Merge pull request #130 from sanger/develop

Merge develop to master - CT channel changes

README.md

@@ -68,3 +68,9 @@ You can also stop a worker by calling `stop` or restart it with `restart`.
 
 If you receive an error about a missing output file under `tmp/pid/` it may be that you need to create this directory manually.
 Once the directory above has been inserted at the root of the repository, the error should go away.
+
+#### How To Section
+
+Cog Uk Ids - These ids are given to positive samples imported through the Lighthouse-UI. This process should automatically record those Ids in the sample table, and also into the lighthouse_sample table.
+To migrate Cog Uk Ids into the lighthouse_sample table manually via SQL, see this Confluence page:
+https://ssg-confluence.internal.sanger.ac.uk/display/PSD/How+to+migrate+Cog+UK+IDs+into+the+lighthouse_sample+table

db/migrate/20200929142921_add_ct_columns_to_lighthouse_samples.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+# Adds the CT channel columns to the lighthouse_sample table
+class AddCtColumnsToLighthouseSamples < ActiveRecord::Migration
+  def change
+    change_table :lighthouse_sample, bulk: true do |t|
+      t.string  :ch1_target, null: true, comment: 'Target for channel 1', after: :lab_id
+      t.string  :ch1_result, null: true, comment: 'Result for channel 1', after: :ch1_target
+      t.decimal :ch1_cq, precision: 11, scale: 8, null: true, comment: 'Cq value for channel 1', after: :ch1_result
+      t.string  :ch2_target, null: true, comment: 'Target for channel 2', after: :ch1_cq
+      t.string  :ch2_result, null: true, comment: 'Result for channel 2', after: :ch2_target
+      t.decimal :ch2_cq, precision: 11, scale: 8, null: true, comment: 'Cq value for channel 2', after: :ch2_result
+      t.string  :ch3_target, null: true, comment: 'Target for channel 3', after: :ch2_cq
+      t.string  :ch3_result, null: true, comment: 'Result for channel 3', after: :ch3_target
+      t.decimal :ch3_cq, precision: 11, scale: 8, null: true, comment: 'Cq value for channel 3', after: :ch3_result
+      t.string  :ch4_target, null: true, comment: 'Target for channel 4', after: :ch3_cq
+      t.string  :ch4_result, null: true, comment: 'Result for channel 4', after: :ch4_target
+      t.decimal :ch4_cq, precision: 11, scale: 8, null: true, comment: 'Cq value for channel 4', after: :ch4_result
+    end
+  end
+end

db/structure.sql

@@ -167,6 +167,18 @@ CREATE TABLE `lighthouse_sample` (
   `date_tested` datetime DEFAULT NULL COMMENT 'date_tested_string in date format',
   `source` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Lighthouse centre that the sample came from',
   `lab_id` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Id of the lab, within the Lighthouse centre',
+  `ch1_target` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Target for channel 1',
+  `ch1_result` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Result for channel 1',
+  `ch1_cq` decimal(11,8) DEFAULT NULL COMMENT 'Cq value for channel 1',
+  `ch2_target` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Target for channel 2',
+  `ch2_result` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Result for channel 2',
+  `ch2_cq` decimal(11,8) DEFAULT NULL COMMENT 'Cq value for channel 2',
+  `ch3_target` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Target for channel 3',
+  `ch3_result` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Result for channel 3',
+  `ch3_cq` decimal(11,8) DEFAULT NULL COMMENT 'Cq value for channel 3',
+  `ch4_target` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Target for channel 4',
+  `ch4_result` varchar(255) COLLATE utf8_unicode_ci DEFAULT NULL COMMENT 'Result for channel 4',
+  `ch4_cq` decimal(11,8) DEFAULT NULL COMMENT 'Cq value for channel 4',
   `created_at` datetime DEFAULT NULL COMMENT 'When this record was inserted',
   `updated_at` datetime DEFAULT NULL COMMENT 'When this record was last updated',
   PRIMARY KEY (`id`),
@@ -474,7 +486,7 @@ CREATE TABLE `study_users` (
 /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
 /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
 
--- Dump completed on 2020-09-21 16:04:05
+-- Dump completed on 2020-09-30 17:50:31
 INSERT INTO schema_migrations (version) VALUES ('20141113110635');
 
 INSERT INTO schema_migrations (version) VALUES ('20141113130813');
@@ -575,3 +587,5 @@ INSERT INTO schema_migrations (version) VALUES ('20200903104439');
 
 INSERT INTO schema_migrations (version) VALUES ('20200909085557');
 
+INSERT INTO schema_migrations (version) VALUES ('20200929142921');
+

spec/factories.rb

@@ -25,6 +25,18 @@
     date_tested Time.new(2020, 4, 1, 1, 0, 0, '+00:00')
     source 'Test Centre'
     lab_id 'TC'
+    ch1_target 'ORF1ab'
+    ch1_result 'Positive'
+    ch1_cq 12.46979445
+    ch2_target 'N gene'
+    ch2_result 'Positive'
+    ch2_cq 13.2452244
+    ch3_target 'S gene'
+    ch3_result 'Positive'
+    ch3_cq 13.07034452
+    ch4_target 'MS2'
+    ch4_result 'Positive'
+    ch4_cq 24.98589115
     created_at Time.new(2020, 4, 2, 1, 0, 0, '+00:00')
     updated_at Time.new(2020, 4, 2, 1, 0, 0, '+00:00')
   end