Issue 1558 hide unauthorized cells in dynamic table

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

@@ -50,7 +50,14 @@ const handleSelect = (e) => {
           if (c.multi_link) {
             data = data && Array.isArray(data) ? data : [data];
             data = data[0]?.id ? data : [];
-            const existingOptions = data.map((e) => `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${e.title}</option>`).join("");
+            const existingOptions = data.map((e) => {
+              isHiddenInput = (e.title == '#HIDDEN')
+              if (isHiddenInput) {
+                return `<option selected="selected" title="ID: hidden" value="hidden">hidden</option>`
+              } else {
+                return `<option selected="selected" title="ID: ${e.id}" value="${e.id}">${e.title}</option>`
+              }
+            }).join("");
             if (options.readonly) {
               return data.map((e) => `<span title="ID: ${e.id}" class="badge">${e.title}</span>`).join(" ");
             } else {
@@ -61,15 +68,15 @@ const handleSelect = (e) => {
               const linkedSamples = retrieveLinkedSamples(url);
               const linkedSampleIds = linkedSamples.map((ls) => ls.id);
               const unLinkedSamples = data.reduce(function(filtered, sample) {
-                if(!linkedSampleIds.includes(parseInt(sample.id))){
+                if(!linkedSampleIds.includes(parseInt(sample.id)) && sample.title != '#HIDDEN'){
                   filtered.push(sample);
                 }
                 return filtered;
               }, []);
               const hasUnlinkedSamples = unLinkedSamples.length > 0 ? true : false;
 
               const extraClass = hasUnlinkedSamples ? 'select2__error' : '';
-              const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as sources. Please correct this issue!` : '';
+              const titleText = hasUnlinkedSamples ? `Sample(s) '${unLinkedSamples.map(uls => uls.title).join(', ')}' not recognised as input. Please correct this issue!` : '';
 
               return objectInputTemp
               .replace(/_NAME_/g, objectInputName)

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

@@ -207,61 +207,78 @@ async function batchDeleteSample(sampleTypes) {
 // Posts the content of the dynamic table to the single_pages_controller,
 // which generates an excel workbook based on a template.
 async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
-    const headerRow = $j(`table[id=${tableName}] thead tr`)["0"];
+  const headerRow = $j(`table[id=${tableName}] thead tr`)["0"];
 
-    // Cells from the table body => Each row = array
-    // For some reason they contain null values, which should be filtered out
-    let bodyCells = $j(`table[id=${tableName}]`).DataTable().data().toArray().map(subarray => subarray.filter(function(el){return el != null}));
+  // Cells from the table body => Each row = array
+  // For some reason they contain null values, which should be filtered out
+  let bodyCells = $j(`table[id=${tableName}]`).DataTable().data().toArray().map(subarray => subarray.filter(function(el){return el != null}));
 
-    // Return array of table header cells from headerRow
-    let headerCells = [];
-    $j.each(headerRow.cells, function (i, v) {
-        headerCells.push(v.textContent);
-    });
+  // Checks whether the dynamic table has errors
+  // The excel export will be aborted as long as the dynamic table has errors
+  hasErrorcells = $j(`table[id=${tableName}]`).find('select.select2__error').size() > 0
+  if (hasErrorcells) {
+    alert('It appears this sample table has some errors. Please correct the errors in the current sample table and try downloading again.');
+    return;
+  }
 
-    // Construct the 'struct' of the table data
-    let data = [];
-    for (let i = 0; i < bodyCells.length; i++) {
-        const row = bodyCells[i];
-        // If a row has been checked / unchecked,
-        // the datatable body gets one extra hidden cell at index 1,
-        // compared to the table header. This has to be removed.
-        if (row.length !== headerCells.length)row.splice(1,1);
-        let obj = {};
-        for (let j = 0; j < headerCells.length; j++) {
-          const attr = headerCells[j];
-          const val = row[j];
+  // Return array of table header cells from headerRow
+  let headerCells = [];
+  $j.each(headerRow.cells, function (i, v) {
+      headerCells.push(v.textContent);
+  });
 
-          // The source inputs are wrapped in an object and must be unwrapped first
-          // And then packaged as a single element
-          if(j === 0) {
-              obj["selected"] = (val === "") ? false : val;
-          } else {
-              obj[attr] = val;
-          }
-          if(obj.selected) data.push(obj);
+  // Construct the 'struct' of the table data
+  let data = [];
+  for (let i = 0; i < bodyCells.length; i++) {
+    const row = bodyCells[i];
+    // If a row has been checked / unchecked,
+    // the datatable body gets one extra hidden cell at index 1,
+    // compared to the table header. This has to be removed.
+    if (row.length !== headerCells.length)row.splice(1,1);
+    let obj = {};
+    let hasHiddenInputs = false;
+    for (let j = 0; j < headerCells.length; j++) {
+      const attr = headerCells[j];
+      const val = row[j];
+
+      // Check whether sample has one or more hidden Inputs or if sample is completely hidden
+      if (attr.toLowerCase().includes('input')) {
+        if (Array.isArray(val)){
+          hasHiddenInputs = val.some(input => input.title === '#HIDDEN'); // Sample has hidden inputs
+        } else {
+          hasHiddenInputs = val === '#HIDDEN'; // Sample is completely hidden
         }
       }
 
-      // Use ajax for POST request with table data in the body
-      // If succes => Redirect to download path for retrieving excel file
-      $j.ajax({
-        type: 'POST',
-        url: '<%= export_to_excel_single_pages_path() %>',
-        data: { sample_data: JSON.stringify(data),
-          sample_type_id: JSON.stringify(sampleTypeId),
-          study_id: JSON.stringify(studyId),
-          assay_id: JSON.stringify(assayId),
-        },
-        success: function(response) {
-          downloadUrl = `<%= download_samples_excel_single_pages_path() %>?uuid=${response.uuid}`;
-          window.location.href = downloadUrl;
-        },
-        error: function(response) {
-            alert(`Failed to export through excel!\nStatus: ${response.status}\nError: ${JSON.stringify(response.error().statusText)}`);
-        }
-    });
+      // The source inputs are wrapped in an object and must be unwrapped first
+      // And then packaged as a single element
+      if(j === 0) {
+        obj["selected"] = (val === "") ? false : val;
+      } else {
+        obj[attr] = val;
+      }
+    }
+    if (!hasHiddenInputs) data.push(obj);
+  }
 
+  // Use ajax for POST request with table data in the body
+  // If succes => Redirect to download path for retrieving excel file
+  $j.ajax({
+    type: 'POST',
+    url: '<%= export_to_excel_single_pages_path() %>',
+    data: { sample_data: JSON.stringify(data),
+      sample_type_id: JSON.stringify(sampleTypeId),
+      study_id: JSON.stringify(studyId),
+      assay_id: JSON.stringify(assayId),
+    },
+    success: function(response) {
+      downloadUrl = `<%= download_samples_excel_single_pages_path() %>?uuid=${response.uuid}`;
+      window.location.href = downloadUrl;
+    },
+    error: function(response) {
+        alert(`Failed to export through excel!\nStatus: ${response.status}\nError: ${JSON.stringify(response.error().statusText)}`);
+    }
+  });
 }
 
 async function batchUpdateSample(sampleTypes) {

app/controllers/single_pages_controller.rb

@@ -70,7 +70,9 @@ def download_samples_excel
     @project = @study.projects.first
     @samples = Sample.where(id: sample_ids)&.authorized_for(:view)&.sort_by(&:id)
 
-    raise 'Nothing to export to Excel.' if @samples.nil? || @samples == [] || sample_type_id.nil?
+    if @samples.nil? || @samples == [] || sample_type_id.nil?
+      raise 'Nothing to export to Excel. Please select samples in the table and try downloading the table again.'
+    end
 
     @sample_type = SampleType.find(sample_type_id)
 
@@ -114,7 +116,7 @@ def download_samples_excel
   def export_to_excel
     cache_uuid = UUID.new.generate
     id_label = "#{Seek::Config.instance_name} id"
-    sample_ids = JSON.parse(params[:sample_data]).map { |sample| sample[id_label] unless sample[id_label] == '#HIDDEN' }
+    sample_ids = JSON.parse(params[:sample_data]).map { |sample| sample[id_label] }
     sample_type_id = JSON.parse(params[:sample_type_id])
     study_id = JSON.parse(params[:study_id])
     assay_id = JSON.parse(params[:assay_id])

app/helpers/dynamic_table_helper.rb

@@ -31,14 +31,34 @@ def link_sequence(sample_type)
 
   def dt_rows(sample_type)
     sample_type.samples.map do |s|
-        if s.can_view?
-          ['', s.id, s.uuid] +
-          JSON(s.json_metadata).values
-        else
-          ['', '#HIDDEN', '#HIDDEN'] +
+      if s.can_view?
+        sanitized_json_metadata = hide_unauthorized_inputs(JSON(s.json_metadata))
+        ['', s.id, s.uuid] +
+          sanitized_json_metadata.values
+      else
+        ['', '#HIDDEN', '#HIDDEN'] +
           Array.new(JSON(s.json_metadata).length, '#HIDDEN')
+      end
+    end
+  end
+
+  def hide_unauthorized_inputs(json_metadata)
+    input_key = json_metadata.keys.detect { |jmdk| jmdk.downcase.include? 'input' }
+
+    unless input_key.nil?
+      json_metadata[input_key] = json_metadata[input_key].map do |input|
+        input_exists = Sample.where(id: input['id']).any?
+        if !input_exists
+          input
+        elsif Sample.find(input['id']).can_view?
+          input
+        else
+          { 'id' => input['id'], 'type' => input['type'], 'title' => '#HIDDEN' }
         end
+      end
     end
+
+    json_metadata
   end
 
   def dt_cols(sample_type)

app/views/isa_studies/_form.html.erb

@@ -24,7 +24,7 @@
 
     <div id="investigation_collection" class="hidden">
       <%= render :partial=>"studies/investigation_list",:locals=>{study:@isa_study.study, :investigations=>Investigation.all.select {|i|current_user.person.member_of? i.projects}} -%>
-    </div>    
+    </div>
 
     <div class="form-group">
       <%= study_fields.label "Study position" -%><br/>
@@ -42,48 +42,56 @@
     <%= render partial: 'projects/implicit_project_selector', locals: { action: action,
                                                                           select_id: '#study_investigation_id',
                                                                           parents: Investigation.authorized_for('edit') } %>
-    
+
     <%= folding_panel("Define #{t(:sample_type)} for Source") do %>
       <%= render partial: 'sample_types_form', locals: {f: f, sample_type: @isa_study.source, id_suffix: "_source_sample_type", action: action } if @isa_study.source %>
     <% end %>
 
 		<%= folding_panel(t(:sop).pluralize) do %>
 			<p class="help-block">The following <%= t(:sop).pluralize %> are associated with this <%= t(:study) %>:</p>
-			
+
       <%= study_fields.fancy_multiselect :sops, { other_projects_checkbox: true, name: "isa_study[study][sop_ids]" } %>
-     
+
 		<% end %>
 
     <%= folding_panel("Define #{t(:sample_type)} for Sample") do %>
       <%= render partial: 'sample_types_form', locals: {f: f, sample_type: @isa_study.sample_collection, id_suffix: "_sample_collection_sample_type", action: action  } if @isa_study.sample_collection %>
     <% end %>
 
-<% end -%> 
+<% end -%>
+
 
 
 
-
 <%= form_submit_buttons(@isa_study.study) %>
 
 <script>
     const templates = <%= load_templates().to_json.html_safe %>
     const initTemplateModal = function(field_name) {
-      Templates.context.description_elem = `#isa_study_${field_name}_description`
-      Templates.context.suffix = "_" + field_name
-      Templates.context.field_name = field_name
-      showTemplateModal()
+      if (templates.length > 0) {
+        Templates.context.description_elem = `#isa_study_${field_name}_description`
+        Templates.context.suffix = "_" + field_name
+        Templates.context.field_name = field_name
+        showTemplateModal()
+      }else{
+        if (confirm("No templates available for this project. Click 'OK' to create a project specific template or 'cancel' to close this window.")){
+          window.open('/templates/new')
+        }
+      }
     }
 
-    $j(document).ready(function () {   
+    $j(document).ready(function () {
       const urlSearchParams = new URLSearchParams(window.location.search);
       const params = Object.fromEntries(urlSearchParams.entries());
       const investigation_id = params["investigation_id"]
       // Prevent setting the hidden field on redirect (query string parameters are missing)
       if(investigation_id) {
-          $j("#isa_study_study_investigation_id").val(investigation_id); 
+          $j("#isa_study_study_investigation_id").val(investigation_id);
           $j("#study_investigation_id").val(investigation_id).change();
-      } 
+      }
 
-      Templates.init($j('#template-attributes'));   
-    }); 
+      if (templates.length > 0) {
+        Templates.init($j('#template-attributes'));
+      }
+    });
 </script>

app/views/isa_studies/new.html.erb

@@ -6,20 +6,11 @@
 	</span>
   <h1>New <%=t('isa_study')%></h1>
 
-  <% if show_batch_miappe_button? %>
-    <h4>Upload studies from file:</h4>
-    <%= link_to "MIAPPE Study batch upload", batch_uploader_studies_path, class: "btn btn-primary" %>
-    <div>
-      <%= link_to "Download MIAPPE template here", asset_path('batch_upload_template/MIAPPE Study batch template.zip', skip_pipeline: true) %>
-    </div>
-    <h4>Or create a study with the form:</h4>
-  <% end %>
-
   <%= render :partial => "templates/template_modal" -%>
 
   <div class="show_basic">
     <%= form_for @isa_study do |f| %>
       <%= render :partial => "form", :locals => { :f => f, :action=>:new } -%>
     <% end -%>
   </div>
-<% end -%>
+<% end -%>