Testing

ELIXIR-Belgium · Jan 8, 2025 · 14764da · 14764da
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Showing 3 changed files with 35 additions and 3 deletions.
diff --git a/lib/seek/isa_templates/template_extractor.rb b/lib/seek/isa_templates/template_extractor.rb
@@ -39,6 +39,7 @@ def self.extract_templates(user)
               current_template_attributes = []
               item['data'].each_with_index do |attribute, j|
                 is_cv = attribute['dataType'].include? 'Controlled Vocabulary'
+                allow_cv_free_text = false
                 if is_cv
                   is_ontology = attribute['ontology'].present?
                   cv_exists = !SampleControlledVocab.find_by(title: attribute['name']).nil?

diff --git a/test/fixtures/files/upload_json_sample_type_template/test_apple_cv_template.json b/test/fixtures/files/upload_json_sample_type_template/test_apple_cv_template.json
@@ -32,6 +32,7 @@
           "dataType": "String",
           "required": true,
           "ontology": null,
+          "allowCVFreeText": null,
           "CVList": null,
           "isaTag": "source_characteristic"
         },
@@ -82,7 +83,7 @@
         },
         {
           "iri": null,
-          "name": "New ontology",
+          "name": "New ontology List",
           "description": "",
           "dataType": "Controlled Vocabulary List",
           "required": false,

diff --git a/test/functional/templates_controller_test.rb b/test/functional/templates_controller_test.rb
@@ -663,8 +663,8 @@ class TemplatesControllerTest < ActionController::TestCase
     # 2. Source Characteristic 1 (String) => New
     # 3. apples controlled (CV) vocab for template => Reuse
     # 4. physics ontology (CV, ontology) => Reuse
-    # 5. New CV (CV) List => New
-    # 6. New ontology (CV, ontology) => New
+    # 5. New CV (CV List) List => New
+    # 6. New ontology List (CV List, ontology) => New
     # New template attributes should be 6
     # New sample controlled vocabs should be 2
     ####################################################################################################################
@@ -687,6 +687,36 @@ class TemplatesControllerTest < ActionController::TestCase
     assert_equal registered_template.template_attributes.detect { |ta| ta.title == 'physics ontology' }.sample_controlled_vocab, physics_ontology
   end
 
+  test 'should allow controlled vocab attributes to have free text in instance-wide templates' do
+    login_as(@admin)
+    ####################################################################################################################
+    # This file contains the JSON definition for 1 template with 6 template attribute:
+    # 1. Source Name (Sting) => allowCVFreeText: null (not present)
+    # 2. Source Characteristic 1 (String) => allowCVFreeText: null
+    # 3. apples controlled vocab for template => allowCVFreeText: true
+    # 4. physics ontology (CV, ontology) => allowCVFreeText: false
+    # 5. New CV List (CV List) => allowCVFreeText: null => Should resolve to false
+    # 6. New ontology (CV List, ontology) => allowCVFreeText: null  => Should resolve to false
+    ####################################################################################################################
+    template_json = fixture_file_upload('upload_json_sample_type_template/test_apple_cv_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
+      assert_difference('TemplateAttribute.count', 6) do
+        perform_enqueued_jobs(only: PopulateTemplatesJob)
+      end
+    end
+
+    registered_template = Template.last
+    refute registered_template.template_attributes.detect { |ta| ta.title == 'Source Name' }.allow_cv_free_text
+    refute registered_template.template_attributes.detect { |ta| ta.title == 'Source Characteristic 1' }.allow_cv_free_text
+    assert registered_template.template_attributes.detect { |ta| ta.title == 'apples controlled vocab for template' }.allow_cv_free_text
+    refute registered_template.template_attributes.detect { |ta| ta.title == 'physics ontology' }.allow_cv_free_text
+    refute registered_template.template_attributes.detect { |ta| ta.title == 'New CV List' }.allow_cv_free_text
+    refute registered_template.template_attributes.detect { |ta| ta.title == 'New ontology List' }.allow_cv_free_text
+  end
+
   def create_template_from_parent_template(parent_template, person= @person, linked_sample_type= nil)
     child_template_attributes = parent_template.template_attributes.map do |ta|
       FactoryBot.create(:template_attribute, parent_attribute_id: ta.id, title: ta.title, isa_tag_id: ta.isa_tag_id, sample_attribute_type: ta.sample_attribute_type, is_title: ta.is_title, required: ta.required, sample_controlled_vocab: ta.sample_controlled_vocab, pos: ta.pos)