Merge pull request #4573 from sanger/Y24-480-store-huMFre-code

store huMFre code by sample

app/controllers/samples_controller.rb

@@ -248,6 +248,7 @@ def default_permitted_metadata_fields
         subject
         treatment
         donor_id
+        huMFre_code
       ]
     }
   end

app/models/api/sample_io.rb

@@ -98,6 +98,7 @@ def json_root
     map_attribute_to_json_attribute(:treatment)
     map_attribute_to_json_attribute(:date_of_consent_withdrawn)
     map_attribute_to_json_attribute(:user_id_of_consent_withdrawn, 'marked_as_consent_withdrawn_by')
+    map_attribute_to_json_attribute(:huMFre_code)
   end
 
   extra_json_attributes do |_object, json_attributes|

app/models/sample.rb

@@ -147,6 +147,8 @@ class Current < ActiveSupport::CurrentAttributes
     custom_attribute(:date_of_consent_withdrawn)
     custom_attribute(:user_id_of_consent_withdrawn)
 
+    custom_attribute(:huMFre_code)
+
     # These fields are warehoused, so need to match the encoding restrictions there
     # This excludes supplementary characters, which include emoji and rare kanji
     # @note phenotype isn't currently broadcast but has a field waiting in the warehouse
@@ -226,6 +228,17 @@ class Current < ActiveSupport::CurrentAttributes
   # Sample::Metadata tracks sample information, either for use in the lab, or passing to
   # the EBI
   class Metadata
+    # HuMFre numbers contain tissue information, which is only relevant for human samples.
+    validates :huMFre_code,
+              length: {
+                maximum: 16
+              },
+              format: {
+                with: %r{\A(?:\d{2}/\d{2,}|\d{2}/\d{4}-\d{3})\z},
+                message: 'must match a valid format, e.g. 12/34 or 12/2023-001'
+              },
+              allow_blank: true
+
     # This constraint doesn't match that described in the manifest, and is more permissive
     # It was added on conversion of out database to utf8 to address concerns that this would
     # lead to an increase in characters that their pipeline cannot process. Only a handful

app/views/shared/metadata/edit/_sample.html.erb

@@ -80,6 +80,8 @@
     <%= metadata_fields.text_field(:disease) %>
     <%= metadata_fields.text_field(:treatment)%>
 
+    <%= metadata_fields.text_field(:huMFre_code)%>
+
     <%  metadata_fields.finalize_related_fields %>
   <% end %>
 <% end %>

app/views/shared/metadata/show/_sample.html.erb

@@ -64,5 +64,7 @@
     <%= metadata_fields.plain_value(:disease) %>
     <%= metadata_fields.plain_value(:treatment)%>
 
+    <%= metadata_fields.plain_value(:huMFre_code)%>
+
   <% end %>
 <% end %>

config/locales/metadata/en.yml

@@ -325,6 +325,8 @@ en:
           edit_info: "EGA"
         genome_size:
           label: Genome Size
+        huMFre_code:
+          label: HuMFre Code
 
     study:
       metadata:

db/migrate/20241211143636_add_hu_m_fre_code_to_sample_metadata.rb

@@ -0,0 +1,6 @@
+# frozen_string_literal: true
+class AddHuMFreCodeToSampleMetadata < ActiveRecord::Migration[7.0]
+  def change
+    add_column :sample_metadata, :huMFre_code, :string, limit: 16
+  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_11_06_103710) do
+ActiveRecord::Schema[7.0].define(version: 2024_12_11_143636) do
   create_table "aliquot_indices", id: :integer, charset: "utf8mb4", collation: "utf8mb4_unicode_ci", options: "ENGINE=InnoDB ROW_FORMAT=DYNAMIC", force: :cascade do |t|
     t.integer "aliquot_id", null: false
     t.integer "lane_id", null: false
@@ -1395,6 +1395,7 @@
     t.integer "user_id_of_consent_withdrawn"
     t.boolean "consent_withdrawn", default: false, null: false
     t.string "collected_by", comment: "Name of persons or institute who collected the specimen"
+    t.string "huMFre_code", limit: 16
     t.index ["sample_ebi_accession_number"], name: "index_sample_metadata_on_sample_ebi_accession_number"
     t.index ["sample_id"], name: "index_sample_metadata_on_sample_id"
     t.index ["supplier_name"], name: "index_sample_metadata_on_supplier_name"

features/samples/xml_interface.feature

@@ -68,6 +68,7 @@ Feature: The XML interface to the samples
           <property><name>Time Point</name><value></value></property>
           <property><name>Donor Id</name><value></value></property>
           <property><name>Collected By</name><value/></property>
+          <property><name>HuMFre Code</name><value/></property>
         </properties>
       </sample>
       """

spec/models/api/sample_io_spec.rb

@@ -62,7 +62,8 @@
         sample_strain_att: 'stuff about strain',
         consent_withdrawn: false,
         donor_id: 2,
-        developmental_stage: 'thing'
+        developmental_stage: 'thing',
+        huMFre_code: '23/21'
       }
     )
   end
@@ -133,7 +134,8 @@
       'developmental_stage' => 'thing',
       'donor_id' => '2',
       'reference_genome' => 'ReferenceGenome1',
-      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }]
+      'component_sample_uuids' => [{ uuid: comp_sample1.uuid }, { uuid: comp_sample2.uuid }],
+      'huMFre_code' => '23/21'
     }
   end
 

spec/models/sample_spec.rb

@@ -259,6 +259,30 @@
     end
   end
 
+  context 'huMFre code' do
+    let(:sample) { create(:sample) }
+
+    it 'defaults to null when not specified' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+
+    it 'fails to update/save when huMFre code value is invalid' do
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+      sample.sample_metadata.huMFre_code = 'humFre1'
+      expect(sample.sample_metadata.save).to be false
+    end
+
+    it 'contains huMFre code value when it is correctly specified' do
+      sample.sample_metadata.update!(huMFre_code: '12/12')
+      expect(sample.sample_metadata.huMFre_code).to eq '12/12'
+    end
+
+    it 'can have the huMFre code blanked' do
+      sample.sample_metadata.update!(huMFre_code: nil)
+      expect(sample.sample_metadata.huMFre_code).to be_nil
+    end
+  end
+
   context '(DPL-148) on updating sample metadata' do
     let(:sample) { create(:sample) }