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Moved some tests to a new test script.
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Moved tests for aggregation across lanes to a new test
scripts. Tests for a new merge by library method will
be added to this new test script.
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@mgcam
mgcam committed Nov 14, 2023
1 parent c9a37bd commit 00ba90e
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Expand Up @@ -395,6 +395,7 @@ t/34-monitor-runfolder-staging.t
t/34-monitor-runfolder.t
t/34-monitor-staging.t
t/35-monitor_one_runfolder.t
t/40-st-lims-merge.t
t/40-st-lims-mlwarehouse.t
t/40-st-lims-ml_warehouse-drivers.t
t/40-st-lims-samplesheet.t
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244 changes: 244 additions & 0 deletions t/40-st-lims-merge.t
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use strict;
use warnings;
use Test::More tests => 4;
use Test::Exception;

use_ok('st::api::lims');

subtest 'Aggregation across lanes for pools' => sub {
plan tests => 85;

local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv';

my $l = st::api::lims->new(rpt_list => '25846:1:3');
throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/,
'method cannot be run for a composition';
$l = st::api::lims->new(id_run => 25846, position => 1);
throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/,
'method cannot be run for a lane-level object';
$l = st::api::lims->new(id_run => 25846, position => 1, tag_index => 4);
throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/,
'method cannot be run for a plex-level object';

$l = st::api::lims->new(id_run => 25846);

throws_ok { $l->aggregate_xlanes(qw/2 10/) }
qr/Requested position 10 does not exists in /,
'error if requested position does not exist';

my @merged = $l->aggregate_xlanes();
is (scalar @merged, 23, 'number of aggregates is number of tags plus two');
my $tag_zero = pop @merged;
my $tag_spiked = pop @merged;
my $tag_last = pop @merged;
my $tag_first = shift @merged;
is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0',
'rpt list for tag zero object');
is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888',
'rpt list for spiked in tag object');
is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21',
'rpt list for tag 21 object');
is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1',
'rpt list for tag 1 object');

@merged = $l->aggregate_xlanes(qw/1 4/);
is (scalar @merged, 23, 'number of aggregates is number of tags plus two');
$tag_zero = pop @merged;
$tag_spiked = pop @merged;
$tag_last = pop @merged;
$tag_first = shift @merged;
is ($tag_zero->rpt_list, '25846:1:0;25846:4:0',
'rpt list for tag zero object');
is ($tag_spiked->rpt_list, '25846:1:888;25846:4:888',
'rpt list for spiked in tag object');
is ($tag_last->rpt_list, '25846:1:21;25846:4:21',
'rpt list for tag 21 object');
is ($tag_first->rpt_list, '25846:1:1;25846:4:1',
'rpt list for tag 1 object');

@merged = $l->aggregate_xlanes(qw/1/);
is (scalar @merged, 23, 'number of aggregates is number of tags plus two');
$tag_zero = pop @merged;
$tag_spiked = pop @merged;
$tag_last = pop @merged;
$tag_first = shift @merged;
is ($tag_zero->rpt_list, '25846:1:0', 'rpt list for tag zero object');
is ($tag_spiked->rpt_list, '25846:1:888', 'rpt list for spiked in tag object');
is ($tag_last->rpt_list, '25846:1:21', 'rpt list for tag 21 object');
is ($tag_first->rpt_list, '25846:1:1', 'rpt list for tag 1 object');

@merged = $l->aggregate_xlanes();
is (scalar @merged, 23, 'number of aggregates is number of tags plus two');
$tag_zero = pop @merged;
$tag_spiked = pop @merged;
$tag_last = pop @merged;
$tag_first = shift @merged;
is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0',
'rpt list for tag zero object');
is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888',
'rpt list for spiked in tag object');
is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21',
'rpt list for tag 21 object');
is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1',
'rpt list for tag 1 object');

my $expected = {
'25846:1:0;25846:2:0;25846:3:0;25846:4:0' => {
'sample_id' => undef,
'sample_name' => undef,
'sample_common_name' => 'Homo sapiens',
'study_id' => 5318,
'study_name' => 'NovaSeq testing',
'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)',
'library_id' => undef,
'library_name' => undef,
'library_type' => 'Standard',
'default_tag_sequence' => undef,
'study_alignments_in_bam' => 1,
'study_contains_nonconsented_human' => 0
},
'25846:1:888;25846:2:888;25846:3:888;25846:4:888' => {
'sample_id' => '1255141',
'sample_name' => 'phiX_for_spiked_buffers',
'sample_common_name' => undef,
'study_id' => 198,
'study_name' => 'Illumina Controls',
'reference_genome' => undef,
'library_id' => '17883061',
'library_name' => '17883061',
'library_type' => undef,
'default_tag_sequence' => 'ACAACGCAATC',
'study_alignments_in_bam' => 1,
'study_contains_nonconsented_human' => 0
},
'25846:1:21;25846:2:21;25846:3:21;25846:4:21' => {
'sample_id' => '3681772',
'sample_name' => '5318STDY7462477',
'sample_common_name' => 'Homo sapiens',
'study_id' => 5318,
'study_name' => 'NovaSeq testing',
'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)',
'library_id' => '21059089',
'library_name' => '21059089',
'library_type' => 'Standard',
'default_tag_sequence' => 'TCGAGCGT',
'study_alignments_in_bam' => 1,
'study_contains_nonconsented_human' => 0
},
'25846:1:1;25846:2:1;25846:3:1;25846:4:1' => {
'sample_id' => '3681752',
'sample_name' => '5318STDY7462457',
'sample_common_name' => 'Homo sapiens',
'study_id' => 5318,
'study_name' => 'NovaSeq testing',
'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)',
'library_id' => '21059039',
'library_name' => '21059039',
'library_type' => 'Standard',
'default_tag_sequence' => 'ATCACGTT',
'study_alignments_in_bam' => 1,
'study_contains_nonconsented_human' => 0
}
};

for my $o (($tag_zero, $tag_spiked, $tag_first, $tag_last)) {
my $rpt_list = $o->rpt_list;
ok (!defined $o->id_run, "id_run not defined for $rpt_list");
for my $method ( qw/
sample_id sample_name sample_common_name
study_id study_name reference_genome
library_id library_name library_type
default_tag_sequence
/) {
is ($o->$method, $expected->{$rpt_list}->{$method}, "$method for $rpt_list");
}
ok ($o->study_alignments_in_bam, "alignment true for $rpt_list");
ok (!$o->study_contains_nonconsented_human, "nonconsented_human false for $rpt_list");
}

ok ($tag_spiked->is_phix_spike, 'is phix spike');
ok (!$tag_first->is_phix_spike, 'is not phix spike');
ok (!$tag_zero->is_phix_spike, 'is not phix spike');

is (join(q[:], $tag_zero->study_names), 'Illumina Controls:NovaSeq testing',
'study names including spiked phix');
is (join(q[:], $tag_zero->study_names(1)), 'Illumina Controls:NovaSeq testing',
'sudy names including spiked phix');
is (join(q[:], $tag_zero->study_names(0)), 'NovaSeq testing',
'study names excluding spiked phix');

my @sample_names = qw/
5318STDY7462457 5318STDY7462458 5318STDY7462459 5318STDY7462460 5318STDY7462461
5318STDY7462462 5318STDY7462463 5318STDY7462464 5318STDY7462465 5318STDY7462466
5318STDY7462467 5318STDY7462468 5318STDY7462469 5318STDY7462470 5318STDY7462471
5318STDY7462472 5318STDY7462473 5318STDY7462474 5318STDY7462475 5318STDY7462476
5318STDY7462477 /;

is (join(q[:], $tag_zero->sample_names(0)), join(q[:], @sample_names),
'sample names excluding spiked phix');
push @sample_names, 'phiX_for_spiked_buffers';
is (join(q[:], $tag_zero->sample_names()), join(q[:], @sample_names),
'sample names including spiked phix');
is (join(q[:], $tag_zero->sample_names(1)), join(q[:], @sample_names),
'sample names including spiked phix');
};

subtest 'Aggregation across lanes for non-pools' => sub {
plan tests => 13;

local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_rapidrun_nopool.csv';
my @merged = st::api::lims->new(id_run => 22672)->aggregate_xlanes();

my $l = $merged[0];
is (scalar @merged, 1, 'one object returned');
is ($l->rpt_list, '22672:1;22672:2', 'correct rpt_list');
ok (!defined $l->id_run, "id_run not defined");
ok (!$l->is_phix_spike, 'is not phix spike');

my $expected = {
'sample_id' => '2917461',
'sample_name' => '4600STDY6702635',
'sample_common_name' => 'Homo sapiens',
'study_id' => 4600,
'study_name' => 'Osteosarcoma_WGBS',
'reference_genome' => 'Not suitable for alignment',
'library_id' => '18914827',
'library_name' => '18914827',
'library_type' => 'Bisulphite pre quality controlled',
'study_alignments_in_bam' => 1,
'study_contains_nonconsented_human' => 0
};

for my $method ( qw/
sample_id sample_name sample_common_name
study_id study_name reference_genome
library_id library_name library_type
/) {
is ($l->$method, $expected->{$method}, "$method");
}
};

subtest 'Aggregation across lanes for a tag' => sub {
plan tests => 13;

local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv';

my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1');

my $e = qr/id_run and position are expected as arguments/;
throws_ok { $l->create_lane_object() } $e, 'no arguments - error';
throws_ok { $l->create_lane_object(1) } $e, 'one argument - error';
throws_ok { $l->create_lane_object(1, 0) } $e,
'one of argument is false - error';

for my $p ((1,2)) {
my $lane_l = $l->create_lane_object(25846, $p);
is ($lane_l->id_run, 25846, 'run id is 25846');
is ($lane_l->position, $p, "position is $p");
is ($lane_l->rpt_list, undef, 'rpt_list is undefined');
is ($lane_l->tag_index, undef, 'tag index is undefined');
ok ($lane_l->is_pool, 'the entity is a pool');
}
};

1;
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