Merge branch 'main' into full-test-suite

Gemfile

@@ -154,7 +154,7 @@ gem 'remotipart', '~> 1.4.4' # Allows file upload in AJAX forms
 
 gem 'rails-static-router'
 
-gem 'caxlsx', '>= 3.0' # Write content to an xlsx file
+gem 'caxlsx', '>= 4.0' # Write content to an xlsx file
 gem 'caxlsx_rails', '~> 0.6.2'
 
 gem 'net-ftp'
@@ -181,10 +181,10 @@ group :development do
   gem "flamegraph", "~> 0.9.5"
   gem "stackprof", "~> 0.2.25"
   gem 'listen', '~> 3.3'
+  gem 'ruby-prof'
 end
 
 group :test do
-  gem 'ruby-prof'
   gem 'test-prof'
   gem 'rails-perftest'
   gem 'minitest', '~> 5.14'

Gemfile.lock

@@ -50,7 +50,7 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    RedCloth (4.3.2)
+    RedCloth (4.3.3)
     actioncable (6.1.7.6)
       actionpack (= 6.1.7.6)
       activesupport (= 6.1.7.6)
@@ -168,7 +168,7 @@ GEM
     builder (3.2.4)
     case_transform (0.2)
       activesupport
-    caxlsx (3.3.0)
+    caxlsx (4.0.0)
       htmlentities (~> 4.3, >= 4.3.4)
       marcel (~> 1.0)
       nokogiri (~> 1.10, >= 1.10.4)
@@ -491,7 +491,7 @@ GEM
     net-smtp (0.3.3)
       net-protocol
     netrc (0.11.0)
-    nio4r (2.5.9)
+    nio4r (2.7.0)
     nokogiri (1.14.5)
       mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
@@ -563,7 +563,7 @@ GEM
     psych (5.1.0)
       stringio
     public_suffix (5.0.0)
-    puma (5.6.7)
+    puma (5.6.8)
       nio4r (~> 2.0)
     pyu-ruby-sasl (0.0.3.3)
     racc (1.7.1)
@@ -979,7 +979,7 @@ DEPENDENCIES
   bootsnap (>= 1.4.4)
   bootstrap-sass (>= 3.4.1)
   bundler (>= 1.8.4)
-  caxlsx (>= 3.0)
+  caxlsx (>= 4.0)
   caxlsx_rails (~> 0.6.2)
   cff (~> 0.9.0)
   citeproc-ruby (~> 2.0.0)

app/assets/javascripts/application.js

@@ -76,3 +76,4 @@
 //= require jquery.splitter/jquery.splitter.min
 //= require select2.full.min
 //= require licenses
+//= require svg-pan-zoom-3.6.1/svg-pan-zoom.min

app/assets/javascripts/application_shared.js.erb

@@ -175,6 +175,9 @@ function digValue(object, path) {
             elements.removeClass(cssClass)
         }, 1100);
     };
+
+    // Fixes select2 in modals: https://github.com/select2/select2/issues/1436
+    $j.fn.modal.Constructor.prototype.enforceFocus = function () {};
 }(jQuery));
 
 $j(document).ready(function () {
@@ -401,6 +404,21 @@ $j(document).ready(function () {
     $j(document).on('click', '.sidebar-backdrop', Sidebar.toggle);
 
     Licenses.init();
+
+    $j('.svg-pan-zoom').each(function () {
+        // Does not seem to work using jQuery load event, so doing it vanilla way
+        this.addEventListener('load', function () {
+            svgPanZoom(this, {
+                zoomEnabled: true,
+                dblClickZoomEnabled: true,
+                mouseWheelZoomEnabled: false,
+                controlIconsEnabled: true,
+                contain: false,
+                fit: true
+            });
+        });
+    });
 });
 
+
 var URL_ROOT = '<%= Rails.application.config.relative_url_root %>';

app/assets/javascripts/controlled_vocabs.js.erb

@@ -86,43 +86,26 @@ CVTerms = {
             $j(':input:not(.destroy-attribute)', row).prop('disabled', false);
         }
     },
-    // processes the JSON response when fetching terms, and populates the term list
-    handleOntologyTermsJSONResponse: function (json) {
-        $j.each(json, function (key, term) {
-            //make a new term
-            CVTerms.addNewTermRow();
-
-            //get the last row and its inputs
-            var row = $j('table#new-terms tr.sample-cv-term').last();
-            var 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);
-        });
+    handleOntologyTermsHTMLResponse: function (html) {
+        $j('#add-term-button-row').before(html);
     },
     // adds a new blank row to the terms list
     addNewTermRow: function () {
-        var newTerm = $j('#new-term-row tbody').clone().html();
+        let newTerm = $j('#new-term-row tbody').clone().html();
 
-        var index = 0;
-        $j('#new-terms tr.sample-cv-term').each(function () {
-            var newIndex = parseInt($j(this).data('index'));
-            if (newIndex > index) {
-                index = newIndex;
-            }
-        });
+        let index = 0;
+
+        //can't be reordered, so the last should always be the highest index
+        if ($j('#new-terms tr.sample-cv-term').length) {
+            index = parseInt($j('#new-terms tr.sample-cv-term').last().data('index'));
+        }
         index++;
 
         newTerm = newTerm.replace(/--index--/g, index);
         $j('#add-term-button-row').before($j(newTerm));
     },
     // reports the error when the ajax method to fetch the terms is unsuccessful
-    reportFetchError: function (json) {
-        var error_message = json.errors[0].details;
+    reportFetchError: function (error_message) {
         $j('div#fetch-error-message').text("An error occurred fetching the terms: " + error_message);
         $j('div#fetch-error-message').show();
     },
@@ -135,23 +118,6 @@ CVTerms = {
             }
         });
     },
-    disableAddTermButton: function(reason) {
-        $j('a#add-term').attr('disabled', true);
-        if (!$j('a#add-term').parent().is('span')) {
-            let span = $j('a#add-term').wrap('<span />').parent();
-            $j(span).attr('data-tooltip', reason);
-            bindTooltips('div#controlled-vocab-terms');
-            $j(span).click(function () {
-                alert(reason);
-            });
-        }
-    },
-    enableAddTermButton: function() {
-        let button = $j('a#add-term');
-        button.attr('disabled',false);
-        button.removeClass('disabled');
-        button.unwrap('span');
-    },
     // sets up and trigger the ajax call to fetch the terms list
     fetchTermsAJAX: function () {
         $j('div#controlled-vocab-terms').hide();
@@ -161,19 +127,19 @@ CVTerms = {
         $j('input#fetch-ontology-terms-submit').prop('disabled', true);
 
         $j.ajax({
-            url: '<%= fetch_ols_terms_sample_controlled_vocabs_path %>',
-            dataType: "json",
+            url: '<%= fetch_ols_terms_html_sample_controlled_vocabs_path %>',
+            dataType: "html",
             data: {
                 source_ontology_id: $j('select#sample_controlled_vocab_source_ontology').val(),
                 root_uri: $j('#sample_controlled_vocab_ols_root_term_uri').val(),
                 include_root_term: $j('#include_root_term:checked').val()
             },
             success: function (resp) {
                 CVTerms.clearAllTerms();
-                CVTerms.handleOntologyTermsJSONResponse((resp));
+                CVTerms.handleOntologyTermsHTMLResponse(resp);
             },
             error: function (resp) {
-                CVTerms.reportFetchError(resp.responseJSON);
+                CVTerms.reportFetchError(resp.responseText);
             },
             complete: function () {
                 $j('#fetch-terms-spinner').spinner('remove');
@@ -209,10 +175,8 @@ CVTerms = {
             if (selected.value == "") {
                 $j('#sample_controlled_vocab_ols_root_term_uri').val('');
                 $j('#ontology-root-uri').hide();
-                CVTerms.enableAddTermButton();
             } else {
                 $j('#ontology-root-uri').show();
-                CVTerms.disableAddTermButton('<%= I18n.t('controlled_vocabs.add_new_term_disabled_reason') %>');
                 var link = $j('a#selected-ols-link');
                 link.text(selected.text);
                 link.attr('href', '<%= Ebi::OlsClient::ROOT_URL %>/ontologies/' + selected.value);