Add required constraint to uuid_sample_lims and improve sample indexing

db/migrate/20241203115427_add_indexes_to_sample.rb

@@ -0,0 +1,11 @@
+class AddIndexesToSample < ActiveRecord::Migration[7.0]
+
+  def change
+    #id_lims and id_sample_lims should be unique together
+    add_index :sample, [:id_lims, :id_sample_lims], unique: true
+
+    #improve search performance
+    add_index :sample, :id_lims, unique: false
+    add_index :sample, :id_sample_lims, unique: false
+  end
+end

db/migrate/20241203134455_add_required_to_uuid_sample_lims_to_sample.rb

@@ -0,0 +1,10 @@
+class AddRequiredToUuidSampleLimsToSample < ActiveRecord::Migration[7.0]
+  def up
+    # uuid_sample_lims should be required
+    change_column_null(:sample, :uuid_sample_lims, false) 
+  end
+
+  def down
+    change_column_null(:sample, :uuid_sample_lims, true)
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_09_19_134424) do
+ActiveRecord::Schema[7.0].define(version: 2024_12_03_134455) 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"
@@ -304,7 +304,7 @@
 
   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 "uuid_sample_lims", limit: 36, null: false, comment: "LIMS-specific sample uuid"
     t.string "id_sample_lims", null: false, comment: "LIMS-specific sample identifier"
     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"
@@ -367,7 +367,10 @@
     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_lims", "id_sample_lims"], name: "index_sample_on_id_lims_and_id_sample_lims", unique: true
+    t.index ["id_lims"], name: "index_sample_on_id_lims"
     t.index ["id_sample_lims", "id_lims"], name: "index_sample_on_id_sample_lims_and_id_lims", unique: true
+    t.index ["id_sample_lims"], name: "index_sample_on_id_sample_lims"
     t.index ["name"], name: "sample_name_index"
     t.index ["sanger_sample_id"], name: "index_sample_on_sanger_sample_id"
     t.index ["supplier_name"], name: "index_sample_on_supplier_name"

spec/models/sample_spec.rb

@@ -24,42 +24,46 @@
   end
 
   context 'without uuid' do
-    it_behaves_like 'a sample resource'
-
-    let(:json) do
-      {
-        'id' => '1' * 255.to_i,
-        'name' => 'name',
-        'reference_genome' => 'reference genome',
-        'organism' => 'organism',
-        'consent_withdrawn' => true,
-        'accession_number' => 'accession number',
-        'common_name' => 'common name',
-        'description' => 'description',
-        'taxon_id' => 'taxon id',
-        'father' => 'father',
-        'mother' => 'mother',
-        'replicate' => 'replicate',
-        'ethnicity' => 'ethnicity',
-        'gender' => 'gender',
-        'cohort' => 'cohort',
-        'country_of_origin' => 'country of origin',
-        'geographical_region' => 'geographical region',
-        'updated_at' => '2012-03-11 10:22:42',
-        'created_at' => '2012-03-11 10:22:42',
-        'sanger_sample_id' => 'sanger sample id',
-        'control' => true,
-        'empty_supplier_sample_name' => true,
-        'supplier_name' => 'supplier name',
-        'public_name' => 'public name',
-        'sample_visibility' => 'sample visibility',
-        'strain' => 'strain',
-        'updated_by_manifest' => true,
-        'donor_id' => '11111111-2222-3333-4444-555555555556',
-        'developmental_stage' => 'Larval: Day 5 ZFS:0000037',
-        'control_type' => 'positive'
-      }
+    it 'should raiser an error if uuid is null' do
+      expect { create(:sample, uuid_sample_lims: nil) }.to raise_error ActiveRecord::NotNullViolation
     end
+
+    # it_behaves_like 'a sample resource'
+
+    # let(:json) do
+    #   {
+    #     'id' => '1' * 255.to_i,
+    #     'name' => 'name',
+    #     'reference_genome' => 'reference genome',
+    #     'organism' => 'organism',
+    #     'consent_withdrawn' => true,
+    #     'accession_number' => 'accession number',
+    #     'common_name' => 'common name',
+    #     'description' => 'description',
+    #     'taxon_id' => 'taxon id',
+    #     'father' => 'father',
+    #     'mother' => 'mother',
+    #     'replicate' => 'replicate',
+    #     'ethnicity' => 'ethnicity',
+    #     'gender' => 'gender',
+    #     'cohort' => 'cohort',
+    #     'country_of_origin' => 'country of origin',
+    #     'geographical_region' => 'geographical region',
+    #     'updated_at' => '2012-03-11 10:22:42',
+    #     'created_at' => '2012-03-11 10:22:42',
+    #     'sanger_sample_id' => 'sanger sample id',
+    #     'control' => true,
+    #     'empty_supplier_sample_name' => true,
+    #     'supplier_name' => 'supplier name',
+    #     'public_name' => 'public name',
+    #     'sample_visibility' => 'sample visibility',
+    #     'strain' => 'strain',
+    #     'updated_by_manifest' => true,
+    #     'donor_id' => '11111111-2222-3333-4444-555555555556',
+    #     'developmental_stage' => 'Larval: Day 5 ZFS:0000037',
+    #     'control_type' => 'positive'
+    #   }
+    # end
   end
 
   context 'compound samples via JSON' do