| 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
|
2026 |
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
|
2026 |
9997 |
if ($line =~ /^id:\s*(\S+)/) { } |
|
|
2 |
9995 |
elsif ($line =~ /^is_anonymous:$r_true_false/) { } |
|
|
2024 |
7971 |
elsif ($line =~ /^name:\s*(.*)/) { } |
|
|
14 |
7957 |
elsif ($line =~ /^namespace:\s*(.*)/) { } |
|
|
9 |
7948 |
elsif ($line =~ /^alt_id:$r_db_acc/) { } |
|
|
1338 |
6610 |
elsif ($line =~ /^def:\s*\"(.*)\"$r_dbxref/) { } |
|
|
194 |
6416 |
elsif ($line =~ /^comment:\s*(.*)/) { } |
|
|
34 |
6382 |
elsif ($line =~ /^subset:\s*(\S+)/) { } |
|
|
573 |
5809 |
elsif ($line =~ /^(exact|narrow|broad|related)_synonym:\s*\"(.*)\"$r_dbxref/) { } |
|
|
1541 |
4268 |
elsif ($line =~ /^synonym:\s*\"(.*)\"$syn_scope(\s+([-\w]+))?$r_dbxref/) { } |
|
|
1167 |
3101 |
elsif ($line =~ /^xref:\s*(.*)/ or $line =~ /^xref_analog:\s*(.*)/ or $line =~ /^xref_unknown:\s*(.*)/) { } |
|
|
2149 |
952 |
elsif ($line =~ /^is_a:$r_db_acc$r_comments/) { } |
|
|
2 |
950 |
elsif ($line =~ m[^intersection_of:\s*([\w/]+)?$r_db_acc$r_comments]) { } |
|
|
0 |
950 |
elsif ($line =~ /^union_of:$r_db_acc$r_comments/) { } |
|
|
15 |
935 |
elsif ($line =~ /^disjoint_from:$r_db_acc$r_comments/) { } |
|
|
898 |
37 |
elsif ($line =~ m[^relationship:\s*([\w/]+)$r_db_acc$r_comments] or $line =~ /^relationship:\s*$r_db_acc$r_db_acc$r_comments/) { } |
|
|
5 |
32 |
elsif ($line =~ /^created_by:\s*(.*)/) { } |
|
|
5 |
27 |
elsif ($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+"([ \302\260'\#~\w:\\\+\?\{\}\$/\(\)\[\]\.=&!%_,-]+)"$r_db_acc>) { } |
|
|
1 |
0 |
elsif ($line =~ /^!/) { } |
|
311
|
2026 |
0 |
if ($line =~ /^id:$r_db_acc/) { } |
|
312
|
0 |
2026 |
if $only_one_id_tag_per_entry |
|
314
|
1622 |
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 |
2024 |
if $only_one_name_tag_per_entry |
|
330
|
0 |
2024 |
if (not defined $1) { } |
|
349
|
34 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
359
|
1537 |
4 |
defined $3 ? : |
|
362
|
5 |
1536 |
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 $target) |
|
447
|
0 |
5 |
unless ($pd) |
|
459
|
0 |
0 |
unless ($pd) |
|
464
|
20 |
0 |
$1 eq 'true' ? : |
|
470
|
0 |
0 |
$1 eq 'true' ? : |
|
478
|
6 |
0 |
unless (defined $r2_type) |
|
492
|
1 |
5 |
if (not defined $last_match) { } |
|
|
5 |
0 |
elsif (defined $last_match) { } |
|
498
|
0 |
1 |
if (defined $target) { } |
|
503
|
1 |
0 |
unless (defined $target) |
|
520
|
5 |
0 |
unless (defined $target) |
|
525
|
0 |
5 |
unless exists $allowed_data_types{$last_match} |
|
546
|
0 |
2026 |
if (defined $term and not defined $term->id) |
|
549
|
0 |
2026 |
if ($intersection_of_counter == 1) |
|
552
|
0 |
2026 |
if ($union_of_counter == 1) |
|
569
|
112 |
490 |
if ($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 =~ /^!/) { } |
|
571
|
75 |
37 |
if (not defined $type) { } |
|
|
0 |
37 |
elsif (defined $type->def->text and $type->def->text ne '') { } |
|
585
|
0 |
0 |
$1 eq 'true' ? : |
|
587
|
0 |
112 |
if $only_one_name_tag_per_entry |
|
603
|
1 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
615
|
13 |
0 |
$1 eq 'true' ? : |
|
617
|
0 |
0 |
$1 eq 'true' ? : |
|
619
|
24 |
0 |
$1 eq 'true' ? : |
|
621
|
2 |
0 |
$1 eq 'true' ? : |
|
623
|
47 |
0 |
$1 eq 'true' ? : |
|
627
|
0 |
62 |
if ($r_id eq $r) |
|
635
|
7 |
55 |
unless (defined $target) |
|
643
|
0 |
0 |
$1 eq 'true' ? : |
|
645
|
1 |
0 |
$1 eq 'true' ? : |
|
649
|
16 |
0 |
defined $3 ? : |
|
652
|
0 |
16 |
if (defined $5) |
|
656
|
0 |
0 |
if ($st->name eq $5) |
|
659
|
0 |
0 |
if defined $default_scope |
|
663
|
0 |
0 |
unless $found |
|
678
|
0 |
0 |
unless (defined $target) |
|
689
|
0 |
0 |
unless (defined $target) |
|
701
|
9 |
4 |
unless (defined $inv_type) |
|
714
|
2 |
12 |
unless (defined $r1_type) |
|
720
|
1 |
13 |
unless (defined $r2_type) |
|
731
|
0 |
0 |
$1 eq 'true' ? : |
|
733
|
0 |
0 |
$1 eq 'true' ? : |
|
739
|
0 |
2 |
unless ($pd) |
|
748
|
0 |
1 |
unless ($pd) |
|
753
|
0 |
0 |
$1 eq 'true' ? : |
|
759
|
5 |
0 |
$1 eq 'true' ? : |
|
767
|
0 |
112 |
unless (defined $type->id) |
|
770
|
0 |
112 |
if ($intersection_of_counter == 1) |
|
773
|
0 |
112 |
if ($union_of_counter == 1) |
|
794
|
5 |
21 |
if ($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 =~ m<^property_value:\s*(\w+)\s+"([ \302\260'\#~\w:\\\+\?\{\}\$/\(\)\[\]\.=&!%_,-]+)"$r_db_acc>) { } |
|
|
0 |
0 |
elsif ($line =~ /^!/) { } |
|
795
|
5 |
0 |
if ($line =~ /^id:$r_db_acc/) { } |
|
796
|
0 |
5 |
if $only_one_id_tag_per_entry |
|
798
|
3 |
2 |
unless (defined $instance) |
|
812
|
0 |
0 |
$1 eq 'true' ? : |
|
814
|
0 |
5 |
if $only_one_name_tag_per_entry |
|
815
|
0 |
5 |
if (not defined $1) { } |
|
835
|
0 |
0 |
if ($result->subset_def_map->contains_key($ss)) { } |
|
845
|
1 |
0 |
defined $3 ? : |
|
848
|
0 |
1 |
if (defined $5) |
|
852
|
0 |
0 |
if ($st->name eq $5) |
|
855
|
0 |
0 |
if defined $default_scope |
|
859
|
0 |
0 |
unless $found |
|
867
|
3 |
2 |
unless (defined $t) |
|
883
|
0 |
0 |
unless (defined $target) |
|
895
|
0 |
0 |
unless (defined $target) |
|
913
|
0 |
0 |
unless (defined $target) |
|
925
|
0 |
0 |
unless ($pd) |
|
934
|
0 |
0 |
unless ($pd) |
|
939
|
0 |
0 |
$1 eq 'true' ? : |
|
946
|
0 |
0 |
$1 eq 'true' ? : |
|
954
|
5 |
3 |
unless (defined $r2_type) |
|
969
|
4 |
4 |
if (not defined $last_match) { } |
|
|
4 |
0 |
elsif (defined $last_match) { } |
|
975
|
0 |
4 |
if (defined $target) { } |
|
980
|
3 |
1 |
unless (defined $target) |
|
997
|
4 |
0 |
unless (defined $target) |
|
1002
|
0 |
4 |
unless exists $allowed_data_types{$last_match} |
|
1023
|
0 |
5 |
if (defined $instance and not defined $instance->id) |
|
1026
|
0 |
5 |
if ($intersection_of_counter == 1) |
|
1030
|
0 |
5 |
if ($union_of_counter == 1) |
|
1044
|
0 |
19 |
unless ($used_subset{$pss}) |
|
1055
|
0 |
5 |
unless ($used_synonym_type_def{$st->name}) |
|
1064
|
0 |
9 |
unless ($result->has_relationship_type_id('is_a')) |