Merge pull request #927 from sanger/develop

[release] Merge Develop into Master for 1.35.2

Author: andrewsparkes

.gitignore

@@ -16,6 +16,7 @@
 /doc
 
 coverage
+lcov.info
 
 # Allow custom config files if desired
 *.local.yml

.release-version

@@ -1 +1 @@
-1.35.1
+1.35.2

db/migrate/20260701094306_alter_o_seq_flowcell_row_format.rb

@@ -0,0 +1,11 @@
+# DBAs requested to adjust table definition in the MLWH database so that the upgrade to MySQL v8.4
+# can proceed smoothly. See Y26-207
+class AlterOSeqFlowcellRowFormat < ActiveRecord::Migration[7.2]
+  def up
+    ActiveRecord::Base.connection.execute("ALTER TABLE `oseq_flowcell` ROW_FORMAT=DYNAMIC;")
+  end
+
+  def down
+    raise ActiveRecord::IrreversibleMigration
+  end
+end

db/migrate/20260701094718_alter_lighthouse_sample_row_format.rb

@@ -0,0 +1,11 @@
+# DBAs requested to adjust table definition in the MLWH database so that the upgrade to MySQL v8.4
+# can proceed smoothly. See Y26-207
+class AlterLighthouseSampleRowFormat < ActiveRecord::Migration[7.2]
+  def up
+    ActiveRecord::Base.connection.execute("ALTER TABLE `lighthouse_sample` ROW_FORMAT=DYNAMIC;")
+  end
+
+  def down
+    raise ActiveRecord::IrreversibleMigration
+  end
+end

db/migrate/20260701125103_extend_aliquot_sample_name_column.rb

@@ -0,0 +1,6 @@
+class ExtendAliquotSampleNameColumn < ActiveRecord::Migration[7.2]
+  def up
+    change_column :aliquot, :sample_name, :string, limit: 512
+    change_column_comment :aliquot, :sample_name, 'The name of the sample, or colon separated list of sample names, that the aliquot was created from'
+  end
+end

db/schema.rb

@@ -10,14 +10,14 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.2].define(version: 2026_05_29_124351) do
+ActiveRecord::Schema[7.2].define(version: 2026_07_01_125103) do
   create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
     t.string "aliquot_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
     t.string "aliquot_type", null: false, comment: "The type of the aliquot"
     t.string "source_type", null: false, comment: "The type of the source of the aliquot"
     t.string "source_barcode", null: false, comment: "The barcode of the source of the aliquot"
-    t.string "sample_name", null: false, comment: "The name of the sample that the aliquot was created from"
+    t.string "sample_name", limit: 512, null: false, comment: "The name of the sample, or colon separated list of sample names, that the aliquot was created from"
     t.string "used_by_type", null: false, comment: "The type of the entity that the aliquot is used by"
     t.string "used_by_barcode", null: false, comment: "The barcode of the entity that the aliquot is used by"
     t.decimal "volume", precision: 10, scale: 2, null: false, comment: "The volume of the aliquot (uL)"
@@ -181,7 +181,7 @@
     t.index ["location_barcode"], name: "index_labware_location_on_location_barcode"
   end
 
-  create_table "lighthouse_sample", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
+  create_table "lighthouse_sample", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.string "mongodb_id", comment: "Auto-generated id from MongoDB"
     t.string "root_sample_id", null: false, comment: "Id for this sample provided by the Lighthouse lab"
     t.string "cog_uk_id", null: false, comment: "Consortium-wide id, generated by Sanger on import to LIMS"
@@ -248,7 +248,7 @@
     t.index ["sample_id"], name: "index_long_read_qc_result_on_sample_id"
   end
 
-  create_table "oseq_flowcell", primary_key: "id_oseq_flowcell_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
+  create_table "oseq_flowcell", primary_key: "id_oseq_flowcell_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.string "id_flowcell_lims", null: false, comment: "LIMs-specific flowcell id"
     t.datetime "last_updated", precision: nil, null: false, comment: "Timestamp of last update"
     t.datetime "recorded_at", precision: nil, null: false, comment: "Timestamp of warehouse update"