From 5b0932e6ecf8a2be05a16571a07b719318d45701 Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Wed, 27 Sep 2023 17:44:09 +0100
Subject: [PATCH] Simplified code for insert size and restored is tests.

---
 lib/st/api/lims.pm | 36 ++++++++++--------------------------
 t/40-st-lims.t     | 37 ++++++++++++++++++++++++++++++++++++-
 2 files changed, 46 insertions(+), 27 deletions(-)

diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm
index 4d5e77da..2790c40e 100644
--- a/lib/st/api/lims.pm
+++ b/lib/st/api/lims.pm
@@ -542,44 +542,28 @@ sub _build_required_insert_size {
   my $self = shift;
 
   my $is_hash = {};
-  my $size_element_defined = 0;
-  if (defined $self->position && !$self->is_control) {
+  if (defined $self->position) {
     my @alims = $self->associated_lims;
-    if (!@alims) {
-      @alims = ($self);
-    }
+    @alims = @alims ? @alims : ($self);
     foreach my $lims (@alims) {
-      $self->_entity_required_insert_size($lims, $is_hash, \$size_element_defined);
-    }
-  }
-  return $is_hash;
-}
-sub _entity_required_insert_size {
-  my ($self, $lims, $is_hash, $isize_defined) = @_;
-
-  if (!$is_hash) {
-    croak q[Isize hash ref should be supplied];
-  }
-  if (!$lims) {
-    croak q[Lims object should be supplied];
-  }
-
-  if (!$lims->is_control) {
-    my $is = $lims->required_insert_size_range;
-    if ($is && keys %{$is}) {
-      ${$isize_defined} = 1;
+      if ($lims->is_control) {
+        next;
+      }
+      my $is = $lims->required_insert_size_range || {};
       foreach my $key (qw/to from/) {
         my $value = $is->{$key};
         if ($value) {
-          my $lib_key = $lims->library_id || $lims->tag_index || $lims->sample_id;
+          my $lib_key = $lims->library_id || $lims->sample_id;
           $is_hash->{$lib_key}->{$key} = $value;
         }
       }
     }
   }
-  return;
+
+  return $is_hash;
 }
 
+
 =head2 seq_qc_state
 
  1 for passes, 0 for failed, undef if the value is not set.
diff --git a/t/40-st-lims.t b/t/40-st-lims.t
index 80a41911..ff92df01 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 => 14;
+use Test::More tests => 15;
 use Test::Exception;
 use Test::Warn;
 use File::Temp qw/ tempdir /;
@@ -620,4 +620,39 @@ subtest 'Dual index' => sub {
   is($plex->purpose, 'standard', 'purpose');
 };
 
+subtest 'Insert size' => sub {
+  plan tests => 14;
+
+  local $ENV{NPG_CACHED_SAMPLESHEET_FILE} =
+    't/data/samplesheet/4pool4libs_extended.csv';
+
+  my $lims = st::api::lims->new(id_run => 9999);
+  is_deeply($lims->required_insert_size, {}, 'no insert size on run level');
+  
+  $lims = st::api::lims->new(id_run => 9999, position => 1);
+  my $id = $lims->library_id;
+  my $insert_size = $lims->required_insert_size;
+  is (keys %{$insert_size}, 1, 'one entry in the insert size hash');
+  is ($insert_size->{$id}->{q[from]}, 400, 'required FROM insert size');
+  is ($insert_size->{$id}->{q[to]}, 550, 'required TO insert size');
+  
+  $lims = st::api::lims->new(id_run => 9999, position => 7);
+  ok ($lims->is_pool, 'lane is a pool');
+  $insert_size = $lims->required_insert_size;
+  is (keys %{$insert_size}, 2, 'two entries in the insert size hash');
+  $id = '8324594';
+  is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size');
+  is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); 
+  $id = '8324595';
+  is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size');
+  is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size');
+  ok (!exists $insert_size->{q[6946_7_ACAACGCAAT]}, 'no required insert size');
+  
+  $lims = st::api::lims->new(id_run => 9999, position => 7, tag_index => 77);
+  $insert_size = $lims->required_insert_size;
+  is (keys %{$insert_size}, 1, 'one entry in the insert size hash');
+  is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size');
+  is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size');
+};
+
 1;