true_false/) { } |
|
|
1 |
133 |
elsif ($line =~ /^is_class_level:$r_true_false/) { } |
|
|
3 |
130 |
elsif ($line =~ /^(exact|narrow|broad|related)_synonym:\s*\"(.*)\"$r_dbxref/) { } |
|
|
16 |
114 |
elsif ($line =~ /^synonym:\s*\"(.*)\"$syn_scope(\s+(\w+))?$r_dbxref/) { } |
|
|
74 |
40 |
elsif ($line =~ /^xref:\s*(.*)/ or $line =~ /^xref_analog:\s*(.*)/ or $line =~ /^xref_unk:\s*(.*)/) { } |
|
|
0 |
40 |
elsif ($line =~ m[^intersection_of:\s*([\w/]+)?$r_db_acc$r_comments]) { } |
|
|
0 |
40 |
elsif ($line =~ /^union_of:\s*(.*)/) { } |
|
|
1 |
39 |
elsif ($line =~ /^disjoint_from:\s*([:\w]+)$r_comments/) { } |
|
|
13 |
26 |
elsif ($line =~ /^inverse_of:\s*([:\w]+)$r_comments/) { } |
|
|
0 |
26 |
elsif ($line =~ /^transitive_over:\s*(.*)/) { } |
|
|
14 |
12 |
elsif ($line =~ /^holds_over_chain:\s*([:\w]+)\s*([:\w]+)$r_comments/) { } |
|
|
0 |
12 |
elsif ($line =~ /^equivalent_to_chain:\s*(.*)/) { } |
|
|
0 |
12 |
elsif ($line =~ /^disjoint_over:\s*(.*)/) { } |
|
|
0 |
12 |
elsif ($line =~ /^is_functional:$r_true_false/) { } |
|
|
0 |
12 |
elsif ($line =~ /^is_inverse_functional:$r_true_false/) { } |
|
|
2 |
10 |
elsif ($line =~ /^created_by:\s*(.*)/) { } |
|
|
2 |
8 |
elsif ($line =~ /^creation_date:\s*(.*)/) { } |
|
|
1 |
7 |
elsif ($line =~ /^modified_by:\s*(.*)/) { } |
|
|
1 |
6 |
elsif ($line =~ /^modification_date:\s*(.*)/) { } |
|
|
0 |
6 |
elsif ($line =~ /^is_obsolete:\s*(.*)/) { } |
|
|
0 |
6 |
elsif ($line =~ /^replaced_by:\s*(.*)/) { } |
|
|
0 |
6 |
elsif ($line =~ /^consider:\s*(.*)/) { } |
|
|
5 |
1 |
elsif ($line =~ /^builtin:$r_true_false/) { } |
|
|
1 |
0 |
elsif ($line =~ /^!/) { } |
|
568
|
75 |
37 |
if (not defined $type) { } |
|
|
0 |
37 |
elsif (defined $type->def->text and $type->def->text ne '') { } |
|
582
|
0 |
0 |
$1 eq 'true' ? : |
|
584
|
0 |
112 |
if $only_one_name_tag_per_entry |
|
600
|
1 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
612
|
13 |
0 |
$1 eq 'true' ? : |
|
614
|
0 |
0 |
$1 eq 'true' ? : |
|
616
|
24 |
0 |
$1 eq 'true' ? : |
|
618
|
2 |
0 |
$1 eq 'true' ? : |
|
620
|
47 |
0 |
$1 eq 'true' ? : |
|
624
|
0 |
62 |
if ($r_id eq $r) |
|
632
|
7 |
55 |
unless (defined $target) |
|
640
|
0 |
0 |
$1 eq 'true' ? : |
|
642
|
1 |
0 |
$1 eq 'true' ? : |
|
646
|
16 |
0 |
defined $3 ? : |
|
649
|
0 |
16 |
if (defined $5) |
|
653
|
0 |
0 |
if ($st->name eq $5) |
|
656
|
0 |
0 |
if defined $default_scope |
|
660
|
0 |
0 |
unless $found |
|
675
|
0 |
0 |
unless (defined $target) |
|
686
|
0 |
0 |
unless (defined $target) |
|
698
|
9 |
4 |
unless (defined $inv_type) |
|
711
|
2 |
12 |
unless (defined $r1_type) |
|
717
|
1 |
13 |
unless (defined $r2_type) |
|
728
|
0 |
0 |
$1 eq 'true' ? : |
|
730
|
0 |
0 |
$1 eq 'true' ? : |
|
736
|
0 |
2 |
unless ($pd) |
|
745
|
0 |
1 |
unless ($pd) |
|
750
|
0 |
0 |
$1 eq 'true' ? : |
|
756
|
5 |
0 |
$1 eq 'true' ? : |
|
764
|
0 |
112 |
unless (defined $type->id) |
|
767
|
0 |
112 |
if ($intersection_of_counter == 1) |
|
770
|
0 |
112 |
if ($union_of_counter == 1) |
|
791
|
5 |
21 |
if ($line =~ /^id:\s*(\S+)/) { } |
|
|
0 |
21 |
elsif ($line =~ /^is_anonymous:$r_true_false/) { } |
|
|
5 |
16 |
elsif ($line =~ /^name:\s*(.*)/) { } |
|
|
1 |
15 |
elsif ($line =~ /^namespace:\s*(.*)/) { } |
|
|
0 |
15 |
elsif ($line =~ /^alt_id:$r_db_acc/) { } |
|
|
0 |
15 |
elsif ($line =~ /^def:\s*\"(.*)\"$r_dbxref/) { } |
|
|
0 |
15 |
elsif ($line =~ /^comment:\s*(.*)/) { } |
|
|
0 |
15 |
elsif ($line =~ /^subset:\s*(\S+)/) { } |
|
|
0 |
15 |
elsif ($line =~ /^(exact|narrow|broad|related)_synonym:\s*\"(.*)\"$r_dbxref/) { } |
|
|
1 |
14 |
elsif ($line =~ /^synonym:\s*\"(.*)\"$syn_scope(\s+([-\w]+))?$r_dbxref/) { } |
|
|
1 |
13 |
elsif ($line =~ /^xref:\s*(.*)/ or $line =~ /^xref_analog:\s*(.*)/ or $line =~ /^xref_unknown:\s*(.*)/) { } |
|
|
5 |
8 |
elsif ($line =~ /^instance_of:$r_db_acc$r_comments/) { } |
|
|
0 |
8 |
elsif ($line =~ m[^intersection_of:\s*([\w/]+)?$r_db_acc$r_comments]) { } |
|
|
0 |
8 |
elsif ($line =~ /^union_of:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^disjoint_from:$r_db_acc$r_comments/) { } |
|
|
0 |
8 |
elsif ($line =~ m[^relationship:\s*([\w/]+)$r_db_acc$r_comments] or $line =~ /^relationship:\s*$r_db_acc$r_db_acc$r_comments/) { } |
|
|
0 |
8 |
elsif ($line =~ /^created_by:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^creation_date:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^modified_by:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^modification_date:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^is_obsolete:$r_true_false/) { } |
|
|
0 |
8 |
elsif ($line =~ /^replaced_by:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^consider:\s*(.*)/) { } |
|
|
0 |
8 |
elsif ($line =~ /^builtin:$r_true_false/) { } |
|
|
8 |
0 |
elsif ($line =~ /^property_value:\s*(\w+)$r_db_acc/ or $line =~ /^property_value:\s*(\w+)\s+"(\w+)"$r_db_acc/) { } |
|
|
0 |
0 |
elsif ($line =~ /^!/) { } |
|
792
|
5 |
0 |
if ($line =~ /^id:$r_db_acc/) { } |
|
793
|
0 |
5 |
if $only_one_id_tag_per_entry |
|
795
|
3 |
2 |
unless (defined $instance) |
|
809
|
0 |
0 |
$1 eq 'true' ? : |
|
811
|
0 |
5 |
if $only_one_name_tag_per_entry |
|
812
|
0 |
5 |
if (not defined $1) { } |
|
832
|
0 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
842
|
1 |
0 |
defined $3 ? : |
|
845
|
0 |
1 |
if (defined $5) |
|
849
|
0 |
0 |
if ($st->name eq $5) |
|
852
|
0 |
0 |
if defined $default_scope |
|
856
|
0 |
0 |
unless $found |
|
864
|
3 |
2 |
unless (defined $t) |
|
880
|
0 |
0 |
unless (defined $target) |
|
892
|
0 |
0 |
unless (defined $target) |
|
910
|
0 |
0 |
unless (defined $target) |
|
922
|
0 |
0 |
unless ($pd) |
|
931
|
0 |
0 |
unless ($pd) |
|
936
|
0 |
0 |
$1 eq 'true' ? : |
|
943
|
0 |
0 |
$1 eq 'true' ? : |
|
947
|
5 |
3 |
unless (defined $r2_type) |
|
962
|
4 |
4 |
if (not defined $3) { } |
|
|
4 |
0 |
elsif (defined $3) { } |
|
968
|
0 |
4 |
if (defined $target) { } |
|
973
|
3 |
1 |
unless (defined $target) |
|
990
|
4 |
0 |
unless (defined $target) |
|
995
|
0 |
4 |
unless exists $allowed_data_types{$3} |
|
1016
|
0 |
5 |
if (defined $instance and not defined $instance->id) |
|
1019
|
0 |
5 |
if ($intersection_of_counter == 1) |
|
1023
|
0 |
5 |
if ($union_of_counter == 1) |
|
1037
|
0 |
19 |
unless ($used_subset{$pss}) |
|
1048
|
0 |
5 |
unless ($used_synonym_type_def{$st->name}) |
|
1057
|
0 |
9 |
unless ($result->has_relationship_type_id('is_a')) |