some final tidying up, in particualr removed the fetch ols as JSON se…

…ek4science#1691
ScilifelabDataCentre · Dec 13, 2023 · 5fcca0c · 5fcca0c
1 parent f4a24ae
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Showing 5 changed files with 1 addition and 102 deletions.
diff --git a/app/assets/javascripts/controlled_vocabs.js.erb b/app/assets/javascripts/controlled_vocabs.js.erb
@@ -89,30 +89,6 @@ CVTerms = {
     handleOntologyTermsHTMLResponse: function (html) {
         $j('#add-term-button-row').before(html);
     },
-    // processes the JSON response when fetching terms, and populates the term list
-    handleOntologyTermsJSONResponse: function (json) {
-        let index=0
-        $j.each(json, function (key, term) {
-            //make a new term
-            let newTerm = $j('#new-term-row tbody').clone().html();
-
-            newTerm = newTerm.replace(/--index--/g, index);
-            $j('#add-term-button-row').before($j(newTerm));
-
-            let row = $j('table#new-terms tr.sample-cv-term').last();
-
-            let inputs = $j(row).find('td input');
-            $j(inputs).prop('readonly',true);
-
-            //inputs 0,1,2 are label, iri, and parent_iri
-
-            $j(inputs[0]).val(term.label);
-            $j(inputs[1]).val(term.iri);
-            $j(inputs[2]).val(term.parent_iri);
-
-            index++;
-        });
-    },
     // adds a new blank row to the terms list
     addNewTermRow: function () {
         let newTerm = $j('#new-term-row tbody').clone().html();
@@ -130,8 +106,6 @@ CVTerms = {
     },
     // reports the error when the ajax method to fetch the terms is unsuccessful
     reportFetchError: function (error_message) {
-//        let json = JSON.parse(response);
-//        const error_message = json.errors[0].details;
         $j('div#fetch-error-message').text("An error occurred fetching the terms: " + error_message);
         $j('div#fetch-error-message').show();
     },

diff --git a/app/controllers/sample_controlled_vocabs_controller.rb b/app/controllers/sample_controlled_vocabs_controller.rb
@@ -85,31 +85,6 @@ def destroy
     end
   end
 
-  def fetch_ols_terms
-    error_msg = nil
-    begin
-      source_ontology = params[:source_ontology_id]
-      root_uri = params[:root_uri]
-
-      raise 'No root URI provided' if root_uri.blank?
-
-      client = Ebi::OlsClient.new
-      terms = client.all_descendants(source_ontology, root_uri)
-      terms.reject! { |t| t[:iri] == root_uri } unless params[:include_root_term] == '1'
-      error_msg = "There are no descendant terms to populate the list." unless terms.present?
-    rescue StandardError => e
-      error_msg = e.message
-    end
-
-    respond_to do |format|
-      if error_msg
-        format.json { render json: { errors: [{ details: error_msg }] }, status: :unprocessable_entity }
-      else
-        format.json { render json: terms.to_json }
-      end
-    end
-  end
-
   def fetch_ols_terms_html
     error_msg = nil
     begin

diff --git a/app/views/sample_controlled_vocabs/_form.html.erb b/app/views/sample_controlled_vocabs/_form.html.erb
@@ -31,7 +31,6 @@
 
     <div class="form-group">
       <label>Ontology</label>
-      <%#= f.select :source_ontology, Ebi::OlsClient.ontology_choices, { include_blank: 'No Ontology' }, class: 'form-control' -%>
       <%= select_cv_source_ontology(@sample_controlled_vocab) %>
       <br/>
 

diff --git a/config/routes.rb b/config/routes.rb
@@ -699,7 +699,6 @@
   resources :sample_controlled_vocabs do
     collection do
       get :typeahead
-      get :fetch_ols_terms
       get :fetch_ols_terms_html
     end
   end

diff --git a/test/functional/sample_controlled_vocabs_controller_test.rb b/test/functional/sample_controlled_vocabs_controller_test.rb
@@ -1,6 +1,7 @@
 require 'test_helper'
 
 class SampleControlledVocabsControllerTest < ActionController::TestCase
+
   include AuthenticatedTestHelper
 
   test 'show' do
@@ -267,55 +268,6 @@ class SampleControlledVocabsControllerTest < ActionController::TestCase
     end
   end
 
-  test 'fetch ols terms as JSON with root term included' do
-    person = FactoryBot.create(:person)
-    login_as(person)
-    VCR.use_cassette('ols/fetch_obo_plant_cell_papilla') do
-      get :fetch_ols_terms, params: { source_ontology_id: 'go',
-                                      root_uri: 'http://purl.obolibrary.org/obo/GO_0090395',
-                                      include_root_term: '1' }, format: :json
-
-      assert_response :success
-      res = JSON.parse(response.body)
-      assert_equal 4, res.length
-      iris = res.map { |term| term['iri'] }
-      assert_includes iris, 'http://purl.obolibrary.org/obo/GO_0090395'
-      assert_includes iris, 'http://purl.obolibrary.org/obo/GO_0090396'
-      assert_includes iris, 'http://purl.obolibrary.org/obo/GO_0090397'
-    end
-  end
-
-  test 'fetch ols terms as JSON without root term included' do
-    person = FactoryBot.create(:person)
-    login_as(person)
-    VCR.use_cassette('ols/fetch_obo_plant_cell_papilla') do
-      get :fetch_ols_terms, params: { source_ontology_id: 'go',
-                                      root_uri: 'http://purl.obolibrary.org/obo/GO_0090395' }, format: :json
-
-      assert_response :success
-      res = JSON.parse(response.body)
-      assert_equal 3, res.length
-      iris = res.map { |term| term['iri'] }
-      refute_includes iris, 'http://purl.obolibrary.org/obo/GO_0090395'
-      assert_includes iris, 'http://purl.obolibrary.org/obo/GO_0090396'
-      assert_includes iris, 'http://purl.obolibrary.org/obo/GO_0090397'
-    end
-  end
-
-  test 'fetch ols terms as JSON with wrong URI' do
-    person = FactoryBot.create(:person)
-    login_as(person)
-    VCR.use_cassette('ols/fetch_obo_bad_term') do
-      get :fetch_ols_terms, params: { source_ontology_id: 'go',
-                                      root_uri: 'http://purl.obolibrary.org/obo/banana',
-                                      include_root_term: '1' }, format: :json
-
-      assert_response :unprocessable_entity
-      res = JSON.parse(response.body)
-      assert_equal '404 Not Found', res.dig('errors', 0, 'details')
-    end
-  end
-
   test 'fetch ols terms as HTML with wrong URI' do
     person = FactoryBot.create(:person)
     login_as(person)