Merge pull request #150 from wtsi-npg/devel

merge from devel to master to create release 6.9.0

Changes

@@ -1,6 +1,12 @@
 LIST OF CHANGES
 ---------------
 
+release 6.9.0
+ - ml warehouse LIMS drivers - define additional delegated
+   to sample objects methods 
+ - DBIx class for a new iseq_heron_product_metrics table
+ - DBIx classes updates for latest changes in ml warehouse database
+
 release 6.8.0
  - capture latest changes/additions in ml warehouse database
 

MANIFEST

@@ -14,6 +14,7 @@ lib/WTSI/DNAP/Warehouse/Schema/Result/CgapSupplierBarcode.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/FlgenPlate.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/IseqFlowcell.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/IseqProductMetric.pm
+lib/WTSI/DNAP/Warehouse/Schema/Result/IseqHeronProductMetric.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/IseqExternalProductMetric.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/IseqExternalProductComponent.pm
 lib/WTSI/DNAP/Warehouse/Schema/Result/IseqProductComponent.pm

lib/WTSI/DNAP/Warehouse/Schema/Result/CgapHeron.pm

@@ -47,7 +47,7 @@ __PACKAGE__->table('cgap_heron');
 
 Internal to this database id. Value can change.
 
-=head2 tube_rack_barcode
+=head2 container_barcode
 
   data_type: 'varchar'
   is_nullable: 0
@@ -56,7 +56,7 @@ Internal to this database id. Value can change.
 =head2 tube_barcode
 
   data_type: 'varchar'
-  is_nullable: 0
+  is_nullable: 1
   size: 32
 
 =head2 supplier_sample_id
@@ -90,6 +90,24 @@ Internal to this database id. Value can change.
   is_nullable: 0
   size: 32
 
+=head2 destination
+
+  data_type: 'varchar'
+  is_nullable: 0
+  size: 32
+
+=head2 wrangled
+
+  data_type: 'timestamp'
+  datetime_undef_if_invalid: 1
+  is_nullable: 1
+
+=head2 sample_state
+
+  data_type: 'varchar'
+  is_nullable: 0
+  size: 32
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -100,10 +118,10 @@ __PACKAGE__->add_columns(
     is_auto_increment => 1,
     is_nullable => 0,
   },
-  'tube_rack_barcode',
+  'container_barcode',
   { data_type => 'varchar', is_nullable => 0, size => 32 },
   'tube_barcode',
-  { data_type => 'varchar', is_nullable => 0, size => 32 },
+  { data_type => 'varchar', is_nullable => 1, size => 32 },
   'supplier_sample_id',
   { data_type => 'varchar', is_nullable => 0, size => 64 },
   'position',
@@ -119,6 +137,16 @@ __PACKAGE__->add_columns(
   },
   'study',
   { data_type => 'varchar', is_nullable => 0, size => 32 },
+  'destination',
+  { data_type => 'varchar', is_nullable => 0, size => 32 },
+  'wrangled',
+  {
+    data_type => 'timestamp',
+    datetime_undef_if_invalid => 1,
+    is_nullable => 1,
+  },
+  'sample_state',
+  { data_type => 'varchar', is_nullable => 0, size => 32 },
 );
 
 =head1 PRIMARY KEY
@@ -139,7 +167,7 @@ __PACKAGE__->set_primary_key('cgap_heron_tmp');
 
 =over 4
 
-=item * L</tube_rack_barcode>
+=item * L</container_barcode>
 
 =item * L</position>
 
@@ -149,7 +177,7 @@ __PACKAGE__->set_primary_key('cgap_heron_tmp');
 
 __PACKAGE__->add_unique_constraint(
   'cgap_heron_rack_and_position',
-  ['tube_rack_barcode', 'position'],
+  ['container_barcode', 'position'],
 );
 
 =head2 C<tube_barcode>
@@ -165,8 +193,8 @@ __PACKAGE__->add_unique_constraint(
 __PACKAGE__->add_unique_constraint('tube_barcode', ['tube_barcode']);
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2020-05-13 12:19:14
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:gaWAXpLadewCkZC4kW+MBA
+# Created by DBIx::Class::Schema::Loader v0.07049 @ 2020-06-11 17:00:43
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:w4fgEfecKEbXiTnwlD55lA
 
 our $VERSION = '0';
 

lib/WTSI/DNAP/Warehouse/Schema/Result/IseqFlowcell.pm

@@ -613,6 +613,8 @@ Readonly my %DELEGATION_TO_SAMPLE => {
     'sample_supplier_name'     => 'supplier_name',
     'sample_cohort'            => 'cohort',
     'sample_donor_id'          => 'donor_id',
+    'sample_is_control'        => 'control',
+    'sample_control_type'      => 'control_type',
 };
 
 Readonly my %DELEGATION_TO_STUDY => {
@@ -866,7 +868,7 @@ Marina Gourtovaia E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2015 Genome Research Limited
+Copyright (C) 2014,2015,2016,2017,2018,2019,2020 Genome Research Ltd.
 
 This file is part of the ml_warehouse package L<https://github.com/wtsi-npg/ml_warehouse>.