Merge pull request #547 from sanger/develop

Develop to master

.release-version

@@ -1 +1 @@
-1.17.1
+1.17.3

db/migrate/20230802153621_add_priority_level_to_sample.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+# Adding priority_level e.g. Medium, High etc to receive this information
+# in a sample message from TOL through traction qc_receptions endpoint
+class AddPriorityLevelToSample < ActiveRecord::Migration[7.0]
+  def change
+    change_table :sample, bulk: true do |t|
+      t.string :priority_level, comment: 'Priority level e.g. Medium, High etc'
+    end
+  end
+end

db/migrate/20230816092204_add_index_long_read_qc_results_sample_id.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# Add index on sample id for long read qc results to be able to join with samples
+class AddIndexLongReadQcResultsSampleId < ActiveRecord::Migration[7.0]
+  def change
+    add_index :long_read_qc_result, :sample_id, unique: false
+  end
+end

db/migrate/20230816100140_add_index_long_read_qc_results_assay_type_key.rb

@@ -0,0 +1,8 @@
+# frozen_string_literal: true
+
+# Index to query long_read_qc_results using assay_type_key
+class AddIndexLongReadQcResultsAssayTypeKey < ActiveRecord::Migration[7.0]
+  def change
+    add_index :long_read_qc_result, :assay_type_key, unique: false
+  end
+end

db/schema.rb

@@ -10,8 +10,8 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2023_07_04_101316) do
-  create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+ActiveRecord::Schema[7.0].define(version: 2023_08_21_100520) do
+  create_table "bmap_flowcell", primary_key: "id_bmap_flowcell_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     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"
     t.integer "id_sample_tmp", null: false, comment: "Sample id, see \"sample.id_sample_tmp\"", unsigned: true
@@ -31,7 +31,7 @@
     t.index ["id_study_tmp"], name: "fk_bmap_flowcell_to_study"
   end
 
-  create_table "flgen_plate", primary_key: "id_flgen_plate_tmp", id: { type: :integer, unsigned: true }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "flgen_plate", primary_key: "id_flgen_plate_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.integer "id_sample_tmp", null: false, comment: "Sample id, see \"sample.id_sample_tmp\"", unsigned: true
     t.integer "id_study_tmp", null: false, comment: "Study id, see \"study.id_study_tmp\"", unsigned: true
     t.string "cost_code", limit: 20, null: false, comment: "Valid WTSI cost code"
@@ -52,7 +52,7 @@
     t.index ["id_study_tmp"], name: "flgen_plate_study_fk"
   end
 
-  create_table "iseq_flowcell", primary_key: "id_iseq_flowcell_tmp", id: { type: :integer, unsigned: true }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "iseq_flowcell", primary_key: "id_iseq_flowcell_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     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"
     t.integer "id_sample_tmp", null: false, comment: "Sample id, see \"sample.id_sample_tmp\"", unsigned: true
@@ -107,7 +107,7 @@
     t.index ["legacy_library_id"], name: "index_iseq_flowcell_legacy_library_id"
   end
 
-  create_table "labware_location", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "labware_location", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "labware_barcode", null: false, comment: "Barcode on the stored labware"
     t.string "location_barcode", null: false, comment: "Barcode associated with storage location"
     t.string "full_location_address", null: false, comment: "Fully qualifed address of the nested location"
@@ -123,7 +123,7 @@
     t.index ["location_barcode"], name: "index_labware_location_on_location_barcode"
   end
 
-  create_table "lighthouse_sample", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "lighthouse_sample", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", 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"
@@ -172,7 +172,7 @@
     t.index ["root_sample_id", "rna_id", "result"], name: "index_lighthouse_sample_on_root_sample_id_and_rna_id_and_result", unique: true
   end
 
-  create_table "long_read_qc_result", primary_key: "id_long_read_qc_result_tmp", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3", force: :cascade do |t|
+  create_table "long_read_qc_result", primary_key: "id_long_read_qc_result_tmp", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "labware_barcode", null: false, comment: "Barcode of the labware that was the source for the QC tests."
     t.string "sample_id", null: false, comment: "External identifier for the sample(s)."
     t.string "assay_type", null: false, comment: "Type of the QC test."
@@ -186,9 +186,11 @@
     t.datetime "recorded_at", precision: nil, comment: "Timestamp of the latest warehouse update."
     t.string "qc_status", comment: "Status of the QC decision eg pass, fail etc"
     t.string "qc_status_decision_by", comment: "Who made the QC status decision eg ToL, Long Read"
+    t.index ["assay_type_key"], name: "index_long_read_qc_result_on_assay_type_key"
+    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 }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_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", 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"
@@ -218,7 +220,7 @@
     t.index ["id_study_tmp"], name: "fk_oseq_flowcell_to_study"
   end
 
-  create_table "pac_bio_run", primary_key: "id_pac_bio_tmp", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "pac_bio_run", primary_key: "id_pac_bio_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     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"
     t.integer "id_sample_tmp", null: false, comment: "Sample id, see \"sample.id_sample_tmp\"", unsigned: true
@@ -255,14 +257,14 @@
     t.index ["id_study_tmp"], name: "fk_pac_bio_run_to_study"
   end
 
-  create_table "psd_sample_compounds_components", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3", comment: "A join table owned by PSD to associate compound samples with their component samples.", force: :cascade do |t|
+  create_table "psd_sample_compounds_components", charset: "utf8mb3", comment: "A join table owned by PSD to associate compound samples with their component samples.", force: :cascade do |t|
     t.integer "compound_id_sample_tmp", null: false, comment: "The warehouse ID of the compound sample in the association."
     t.integer "component_id_sample_tmp", null: false, comment: "The warehouse ID of the component sample in the association."
     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."
   end
 
-  create_table "qc_result", primary_key: "id_qc_result_tmp", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "qc_result", primary_key: "id_qc_result_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.integer "id_sample_tmp", null: false, unsigned: true
     t.string "id_qc_result_lims", limit: 20, null: false, comment: "LIMS-specific qc_result identifier"
     t.string "id_lims", limit: 10, null: false, comment: "LIMS system identifier (e.g. SEQUENCESCAPE)"
@@ -282,7 +284,7 @@
     t.index ["id_sample_tmp"], name: "fk_qc_result_to_sample"
   end
 
-  create_table "sample", primary_key: "id_sample_tmp", id: { type: :integer, unsigned: true }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "sample", primary_key: "id_sample_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", limit: 10, null: false, comment: "LIM system identifier, e.g. CLARITY-GCLP, SEQSCAPE"
     t.string "uuid_sample_lims", limit: 36, comment: "LIMS-specific sample uuid"
     t.string "id_sample_lims", limit: 20, null: false, comment: "LIMS-specific sample identifier"
@@ -345,6 +347,7 @@
     t.string "customer_measured_volume"
     t.string "gc_content"
     t.string "dna_source"
+    t.string "priority_level", comment: "Priority level eg Medium, High etc"
     t.index ["accession_number"], name: "sample_accession_number_index"
     t.index ["id_sample_lims", "id_lims"], name: "index_sample_on_id_sample_lims_and_id_lims", unique: true
     t.index ["name"], name: "sample_name_index"
@@ -353,7 +356,7 @@
     t.index ["uuid_sample_lims"], name: "sample_uuid_sample_lims_index", unique: true
   end
 
-  create_table "samples_extraction_activity", primary_key: "id_activity_tmp", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "samples_extraction_activity", primary_key: "id_activity_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_activity_lims", null: false, comment: "LIMs-specific activity id"
     t.integer "id_sample_tmp", null: false, comment: "Sample id, see \"sample.id_sample_tmp\"", unsigned: true
     t.string "activity_type", null: false, comment: "The type of the activity performed"
@@ -372,7 +375,7 @@
     t.index ["id_sample_tmp"], name: "fk_rails_bbdd0468f0"
   end
 
-  create_table "stock_resource", primary_key: "id_stock_resource_tmp", id: :integer, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "stock_resource", primary_key: "id_stock_resource_tmp", id: :integer, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     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"
     t.datetime "created", precision: nil, null: false, comment: "Timestamp of initial registration of stock in LIMS"
@@ -398,7 +401,7 @@
     t.index ["id_study_tmp"], name: "fk_stock_resource_to_study"
   end
 
-  create_table "study", primary_key: "id_study_tmp", id: { type: :integer, unsigned: true }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "study", primary_key: "id_study_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", limit: 10, null: false, comment: "LIM system identifier, e.g. GCLP-CLARITY, SEQSCAPE"
     t.string "uuid_study_lims", limit: 36, comment: "LIMS-specific study uuid"
     t.string "id_study_lims", limit: 20, null: false, comment: "LIMS-specific study identifier"
@@ -444,7 +447,7 @@
     t.index ["uuid_study_lims"], name: "study_uuid_study_lims_index", unique: true
   end
 
-  create_table "study_users", primary_key: "id_study_users_tmp", id: { type: :integer, unsigned: true }, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_unicode_ci", force: :cascade do |t|
+  create_table "study_users", primary_key: "id_study_users_tmp", id: { type: :integer, unsigned: true }, charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.integer "id_study_tmp", null: false, comment: "Study id, see \"study.id_study_tmp\"", unsigned: true
     t.datetime "last_updated", precision: nil, null: false, comment: "Timestamp of last update"
     t.string "role"