Merge seek 1.15.1 into LDH

Gemfile

@@ -54,7 +54,7 @@ gem 'will_paginate', '~> 3.1'
 gem 'yaml_db'
 gem 'rails_autolink'
 gem 'rfc-822'
-gem 'nokogiri', '~> 1.16.2'
+gem 'nokogiri', '~> 1.16'
 #necessary for newer hashie dependency, original api_smith is no longer active
 gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b'
 gem 'rdf-virtuoso', '>= 0.2.0'

Gemfile.lock

@@ -51,40 +51,40 @@ GEM
   remote: https://rubygems.org/
   specs:
     RedCloth (4.3.3)
-    actioncable (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actioncable (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       nio4r (~> 2.0)
       websocket-driver (>= 0.6.1)
-    actionmailbox (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      activejob (= 6.1.7.7)
-      activerecord (= 6.1.7.7)
-      activestorage (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actionmailbox (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      activejob (= 6.1.7.8)
+      activerecord (= 6.1.7.8)
+      activestorage (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       mail (>= 2.7.1)
-    actionmailer (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      actionview (= 6.1.7.7)
-      activejob (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actionmailer (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      actionview (= 6.1.7.8)
+      activejob (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       mail (~> 2.5, >= 2.5.4)
       rails-dom-testing (~> 2.0)
-    actionpack (6.1.7.7)
-      actionview (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actionpack (6.1.7.8)
+      actionview (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       rack (~> 2.0, >= 2.0.9)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actiontext (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      activerecord (= 6.1.7.7)
-      activestorage (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actiontext (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      activerecord (= 6.1.7.8)
+      activestorage (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       nokogiri (>= 1.8.5)
-    actionview (6.1.7.7)
-      activesupport (= 6.1.7.7)
+    actionview (6.1.7.8)
+      activesupport (= 6.1.7.8)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
@@ -94,14 +94,14 @@ GEM
       activemodel (>= 4.1, < 7.1)
       case_transform (>= 0.2)
       jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
-    activejob (6.1.7.7)
-      activesupport (= 6.1.7.7)
+    activejob (6.1.7.8)
+      activesupport (= 6.1.7.8)
       globalid (>= 0.3.6)
-    activemodel (6.1.7.7)
-      activesupport (= 6.1.7.7)
-    activerecord (6.1.7.7)
-      activemodel (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    activemodel (6.1.7.8)
+      activesupport (= 6.1.7.8)
+    activerecord (6.1.7.8)
+      activemodel (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
     activerecord-import (1.3.0)
       activerecord (>= 4.2)
     activerecord-session_store (2.0.0)
@@ -110,14 +110,14 @@ GEM
       multi_json (~> 1.11, >= 1.11.2)
       rack (>= 2.0.8, < 3)
       railties (>= 5.2.4.1)
-    activestorage (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      activejob (= 6.1.7.7)
-      activerecord (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    activestorage (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      activejob (= 6.1.7.8)
+      activerecord (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       marcel (~> 1.0)
       mini_mime (>= 1.1.0)
-    activesupport (6.1.7.7)
+    activesupport (6.1.7.8)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -198,7 +198,7 @@ GEM
       execjs
     coffee-script-source (1.12.2)
     commonmarker (0.23.10)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.1)
     connection_pool (2.3.0)
     countries (5.2.0)
       unaccent (~> 0.3)
@@ -322,7 +322,7 @@ GEM
     httpclient (2.8.3)
     httpi (1.1.1)
       rack
-    i18n (1.14.4)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
     i18n-js (3.9.0)
       i18n (>= 0.6.6)
@@ -460,7 +460,7 @@ GEM
       nokogiri (~> 1)
       rake
     mini_mime (1.1.5)
-    mini_portile2 (2.8.5)
+    mini_portile2 (2.8.7)
     minitest (5.20.0)
     minitest-reporters (1.5.0)
       ansi
@@ -492,7 +492,7 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.7.0)
-    nokogiri (1.16.2)
+    nokogiri (1.16.5)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     nori (1.1.5)
@@ -566,8 +566,8 @@ GEM
     puma (5.6.8)
       nio4r (~> 2.0)
     pyu-ruby-sasl (0.0.3.3)
-    racc (1.7.3)
-    rack (2.2.8.1)
+    racc (1.8.0)
+    rack (2.2.9)
     rack-attack (6.6.0)
       rack (>= 1.0, < 3)
     rack-cors (1.1.1)
@@ -584,20 +584,20 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rails (6.1.7.7)
-      actioncable (= 6.1.7.7)
-      actionmailbox (= 6.1.7.7)
-      actionmailer (= 6.1.7.7)
-      actionpack (= 6.1.7.7)
-      actiontext (= 6.1.7.7)
-      actionview (= 6.1.7.7)
-      activejob (= 6.1.7.7)
-      activemodel (= 6.1.7.7)
-      activerecord (= 6.1.7.7)
-      activestorage (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    rails (6.1.7.8)
+      actioncable (= 6.1.7.8)
+      actionmailbox (= 6.1.7.8)
+      actionmailer (= 6.1.7.8)
+      actionpack (= 6.1.7.8)
+      actiontext (= 6.1.7.8)
+      actionview (= 6.1.7.8)
+      activejob (= 6.1.7.8)
+      activemodel (= 6.1.7.8)
+      activerecord (= 6.1.7.8)
+      activestorage (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       bundler (>= 1.15.0)
-      railties (= 6.1.7.7)
+      railties (= 6.1.7.8)
       sprockets-rails (>= 2.0.0)
     rails-controller-testing (1.0.5)
       actionpack (>= 5.0.1.rc1)
@@ -625,9 +625,9 @@ GEM
       json
       require_all (~> 3.0)
       ruby-progressbar
-    railties (6.1.7.7)
-      actionpack (= 6.1.7.7)
-      activesupport (= 6.1.7.7)
+    railties (6.1.7.8)
+      actionpack (= 6.1.7.8)
+      activesupport (= 6.1.7.8)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -728,7 +728,8 @@ GEM
       netrc (~> 0.8)
     reverse_markdown (2.1.1)
       nokogiri
-    rexml (3.2.5)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rfc-822 (0.4.1)
     rmagick (5.3.0)
       pkg-config (~> 1.4)
@@ -861,6 +862,7 @@ GEM
     sqlite3 (1.4.2)
     stackprof (0.2.25)
     stringio (3.0.1.1)
+    strscan (3.1.0)
     sunspot (2.6.0)
       pr_geohash (~> 1.0)
       rsolr (>= 1.1.1, < 3)
@@ -950,7 +952,7 @@ GEM
       rails (>= 3.0)
       rake (>= 0.8.7)
     yard (0.9.36)
-    zeitwerk (2.6.13)
+    zeitwerk (2.6.15)
     zip-container (4.0.2)
       rubyzip (~> 2.0.0)
 
@@ -1028,7 +1030,7 @@ DEPENDENCIES
   my_responds_to_parent!
   mysql2
   net-ftp
-  nokogiri (~> 1.16.2)
+  nokogiri (~> 1.16)
   omniauth (~> 2.1.0)
   omniauth-github
   omniauth-rails_csrf_protection

app/assets/javascripts/single_page/dynamic_table.js.erb

@@ -48,7 +48,7 @@ function sanitizeData(data) {
 
 const objectInputTemp = '<input type="hidden" name="_NAME_[]" id="inpt-_NAME_" value="" autocomplete="off" />' +
   '<select name="_NAME_[]" id="select-_NAME_" class="form-control _EXTRACLASS_" title="_TITLE_" data-role="seek-objectsinput" ' +
-  'data-tags-limit="100" _MULTIPLE?_ style="background-color: coral;" data-typeahead-template="_TYPEHEAD_"' +
+  'data-tags-limit="_LIMIT?_" multiple style="background-color: coral;" data-typeahead-template="_TYPEHEAD_"' +
   'data-typeahead-query-url="_URL_" data-allow-new-items=_ALLOW_FREE_TEXT_>_OPTIONS_</select>';
 
 const typeaheadSamplesUrl = "<%= typeahead_samples_path(linked_sample_type_id: '_LINKED_') %>";
@@ -86,11 +86,12 @@ const handleSelect = (e) => {
         }
 
         c["render"] = function(data_, type, full, meta) {
-          sanitizedData = sanitizeData(data_);
+          let sanitizedData = sanitizeData(data_);
+          let data;
           if(c.linked_sample_type){
             data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData];
             data = data[0]?.id ? data : [];
-            return inputObjectsInput(c, data, options, linkedSamplesUrl);
+            return registeredSamplesObjectsInput(c, data, options, linkedSamplesUrl);
           } else if(c.is_cv_list && sanitizedData !== "#HIDDEN"){
               data = sanitizedData && Array.isArray(sanitizedData) ? sanitizedData : [sanitizedData];
               data = data.map((e) => {
@@ -569,7 +570,7 @@ function retrieveLinkedSamples(url){
   return linkedSamples;
 }
 
-function inputObjectsInput(column, data, options, url){
+function registeredSamplesObjectsInput(column, data, options, url){
   const existingOptions = data.map((e) => {
     isHiddenInput = (e.title == '#HIDDEN');
     if (isHiddenInput) {
@@ -584,7 +585,6 @@ function inputObjectsInput(column, data, options, url){
     const typeaheadTemplate = 'typeahead/single_pages_samples'
     const objectInputName = data.map((e) => e.id).join('-') + '-' + crypto.randomUUID();
 
-
     const unLinkedSamples = data.reduce(function(filtered, sample) {
       if(!column.linkedSampleIds.includes(parseInt(sample.id)) && sample.title != '#HIDDEN'){
         filtered.push(sample);
@@ -593,7 +593,7 @@ function inputObjectsInput(column, data, options, url){
     }, []);
     const hasUnlinkedSamples = unLinkedSamples.length > 0 ? true : false;
 
-    const hasMultipleInputs = column.multi_link ? 'multiple="multiple"' : ''
+    const hasMultipleInputs = column.multi_link ? '100' : '1'
     const extraClass = hasUnlinkedSamples ? 'select2__error' : '';
     const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as input. Please correct this issue!` : '';
     setTimeout(ObjectsInput.init);
@@ -605,7 +605,7 @@ function inputObjectsInput(column, data, options, url){
     .replace('_OPTIONS_', existingOptions)
     .replace('_EXTRACLASS_', extraClass)
     .replace('_TITLE_', titleText)
-    .replace('_MULTIPLE?_', hasMultipleInputs)
+    .replace('_LIMIT?_', hasMultipleInputs)
     .replace('_ALLOW_FREE_TEXT_', false);
   }
 }
@@ -629,7 +629,7 @@ function cvListObjectsInput(column, data, options, url){
     .replace('_OPTIONS_', existingOptions)
     .replace('_EXTRACLASS_', extraClass)
     .replace('_TITLE_', titleText)
-    .replace('_MULTIPLE?_', 'multiple="multiple"')
+    .replace('_LIMIT?_', '')
     .replace('_ALLOW_FREE_TEXT_', allowNewItems);
   }
 }

app/assets/javascripts/templates.js

@@ -222,6 +222,7 @@ const applyTemplate = () => {
   $j('#template_level').val(data.level);
   $j('#template_parent_id').val(data.template_id);
 
+  const appliedToSampleType = $j('#template_level')[0] === undefined || $j('#template_level')[0] === null;
   // Make sure default sorted attributes are added to the table
   Templates.table.order([9, "asc"]).draw();
   $j.each(Templates.table.rows().data(), (i, row) => {
@@ -239,24 +240,25 @@ const applyTemplate = () => {
         row[7] === "Registered Sample List" &&
         row[1].includes("Input") &&
         row[11] === null;
-    const isInherited = row[14] !== "undefined" || row[14] !== null;
     const isRequired = row[0] ? "checked" : "";
     newRow = $j(newRow.replace(/replace-me/g, index));
     $j(newRow).find('[data-attr="required"]').prop("checked", row[0]);
+    if (appliedToSampleType) $j(newRow).find('[data-attr="required"]').addClass("disabled");
+    $j(newRow).find(".sample-type-is-title").prop("checked", row[8]);
+    if (appliedToSampleType) $j(newRow).find('.sample-type-is-title').addClass("disabled");
     $j(newRow).find('[data-attr="title"]').val(row[1]);
-    $j(newRow).find('[data-attr="title"]').addClass("disabled");
+    if (appliedToSampleType) $j(newRow).find('[data-attr="title"]').addClass("disabled");
     $j(newRow).find('[data-attr="description"]').val(row[2]);
     $j(newRow).find('[data-attr="type"]').val(row[3]);
-    $j(newRow).find('[data-attr="type"]').addClass("disabled");
+    if (appliedToSampleType) $j(newRow).find('[data-attr="type"]').addClass("disabled");
     $j(newRow).find('[data-attr="cv_id"]').val(row[4]);
-    $j(newRow).find('[data-attr="cv_id"]').parent().addClass("disabled");
+    if (appliedToSampleType) $j(newRow).find('[data-attr="cv_id"]').parent().addClass("disabled");
     $j(newRow).find('[data-attr="allow_cv_free_text"]').prop("checked", row[5]);
-    $j(newRow)
-        .find('[data-attr="allow_cv_free_text"]')
-        .addClass("disabled");
+    if (appliedToSampleType) $j(newRow)
+                                .find('[data-attr="allow_cv_free_text"]')
+                                .addClass("disabled");
     $j(newRow).find('[data-attr="unit"]').val(row[6]);
-    $j(newRow).find('[data-attr="unit"]').addClass("disabled");
-    $j(newRow).find(".sample-type-is-title").prop("checked", row[8]);
+    if (appliedToSampleType)  $j(newRow).find('[data-attr="unit"]').addClass("disabled");
     $j(newRow).find('[data-attr="pid"]').val(row[9]);
     $j(newRow).find('[data-attr="isa_tag_id"]').val(row[11]);
     $j(newRow).find('[data-attr="isa_tag_title"]').val(row[11]);
@@ -265,7 +267,10 @@ const applyTemplate = () => {
         .addClass("disabled");
     $j(newRow).find('[data-attr="template_attribute_id"]').val(row[14]); // In case of a sample type
     $j(newRow).find('[data-attr="parent_attribute_id"]').val(row[14]); // In case of a template
-    if (isRequired) {
+
+    // Hide the remove button if the attribute is required and it is applied to a sample type.
+    // Template attributes should always be removeable
+    if (isRequired && appliedToSampleType) {
       $j(newRow).find('label.btn.btn-danger').addClass("hidden");
     }
 
@@ -293,9 +298,12 @@ const applyTemplate = () => {
   const template_id_tag = $j(`#isa_study${suffix}template_parent_id`);
   if (template_id_tag) $j(template_id_tag).val(id);
 
+  // Removes the hidden from the new attribute button
+  $j(`${attribute_table} ${addAttributeRow}`).find('#add-attribute').removeClass("hidden");
+
   SampleTypes.recalculatePositions();
   SampleTypes.bindSortable();
-	$j(".sample-type-attribute-type").trigger("change", [false]);
+  $j(".sample-type-attribute-type").trigger("change", [false]);
 };
 
 // Shows the modal form