2312 change text in sample type buttons

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

@@ -94,11 +94,11 @@ const handleSelect = (e) => {
         let isRegisteredDataFile = false;
         let isRegisteredStrain = false;
         if (c.attribute_type) {
-          isRegisteredSample = c.attribute_type.base_type.includes("SeekSample");
-          isCVList = c.attribute_type.base_type === "CVList";
-          isRegisteredSop = c.attribute_type.base_type === "SeekSop";
-          isRegisteredDataFile = c.attribute_type.base_type === "SeekDataFile";
-          isRegisteredStrain = c.attribute_type.base_type === "SeekStrain";
+          isRegisteredSample = c.attribute_type.includes("SeekSample");
+          isCVList = c.attribute_type === "CVList";
+          isRegisteredSop = c.attribute_type === "SeekSop";
+          isRegisteredDataFile = c.attribute_type === "SeekDataFile";
+          isRegisteredStrain = c.attribute_type === "SeekStrain";
         }
 
         if (isRegisteredSample) {
@@ -173,17 +173,43 @@ const handleSelect = (e) => {
       });
       // Retrieve the column index of the multi-input cells (select2 items)
       // if column has a multi-input cell, it adds the index to the t array (=accumulator)
-      let multi_link_idx = columns.reduce((t, c, i) => (c.multi_link ? [...t, i + 1] : t), []);
-      // If it's Assay level table keep the first, otherwise hide all of them
-      if (options.level == "assay") multi_link_idx = multi_link_idx.slice(1);
-      this.hiddenColumns = multi_link_idx;
+      let input_col_ids = columns.reduce((t, c, i) => (c.is_input ? [...t, i + 1] : t), []);
+
+      if (options.readonly) {
+        this.hiddenColumns = columns
+          .map((col, index) => {
+          if (
+            // If it's Assay level table keep the first input in the experiment overview,
+            // otherwise hide all inputs.
+            (col.is_input && !col.is_first_input) ||
+            // Hide ID related fields (id, uuid, ...)
+            col.is_id_field ||
+            // Hide the status column
+            col.title === 'status'
+          ){
+            return index + 1;
+          } else {
+            return -1;
+          }
+        })
+          .filter(index => index !== -1);
+      } else {
+        this.hiddenColumns = columns
+          .map((col, index) => {
+            // Hide the status column
+            if (col.title === 'status') {
+              return index + 1;
+            } else {
+              return -1;
+            }
+          })
+          .filter(index => index !== -1);
+      }
       columns.unshift(...defaultCols);
 
-      const columnDefs = [{
-        targets: options.readonly ? [0] : [0, 1]
-      },
+      const columnDefs = [
         {
-          targets: options.readonly ? [0, ...multi_link_idx] : [1],
+          targets: options.readonly ? [0, ...this.hiddenColumns] : [1, 3, ...this.hiddenColumns],
           visible: false,
           searchable: false
         },
@@ -590,7 +616,7 @@ function getNonTextAttributes(st_attributes) {
   return st_attributes
     .filter(
       (attr) => {
-        const baseType = attr?.attribute_type?.base_type ?? stringType;
+        const baseType = attr?.attribute_type ?? stringType;
         return baseType !== stringType;
       })
     .map(function (attr) {

app/helpers/dynamic_table_helper.rb

@@ -25,7 +25,7 @@ def dt_aggregated(study, assay = nil)
       end
     columns = dt_cumulative_cols(sample_types)
     rows = dt_cumulative_rows(sample_types, columns.length)
-    { columns:, rows:, sample_types: sample_types.map { |s| { title: s.title, id: s.id } } }
+    { columns:, rows:, sample_types: sample_types.map { |s| { title: s.title, id: s.id, assay_title: s.assays.first&.title } } }
   end
 
   private
@@ -99,15 +99,19 @@ def transform_registered_sample_single(json_metadata, input_key)
   def dt_cols(sample_type)
     attribs = sample_type.sample_attributes.map do |a|
       attribute = { title: a.title, name: sample_type.id.to_s, required: a.required, description: a.description,
-                    is_title: a.is_title, attribute_type: a.sample_attribute_type }
+                    is_title: a.is_title, attribute_type: a.sample_attribute_type&.base_type }
 
       if a.sample_attribute_type&.controlled_vocab?
         cv_allows_free_text = a.allow_cv_free_text
         attribute.merge!({ cv_allows_free_text: cv_allows_free_text, cv_id: a.sample_controlled_vocab_id })
       end
 
       if a.sample_attribute_type&.seek_sample_multi? || a.sample_attribute_type&.seek_sample?
-        attribute.merge!({ multi_link: a.sample_attribute_type&.seek_sample_multi?, linked_sample_type: a.linked_sample_type_id })
+        attribute.merge!(linked_sample_type: a.linked_sample_type_id)
+      end
+
+      if a.input_attribute?
+        attribute.merge!(is_input: true)
       end
 
       attribute
@@ -156,18 +160,21 @@ def get_full_rows(x, depth, row = [], i = 0, rows = [])
   end
 
   def dt_cumulative_cols(sample_types)
-    sample_types.flat_map do |s|
+    sample_types.flat_map.with_index do |s, i|
       s.sample_attributes.map do |a|
         attribute = { title: a.title, name: s.id.to_s, required: a.required, description: a.description,
-                      is_title: a.is_title, attribute_type: a.sample_attribute_type }
+                      is_title: a.is_title, attribute_type: a.sample_attribute_type&.base_type }
         is_seek_sample_multi = a.sample_attribute_type.seek_sample_multi?
         is_seek_sample = a.sample_attribute_type.seek_sample?
         is_cv_list = a.sample_attribute_type.seek_cv_list?
-        attribute.merge!({ multi_link: true, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample_multi
-        attribute.merge!({ multi_link: false, linked_sample_type: a.linked_sample_type.id }) if is_seek_sample
-        attribute.merge!({ is_cv_list: true }) if is_cv_list
+        is_input = a.input_attribute?
+        attribute.merge!(linked_sample_type: a.linked_sample_type.id) if is_seek_sample_multi || is_seek_sample
+        # The first input has to show up in the experiment view,
+        # that's why when i=0, the `is_first_input` flag is set to true.
+        attribute.merge!({ is_input: true, is_first_input: i == 0 }) if is_input
+        attribute.merge!(is_cv_list: true) if is_cv_list
         attribute
-      end.unshift({ title: 'id' }, { title: 'uuid' })
+      end.unshift({ title: 'id', is_id_field: true }, { title: 'uuid', is_id_field: true })
     end
   end
 end

app/views/isa_assays/_assay_table.html.erb

@@ -40,7 +40,8 @@
         function createSampleTypeOptions(types){
             $j("#options_container").append('<div id="checkbox_group" class="btn-group" data-toggle="buttons"></div>')
                 types.forEach( (t, i) => {
-                    let elem = `<label class="btn btn-default active sp-btn-variant-${i%2}"><input id="checkbox-${t.id}" type="checkbox" checked onchange="toggleSampleType(${t.id}, $j(this))" />${t.title}</label>`
+                    let assayTitle = t.assay_title;
+                    let elem = `<label class="btn btn-default active sp-btn-variant-${i%2}"><input id="checkbox-${t.id}" type="checkbox" checked onchange="toggleSampleType(${t.id}, $j(this))" />${assayTitle}</label>`
                     $j("#checkbox_group").append(elem)
                 })
         }

app/views/isa_studies/_study_table.html.erb

@@ -1,7 +1,7 @@
 <%# The study experiment overview table %>
 
 <% study ||= nil %>
-<% valid_study = study&.sample_types&.second %>
+<% valid_study = study&.sample_types&.count == 2 %>
 
 <div style="padding: 0 20px 20px 20px;">
     <div class="row" id="options_container" style="margin-bottom:15px">
@@ -28,7 +28,7 @@
                         studyTableInitialLoad = false;
                         return;
                     }
-                    d.study_id = '<%=study.id%>';
+                    d.study_id = '<%=study&.id%>';
                     d.rows_pad = "true";
                 }
             }
@@ -41,10 +41,14 @@
 
         function createSampleTypeOptions(types){
             $j("#options_container").append('<div id="checkbox_group" class="btn-group" data-toggle="buttons"></div>')
-                types.forEach( (t, i) => {
-                    let elem = `<label class="btn btn-default active sp-btn-variant-${i%2}"><input id="checkbox-${t.id}" type="checkbox" checked onchange="toggleSampleType(${t.id}, $j(this))" />${t.title}</label>`
-                    $j("#checkbox_group").append(elem)
-                })
+            let studyTitle = '<%= study&.title || 'Study' %>';
+            let sourceSampleType = types[0];
+            let sampleSampleType = types[1];
+            let source_elem = `<label class="btn btn-default active sp-btn-variant-0"><input id="checkbox-${sourceSampleType.id}" type="checkbox" checked onchange="toggleSampleType(${sourceSampleType.id}, $j(this))" />${studyTitle} - sources</label>`;
+            let sample_elem = `<label class="btn btn-default active sp-btn-variant-1"><input id="checkbox-${sampleSampleType.id}" type="checkbox" checked onchange="toggleSampleType(${sampleSampleType.id}, $j(this))" />${studyTitle} - samples</label>`;
+            [source_elem, sample_elem].forEach((elem) => {
+                $j("#checkbox_group").append(elem);
+            });
         }
 
         function toggleSampleType(sample_type, e){