Merge pull request #123 from sanger/develop

Develop into Master

db/migrate/20200909085557_add_tag2_to_pac_bio_run.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+# Add tag2 information to the pac_bio_run table so we can do dual indexing
+class AddTag2ToPacBioRun < ActiveRecord::Migration
+  def change
+    change_table :pac_bio_run, bulk: true do |t|
+      t.string   'tag2_sequence',    limit: 30,  comment: 'Tag sequence for tag 2', after: :tag_set_name
+      t.string   'tag2_set_id_lims', limit: 20,  comment: 'LIMs-specific identifier of the tag set for tag 2', after: :tag2_sequence
+      t.string   'tag2_set_name',    limit: 100, comment: 'WTSI-wide tag set name for tag 2', after: :tag2_set_id_lims
+      t.string   'tag2_identifier', limit: 30, comment: 'The position of tag2 within the tag group', after: :tag2_set_name
+    end
+  end
+end

db/structure.sql

@@ -1,4 +1,4 @@
--- MySQL dump 10.13  Distrib 8.0.19, for osx10.15 (x86_64)
+-- MySQL dump 10.13  Distrib 8.0.19, for osx10.14 (x86_64)
 --
 -- Host: localhost    Database: unified_warehouse_development
 -- ------------------------------------------------------
@@ -205,6 +205,10 @@ CREATE TABLE `pac_bio_run` (
   `tag_sequence` varchar(30) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Tag sequence for tag',
   `tag_set_id_lims` varchar(20) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'LIMs-specific identifier of the tag set for tag',
   `tag_set_name` varchar(100) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'WTSI-wide tag set name for tag',
+  `tag2_sequence` varchar(30) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Tag sequence for tag 2',
+  `tag2_set_id_lims` varchar(20) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'LIMs-specific identifier of the tag set for tag 2',
+  `tag2_set_name` varchar(100) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'WTSI-wide tag set name for tag 2',
+  `tag2_identifier` varchar(30) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'The position of tag2 within the tag group',
   `plate_barcode` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The human readable barcode for the plate loaded onto the machine',
   `plate_uuid_lims` varchar(36) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The plate uuid',
   `well_label` varchar(255) COLLATE utf8_unicode_ci NOT NULL COMMENT 'The well identifier for the plate, A1-H12',
@@ -441,7 +445,7 @@ CREATE TABLE `study_users` (
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2020-05-18 11:09:26
+-- Dump completed on 2020-09-10 10:12:23
 INSERT INTO schema_migrations (version) VALUES ('20141113110635');
 
 INSERT INTO schema_migrations (version) VALUES ('20141113130813');
@@ -538,3 +542,5 @@ INSERT INTO schema_migrations (version) VALUES ('20200512152113');
 
 INSERT INTO schema_migrations (version) VALUES ('20200518083730');
 
+INSERT INTO schema_migrations (version) VALUES ('20200909085557');
+

spec/models/pac_bio_run_spec.rb

@@ -46,6 +46,10 @@
               "cost_code" => "cost_code1",
               "tag_set_name" => "Sanger_168tags - 10 mer tags",
               "study_uuid" => '000000-0000-0000-0000-0000000001',
+              'tag2_identifier' => '1',
+              'tag2_sequence' => 'GTCA',
+              'tag2_set_id_lims' => '2',
+              'tag2_set_name' => 'tag_set_2'
             },
             {
               "sample_uuid" => '000000-0000-0000-0000-0000000000',
@@ -58,6 +62,10 @@
               "cost_code" => "cost_code1",
               "tag_set_name" => "Sanger_168tags - 10 mer tags",
               "study_uuid" => '000000-0000-0000-0000-0000000001',
+              'tag2_identifier' => '1',
+              'tag2_sequence' => 'GTCA',
+              'tag2_set_id_lims' => '2',
+              'tag2_set_name' => 'tag_set_2'
             }
           ]
         },