diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 73d769c239..c709e4f104 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -247,7 +247,7 @@ def query
       end
     end
 
-    if params[:input_template_id].present? # linked
+    if params[:input_template_id].present? && params[:input_attribute_id].present? # linked
       input_template_attribute =
         TemplateAttribute.find(params[:input_attribute_id])
       @result = filter_linked_samples(@result, :linked_samples,
@@ -256,7 +256,7 @@ def query
           template_id: params[:input_template_id] }, input_template_attribute)
     end
 
-    if params[:output_template_id].present? # linking
+    if params[:output_template_id].present? && params[:output_attribute_id].present? # linking
       output_template_attribute =
         TemplateAttribute.find(params[:output_attribute_id])
       @result = filter_linked_samples(@result, :linking_samples,
diff --git a/app/controllers/templates_controller.rb b/app/controllers/templates_controller.rb
index 3228799377..b163fa1613 100644
--- a/app/controllers/templates_controller.rb
+++ b/app/controllers/templates_controller.rb
@@ -107,7 +107,7 @@ def populate_template
 
     begin
       running!
-      PopulateTemplatesJob.new.queue_job
+      PopulateTemplatesJob.perform_later(@current_user)
     rescue StandardError
       done!
     end
diff --git a/app/jobs/populate_templates_job.rb b/app/jobs/populate_templates_job.rb
index c1827711f3..07c54daaf4 100644
--- a/app/jobs/populate_templates_job.rb
+++ b/app/jobs/populate_templates_job.rb
@@ -2,9 +2,9 @@
 class PopulateTemplatesJob < ApplicationJob
   queue_with_priority 1
   queue_as QueueNames::TEMPLATES
-  def perform
+  def perform(user)
     return unless Seek::Config.isa_json_compliance_enabled
 
-    Seek::ISATemplates::TemplateExtractor.extract_templates
+    Seek::ISATemplates::TemplateExtractor.extract_templates(user)
   end
 end
diff --git a/app/views/samples/query.js.erb b/app/views/samples/query.js.erb
index 116b356e01..5c8473cb31 100644
--- a/app/views/samples/query.js.erb
+++ b/app/views/samples/query.js.erb
@@ -1,3 +1,3 @@
 $j('#samples-table').html('<%= escape_javascript(render(partial: "table_view", locals: { samples: @result, link: true, show_extra_info: true })) -%>');
-$j('#sample-count').html('<%= "#{@visible_samples} sample(s) visible to you" %>')
+$j('#sample-count').html('<span><%= "#{@visible_samples}"%> sample(s) visible to you' + '</span> - <span class=\"text-success\"> Successful query @ <%= "#{Time.now.strftime("%d/%m/%Y %H:%M:%S")}" %></span>')
 Samples.initTable($j('#samples-table'), false, { hideEmptyColumns: true });
diff --git a/app/views/samples/query_form.html.erb b/app/views/samples/query_form.html.erb
index 72e351a2f2..fa6b0dd2b4 100644
--- a/app/views/samples/query_form.html.erb
+++ b/app/views/samples/query_form.html.erb
@@ -121,6 +121,9 @@
 	<div class="row">
 		<div class="col-md-4" style="margin-bottom:20px">
 			<button id="btn_submit" class="btn btn-primary" onclick="submit()">Query</button>
+			<div id= "sample-query-spinner">
+				<%= image("spinner") %>
+			</div>
 			<br>
 			<em id="sample-count"></em>
 		</div>
@@ -137,6 +140,7 @@
 	$j(document).ready(function () {
 		initSelect2($j('.select2'), $j('#query_samples'))
 		Samples.initTable($j('#samples-table'));
+		$j('#sample-query-spinner').hide();
 	});
 
 	$j("#template").on("change", function(){
@@ -187,7 +191,18 @@
 		$j.ajax({
 				url: "<%=query_samples_path%>",
 				method: "POST",
-				data
+				data,
+				beforeSend: function(){
+					$j('#sample-count').html("");
+					$j("#sample-query-spinner").show();
+					$j('#samples-table').html("");
+				},
+				error: function(err){
+					$j('#sample-count').html(`<b><p class="text-danger">Error [code ${err.status}]: Failed to fetch query results!</p></b>`)
+				},
+				complete: function(){
+					$j("#sample-query-spinner").hide()
+				}
 		})
 	}
 </script>
diff --git a/lib/seek/isa_templates/template_attributes_schema.json b/lib/seek/isa_templates/template_attributes_schema.json
index ceed37ba58..334f831d7c 100644
--- a/lib/seek/isa_templates/template_attributes_schema.json
+++ b/lib/seek/isa_templates/template_attributes_schema.json
@@ -1,112 +1,140 @@
 {
-	"$schema": "http://json-schema.org/draft-04/schema",
-	"title": "ISA tempalte attribute schema",
-	"description": "JSON-schema representing an ISA template attribute in DataHub",
-	"type": "object",
-	"properties": {
-		"iri": {
-			"anyOf": [
-				{
-					"type": "string",
-					"format": "uri"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"name": { "type": "string" },
-		"description": { "type": "string" },
-		"required": {
-			"anyOf": [
-				{
-					"type": "boolean"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"ontology": {
-			"anyOf": [
-				{
-					"type": "object",
-					"properties": {
-						"name": { "type": "string" },
-						"version": {
-							"anyOf": [{ "type": "string" }, { "type": "number" }]
-						},
-						"description": { "type": "string" },
-						"rootTermURI": { "type": "string", "format": "uri" }
-					}
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"dataType": {
-			"type": "string",
-			"enum": [
-				"Date time",
-				"Date",
-				"Real number",
-				"Integer",
-				"Web link",
-				"Email address",
-				"Text",
-				"String",
-				"Boolean",
-				"Registered Sample",
-				"Registered Sample List",
-				"Controlled Vocabulary",
-				"URI",
-				"Registered Data file",
-				"ENA custom date"
-			]
-		},
-		"CVList": {
-			"anyOf": [
-				{
-					"type": "array"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"isaTag": {
-			"anyOf": [
-				{
-					"type": "string",
-					"enum": [
-						"source",
-						"sample",
-						"protocol",
-						"source_characteristic",
-						"sample_characteristic",
-						"other_material",
-						"other_material_characteristic",
-						"data_file",
-						"data_file_comment",
-						"parameter_value"
-					]
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"title": {
-			"anyOf": [
-				{
-					"type": "boolean"
-				},
-				{
-					"type": "null"
-				}
-			]
-		}
-	},
-	"additionalProperties": false
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "ISA tempalte attribute schema",
+  "description": "JSON-schema representing an ISA template attribute in DataHub",
+  "type": "object",
+  "properties": {
+    "iri": {
+      "anyOf": [
+        {
+          "type": "string",
+          "format": "uri"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "name": {
+      "type": "string"
+    },
+    "description": {
+      "type": "string"
+    },
+    "required": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "ontology": {
+      "anyOf": [
+        {
+          "type": "object",
+          "properties": {
+            "name": {
+              "type": "string"
+            },
+            "version": {
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "type": "number"
+                }
+              ]
+            },
+            "description": {
+              "type": "string"
+            },
+            "rootTermURI": {
+              "type": "string",
+              "format": "uri"
+            }
+          }
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "dataType": {
+      "type": "string",
+      "enum": [
+        "Date time",
+        "Date",
+        "Real number",
+        "Integer",
+        "Web link",
+        "Email address",
+        "Text",
+        "String",
+        "Boolean",
+        "Registered Sample",
+        "Registered Sample List",
+        "Controlled Vocabulary",
+        "URI",
+        "Registered Data file",
+        "ENA custom date"
+      ]
+    },
+    "allowCVFreeText": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "CVList": {
+      "anyOf": [
+        {
+          "type": "array"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "isaTag": {
+      "anyOf": [
+        {
+          "type": "string",
+          "enum": [
+            "source",
+            "sample",
+            "protocol",
+            "source_characteristic",
+            "sample_characteristic",
+            "other_material",
+            "other_material_characteristic",
+            "data_file",
+            "data_file_comment",
+            "parameter_value"
+          ]
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "title": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    }
+  },
+  "additionalProperties": false
 }
diff --git a/lib/seek/isa_templates/template_attributes_schema_test.json b/lib/seek/isa_templates/template_attributes_schema_test.json
index 23528693ba..b2d16f4092 100644
--- a/lib/seek/isa_templates/template_attributes_schema_test.json
+++ b/lib/seek/isa_templates/template_attributes_schema_test.json
@@ -1,99 +1,152 @@
 {
-	"$schema": "http://json-schema.org/draft-04/schema",
-	"title": "ISA tempalte attribute schema",
-	"description": "JSON-schema representing an ISA template attribute in DataHub",
-	"type": "object",
-	"properties": {
-		"iri": {
-			"anyOf": [
-				{
-					"type": "string",
-					"format": "uri"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"name": { "type": "string" },
-		"description": { "type": "string" },
-		"required": {
-			"anyOf": [
-				{
-					"type": "boolean"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"ontology": {
-			"anyOf": [
-				{
-					"type": "object",
-					"properties": {
-						"name": { "type": "string" },
-						"version": {
-							"anyOf": [{ "type": "string" }, { "type": "number" }]
-						},
-						"description": { "type": "string" },
-						"rootTermURI": { "type": "string", "format": "uri" }
-					}
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"dataType": {
-			"type": "string",
-			"enum": [
-				"String attribute type 1",
-				"Sample multi attribute type 1"
-			]
-		},
-		"CVList": {
-			"anyOf": [
-				{
-					"type": "array"
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"isaTag": {
-			"anyOf": [
-				{
-					"type": "string",
-					"enum": [
-						"source",
-						"sample",
-						"protocol",
-						"source_characteristic",
-						"sample_characteristic",
-						"other_material",
-						"other_material_characteristic",
-						"data_file",
-						"data_file_comment",
-						"parameter_value"
-					]
-				},
-				{
-					"type": "null"
-				}
-			]
-		},
-		"title": {
-			"anyOf": [
-				{
-					"type": "boolean"
-				},
-				{
-					"type": "null"
-				}
-			]
-		}
-	},
-	"additionalProperties": false
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "ISA template attribute schema",
+  "description": "JSON-schema representing an ISA template attribute in DataHub",
+  "type": "object",
+  "properties": {
+    "iri": {
+      "anyOf": [
+        {
+          "type": "string",
+          "format": "uri"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "name": {
+      "type": "string"
+    },
+    "description": {
+      "type": "string"
+    },
+    "required": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "ontology": {
+      "anyOf": [
+        {
+          "type": "object",
+          "properties": {
+            "name": {
+              "type": "string"
+            },
+            "version": {
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "type": "number"
+                }
+              ]
+            },
+            "description": {
+              "type": "string"
+            },
+            "rootTermURI": {
+              "type": "string",
+              "format": "uri"
+            }
+          }
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "dataType": {
+      "type": "string",
+      "enum": [
+        "Date time",
+        "Date",
+        "Real number",
+        "Integer",
+        "Web link",
+        "Email address",
+        "Text",
+        "String",
+        "ChEBI",
+        "ECN",
+        "MetaNetX chemical",
+        "MetaNetX reaction",
+        "MetaNetX compartment",
+        "InChI",
+        "ENA custom date",
+        "Boolean",
+        "Registered Strain",
+        "Registered Sample",
+        "Registered Sample List",
+        "Controlled Vocabulary",
+        "Controlled Vocabulary List",
+        "URI",
+        "DOI",
+        "NCBI ID",
+        "Registered Data file",
+        "Linked Extended Metadata",
+        "Linked Extended Metadata (multiple)"
+      ]
+    },
+    "allowCVFreeText": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "CVList": {
+      "anyOf": [
+        {
+          "type": "array"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "isaTag": {
+      "anyOf": [
+        {
+          "type": "string",
+          "enum": [
+            "source",
+            "sample",
+            "protocol",
+            "source_characteristic",
+            "sample_characteristic",
+            "other_material",
+            "other_material_characteristic",
+            "data_file",
+            "data_file_comment",
+            "parameter_value"
+          ]
+        },
+        {
+          "type": "null"
+        }
+      ]
+    },
+    "title": {
+      "anyOf": [
+        {
+          "type": "boolean"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    }
+  },
+  "additionalProperties": false
 }
diff --git a/lib/seek/isa_templates/template_extractor.rb b/lib/seek/isa_templates/template_extractor.rb
index 30c50ffb92..10d1e8ceb9 100644
--- a/lib/seek/isa_templates/template_extractor.rb
+++ b/lib/seek/isa_templates/template_extractor.rb
@@ -3,13 +3,12 @@
 module Seek
   module ISATemplates
     module TemplateExtractor
-      def self.extract_templates
+      def self.extract_templates(user)
         FileUtils.touch(resultfile)
         result = StringIO.new
         seed_isa_tags
 
-        disable_authorization_checks do
-          client = Ebi::OlsClient.new
+        User.with_current_user(user) do
           project = Project.find_or_create_by(title: 'Default Project')
           directory = Seek::Config.append_filestore_path('source_types')
           @directory_files = Dir.exist?(directory) ? Dir.glob("#{directory}/*.json") : []
@@ -38,54 +37,16 @@ def self.extract_templates
 
               current_template_attributes = []
               item['data'].each_with_index do |attribute, j|
-                is_ontology = attribute['ontology'].present?
-                is_cv = attribute['CVList'].present?
-                if is_ontology || is_cv
-                  scv =
-                    SampleControlledVocab.new(
-                      {
-                        title: attribute['name'],
-                        source_ontology: is_ontology ? attribute['ontology']['name'] : nil,
-                        ols_root_term_uris: is_ontology ? attribute['ontology']['rootTermURI'] : nil
-                      }
-                    )
-                end
-
-                if is_ontology
-                  if attribute['ontology']['rootTermURI'].present?
-                    begin
-                      terms = client.all_descendants(attribute['ontology']['name'],
-                                                     attribute['ontology']['rootTermURI'])
-                    rescue StandardError => e
-                      scv.save(validate: false)
-                      next
-                    end
-                    terms.each_with_index do |term, i|
-                      puts "#{j}) #{i + 1} FROM #{terms.length}"
-                      if i.zero?
-                        # Skip the parent name
-                        des = term[:description]
-                        scv[:description] = des.is_a?(Array) ? des[0] : des
-                      elsif term[:label].present? && term[:iri].present?
-                        cvt =
-                          SampleControlledVocabTerm.new(
-                            { label: term[:label], iri: term[:iri], parent_iri: term[:parent_iri] }
-                          )
-                        scv.sample_controlled_vocab_terms << cvt
-                      end
-                    end
-                  end
-                elsif is_cv
-                  # the CV terms
-                  if attribute['CVList'].present?
-                    attribute['CVList'].each do |term|
-                      cvt = SampleControlledVocabTerm.new({ label: term })
-                      scv.sample_controlled_vocab_terms << cvt
-                    end
-                  end
+                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?
+                  allow_cv_free_text = attribute['allowCVFreeText'].present? ? attribute['allowCVFreeText'] : false
+
+                  scv = cv_exists ? SampleControlledVocab.find_by(title: attribute['name']) : initialize_sample_controlled_vocab(template_details, attribute, is_ontology)
                 end
-
-                p scv.errors if (is_ontology || is_cv) && !scv.save(validate: false)
+                p scv.errors if is_cv && !scv.save(validate: false)
 
                 ta = TemplateAttribute.new(is_title: (attribute['title'] || 0),
                                      isa_tag_id: get_isa_tag_id(attribute['isaTag']),
@@ -95,12 +56,13 @@ def self.extract_templates
                                      sample_controlled_vocab_id: scv&.id,
                                      pid: attribute['pid'],
                                      sample_attribute_type_id: get_sample_attribute_type(attribute['dataType']),
-                                     allow_cv_free_text: attribute['ontology'].present?,
+                                     allow_cv_free_text: allow_cv_free_text,
                                      title: attribute['name'])
 
                 current_template_attributes.append ta
               end
               template.template_attributes << current_template_attributes
+              template.contributor = nil
               template.save! unless @errors.present?
             end
 
@@ -118,6 +80,51 @@ def self.extract_templates
         FileUtils.rm_f(@directory_files) unless @directory_files.blank?
       end
 
+      def self.initialize_sample_controlled_vocab(template_details, attribute, is_ontology = false)
+        scv = SampleControlledVocab.new(
+          {
+            title: attribute['name'],
+            source_ontology: is_ontology ? attribute['ontology']['name'] : nil,
+            ols_root_term_uris: is_ontology ? attribute['ontology']['rootTermURI'] : nil
+          }
+        )
+
+        if is_ontology
+          client = Ebi::OlsClient.new
+          if attribute['ontology']['rootTermURI'].present?
+            begin
+              terms = client.all_descendants(attribute['ontology']['name'],
+                                             attribute['ontology']['rootTermURI'])
+            rescue StandardError => e
+              add_log(template_details, "Failed to fetch terms from OLS for attribute '#{attribute['name']}'. Please add terms manually!")
+              Rails.logger.debug("Failed to fetch terms from OLS for attribute '#{attribute['name']}'. Error: #{e}")
+              terms = []
+            end
+            terms.each_with_index do |term, i|
+              puts "#{j}) #{i + 1} FROM #{terms.length}"
+              if i.zero?
+                # Skip the parent name
+                des = term[:description]
+                scv[:description] = des.is_a?(Array) ? des[0] : des
+              elsif term[:label].present? && term[:iri].present?
+                cvt =
+                  SampleControlledVocabTerm.new(
+                    { label: term[:label], iri: term[:iri], parent_iri: term[:parent_iri] }
+                  )
+                scv.sample_controlled_vocab_terms << cvt
+              end
+            end
+          end
+        else
+          # the CV terms
+          attribute['CVList'].each do |term|
+            cvt = SampleControlledVocabTerm.new({ label: term })
+            scv.sample_controlled_vocab_terms << cvt
+          end
+        end
+        scv
+      end
+
       def self.init_template(metadata)
         {
           title: metadata['name'],
@@ -169,7 +176,7 @@ def self.valid_isa_json?(json)
       end
 
       def self.get_sample_attribute_type(title)
-        sa = SampleAttributeType.find_by(title:)
+        sa = SampleAttributeType.find_by(title: title)
         @errors.append "<li>Could not find a Sample Attribute Type named '#{title}'</li>" if sa.nil?
 
         return if sa.nil?
@@ -180,10 +187,10 @@ def self.get_sample_attribute_type(title)
       def self.get_isa_tag_id(title)
         return nil if title.blank?
 
-        it = ISATag.find_by(title:)
+        it = ISATag.find_by(title: title)
         @errors.append "<li>Could not find an ISA Tag named '#{title}'</li>" if it.nil?
 
-        it.id
+        it&.id
       end
 
       def self.seed_isa_tags
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
new file mode 100644
index 0000000000..4eaef0dd67
--- /dev/null
+++ b/test/fixtures/files/upload_json_sample_type_template/test_apple_cv_template.json
@@ -0,0 +1,102 @@
+{
+  "data": [
+    {
+      "metadata": {
+        "name": "Test Apple CV Template",
+        "group": "SEEK Test",
+        "group_order": 1,
+        "temporary_name": "1_test_apple_cv_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": "Source Characteristic 1",
+          "description": "A characteristic of the source",
+          "dataType": "String",
+          "required": true,
+          "ontology": null,
+          "allowCVFreeText": null,
+          "CVList": null,
+          "isaTag": "source_characteristic"
+        },
+        {
+          "iri": null,
+          "name": "apples controlled vocab for template",
+          "description": "",
+          "dataType": "Controlled Vocabulary",
+          "required": false,
+          "ontology": null,
+          "allowCVFreeText": true,
+          "CVList": [
+            "Granny Smith",
+            "Golden Delicious",
+            "Bramley",
+            "Cox's Orange Pippin"
+          ],
+          "isaTag": "source_characteristic"
+        },
+        {
+          "iri": null,
+          "name": "physics ontology",
+          "description": "",
+          "dataType": "Controlled Vocabulary List",
+          "required": false,
+          "ontology": {
+            "name": "edam",
+            "version": "",
+            "description": "The study of matter, space and time, and related concepts such as energy and force.",
+            "rootTermURI": "http://edamontology.org/topic_3318"
+          },
+          "allowCVFreeText": false,
+          "CVList": null,
+          "isaTag": "source_characteristic"
+        },
+        {
+          "iri": null,
+          "name": "New CV List",
+          "description": "",
+          "dataType": "Controlled Vocabulary List",
+          "required": false,
+          "ontology": null,
+          "CVList": [
+            "term 1",
+            "term 2"
+          ],
+          "isaTag": "source_characteristic"
+        },
+        {
+          "iri": null,
+          "name": "New ontology List",
+          "description": "",
+          "dataType": "Controlled Vocabulary List",
+          "required": false,
+          "ontology": {
+            "name": "FBbi",
+            "version": "",
+            "description": "Imaging method",
+            "rootTermURI": "http://purl.obolibrary.org/obo/FBbi_00000222"
+          },
+          "CVList": null,
+          "isaTag": "source_characteristic"
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file
diff --git a/test/fixtures/files/upload_json_sample_type_template/test_templates.json b/test/fixtures/files/upload_json_sample_type_template/test_templates.json
index ce4e2f20cc..0643aee1af 100644
--- a/test/fixtures/files/upload_json_sample_type_template/test_templates.json
+++ b/test/fixtures/files/upload_json_sample_type_template/test_templates.json
@@ -20,7 +20,7 @@
 					"iri": null,
 					"name": "Source Name",
 					"description": "Sources are considered as the starting biological material used in a study.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"title": true,
 					"required": true,
 					"isaTag": "source"
@@ -29,7 +29,7 @@
 					"iri": null,
 					"name": "Source Characteristic 1",
 					"description": "A characteristic of the source.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -57,7 +57,7 @@
 					"iri": null,
 					"name": "Input",
 					"description": "Registered Samples in the platform used as input for this protocol.",
-					"dataType": "Sample multi attribute type 1",
+					"dataType": "Registered Sample List",
 					"required": true,
 					"isaTag": null
 				},
@@ -65,7 +65,7 @@
 					"iri": null,
 					"name": "Name of a protocol with samples as outputs",
 					"description": "Type of experimental step that generates samples as outputs from the study sources.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -75,7 +75,7 @@
 					"iri": null,
 					"name": "Name of protocol parameter 1",
 					"description": "A parameter for the protocol.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -85,7 +85,7 @@
 					"iri": null,
 					"name": "Sample Name",
 					"description": "Samples are considered as biological material sampled from sources and used in the study.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"title": true,
 					"required": true,
 					"isaTag": "sample"
@@ -94,7 +94,7 @@
 					"iri": null,
 					"name": "Sample Characteristic 1",
 					"description": "A characteristic of the sample.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -122,7 +122,7 @@
 					"iri": null,
 					"name": "Input",
 					"description": "Registered Samples in the platform used as input for this protocol.",
-					"dataType": "Sample multi attribute type 1",
+					"dataType": "Registered Sample List",
 					"required": true,
 					"isaTag": null
 				},
@@ -130,7 +130,7 @@
 					"iri": null,
 					"name": "Name of a protocol with material output",
 					"description": "Type of assay or experimental step performed that generates a material output.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -140,7 +140,7 @@
 					"iri": null,
 					"name": "Name of protocol parameter 1",
 					"description": "A parameter for the protocol.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -150,7 +150,7 @@
 					"iri": null,
 					"name": "Output material Name",
 					"description": "Name of the major material output resulting from the application of the protocol.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"title": true,
 					"required": true,
 					"isaTag": "other_material"
@@ -159,7 +159,7 @@
 					"iri": null,
 					"name": "Output material characteristic 1",
 					"description": "Characteristic 1 of the output material.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -187,7 +187,7 @@
 					"iri": null,
 					"name": "Input",
 					"description": "Registered Samples in the platform used as input for this protocol.",
-					"dataType": "Sample multi attribute type 1",
+					"dataType": "Registered Sample List",
 					"required": true,
 					"isaTag": null
 				},
@@ -195,7 +195,7 @@
 					"iri": null,
 					"name": "Name of a protocol with data file output",
 					"description": "Type of assay or experimental step performed that generates a data file output.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -205,7 +205,7 @@
 					"iri": null,
 					"name": "Name of protocol parameter 1",
 					"description": "A parameter for the protocol.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
@@ -215,7 +215,7 @@
 					"iri": null,
 					"name": "Data file Name",
 					"description": "Name of the major data file output resulting from the application of the protocol.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"title": true,
 					"required": true,
 					"isaTag": "data_file"
@@ -224,7 +224,7 @@
 					"iri": null,
 					"name": "Data file characteristic 1",
 					"description": "Characteristic 1 of the data file output.",
-					"dataType": "String attribute type 1",
+					"dataType": "String",
 					"required": true,
 					"ontology": null,
 					"CVList": null,
diff --git a/test/functional/templates_controller_test.rb b/test/functional/templates_controller_test.rb
index 566f16496f..9673aeab8d 100644
--- a/test/functional/templates_controller_test.rb
+++ b/test/functional/templates_controller_test.rb
@@ -14,17 +14,18 @@ class TemplatesControllerTest < ActionController::TestCase
 
     FactoryBot.create(:person) # to prevent person being first person and therefore admin
     @person = FactoryBot.create(:project_administrator)
+    @admin = FactoryBot.create(:admin)
     @project = @person.projects.first
     @project_ids = [@project.id]
     refute_nil @project
     login_as(@person)
     @template = FactoryBot.create(:min_template, project_ids: @project_ids, contributor: @person)
-    @string_type = FactoryBot.create(:string_sample_attribute_type)
-    @int_type = FactoryBot.create(:integer_sample_attribute_type)
-    @registered_sample_attribute_type = FactoryBot.create(:sample_sample_attribute_type)
-    @registered_sample_multi_attribute_type = FactoryBot.create(:sample_multi_sample_attribute_type)
-    @controlled_vocab_type = FactoryBot.create(:controlled_vocab_attribute_type)
-    @controlled_vocab_list_type = FactoryBot.create(:cv_list_attribute_type)
+    @string_type = SampleAttributeType.find_by(title: "String").nil? ? FactoryBot.create(:string_sample_attribute_type, title: "string") : SampleAttributeType.find_by(title: "String")
+    @int_type = SampleAttributeType.find_by(title: "Integer").nil? ? FactoryBot.create(:integer_sample_attribute_type) : SampleAttributeType.find_by(title: "Integer")
+    @registered_sample_attribute_type = SampleAttributeType.find_by(title: "Registered Sample").nil? ? FactoryBot.create(:sample_sample_attribute_type) : SampleAttributeType.find_by(title: "Registered Sample")
+    @registered_sample_multi_attribute_type = SampleAttributeType.find_by(title: "Registered Sample List").nil? ? FactoryBot.create(:sample_multi_sample_attribute_type) : SampleAttributeType.find_by(title: "Registered Sample List")
+    @controlled_vocab_type = SampleAttributeType.find_by(title: "Controlled Vocabulary").nil? ? FactoryBot.create(:controlled_vocab_attribute_type) : SampleAttributeType.find_by(title: "Controlled Vocabulary")
+    @controlled_vocab_list_type = SampleAttributeType.find_by(title: "Controlled Vocabulary List").nil? ? FactoryBot.create(:cv_list_attribute_type) : SampleAttributeType.find_by(title: "Controlled Vocabulary List")
     @default_isa_tag = FactoryBot.create(:default_isa_tag)
   end
 
@@ -650,6 +651,72 @@ class TemplatesControllerTest < ActionController::TestCase
     assert_select 'script#project-selector-possibilities-json', text: /#{options}/, count: 1
   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")
+    assert_equal SampleControlledVocab.count, 2
+
+    login_as(@admin)
+    ####################################################################################################################
+    # This file contains the JSON definition for 1 template with 6 template attributes:
+    # 1. Source Name (Sting) => New
+    # 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) List => New
+    # 6. New ontology List (CV List, ontology) => New
+    # New template attributes should be 6
+    # New sample controlled vocabs should be 2
+    ####################################################################################################################
+    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
+        assert_difference('SampleControlledVocab.count', 2) do
+          perform_enqueued_jobs(only: PopulateTemplatesJob)
+        end
+      end
+    end
+    registered_template = Template.last
+    assert_equal registered_template.template_attributes.detect { |ta| ta.title == 'apples controlled vocab for template' }.sample_controlled_vocab, apples_cv
+    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)
diff --git a/test/unit/jobs/populate_templates_job_test.rb b/test/unit/jobs/populate_templates_job_test.rb
index 0558063667..8b91d8c7df 100644
--- a/test/unit/jobs/populate_templates_job_test.rb
+++ b/test/unit/jobs/populate_templates_job_test.rb
@@ -4,8 +4,8 @@ class PopulateTemplatesJobTest < ActiveSupport::TestCase
   def setup
     # Create the SampleAttributeTypes
     # The title MUST be set manually!
-    FactoryBot.create(:string_sample_attribute_type, title: 'String attribute type 1')
-    FactoryBot.create(:sample_multi_sample_attribute_type, title: 'Sample multi attribute type 1')
+    FactoryBot.create(:string_sample_attribute_type, title: 'String') if SampleAttributeType.find_by(title: 'String').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
     %i[source_isa_tag sample_isa_tag protocol_isa_tag source_characteristic_isa_tag sample_characteristic_isa_tag 
@@ -16,6 +16,7 @@ def setup
 
     # Set isa_json_compliance_enabled to true
     Seek::Config.isa_json_compliance_enabled = true
+    @admin = FactoryBot.create(:admin)
   end
 
   def teardown
@@ -31,7 +32,7 @@ def teardown
 
     assert_nothing_raised do
       assert_difference('Template.count', 4) do
-        PopulateTemplatesJob.perform_now
+        PopulateTemplatesJob.perform_now(@admin)
       end
     end
   end
@@ -44,8 +45,8 @@ def teardown
 
     assert_no_difference('Template.count') do
       assert_raises(RuntimeError, 
-'<ul><li>The property \'#/data/0/data/1/dataType\' value \"Invalid String attribute type 1\" did not match one of the following values: String attribute type 1, Sample multi attribute type 1 in schema file:///home/kepel/projects/seek/lib/seek/isa_templates/template_attributes_schema_test.json#</li><li>Could not find a Sample Attribute Type named \'Invalid String attribute type 1\'</li></ul>') do
-        PopulateTemplatesJob.perform_now
+'<ul><li>The property \'#/data/0/data/1/dataType\' value \"Invalid String attribute type 1\" did not match one of the following values: ') do
+        PopulateTemplatesJob.perform_now(@admin)
       end
     end
   end