Merge pull request #223 from wtsi-npg/devel

pull from devel to master to create release 6.30.0

Changes

@@ -1,6 +1,13 @@
 LIST OF CHANGES
 ---------------
 
+release 6.30.0
+ - To help with detecting recent changes, add `last_changed` column
+   to PacBio NPG tables and update relevant DBIx classes.
+ - Updated DBIx classes from the prod database schema. Two types of changes:
+      1. due to a aserver upgrade tp MySQL v.8+
+      2. due to database schema changes.
+
 release 6.29.1
  - Switch to Perlbrew to obtain multiple Perl versions
 

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

@@ -252,7 +252,7 @@ __PACKAGE__->belongs_to(
   'sample',
   'WTSI::DNAP::Warehouse::Schema::Result::Sample',
   { id_sample_tmp => 'id_sample_tmp' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 =head2 study
@@ -267,12 +267,12 @@ __PACKAGE__->belongs_to(
   'study',
   'WTSI::DNAP::Warehouse::Schema::Result::Study',
   { id_study_tmp => 'id_study_tmp' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07036 @ 2015-01-19 16:35:18
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Df/CLIOB+DW9/6zUgYLM6A
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:lD09a55ctFBQGOiCkQis4Q
 
 our $VERSION = '0';
 

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

@@ -78,7 +78,7 @@ Location of data file
   data_type: 'integer'
   extra: {unsigned => 1}
   is_foreign_key: 1
-  is_nullable: 0
+  is_nullable: 1
 
 Study for this item
 
@@ -87,14 +87,14 @@ Study for this item
   data_type: 'integer'
   extra: {unsigned => 1}
   is_foreign_key: 1
-  is_nullable: 0
+  is_nullable: 1
 
 Sample info for this item
 
 =head2 library_name
 
   data_type: 'varchar'
-  is_nullable: 0
+  is_nullable: 1
   size: 40
 
 Supplier library name
@@ -131,6 +131,14 @@ Lab supplying the data
 
 ENA run accession, populated on ENA submission
 
+=head2 ena_upload
+
+  data_type: 'tinyint'
+  default_value: 0
+  is_nullable: 0
+
+Identifies if the sample is eligible for ENA upload
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -162,17 +170,17 @@ __PACKAGE__->add_columns(
     data_type => 'integer',
     extra => { unsigned => 1 },
     is_foreign_key => 1,
-    is_nullable => 0,
+    is_nullable => 1,
   },
   'id_sample_tmp',
   {
     data_type => 'integer',
     extra => { unsigned => 1 },
     is_foreign_key => 1,
-    is_nullable => 0,
+    is_nullable => 1,
   },
   'library_name',
-  { data_type => 'varchar', is_nullable => 0, size => 40 },
+  { data_type => 'varchar', is_nullable => 1, size => 40 },
   'library_type',
   { data_type => 'varchar', is_nullable => 0, size => 40 },
   'instrument_model',
@@ -181,6 +189,8 @@ __PACKAGE__->add_columns(
   { data_type => 'varchar', is_nullable => 0, size => 100 },
   'run_accession',
   { data_type => 'varchar', is_nullable => 1, size => 40 },
+  'ena_upload',
+  { data_type => 'tinyint', default_value => 0, is_nullable => 0 },
 );
 
 =head1 PRIMARY KEY
@@ -235,7 +245,12 @@ __PACKAGE__->belongs_to(
   'sample',
   'WTSI::DNAP::Warehouse::Schema::Result::Sample',
   { id_sample_tmp => 'id_sample_tmp' },
-  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
+  {
+    is_deferrable => 1,
+    join_type     => 'LEFT',
+    on_delete     => 'RESTRICT',
+    on_update     => 'RESTRICT',
+  },
 );
 
 =head2 study
@@ -250,12 +265,17 @@ __PACKAGE__->belongs_to(
   'study',
   'WTSI::DNAP::Warehouse::Schema::Result::Study',
   { id_study_tmp => 'id_study_tmp' },
-  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
+  {
+    is_deferrable => 1,
+    join_type     => 'LEFT',
+    on_delete     => 'RESTRICT',
+    on_update     => 'RESTRICT',
+  },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-02-09 15:29:50
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:ooVmo3tgjndSeKcqD6ynHw
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:kLSRN187cu2gr+3cdSypqw
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

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

@@ -149,12 +149,12 @@ __PACKAGE__->belongs_to(
   'iseq_product_ext',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqExternalProductMetric',
   { id_iseq_product => 'id_iseq_product_ext' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2019-10-18 16:31:06
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:MZF9h1iwW2028nqp+S3KRA
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:6qZDsJfhvxqvyeZkvdBsnw
 
 our $VERSION = '0';
 

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

@@ -563,7 +563,7 @@ __PACKAGE__->belongs_to(
   'sample',
   'WTSI::DNAP::Warehouse::Schema::Result::Sample',
   { id_sample_tmp => 'id_sample_tmp' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 =head2 study
@@ -581,14 +581,14 @@ __PACKAGE__->belongs_to(
   {
     is_deferrable => 1,
     join_type     => 'LEFT',
-    on_delete     => 'NO ACTION',
-    on_update     => 'NO ACTION',
+    on_delete     => 'RESTRICT',
+    on_update     => 'RESTRICT',
   },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2022-05-16 15:36:45
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WKXNoBer1TGZJNTUsLE3TA
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:VjDSKdvECkCYaV1Nypjnzw
 
 use MooseX::Aliases;
 use Readonly;

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

@@ -89,7 +89,6 @@ __PACKAGE__->table('iseq_heron_climb_status');
 =head2 anonymous_sample_id
 
   data_type: 'varchar'
-  default_value: (empty string)
   is_nullable: 1
   size: 15
 
@@ -130,7 +129,7 @@ __PACKAGE__->add_columns(
     is_nullable => 0,
   },
   'anonymous_sample_id',
-  { data_type => 'varchar', default_value => '', is_nullable => 1, size => 15 },
+  { data_type => 'varchar', is_nullable => 1, size => 15 },
 );
 
 =head1 PRIMARY KEY
@@ -146,8 +145,8 @@ __PACKAGE__->add_columns(
 __PACKAGE__->set_primary_key('id');
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-07-21 23:04:20
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:jToP8sVQEQTYrsDJMuxwrw
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:3XOtKycEV9IycXJtXeepZQ
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

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

@@ -253,12 +253,12 @@ __PACKAGE__->belongs_to(
   'iseq_product',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqProductMetric',
   { id_iseq_product => 'id_iseq_product' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2020-09-29 13:29:47
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:BU6yKQbGElrb3nXbK9ZqIA
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:U1ZHxtXu3hCdlMfUM81Hsg
 
 our $VERSION = '0';
 

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

@@ -157,7 +157,7 @@ __PACKAGE__->belongs_to(
   'iseq_product',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqProductMetric',
   { id_iseq_pr_metrics_tmp => 'id_iseq_pr_tmp' },
-  { is_deferrable => 1, on_delete => 'CASCADE', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'CASCADE', on_update => 'RESTRICT' },
 );
 
 =head2 iseq_product_component
@@ -172,12 +172,12 @@ __PACKAGE__->belongs_to(
   'iseq_product_component',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqProductMetric',
   { id_iseq_pr_metrics_tmp => 'id_iseq_pr_component_tmp' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2019-02-22 16:03:28
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wsP1sEBK1oRYk5C8X4RRag
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:S3T1/dAm6L5h7cAAumcITw
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

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

@@ -1001,7 +1001,7 @@ __PACKAGE__->belongs_to(
     is_deferrable => 1,
     join_type     => 'LEFT',
     on_delete     => 'SET NULL',
-    on_update     => 'NO ACTION',
+    on_update     => 'RESTRICT',
   },
 );
 
@@ -1068,13 +1068,13 @@ __PACKAGE__->belongs_to(
     is_deferrable => 1,
     join_type     => 'LEFT',
     on_delete     => 'CASCADE',
-    on_update     => 'NO ACTION',
+    on_update     => 'RESTRICT',
   },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2022-06-30 16:24:05
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:h1WsGh1UGAW4XYqkn1085Q
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Rf7TGwVeXRjNW5a9wU8baQ
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

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

@@ -94,12 +94,12 @@ __PACKAGE__->belongs_to(
   'run',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqRun',
   { id_run => 'id_run' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07049 @ 2022-04-01 17:33:44
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dboQ2bkPkWQ+PRCfjf/+0A
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QXTesYz1PmqbMqAWCD7FLQ
 
 
 # You can replace this text with custom code or comments, and it will be preserved on regeneration

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

@@ -126,12 +126,12 @@ __PACKAGE__->belongs_to(
   'run_status_dict',
   'WTSI::DNAP::Warehouse::Schema::Result::IseqRunStatusDict',
   { id_run_status_dict => 'id_run_status_dict' },
-  { is_deferrable => 1, on_delete => 'NO ACTION', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'RESTRICT', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-10-29 11:55:17
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:V+5Wt0FmO7gsFYyZ6NKKOQ
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:35:44
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:0YSdRUTGM7gZDMHVT3JCTg
 
 our $VERSION = '0';
 

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

@@ -79,6 +79,15 @@ Product id
 
 The final QC outcome of the product as 0(failed), 1(passed) or NULL
 
+=head2 last_changed
+
+  data_type: 'datetime'
+  datetime_undef_if_invalid: 1
+  default_value: 'CURRENT_TIMESTAMP'
+  is_nullable: 1
+
+Date this record was created or changed
+
 =cut
 
 __PACKAGE__->add_columns(
@@ -92,6 +101,13 @@ __PACKAGE__->add_columns(
   { data_type => 'char', is_nullable => 0, size => 64 },
   'qc',
   { data_type => 'tinyint', is_nullable => 1 },
+  'last_changed',
+  {
+    data_type => 'datetime',
+    datetime_undef_if_invalid => 1,
+    default_value => 'CURRENT_TIMESTAMP',
+    is_nullable => 1,
+  },
 );
 
 =head1 PRIMARY KEY
@@ -155,7 +171,7 @@ __PACKAGE__->belongs_to(
     is_deferrable => 1,
     join_type     => 'LEFT',
     on_delete     => 'SET NULL',
-    on_update     => 'NO ACTION',
+    on_update     => 'RESTRICT',
   },
 );
 
@@ -171,12 +187,12 @@ __PACKAGE__->belongs_to(
   'pac_bio_rw_metrics',
   'WTSI::DNAP::Warehouse::Schema::Result::PacBioRunWellMetric',
   { id_pac_bio_rw_metrics_tmp => 'id_pac_bio_rw_metrics_tmp' },
-  { is_deferrable => 1, on_delete => 'CASCADE', on_update => 'NO ACTION' },
+  { is_deferrable => 1, on_delete => 'CASCADE', on_update => 'RESTRICT' },
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-02-23 11:19:02
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:atOKMZwtqWTqeE7XYU1hlw
+# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 16:47:29
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:hTT2fzNhcm/86YuT61o2Qw
 
 use Carp;