Support allow_free_text in extended metadata controlled vocab attributes

app/serializers/extended_metadata_type_serializer.rb

@@ -18,6 +18,7 @@ def get_extended_metadata_attribute(attribute)
       "sample_attribute_type": get_sample_attribute_type(attribute),
       "required": attribute.required,
       "pos": attribute.pos,
+      "allow_cv_free_text": attribute.allow_cv_free_text,
       "sample_controlled_vocab_id": attribute.sample_controlled_vocab_id&.to_s,
       "linked_extended_metadata_type_id": attribute.linked_extended_metadata_type_id&.to_s
     }

lib/seek/extended_metadata_type/extended_metadata_type_extractor.rb

@@ -25,6 +25,7 @@ def self.extract_extended_metadata_type(file)
       def self.valid_emt_json?(json)
 
         raise StandardError, "The schema file is not readable!" unless File.readable?(SCHEMA_PATH)
+        raise StandardError, "The schema file is not readable!" unless File.readable?(SCHEMA_PATH)
 
         schema = JSON.parse(File.read(SCHEMA_PATH))
         errors = JSON::Validator.fully_validate(schema, json)
@@ -62,12 +63,13 @@ def self.create_extended_metadata_type_from_json(data)
             sample_attribute_type: sample_attribute_type,
             sample_controlled_vocab: sample_controlled_vocab,
             linked_extended_metadata_type: linked_extended_metadata_type,
-            required: attr['required'].present? ? attr['required'] : false,
+            required: attr.key?('required') ? attr['required'] : false,
+            allow_cv_free_text: attr.key?('allow_cv_free_text') ? attr['allow_cv_free_text'] : false,
             pid: attr['pid'].present? ? attr['pid'] : nil
           )
         end
         emt
       end
     end
   end
-end
+end

lib/seek/extended_metadata_type/extended_metadata_type_schema.json

@@ -31,6 +31,9 @@
               "description": {
                 "type": ["string", "null"]
               },
+              "allow_cv_free_text": {
+                "type": "boolean"
+              },
               "label": {
                 "type": "string"
               },
@@ -64,6 +67,9 @@
               "description": {
                 "type": ["string", "null"]
               },
+              "allow_cv_free_text": {
+                "type": "boolean"
+              },
               "label": {
                 "type": "string"
               },
@@ -86,4 +92,4 @@
   },
   "required": ["title", "supported_type", "enabled", "attributes"],
   "additionalProperties": false
-}
+}

public/api/definitions/_schemas.yml

@@ -4840,6 +4840,8 @@ extendedMetadataTypeExtendedMetadataAttributeResponse:
       type: boolean
     pos:
       $ref: "#/components/schemas/nullableInteger"
+    allow_cv_free_text:
+      type: boolean
     sample_controlled_vocab_id:
       $ref: "#/components/schemas/nullableNonEmptyString"
     linked_extended_metadata_type_id:

test/factories/extended_metadata_types.rb

@@ -57,10 +57,10 @@
     after(:build) do |a|
       a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, title:'apple name')
       cv_list_attribute = ExtendedMetadataAttribute.new(title: 'apple list', sample_attribute_type: FactoryBot.create(:cv_list_attribute_type),
-                                                      sample_controlled_vocab: FactoryBot.create(:apples_sample_controlled_vocab), description: "apple samples list", label: "apple samples list")
+                                                      sample_controlled_vocab: FactoryBot.create(:apples_sample_controlled_vocab), description: "apple samples list", label: "apple samples list", allow_cv_free_text: true)
       a.extended_metadata_attributes << cv_list_attribute
       cv_attribute = ExtendedMetadataAttribute.new(title: 'apple controlled vocab', sample_attribute_type: FactoryBot.create(:controlled_vocab_attribute_type),
-                                                 sample_controlled_vocab: FactoryBot.create(:apples_sample_controlled_vocab), description: "apple samples controlled vocab", label: "apple samples controlled vocab")
+                                                 sample_controlled_vocab: FactoryBot.create(:apples_sample_controlled_vocab), description: "apple samples controlled vocab", label: "apple samples controlled vocab", allow_cv_free_text: false)
       a.extended_metadata_attributes << cv_attribute
     end
   end

test/fixtures/files/extended_metadata_type/valid_emt_with_cv_with_ontologies.json

@@ -8,6 +8,7 @@
       "description": "Topics, used for annotating. Describes the domain, field of interest, of study, application, work, data, or technology. Initially seeded from the EDAM ontology.",
       "type": "Controlled Vocabulary",
       "required": true,
+      "allow_cv_free_text": true,
       "pos": 1,
       "pid": "http://edamontology.org/topic_0003",
       "ID": "CV_TOPICS_ID"

test/unit/extended_metadatas/emt_extractor_test.rb

@@ -89,6 +89,7 @@ class EmtExtractorTest < ActiveSupport::TestCase
     assert_equal SampleAttributeType.find_by(title: 'Controlled Vocabulary'), topics_attr.sample_attribute_type
     assert topics_attr.required
     assert_equal 'http://edamontology.org/topic_0003', topics_attr.pid
+    assert topics_attr.allow_cv_free_text
 
     assert_equal topic_cv, topics_attr.sample_controlled_vocab
     assert_equal 4, topics_attr.sample_controlled_vocab.sample_controlled_vocab_terms.count
@@ -153,4 +154,3 @@ def update_id(emt_file_name, person_emt, replaced)
 
 end
 
-