| line |
true |
false |
branch |
|
241
|
0 |
45 |
unless exists $FIELDS{$e} |
|
248
|
0 |
32 |
unless exists $FIELDS{$e} |
|
258
|
9 |
27 |
if defined $self->infile |
|
263
|
0 |
27 |
if ($self->with_condition_name and $self->action ne "decode") |
|
268
|
16 |
11 |
if ($self->action eq 'encode') { } |
|
|
11 |
0 |
elsif ($self->action eq 'decode') { } |
|
272
|
0 |
16 |
unless @conds |
|
275
|
0 |
16 |
if (@conds > $self->max_conditions) |
|
284
|
0 |
16 |
unless my $pat_cfg = $self->codebook->{'entities'}{$self->entity}{'condition_pattern'} |
|
286
|
0 |
16 |
unless my $re = $pat_cfg->{'regex'} |
|
290
|
0 |
19 |
unless $c =~ /^$re$/ |
|
299
|
2 |
154 |
if $field eq "batch" and not defined $self->batch |
|
300
|
2 |
152 |
if $field eq "replicate" and not defined $self->replicate |
|
301
|
0 |
152 |
unless defined $self->$field |
|
308
|
0 |
11 |
unless defined $self->clar_id |
|
330
|
4 |
32 |
if ($self->action eq "decode" and $self->with_condition_name) |
|
331
|
0 |
4 |
unless -e $self->icd10_map |
|
333
|
0 |
4 |
unless open my $jh, "<", $self->icd10_map |
|
342
|
9 |
27 |
if (defined(my $infile = $self->infile)) |
|
345
|
0 |
9 |
if ($infile =~ /\.gz$/) { } |
|
346
|
0 |
0 |
unless $in_fh = "IO::Uncompress::Gunzip"->new($infile) |
|
350
|
0 |
9 |
unless open my $fh_in, "<", $infile |
|
356
|
0 |
9 |
if (defined $self->outfile) { } |
|
357
|
0 |
0 |
if ($self->outfile =~ /\.gz$/) { } |
|
358
|
0 |
0 |
unless $out_fh = "IO::Compress::Gzip"->new($self->outfile) |
|
362
|
0 |
0 |
unless open my $fh_out, ">", $self->outfile |
|
382
|
27 |
0 |
exists $full->{'entities'} ? : |
|
383
|
0 |
27 |
unless my $cb = $$root{$self->entity} |
|
385
|
16 |
11 |
if ($self->action eq 'encode') { } |
|
398
|
2 |
8 |
if ($self->with_condition_name) |
|
424
|
0 |
9 |
unless my $hdr = $csv->getline($in_fh) |
|
430
|
9 |
0 |
exists $full->{'entities'} ? : |
|
431
|
0 |
9 |
unless my $cb = $$root{$self->entity} |
|
435
|
4 |
5 |
if ($self->action eq 'encode') { } |
|
436
|
2 |
2 |
$self->format eq 'stub' ? : |
|
441
|
2 |
3 |
if $self->with_condition_name |
|
448
|
13 |
17 |
if ($self->action eq 'encode') { } |
|
452
|
0 |
13 |
unless @conds |
|
453
|
0 |
13 |
if (@conds > $self->max_conditions) |
|
461
|
0 |
13 |
unless my $pat_cfg = $cb->{'condition_pattern'} |
|
463
|
0 |
13 |
unless my $re = $pat_cfg->{'regex'} |
|
465
|
0 |
16 |
unless $c =~ /^$re$/ |
|
480
|
13 |
4 |
if ($self->format eq 'human') { } |
|
490
|
0 |
17 |
unless defined $row->{$id_col} |
|
495
|
5 |
12 |
if ($self->with_condition_name and $code2name) |
|
513
|
0 |
120 |
unless defined $v and exists $fmap->{$v} |
|
524
|
36 |
24 |
$mode eq 'human' ? : |
|
526
|
36 |
24 |
$mode eq 'human' ? : |
|
539
|
0 |
47 |
unless defined $val |
|
540
|
0 |
47 |
unless $pcfg and $pcfg->{'regex'} |
|
543
|
1 |
46 |
unless $val =~ /$re/ |
|
546
|
0 |
46 |
if @caps > $need |
|
548
|
46 |
0 |
@caps ? : |
|
|
46 |
0 |
$need ? : |
|
556
|
0 |
0 |
if ($map and ref $map eq "HASH" and exists $map->{$val}) |
|
557
|
0 |
0 |
$mode eq 'human' ? : |
|
558
|
0 |
0 |
if defined $map->{$val}{$k} |
|
562
|
0 |
13 |
unless defined $val |
|
565
|
13 |
0 |
if ($pcfg and $pcfg->{'regex'}) |
|
567
|
0 |
13 |
unless $val =~ /$re/ |
|
570
|
0 |
13 |
if @caps > $need |
|
573
|
0 |
0 |
if (not @caps and $need == 1 and $mode eq "stub") |
|
578
|
13 |
0 |
@caps ? : |
|
596
|
0 |
9 |
unless (exists $cb->{'project'}{$pr}) |
|
598
|
0 |
0 |
if exists $cb->{'project'}{$alt} |
|
600
|
0 |
9 |
unless exists $cb->{'project'}{$pr} |
|
611
|
0 |
9 |
unless $pad =~ /^\d+$/ and $pad > 0 |
|
613
|
0 |
9 |
unless $sid =~ /^\d+$/ and $sid >= 0 and $sid <= $max |
|
636
|
7 |
1 |
defined $ba ? : |
|
642
|
7 |
1 |
defined $re ? : |
|
654
|
7 |
1 |
if defined $batch_code |
|
655
|
7 |
1 |
if defined $rep_code |
|
664
|
0 |
13 |
unless @p >= 9 |
|
669
|
0 |
13 |
unless defined $project |
|
672
|
0 |
13 |
unless defined $species |
|
675
|
0 |
13 |
unless defined $tissue |
|
678
|
0 |
13 |
unless defined $stype |
|
680
|
0 |
13 |
unless defined $assay |
|
684
|
0 |
13 |
unless $pad =~ /^\d+$/ and $pad > 0 |
|
685
|
0 |
13 |
unless $sid =~ /^\d{$pad}$/ |
|
691
|
11 |
2 |
if (@rest) |
|
694
|
11 |
0 |
if ($rest[-1] =~ /^R(\d{2})$/) |
|
700
|
11 |
0 |
if (@rest and $rest[-1] =~ /^B(\d{2})$/) |
|
709
|
0 |
13 |
unless defined $timepoint |
|
717
|
0 |
17 |
if (exists $cb->{'condition'}{$code}) { } |
|
722
|
0 |
17 |
if (not $code =~ /\./ and length $code > 3) |
|
733
|
2 |
11 |
unless defined $batch |
|
734
|
2 |
11 |
unless defined $replicate |
|
767
|
0 |
8 |
unless $w =~ /^\d+$/ and $w > 0 |
|
768
|
0 |
8 |
unless defined $sid and $sid =~ /^\d+$/ and $sid <= 62 ** $w - 1 |
|
774
|
0 |
0 |
defined $co ? : |
|
|
8 |
0 |
$conds_aref ? : |
|
778
|
0 |
8 |
unless @conds |
|
779
|
0 |
8 |
if @conds > $self->max_conditions |
|
787
|
0 |
8 |
unless exists $self->icd10_order->{$c} |
|
804
|
8 |
0 |
defined $ba ? : |
|
808
|
8 |
0 |
defined $re ? : |
|
826
|
0 |
3 |
unless defined $id and length $id |
|
839
|
0 |
3 |
if (not defined $replicate and $id =~ s/(\d{2})$//) |
|
840
|
0 |
3 |
if (not defined $batch and $id =~ s/(\d{2})$//) |
|
843
|
0 |
3 |
unless $id =~ s/(\d+)([DWMYN])$// |
|
845
|
1 |
2 |
if $d_unit eq "N" and $d_num != 0 |
|
854
|
2 |
4 |
if ($id =~ s/\Q$stub\E$//) |
|
856
|
0 |
2 |
unless defined $timepoint |
|
859
|
0 |
2 |
unless $id =~ s/(\d{2})$// |
|
861
|
0 |
2 |
unless $cond_count > 0 |
|
871
|
2 |
2 |
if ($head =~ s/^\Q$stub\E//) |
|
873
|
0 |
2 |
unless defined $project |
|
880
|
0 |
2 |
unless exists $sp_by{$spec_stub} |
|
885
|
0 |
2 |
unless $w =~ /^\d+$/ and $w > 0 |
|
895
|
2 |
20 |
if ($head =~ s/^\Q$stub\E//) |
|
897
|
0 |
2 |
unless defined $tissue |
|
904
|
2 |
4 |
if ($head =~ s/^\Q$stub\E//) |
|
906
|
0 |
2 |
unless defined $stype |
|
913
|
2 |
20 |
if ($head =~ s/^\Q$stub\E//) |
|
915
|
0 |
2 |
unless defined $assay |
|
918
|
0 |
2 |
unless length($head) % 3 == 0 |
|
920
|
0 |
2 |
unless @c_stubs == $cond_count |
|
928
|
0 |
2 |
unless $ord >= 1 and $ord < @{$self->icd10_by_order;} |
|
973
|
0 |
6 |
unless $pad =~ /^\d+$/ and $pad > 0 |
|
976
|
0 |
6 |
unless defined $sid and $sid =~ /^\d+$/ and $sid <= $max |
|
981
|
6 |
0 |
defined $co ? : |
|
982
|
0 |
6 |
unless @conds |
|
985
|
0 |
7 |
unless my $pat_cfg = $cb->{'condition_pattern'} |
|
986
|
0 |
7 |
unless $c =~ /^$pat_cfg->{'regex'}$/ |
|
1009
|
0 |
6 |
unless @p == 6 |
|
1014
|
0 |
6 |
unless defined $ag_key |
|
1043
|
0 |
6 |
unless exists $cb->{'type'}{$type} |
|
1044
|
0 |
6 |
unless exists $cb->{'sex'}{$sex} |
|
1046
|
0 |
6 |
unless exists $cb->{'age_group'}{$age_group} |
|
1053
|
0 |
6 |
unless $w =~ /^\d+$/ and $w > 0 |
|
1058
|
0 |
6 |
unless @conds |
|
1059
|
0 |
6 |
if @conds > 99 |
|
1062
|
0 |
7 |
unless exists $self->icd10_order->{$c} |
|
1084
|
0 |
6 |
unless defined $w and $w =~ /^\d+$/ and $w > 0 |
|
1096
|
0 |
6 |
unless length $rest >= 2 |
|
1101
|
0 |
6 |
unless $cond_count > 0 |
|
1106
|
0 |
6 |
unless length $rest >= $conds_len |
|
1112
|
0 |
6 |
unless length $rest >= 1 |
|
1117
|
0 |
6 |
unless length $rest >= $w |
|
1151
|
0 |
6 |
unless defined $type |
|
1155
|
0 |
6 |
unless defined $sex_key |
|
1159
|
0 |
6 |
unless defined $age_group_key |
|
1163
|
0 |
6 |
unless @rev_chunks == $cond_count |
|
1174
|
0 |
7 |
unless $ord >= 1 and $ord < @{$self->icd10_by_order;} |
|
1218
|
0 |
29 |
unless defined $id and $id =~ /^\d+$/ and $id >= 0 |
|
1221
|
0 |
29 |
if $id == 0 |
|
1239
|
0 |
17 |
unless defined $stub and $stub =~ /^[0-9A-Za-z]+$/ |
|
1243
|
0 |
52 |
unless exists $BASE62_REV{$char} |
|
1253
|
0 |
9 |
if $code =~ /\./ or length $code <= 3 |
|
1259
|
0 |
36 |
unless my $ents = $doc->{'entities'} |
|
1263
|
0 |
72 |
unless my $cat = $ents->{$entity} |
|
1268
|
0 |
540 |
if $slot eq "_defaults" |
|
1296
|
6 |
0 |
if ($$sref =~ s/$re//) |