2622 implement unit for global templates

lib/seek/isa_templates/template_attributes_schema.json

@@ -138,6 +138,16 @@
           "type": "null"
         }
       ]
+    },
+    "unit": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ]
     }
   },
   "additionalProperties": false

lib/seek/isa_templates/template_attributes_schema_test.json

@@ -148,6 +148,16 @@
           "type": "null"
         }
       ]
+    },
+    "unit": {
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "null"
+        }
+      ]
     }
   },
   "additionalProperties": false

lib/seek/isa_templates/template_extractor.rb

@@ -55,6 +55,7 @@ def self.extract_templates(user)
                                      description: attribute['description'],
                                      sample_controlled_vocab_id: scv&.id,
                                      pid: attribute['pid'],
+                                     unit_id: get_unit_id(attribute['unit']),
                                      sample_attribute_type_id: get_sample_attribute_type(attribute['dataType']),
                                      allow_cv_free_text: allow_cv_free_text,
                                      title: attribute['name'])
@@ -192,6 +193,15 @@ def self.get_isa_tag_id(title)
         it&.id
       end
 
+      def self.get_unit_id(symbol)
+        return nil if symbol.blank?
+
+        unit = Unit.find_by(symbol: symbol)
+        @errors.append "<li>Could not find a Unit with symbol '#{symbol}'</li>" if unit.nil?
+
+        unit&.id
+      end
+
       def self.seed_isa_tags
         Rake::Task['db:seed:015_isa_tags'].invoke if ISATag.all.blank?
       end

test/fixtures/files/upload_json_sample_type_template/invalid_unit_template.json

@@ -0,0 +1,42 @@
+{
+  "data": [
+    {
+      "metadata": {
+        "name": "Invalid Unit Test Template",
+        "group": "ISA Test",
+        "group_order": 1,
+        "temporary_name": "1_invalid_unit_test_template",
+        "version": "1.0.0",
+        "isa_config": null,
+        "isa_measurement_type": null,
+        "isa_technology_type": null,
+        "isa_protocol_type": null,
+        "repo_schema_id": null,
+        "organism": "any",
+        "level": "study source"
+      },
+      "data": [
+        {
+          "iri": null,
+          "name": "Source Name",
+          "description": "Sources are considered as the starting biological material used in a study.",
+          "dataType": "String",
+          "title": true,
+          "required": true,
+          "isaTag": "source"
+        },
+        {
+          "iri": null,
+          "name": "Weight",
+          "description": "Weight with an unrecognised unit symbol.",
+          "dataType": "Integer",
+          "required": false,
+          "ontology": null,
+          "CVList": null,
+          "isaTag": "source_characteristic",
+          "unit": "INVALID_UNIT_XYZ"
+        }
+      ]
+    }
+  ]
+}

test/fixtures/files/upload_json_sample_type_template/test_unit_template.json

@@ -0,0 +1,42 @@
+{
+  "data": [
+    {
+      "metadata": {
+        "name": "Unit Test Template",
+        "group": "ISA Test",
+        "group_order": 1,
+        "temporary_name": "1_unit_test_template",
+        "version": "1.0.0",
+        "isa_config": null,
+        "isa_measurement_type": null,
+        "isa_technology_type": null,
+        "isa_protocol_type": null,
+        "repo_schema_id": null,
+        "organism": "any",
+        "level": "study source"
+      },
+      "data": [
+        {
+          "iri": null,
+          "name": "Source Name",
+          "description": "Sources are considered as the starting biological material used in a study.",
+          "dataType": "String",
+          "title": true,
+          "required": true,
+          "isaTag": "source"
+        },
+        {
+          "iri": null,
+          "name": "Weight",
+          "description": "Weight of the source material in grams.",
+          "dataType": "Integer",
+          "required": false,
+          "ontology": null,
+          "CVList": null,
+          "isaTag": "source_characteristic",
+          "unit": "g"
+        }
+      ]
+    }
+  ]
+}

test/functional/templates_controller_test.rb

@@ -652,6 +652,81 @@ class TemplatesControllerTest < ActionController::TestCase
     assert_select 'script#project-selector-possibilities-json', text: /#{options}/, count: 1
   end
 
+  test 'should create template attribute with unit' do
+    unit = Unit.find_or_create_by(symbol: 'g')
+
+    assert_difference('Template.count') do
+      post :create, params: { template: { title: 'Template with unit',
+                                          project_ids: @project_ids,
+                                          level: 'study source',
+                                          organism: 'any',
+                                          version: '1.0.0',
+                                          template_attributes_attributes: {
+                                            '0' => {
+                                              pos: '1',
+                                              title: 'Weight',
+                                              required: '1',
+                                              description: 'weight in grams',
+                                              sample_attribute_type_id: @int_type.id,
+                                              unit_id: unit.id,
+                                              _destroy: '0',
+                                              isa_tag_id: @default_isa_tag
+                                            }
+                                          }
+                                        }
+                            }
+    end
+
+    template = assigns(:template)
+    assert_redirected_to template_path(template)
+    weight = template.template_attributes.find_by(title: 'Weight')
+    assert_not_nil weight
+    assert_equal unit, weight.unit
+  end
+
+  test 'should update template attribute to set unit' do
+    unit = Unit.find_or_create_by(symbol: 'g')
+    template = FactoryBot.create(:min_template, project_ids: @project_ids, contributor: @person, title: 'unit_update_template')
+    attribute = template.template_attributes.first
+
+    fields = {
+      '0' => {
+        id: attribute.id,
+        pos: attribute.pos,
+        title: attribute.title,
+        required: (attribute.required ? '1' : '0'),
+        sample_attribute_type_id: attribute.sample_attribute_type_id,
+        unit_id: unit.id,
+        _destroy: '0',
+        isa_tag_id: attribute.isa_tag_id
+      }
+    }
+
+    put :update, params: { id: template, template: { title: template.title, template_attributes_attributes: fields } }
+
+    assert_redirected_to template_path(assigns(:template))
+    assert_equal unit, assigns(:template).template_attributes.first.unit
+  end
+
+  test 'should populate template with unit from json upload' do
+    login_as(@admin)
+    unit = Unit.find_or_create_by(symbol: 'g')
+
+    template_json = fixture_file_upload('upload_json_sample_type_template/test_unit_template.json', 'application/json')
+
+    assert_enqueued_jobs 1, only: PopulateTemplatesJob do
+      post :populate_template, params: { template_json_file: template_json }
+    end
+
+    assert_difference('Template.count', 1) do
+      perform_enqueued_jobs(only: PopulateTemplatesJob)
+    end
+
+    weight_attribute = Template.last.template_attributes.find_by(title: 'Weight')
+    assert_not_nil weight_attribute
+    assert_equal unit, weight_attribute.unit
+  end
+
   test 'should reuse existing controlled vocabularies' do
     apples_cv = FactoryBot.create(:apples_sample_controlled_vocab, title: "apples controlled vocab for template", )
     physics_ontology = FactoryBot.create(:sample_controlled_vocab, title: "physics ontology", source_ontology: "edam", ols_root_term_uris: "http://edamontology.org/topic_3318")

test/unit/jobs/populate_templates_job_test.rb

@@ -5,6 +5,7 @@ def setup
     # Create the SampleAttributeTypes
     # The title MUST be set manually!
     FactoryBot.create(:string_sample_attribute_type, title: 'String') if SampleAttributeType.find_by(title: 'String').nil?
+    FactoryBot.create(:integer_sample_attribute_type, title: 'Integer') if SampleAttributeType.find_by(title: 'Integer').nil?
     FactoryBot.create(:sample_multi_sample_attribute_type, title: 'Registered Sample List') if SampleAttributeType.find_by(title: 'Registered Sample List').nil?
 
     # Create the ISA Tags
@@ -64,4 +65,46 @@ def teardown
     end
   end
 
+  test 'perform sets unit on template attribute from json' do
+    unit = Unit.find_or_create_by(symbol: 'g')
+
+    src = Rails.root.join('test', 'fixtures', 'files', 'upload_json_sample_type_template', 'test_unit_template.json')
+    dest = Seek::Config.append_filestore_path('source_types')
+    FileUtils.cp(src, dest)
+
+    assert_difference('Template.count', 1) do
+      PopulateTemplatesJob.perform_now(@admin)
+    end
+
+    weight_attribute = Template.last.template_attributes.find_by(title: 'Weight')
+    assert_not_nil weight_attribute
+    assert_equal unit, weight_attribute.unit
+  end
+
+  test 'perform with null unit leaves unit blank on template attribute' do
+    src = Rails.root.join('test', 'fixtures', 'files', 'upload_json_sample_type_template', 'test_templates.json')
+    dest = Seek::Config.append_filestore_path('source_types')
+    FileUtils.cp(src, dest)
+
+    assert_difference('Template.count', 4) do
+      PopulateTemplatesJob.perform_now(@admin)
+    end
+
+    Template.last.template_attributes.each do |ta|
+      assert_nil ta.unit
+    end
+  end
+
+  test 'perform with json containing invalid unit symbol raises error' do
+    src = Rails.root.join('test', 'fixtures', 'files', 'upload_json_sample_type_template', 'invalid_unit_template.json')
+    dest = Seek::Config.append_filestore_path('source_types')
+    FileUtils.cp(src, dest)
+
+    assert_no_difference('Template.count') do
+      assert_raises(RuntimeError) do
+        PopulateTemplatesJob.perform_now(@admin)
+      end
+    end
+  end
+
 end