From 00ba90ef3ab61158b7c11eb429afa25baf65d550 Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Tue, 14 Nov 2023 12:51:49 +0000
Subject: [PATCH] Moved some tests to a new test script.

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.
---
 MANIFEST             |   1 +
 t/40-st-lims-merge.t | 244 +++++++++++++++++++++++++++++++++++++++++++
 t/40-st-lims.t       | 238 +----------------------------------------
 3 files changed, 246 insertions(+), 237 deletions(-)
 create mode 100644 t/40-st-lims-merge.t

diff --git a/MANIFEST b/MANIFEST
index 346e5a4b..b06146ca 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -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
diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t
new file mode 100644
index 00000000..01bc15e3
--- /dev/null
+++ b/t/40-st-lims-merge.t
@@ -0,0 +1,244 @@
+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;
diff --git a/t/40-st-lims.t b/t/40-st-lims.t
index e9bd09d9..37dba533 100644
--- a/t/40-st-lims.t
+++ b/t/40-st-lims.t
@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 19;
+use Test::More tests => 16;
 use Test::Exception;
 use Test::Warn;
 use File::Temp qw/ tempdir /;
@@ -343,242 +343,6 @@ subtest 'Samplesheet driver for arbitrary compositions' => sub {
   is ($ss->tag_index, 4, 'correct tag_index');
 };
 
-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');
-  }
-};
-
 subtest 'Creating tag zero object' => sub {
   plan tests => 4;