From f3b3afbf78ae64f8158a883ca480a9c4f710ae75 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 5 May 2023 11:03:27 +0200
Subject: [PATCH 01/54] Added the roo and roo-xls gems

---
 Gemfile      |  4 ++++
 Gemfile.lock | 18 ++++++++++++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/Gemfile b/Gemfile
index 7d70edf3a0..e612c80443 100644
--- a/Gemfile
+++ b/Gemfile
@@ -157,6 +157,10 @@ gem "net-http"
 gem "net-ftp"
 gem "uri", "0.10.0.2"
 
+# Reading excel spreadsheets
+gem "roo", "~> 2.10.0"
+gem 'roo-xls', '~> 1.1'
+
 group :production do
   gem 'passenger'
 end
diff --git a/Gemfile.lock b/Gemfile.lock
index 6085eeb01e..4289bb056d 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -441,7 +441,6 @@ GEM
       nokogiri (~> 1)
       rake
     mini_mime (1.1.2)
-    mini_portile2 (2.8.1)
     minitest (5.18.0)
     minitest-reporters (1.5.0)
       ansi
@@ -475,8 +474,7 @@ GEM
       net-protocol
     netrc (0.11.0)
     nio4r (2.5.8)
-    nokogiri (1.13.10)
-      mini_portile2 (~> 2.8.0)
+    nokogiri (1.13.10-x86_64-linux)
       racc (~> 1.4)
     nori (1.1.5)
     oauth2 (2.0.9)
@@ -714,6 +712,13 @@ GEM
     ro-crate (0.5.1)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
+    roo (2.10.0)
+      nokogiri (~> 1)
+      rubyzip (>= 1.3.0, < 3.0.0)
+    roo-xls (1.2.0)
+      nokogiri
+      roo (>= 2.0.0, < 3)
+      spreadsheet (> 0.9.0)
     rsolr (2.4.0)
       builder (>= 2.1.2)
       faraday (>= 0.9.0)
@@ -745,6 +750,7 @@ GEM
       unicode-display_width (>= 1.4.0, < 3.0)
     rubocop-ast (1.15.1)
       parser (>= 3.0.1.1)
+    ruby-ole (1.2.12.2)
     ruby-prof (1.4.3)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
@@ -820,6 +826,8 @@ GEM
     sparql-client (3.2.0)
       net-http-persistent (~> 4.0, >= 4.0.1)
       rdf (~> 3.2)
+    spreadsheet (1.3.0)
+      ruby-ole
     sprockets (4.2.0)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -925,7 +933,7 @@ GEM
       rubyzip (~> 2.0.0)
 
 PLATFORMS
-  ruby
+  x86_64-linux
 
 DEPENDENCIES
   RedCloth (>= 4.3.0)
@@ -1037,6 +1045,8 @@ DEPENDENCIES
   rmagick (= 2.15.2)
   ro-bundle (~> 0.3.0)
   ro-crate (~> 0.5.1)
+  roo (~> 2.10.0)
+  roo-xls (~> 1.1)
   rspec-rails (~> 5.1)
   rubocop
   ruby-prof

From 8126b2aeab16b1d7d850fecfc65a0c1428fa12bf Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 8 May 2023 09:55:30 +0200
Subject: [PATCH 02/54] Working on uploading the samples via spreadsheet

- added route to routes.rb
- Extraction of sample information in the controller
- Added a partial form with a button to upload the spreadsheet
---
 app/controllers/single_pages_controller.rb | 42 ++++++++++++++++++++++
 app/views/isa_studies/_buttons.html.erb    |  7 ++++
 config/routes.rb                           |  1 +
 3 files changed, 50 insertions(+)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index c925cd6d6d..33dcb0416a 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -1,4 +1,7 @@
 require 'isatab_converter'
+require 'roo'
+require 'roo-xls'
+
 class SinglePagesController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Sharing::SharingCommon
@@ -59,6 +62,45 @@ def export_isa
     end
   end
 
+  def upload_samples
+    wb = Roo::Excelx.new(params[:file].path)
+    puts params
+    # Extract Samples metadata
+    puts wb.cell(2, 2, sheet = 'Metadata').to_i
+    puts wb.cell(5, 2, sheet = 'Metadata').to_i
+    puts wb.cell(8, 2, sheet = 'Metadata').to_i
+
+    @study = Study.find(wb.cell(2, 2, sheet = 'Metadata').to_i)
+    @sample_type = SampleType.find(wb.cell(5, 2, sheet = 'Metadata').to_i)
+    @template = Template.find(wb.cell(8, 2, sheet = 'Metadata').to_i)
+
+    sample_fields = wb.row(1, sheet = 'Samples')
+    samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
+
+    @excel_samples = samples_data.map do |excel_sample|
+      obj = {}
+      (0..sample_fields.size - 1).map do |i|
+        obj.merge!(sample_fields[i] => excel_sample[i])
+      end
+      obj
+    end
+
+    @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
+    @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
+
+    @db_samples = @existing_excel_samples.map { |sample| JSON.parse(Sample.find(sample['id'])[:json_metadata]) }
+
+    [@study, @sample_type, @template, @excel_samples, @existing_excel_samples, @new_excel_samples, @db_samples].each do |var|
+      puts '#' * 100
+      puts var.inspect
+    end
+    puts '#' * 100
+
+    # respond_to do |format|
+    #   format.html { redirect_to single_page_path(@study.projects.first) }
+    # end
+  end
+
   private
 
   def set_up_instance_variable
diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 388e37f75e..720bec20f1 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -15,6 +15,13 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
   <button class="btn btn-primary dt-action" id="btn_save_assay_sample" onClick=<%=save%>>Save</button>
 </div>
 
+<div>
+  <%= form_with url: upload_samples_single_page_url() , multipart: true do |form| %>
+    <%= form.file_field :file %>
+    <%= form.submit 'Upload' %>
+  <% end %>
+</div>
+
 <script>
   function loadBatchPermission(dtName, e){
     const sample_ids = window[dtName].selectedSampleIds()
diff --git a/config/routes.rb b/config/routes.rb
index 3a5d42e900..9278318bfa 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -748,6 +748,7 @@
     member do
       get :dynamic_table_data
       get :export_isa, action: :export_isa
+      post :upload_samples, action: :upload_samples
     end
     collection do
       get :batch_sharing_permission_preview

From 61a00580fb42578778db2e3732e0225e1b02c007 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:39:30 +0200
Subject: [PATCH 03/54] Added functionality to read excel spreadsheets of
 source samples table

---
 app/controllers/single_pages_controller.rb | 82 ++++++++++++++++++----
 1 file changed, 67 insertions(+), 15 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 33dcb0416a..613446b6e4 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -66,15 +66,15 @@ def upload_samples
     wb = Roo::Excelx.new(params[:file].path)
     puts params
     # Extract Samples metadata
-    puts wb.cell(2, 2, sheet = 'Metadata').to_i
-    puts wb.cell(5, 2, sheet = 'Metadata').to_i
-    puts wb.cell(8, 2, sheet = 'Metadata').to_i
+    study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
+    sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
+    template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
 
-    @study = Study.find(wb.cell(2, 2, sheet = 'Metadata').to_i)
-    @sample_type = SampleType.find(wb.cell(5, 2, sheet = 'Metadata').to_i)
-    @template = Template.find(wb.cell(8, 2, sheet = 'Metadata').to_i)
+    @study = Study.find(study_id)
+    @sample_type = SampleType.find(sample_type_id)
+    @template = Template.find(template_id)
 
-    sample_fields = wb.row(1, sheet = 'Samples')
+    sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
 
     @excel_samples = samples_data.map do |excel_sample|
@@ -88,17 +88,69 @@ def upload_samples
     @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
     @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
-    @db_samples = @existing_excel_samples.map { |sample| JSON.parse(Sample.find(sample['id'])[:json_metadata]) }
+    @db_samples = @existing_excel_samples.map do |sample|
+      raw_sample = Sample.find(sample['id'])
+      attributes = JSON.parse(raw_sample[:json_metadata])
+      { 'id' => raw_sample.id,
+        'uuid' => raw_sample.uuid }.merge(attributes)
+    end
+
+    # Determine whether samples have been modified or not
+    @update_samples = @existing_excel_samples.map do |ees|
+      db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
+      # An exception is raised if the ID of an existing Sample cannot be found in the DB
+      raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
+      is_changed = false
+
+      db_sample.map do |k, v|
+        unless ees[k] == v
+          is_changed = true
+          break
+        end
+      end
 
-    [@study, @sample_type, @template, @excel_samples, @existing_excel_samples, @new_excel_samples, @db_samples].each do |var|
-      puts '#' * 100
-      puts var.inspect
+      ees if is_changed
+    end
+    @update_samples.compact!
+
+    # Determine if the new samples are no duplicates of existing ones,
+    # based on the attribute values
+    @possible_duplicates = []
+    @new_samples = []
+    @new_excel_samples.map do |nes|
+      is_duplicate = true
+
+      @existing_excel_samples.map do |ees|
+        ees.map do |k, v|
+          unless %w[id uuid].include?(k)
+            is_duplicate = (nes[k] == v)
+            break unless is_duplicate
+          end
+        end
+        if is_duplicate
+          @possible_duplicates.append(nes.merge({ 'duplicate' => ees }))
+          break
+        end
+      end
+      @new_samples.append(nes) unless is_duplicate
     end
-    puts '#' * 100
 
-    # respond_to do |format|
-    #   format.html { redirect_to single_page_path(@study.projects.first) }
-    # end
+    upload_data = { study: @study,
+                    sampleType: @sample_type,
+                    template: @template,
+                    excelSamples: @excel_samples,
+                    existingExcelSamples: @existing_excel_samples,
+                    newExcelSamples: @new_excel_samples,
+                    updateSamples: @update_samples,
+                    newSamples: @new_samples,
+                    possibleDuplicates: @possible_duplicates,
+                    dbSamples: @db_samples }
+
+
+    respond_to do |format|
+      format.json { render json: { uploadData: upload_data } }
+      format.html { render 'single_pages/sample_upload_content', { layout: false } }
+    end
   end
 
   private

From 60ed3ec0e868b473ac8a1a0fd2b03d52f8899b09 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:40:42 +0200
Subject: [PATCH 04/54] Changed form to html button that calls an ajax function

---
 app/views/isa_studies/_buttons.html.erb | 53 ++++++++++++++++++++-----
 1 file changed, 44 insertions(+), 9 deletions(-)

diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 720bec20f1..573b906e30 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -15,11 +15,18 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
   <button class="btn btn-primary dt-action" id="btn_save_assay_sample" onClick=<%=save%>>Save</button>
 </div>
 
-<div>
-  <%= form_with url: upload_samples_single_page_url() , multipart: true do |form| %>
-    <%= form.file_field :file %>
-    <%= form.submit 'Upload' %>
-  <% end %>
+<div class="container-sm">
+  <form id="upload_excel_form" action="<%= upload_samples_single_page_url() %>" method="post" enctype="multipart/form-data">
+    <div class="mb-3">
+      <label for="file" class="form-label">Upload excel file:</label>
+    </div>
+    <div class="mb-3">
+      <input id="fileUpload" name="fileUpload" type="file" class="form-control form-control-lg"/>
+    </div>
+    <div class="mb-3">
+      <button class="btn btn-default">Upload</button>
+    </div>
+  </form>
 </div>
 
 <script>
@@ -30,7 +37,7 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
       method: "GET",
       url: "<%= batch_sharing_permission_preview_single_pages_path %>",
       data: { sample_ids, single_page: true },
-      success: (res) => { 
+      success: (res) => {
         if (res?.status == "unprocessable_entity"){
           alert(res?.error)
         } else {
@@ -39,11 +46,39 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
           ObjectsInput.init();
         }
       },
-      error: (e) => { 
+      error: (e) => {
         console.log(e);
         alert("An error occurred while fetching data from the server.")
       }
     });
-  
+
   }
-</script>
\ No newline at end of file
+
+async function handleUploadSubmit(e){
+  const form = e.target;
+  const url = new URL(form.action);
+  let formData = new FormData();
+  formData.append('file', fileUpload.files[0]);
+
+
+  $j.ajax({
+    type: 'POST',
+    url: url,
+    data: formData,
+    dataType: 'html',
+    processData: false,
+    contentType: false,
+    enctype: 'multipart/form-data',
+    success: function(response){
+      $j('#upload-excel-modal').modal('show').focus();
+      $j('#upload-excel').html(response);
+    },
+    error: function(err){
+      alert(`The following error occurred!\n${err}`);
+    }
+  });
+  e.preventDefault();
+}
+  const uploadExcelForm = document.getElementById("upload_excel_form");
+  uploadExcelForm.addEventListener('submit', handleUploadSubmit);
+</script>

From f8128b3683255a9f991f051d65bbb07f335535c3 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:41:46 +0200
Subject: [PATCH 05/54] Added a modal form for the overview  of the upload
 actions

---
 .../sample_upload_content.html.erb            | 134 ++++++++++++++++++
 app/views/single_pages/show.html.erb          |  19 ++-
 2 files changed, 147 insertions(+), 6 deletions(-)
 create mode 100644 app/views/single_pages/sample_upload_content.html.erb

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
new file mode 100644
index 0000000000..572a3637a5
--- /dev/null
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -0,0 +1,134 @@
+<div id="upload-summary">
+  <%= folding_panel("General Inforamtion", true, :id => "general-information-panel") do %>
+    <% [@study, @sample_type, @template]. map do | entity | %>
+      <h4> <%= entity.class.to_s.singularize %> </h4>
+      <p><b>ID: </b><span><%= entity.id%></span></p>
+      <p><b>UUID: </b><span><%= entity.uuid %></span></p>
+      <p><b>Title: </b><span><%= entity.title %></span></p>
+      <hr>
+    <% end %>
+  <% end %>
+
+  <% unless @new_samples.nil? or @new_samples.compact == [] %>
+  <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
+  :help_text => "These samples have been detected as new samples and will be created.") do %>
+    <div class="table-responsive">
+      <table id="create-sample-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @new_samples[0].keys %>
+            <th><%= key unless %w[uuid].include?(key) %></th>
+          <% end %>
+        </tr>
+        <% for new_sample in @new_samples %>
+          <% new_sample_id = UUID.generate %>
+          <tr id='<%= "new-sample-#{new_sample_id}" %>'>
+            <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+              <% new_sample.map do |key, val| %>
+                <% val = '<new>' if key =='id' %>
+                <td><%= val unless %w[uuid].include?(key) %></td>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
+
+ <% unless @update_samples.nil? or @update_samples.compact == [] %>
+  <%= folding_panel("Samples to Update <span class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+  :help_text => "These samples were detected existing samples and will be updated.") do %>
+    <div class="table-responsive">
+      <table id="update-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @update_samples[0].keys %>
+            <th><%= key unless key == 'uuid' %></th>
+          <% end %>
+        </tr>
+        <% for update_sample in @update_samples %>
+          <tr id='<%= "update-sample-#{update_sample['id']}-1" %>' >
+            <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
+            <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
+            <% update_sample.map do |key, val| %>
+              <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' >
+                <%= val unless key == 'uuid' %>
+              </td>
+            <% end %>
+          </tr>
+          <tr id='<%= "update-sample-#{update_sample['id']}-2" %>' >
+            <% db_sample.map do |key, val| %>
+              <td>
+                <%= val unless key == 'uuid' %>
+              </td>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
+
+<% unless @possible_duplicates.nil? or @possible_duplicates.compact == [] %>
+  <%= folding_panel("Possible Duplicates <span class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+                  :help_text => "These new samples have been matched to already existing samples.") do %>
+    <div class="table-responsive">
+      <table id="duplicate-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @possible_duplicates[0].keys %>
+            <th>
+              <%= key unless %w[uuid duplicate].include?(key) %>
+            </th>
+          <% end %>
+        </tr>
+        <% for dupl_sample in @possible_duplicates %>
+          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
+            <td rowspan=2>
+              <button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button>
+          </td>
+        <% dupl_sample.map do |key, val| %>
+          <% val = '<new>' if key =='id' %>
+          <td rowspan=1 class="table-danger">
+            <%= val unless %w[uuid duplicate].include?(key) %>
+          </td>
+        <% end %>
+            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
+              <% dupl_sample['duplicate'].map do |key, val| %>
+                <td rowspan=1>
+                  <%= val unless %w[uuid duplicate].include?(key) %>
+                </td>
+              <% end %>
+            </tr>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+  <% end %>
+
+
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
+</div>
+<script type="text/javascript">
+  function removeSample(elementName){
+    console.log("elementName", elementName);
+    $j(`tr[id*='${elementName}']`).remove();
+  }
+
+  function submitUpload(){
+    $j.ajax({
+      method: "POST",
+      url: '<%= batch_change_permission_for_selected_items_single_pages_path -%>?single_page=true',
+      data: $j("#change-permission-preview-form").serialize(),
+      success: (res) => {
+        $j('#change-batch-permission').html(res);
+        // Handling 'remaining backdrop' issue when multiple modals
+        $j('#add-person-permission-modal').data("backdrop", "");
+        $j('#add-project-permission-modal').data("backdrop", "");
+        ObjectsInput.init();
+      },
+      error: (e) => { console.log(e) }
+    });
+  }
+</script>
diff --git a/app/views/single_pages/show.html.erb b/app/views/single_pages/show.html.erb
index 97cc879676..29c6185021 100644
--- a/app/views/single_pages/show.html.erb
+++ b/app/views/single_pages/show.html.erb
@@ -16,7 +16,7 @@
                     <li ><a href="#"><span>Assay</span></a></li>
                     </ul>
                     <div class="treeview-toggle">
-                        Toggle: 
+                        Toggle:
                         <button class="active" onClick="toggleItem(this, 'investigation')">Investigations</button>
                         <button class="active" onClick="toggleItem(this, 'study')">Studies</button>
                         <button class="active" onClick="toggleItem(this, 'assay')">Assays</button>
@@ -56,11 +56,18 @@
       <% end %>
     <% end %>
 
+    <%= modal(id: 'upload-excel-modal', size: 'xl') do %>
+      <%= modal_header("Upload from spreadsheet") %>
+      <%= modal_body do %>
+        <div id="upload-excel">...</div>
+      <% end %>
+    <% end %>
+
 </div>
 
 <script type="text/javascript">
     var selectedItem = {type:"",id:""}, pid, uid, projectDefaultPolicy, dynamicTableDataPath
-		
+
 		$j(document).ready(function() {
 			  $j("#content .container-fluid").removeClass("container-fluid").addClass("container-fluid-single-page")
 
@@ -79,7 +86,7 @@
         $j('html').click(function(e) {
           if($j(e.target).hasClass("modal-backdrop")) {
             $j('.modal-backdrop').remove();
-          } 
+          }
         });
     });
 
@@ -97,7 +104,7 @@
 			const parent = $j(`a[_type="${params.item_type}"][_id="${params.item_id}"]`)
 			$j(parent).addClass("jstree-clicked").click()
 		}
-		
+
 		function setSplitters() {
 			if(!isMobile()) {
 				$j('#widget').width('').height(768).split({
@@ -123,5 +130,5 @@
       updateLocationHash(item, id)
       setTimeout(() => updateContainerHeight(), 1000)
     }
-    
-</script>
\ No newline at end of file
+
+</script>

From bcd77623a45a9623ca12b064e0a625ba7436eff5 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:15:42 +0200
Subject: [PATCH 06/54] Added `project` and changed `db_samples` to match the
 samples from the database the current user has at least editing authorization
 for.

---
 app/controllers/single_pages_controller.rb | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 613446b6e4..372b8a9452 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -25,7 +25,8 @@ def show
   def index; end
 
   def project_folders
-    return if !Seek::Config.project_single_page_folders_enabled
+    return unless Seek::Config.project_single_page_folders_enabled
+
     project_folders = ProjectFolder.root_folders(@project)
     if project_folders.empty?
       project_folders = ProjectFolder.initialize_default_folders(@project)
@@ -73,6 +74,7 @@ def upload_samples
     @study = Study.find(study_id)
     @sample_type = SampleType.find(sample_type_id)
     @template = Template.find(template_id)
+    @project = @study.projects.first # In Single Page a study can only belong to one project
 
     sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
@@ -88,11 +90,10 @@ def upload_samples
     @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
     @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
-    @db_samples = @existing_excel_samples.map do |sample|
-      raw_sample = Sample.find(sample['id'])
-      attributes = JSON.parse(raw_sample[:json_metadata])
-      { 'id' => raw_sample.id,
-        'uuid' => raw_sample.uuid }.merge(attributes)
+    @db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
+      attributes = JSON.parse(sample[:json_metadata])
+      { 'id' => sample.id,
+        'uuid' => sample.uuid }.merge(attributes)
     end
 
     # Determine whether samples have been modified or not
@@ -120,15 +121,15 @@ def upload_samples
     @new_excel_samples.map do |nes|
       is_duplicate = true
 
-      @existing_excel_samples.map do |ees|
-        ees.map do |k, v|
+      @db_samples.map do |dbs|
+        dbs.map do |k, v|
           unless %w[id uuid].include?(k)
             is_duplicate = (nes[k] == v)
             break unless is_duplicate
           end
         end
         if is_duplicate
-          @possible_duplicates.append(nes.merge({ 'duplicate' => ees }))
+          @possible_duplicates.append(nes.merge({ 'duplicate' => dbs }))
           break
         end
       end

From 2cdc97b2f8fe065c79595efd18bc146f2d0ef2df Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:17:09 +0200
Subject: [PATCH 07/54] Implemented javascript functions to submit samples to
 update and samples to create.

---
 .../sample_upload_content.html.erb            | 138 ++++++++++++++++--
 1 file changed, 126 insertions(+), 12 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 572a3637a5..2ead616ef0 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -110,6 +110,7 @@
 
   <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
 </div>
+
 <script type="text/javascript">
   function removeSample(elementName){
     console.log("elementName", elementName);
@@ -117,18 +118,131 @@
   }
 
   function submitUpload(){
-    $j.ajax({
-      method: "POST",
-      url: '<%= batch_change_permission_for_selected_items_single_pages_path -%>?single_page=true',
-      data: $j("#change-permission-preview-form").serialize(),
-      success: (res) => {
-        $j('#change-batch-permission').html(res);
-        // Handling 'remaining backdrop' issue when multiple modals
-        $j('#add-person-permission-modal').data("backdrop", "");
-        $j('#add-project-permission-modal').data("backdrop", "");
-        ObjectsInput.init();
-      },
-      error: (e) => { console.log(e) }
+    const newSamples = { data: getNewSamples() };
+    const updatedSamples= { data: getUpdateSamples() };
+
+    console.log('newSamples', newSamples);
+    console.log('updatedSamples', updatedSamples);
+
+    if(true){
+      uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
+      uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
+    }
+
+    closeModalForm();
+    location.reload();
+  }
+
+  // Retrieves the samples from the create-samples-table and the duplicate-samples-table
+  function getNewSamples(){
+    const newRows = $j('#create-samples-table tr:not(:has(th))').toArray();
+    const duplicatedRows = $j('#duplicate-samples-table tr:not([class="danger"]):not(:has(th))').toArray();
+    let createRows = newRows;
+
+    if (duplicatedRows.length > 0 && confirm("Are you sure you want to add potentially duplicated rows?")) {
+      createRows = createRows.concat(duplicatedRows);
+    }
+    console.log('createRows', createRows);
+    const sampleObjects = createRows.map((cr, index) => createSampleObject(cr, "new", index));
+
+   return sampleObjects
+  }
+
+  function getUpdateSamples(){
+    const updateRows = $j('#update-samples-table [id*="updated"]').toArray();
+
+    const sampleObjects = updateRows.map((ur, index) => createSampleObject(ur, "update", index));
+
+    return sampleObjects
+  }
+
+  function createSampleObject(row, action, index){
+
+    cells = $j(row).find('td:not(:has(".danger"))').toArray();
+    samplesObj = {};
+    cells.map(function(cell){
+      val = cell.textContent;
+      key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
+      samplesObj[key] = val;
     });
+
+    const {id: objId, ...attrMap} = samplesObj;
+
+    attrMap["status"] = action;
+
+    if (action === "update"){
+      return {
+        id: objId,
+        ex_id: `update-${index}-<%= @sample_type.id %>`,
+        data: {
+          type: "samples",
+          attributes: {
+            attribute_map: attrMap
+          }
+        }
+      };
+    } else {
+        return {
+          ex_id: `new-${index}-<%= @sample_type.id %>`,
+            data:{
+              type: "samples",
+              tags: null,
+              attributes: {
+              policy: {
+                access: getAccess(projectDefaultPolicy),
+                permissions: [
+                  {
+                    resource: { type: "Project", id: <%= @project.id %> },
+                    access: getPermission(projectDefaultPolicy, <%= @project.id %>)
+                  }
+                ]
+              },
+              attribute_map: attrMap
+              },
+              relationships: {
+                projects: {
+                  data: [
+                    {type: "projects", id: <%= @project.id %>}
+                  ]
+                },
+                sample_type: {
+                  data: {
+                    type: "sample_types",
+                    id: <%= @sample_type.id %>
+                  }
+                }
+              }
+            }
+        };
+    }
+  }
+  function closeModalForm(){
+    $j('#upload-excel-modal').modal('hide');
   }
+
+  const uploadAjaxCall = (url, method, params) => {
+    const { data, cache, dataType } = params;
+    if (!url || !method) throw new Error("Parameter(s) missing");
+    return $j.ajax({
+      method,
+      url,
+      data,
+      dataType,
+      cache: cache || false,
+      headers: {
+        "Content-Type": "application/json",
+        Accept: "application/json"
+      },
+      beforeSend: function () {
+        $j('#check-excel-upload-result').html('<h2>Updating Samples...</h2>');
+      },
+      success: function(res) {
+        console.log("res", res);
+      },
+      error: function(err) {
+        console.log("err", err);
+      }
+    });
+  };
+
 </script>

From bcd9f56d21f22b19f858e23657fb262420e91e19 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:20:00 +0200
Subject: [PATCH 08/54] Changed the sample upload modal:

- Removed trailing `\n` from cells
- Added more information to 'General Information' pane
---
 .../sample_upload_content.html.erb            | 90 +++++++++++--------
 1 file changed, 55 insertions(+), 35 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 2ead616ef0..48636bebc9 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,10 +1,24 @@
 <div id="upload-summary">
-  <%= folding_panel("General Inforamtion", true, :id => "general-information-panel") do %>
-    <% [@study, @sample_type, @template]. map do | entity | %>
-      <h4> <%= entity.class.to_s.singularize %> </h4>
-      <p><b>ID: </b><span><%= entity.id%></span></p>
-      <p><b>UUID: </b><span><%= entity.uuid %></span></p>
-      <p><b>Title: </b><span><%= entity.title %></span></p>
+  <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
+    <% [@project, @study, @sample_type, @template]. map do | asset | %>
+      <% asset_name = asset.class.to_s.singularize %>
+      <h4> <%= asset_name %> </h4>
+      <p><b>ID: </b><span><%= asset.id%></span></p>
+      <p><b>UUID: </b><span><%= asset.uuid %></span></p>
+      <p><b>Title: </b><span><%= asset.title %></span></p>
+      <% if asset_name == "Project"%>
+        <% if current_user.person.member_of?(asset)%>
+          <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% else %>
+          <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% end %>
+      <% else %>
+        <% if asset.can_manage?%>
+          <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% else %>
+          <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% end %>
+      <% end %>
       <hr>
     <% end %>
   <% end %>
@@ -13,11 +27,13 @@
   <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
   :help_text => "These samples have been detected as new samples and will be created.") do %>
     <div class="table-responsive">
-      <table id="create-sample-table" class="table">
+      <table id="create-samples-table" class="table">
         <tr>
           <th></th>
           <% for key in @new_samples[0].keys %>
-            <th><%= key unless %w[uuid].include?(key) %></th>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for new_sample in @new_samples %>
@@ -26,7 +42,9 @@
             <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
               <% new_sample.map do |key, val| %>
                 <% val = '<new>' if key =='id' %>
-                <td><%= val unless %w[uuid].include?(key) %></td>
+              <% unless key == 'uuid' %>
+                <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
         <% end %>
@@ -43,24 +61,26 @@
         <tr>
           <th></th>
           <% for key in @update_samples[0].keys %>
-            <th><%= key unless key == 'uuid' %></th>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for update_sample in @update_samples %>
-          <tr id='<%= "update-sample-#{update_sample['id']}-1" %>' >
+          <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
             <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
             <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
             <% update_sample.map do |key, val| %>
-              <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' >
-                <%= val unless key == 'uuid' %>
-              </td>
+              <% unless key == 'uuid' %>
+                <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
-          <tr id='<%= "update-sample-#{update_sample['id']}-2" %>' >
+          <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
             <% db_sample.map do |key, val| %>
-              <td>
-                <%= val unless key == 'uuid' %>
-              </td>
+              <% unless key == 'uuid' %>
+                <td><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
         <% end %>
@@ -77,27 +97,25 @@
         <tr>
           <th></th>
           <% for key in @possible_duplicates[0].keys %>
-            <th>
-              <%= key unless %w[uuid duplicate].include?(key) %>
-            </th>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for dupl_sample in @possible_duplicates %>
           <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-            <td rowspan=2>
-              <button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button>
-          </td>
-        <% dupl_sample.map do |key, val| %>
-          <% val = '<new>' if key =='id' %>
-          <td rowspan=1 class="table-danger">
-            <%= val unless %w[uuid duplicate].include?(key) %>
-          </td>
-        <% end %>
+            <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+          <% dupl_sample.map do |key, val| %>
+            <% val = '<new>' if key =='id' %>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+            <% end %>
+          <% end %>
             <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
               <% dupl_sample['duplicate'].map do |key, val| %>
-                <td rowspan=1>
-                  <%= val unless %w[uuid duplicate].include?(key) %>
-                </td>
+                <% unless %w[uuid duplicate].include?(key) %>
+                  <td><%= val %></td>
+                <% end %>
               <% end %>
             </tr>
           </tr>
@@ -105,10 +123,12 @@
       </table>
     </div>
   <% end %>
-  <% end %>
+<% end %>
 
+<div id='check-excel-upload-result'></div>
 
-  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" %>
+  <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 
 <script type="text/javascript">

From 938225624cdc4cff366677afeb57020f8a5b2d12 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:37:00 +0200
Subject: [PATCH 09/54] Added error message to the bottom of the form.

---
 .../sample_upload_content.html.erb             | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 48636bebc9..7674c4c627 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,3 +1,4 @@
+<% can_upload = true %>
 <div id="upload-summary">
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
     <% [@project, @study, @sample_type, @template]. map do | asset | %>
@@ -11,12 +12,19 @@
           <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
           <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+          <% can_upload = false %>
         <% end %>
       <% else %>
         <% if asset.can_manage?%>
           <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
           <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+ <%
+=begin%>
+ <% can_upload = false %>
+<%
+=end%>
+ <% can_upload = false unless asset_name == "Template" %>
         <% end %>
       <% end %>
       <hr>
@@ -126,8 +134,16 @@
 <% end %>
 
 <div id='check-excel-upload-result'></div>
+<% unless can_upload %>
+  <div class="alert alert-danger alert-dismissible" role="alert">
+      <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+      <h3>Error</h3>
+      <strong>Unable to upload the current set of samples!</strong>
+      <p>Please expand the 'General Information' pane for more information.</p>
+  </div>
+<% end %>
 
-  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" %>
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 

From d8c4444061cb2e93ea6aff3921871f8d4eac96c5 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 27 Jun 2023 09:40:43 +0200
Subject: [PATCH 10/54] Change `can_manage?` to `can_edit?` and removed the
 template from the general information.

---
 .../single_pages/sample_upload_content.html.erb   | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 7674c4c627..557ab82d94 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,7 +1,7 @@
 <% can_upload = true %>
 <div id="upload-summary">
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
-    <% [@project, @study, @sample_type, @template]. map do | asset | %>
+    <% [@project, @study, @sample_type]. map do | asset | %>
       <% asset_name = asset.class.to_s.singularize %>
       <h4> <%= asset_name %> </h4>
       <p><b>ID: </b><span><%= asset.id%></span></p>
@@ -15,16 +15,11 @@
           <% can_upload = false %>
         <% end %>
       <% else %>
-        <% if asset.can_manage?%>
-          <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% if asset.can_edit?%>
+          <p><b><%= current_user.person.name %> can edit: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
-          <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
- <%
-=begin%>
- <% can_upload = false %>
-<%
-=end%>
- <% can_upload = false unless asset_name == "Template" %>
+          <p><b><%= current_user.person.name %> can edit: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% can_upload = false %>
         <% end %>
       <% end %>
       <hr>

From f6b9b1b44c5150210541f7765d9a86ad8d94ca10 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 5 May 2023 11:03:27 +0200
Subject: [PATCH 11/54] Added the roo and roo-xls gems

---
 Gemfile      |  4 ++++
 Gemfile.lock | 14 +++++++++++++-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/Gemfile b/Gemfile
index 37721643a9..d99819dfdd 100644
--- a/Gemfile
+++ b/Gemfile
@@ -155,6 +155,10 @@ gem 'rails-static-router'
 
 gem 'net-ftp'
 
+# Reading excel spreadsheets
+gem "roo", "~> 2.10.0"
+gem 'roo-xls', '~> 1.1'
+
 group :production do
   gem 'passenger'
 end
diff --git a/Gemfile.lock b/Gemfile.lock
index d0cc6cece7..d9e3b26f43 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -717,6 +717,13 @@ GEM
     ro-crate (0.5.1)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
+    roo (2.10.0)
+      nokogiri (~> 1)
+      rubyzip (>= 1.3.0, < 3.0.0)
+    roo-xls (1.2.0)
+      nokogiri
+      roo (>= 2.0.0, < 3)
+      spreadsheet (> 0.9.0)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -748,6 +755,7 @@ GEM
       unicode-display_width (>= 1.4.0, < 3.0)
     rubocop-ast (1.15.1)
       parser (>= 3.0.1.1)
+    ruby-ole (1.2.12.2)
     ruby-prof (1.4.3)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
@@ -823,6 +831,8 @@ GEM
     sparql-client (3.2.0)
       net-http-persistent (~> 4.0, >= 4.0.1)
       rdf (~> 3.2)
+    spreadsheet (1.3.0)
+      ruby-ole
     sprockets (4.2.0)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -927,7 +937,7 @@ GEM
       rubyzip (~> 2.0.0)
 
 PLATFORMS
-  ruby
+  x86_64-linux
 
 DEPENDENCIES
   RedCloth (>= 4.3.0)
@@ -1038,6 +1048,8 @@ DEPENDENCIES
   rmagick (= 4.2.5)
   ro-bundle (~> 0.3.0)
   ro-crate (~> 0.5.1)
+  roo (~> 2.10.0)
+  roo-xls (~> 1.1)
   rspec-rails (~> 5.1)
   rubocop
   ruby-prof

From 74e401f9cc513796e9d34bcd6671d2f3c9af725c Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 8 May 2023 09:55:30 +0200
Subject: [PATCH 12/54] Working on uploading the samples via spreadsheet

- added route to routes.rb
- Extraction of sample information in the controller
- Added a partial form with a button to upload the spreadsheet
---
 app/controllers/single_pages_controller.rb | 42 ++++++++++++++++++++++
 app/views/isa_studies/_buttons.html.erb    |  7 ++++
 config/routes.rb                           |  1 +
 3 files changed, 50 insertions(+)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index fa379084ae..a4390727c0 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -1,4 +1,7 @@
 require 'isatab_converter'
+require 'roo'
+require 'roo-xls'
+
 class SinglePagesController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Sharing::SharingCommon
@@ -60,6 +63,45 @@ def export_isa
     end
   end
 
+  def upload_samples
+    wb = Roo::Excelx.new(params[:file].path)
+    puts params
+    # Extract Samples metadata
+    puts wb.cell(2, 2, sheet = 'Metadata').to_i
+    puts wb.cell(5, 2, sheet = 'Metadata').to_i
+    puts wb.cell(8, 2, sheet = 'Metadata').to_i
+
+    @study = Study.find(wb.cell(2, 2, sheet = 'Metadata').to_i)
+    @sample_type = SampleType.find(wb.cell(5, 2, sheet = 'Metadata').to_i)
+    @template = Template.find(wb.cell(8, 2, sheet = 'Metadata').to_i)
+
+    sample_fields = wb.row(1, sheet = 'Samples')
+    samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
+
+    @excel_samples = samples_data.map do |excel_sample|
+      obj = {}
+      (0..sample_fields.size - 1).map do |i|
+        obj.merge!(sample_fields[i] => excel_sample[i])
+      end
+      obj
+    end
+
+    @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
+    @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
+
+    @db_samples = @existing_excel_samples.map { |sample| JSON.parse(Sample.find(sample['id'])[:json_metadata]) }
+
+    [@study, @sample_type, @template, @excel_samples, @existing_excel_samples, @new_excel_samples, @db_samples].each do |var|
+      puts '#' * 100
+      puts var.inspect
+    end
+    puts '#' * 100
+
+    # respond_to do |format|
+    #   format.html { redirect_to single_page_path(@study.projects.first) }
+    # end
+  end
+
   private
 
   def set_up_instance_variable
diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 388e37f75e..720bec20f1 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -15,6 +15,13 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
   <button class="btn btn-primary dt-action" id="btn_save_assay_sample" onClick=<%=save%>>Save</button>
 </div>
 
+<div>
+  <%= form_with url: upload_samples_single_page_url() , multipart: true do |form| %>
+    <%= form.file_field :file %>
+    <%= form.submit 'Upload' %>
+  <% end %>
+</div>
+
 <script>
   function loadBatchPermission(dtName, e){
     const sample_ids = window[dtName].selectedSampleIds()
diff --git a/config/routes.rb b/config/routes.rb
index 33f71904cf..e5b43e3fa1 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -750,6 +750,7 @@
     member do
       get :dynamic_table_data
       get :export_isa, action: :export_isa
+      post :upload_samples, action: :upload_samples
     end
     collection do
       get :batch_sharing_permission_preview

From 0db4b896887891ff20eeec051f12cfd0f26d0de3 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:39:30 +0200
Subject: [PATCH 13/54] Added functionality to read excel spreadsheets of
 source samples table

---
 app/controllers/single_pages_controller.rb | 82 ++++++++++++++++++----
 1 file changed, 67 insertions(+), 15 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index a4390727c0..f67affdd27 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -67,15 +67,15 @@ def upload_samples
     wb = Roo::Excelx.new(params[:file].path)
     puts params
     # Extract Samples metadata
-    puts wb.cell(2, 2, sheet = 'Metadata').to_i
-    puts wb.cell(5, 2, sheet = 'Metadata').to_i
-    puts wb.cell(8, 2, sheet = 'Metadata').to_i
+    study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
+    sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
+    template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
 
-    @study = Study.find(wb.cell(2, 2, sheet = 'Metadata').to_i)
-    @sample_type = SampleType.find(wb.cell(5, 2, sheet = 'Metadata').to_i)
-    @template = Template.find(wb.cell(8, 2, sheet = 'Metadata').to_i)
+    @study = Study.find(study_id)
+    @sample_type = SampleType.find(sample_type_id)
+    @template = Template.find(template_id)
 
-    sample_fields = wb.row(1, sheet = 'Samples')
+    sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
 
     @excel_samples = samples_data.map do |excel_sample|
@@ -89,17 +89,69 @@ def upload_samples
     @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
     @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
-    @db_samples = @existing_excel_samples.map { |sample| JSON.parse(Sample.find(sample['id'])[:json_metadata]) }
+    @db_samples = @existing_excel_samples.map do |sample|
+      raw_sample = Sample.find(sample['id'])
+      attributes = JSON.parse(raw_sample[:json_metadata])
+      { 'id' => raw_sample.id,
+        'uuid' => raw_sample.uuid }.merge(attributes)
+    end
+
+    # Determine whether samples have been modified or not
+    @update_samples = @existing_excel_samples.map do |ees|
+      db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
+      # An exception is raised if the ID of an existing Sample cannot be found in the DB
+      raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
+      is_changed = false
+
+      db_sample.map do |k, v|
+        unless ees[k] == v
+          is_changed = true
+          break
+        end
+      end
 
-    [@study, @sample_type, @template, @excel_samples, @existing_excel_samples, @new_excel_samples, @db_samples].each do |var|
-      puts '#' * 100
-      puts var.inspect
+      ees if is_changed
+    end
+    @update_samples.compact!
+
+    # Determine if the new samples are no duplicates of existing ones,
+    # based on the attribute values
+    @possible_duplicates = []
+    @new_samples = []
+    @new_excel_samples.map do |nes|
+      is_duplicate = true
+
+      @existing_excel_samples.map do |ees|
+        ees.map do |k, v|
+          unless %w[id uuid].include?(k)
+            is_duplicate = (nes[k] == v)
+            break unless is_duplicate
+          end
+        end
+        if is_duplicate
+          @possible_duplicates.append(nes.merge({ 'duplicate' => ees }))
+          break
+        end
+      end
+      @new_samples.append(nes) unless is_duplicate
     end
-    puts '#' * 100
 
-    # respond_to do |format|
-    #   format.html { redirect_to single_page_path(@study.projects.first) }
-    # end
+    upload_data = { study: @study,
+                    sampleType: @sample_type,
+                    template: @template,
+                    excelSamples: @excel_samples,
+                    existingExcelSamples: @existing_excel_samples,
+                    newExcelSamples: @new_excel_samples,
+                    updateSamples: @update_samples,
+                    newSamples: @new_samples,
+                    possibleDuplicates: @possible_duplicates,
+                    dbSamples: @db_samples }
+
+
+    respond_to do |format|
+      format.json { render json: { uploadData: upload_data } }
+      format.html { render 'single_pages/sample_upload_content', { layout: false } }
+    end
   end
 
   private

From 9f34bd87d6bdb6f203c4a438c8ae53f98e240999 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:40:42 +0200
Subject: [PATCH 14/54] Changed form to html button that calls an ajax function

---
 app/views/isa_studies/_buttons.html.erb | 53 ++++++++++++++++++++-----
 1 file changed, 44 insertions(+), 9 deletions(-)

diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 720bec20f1..573b906e30 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -15,11 +15,18 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
   <button class="btn btn-primary dt-action" id="btn_save_assay_sample" onClick=<%=save%>>Save</button>
 </div>
 
-<div>
-  <%= form_with url: upload_samples_single_page_url() , multipart: true do |form| %>
-    <%= form.file_field :file %>
-    <%= form.submit 'Upload' %>
-  <% end %>
+<div class="container-sm">
+  <form id="upload_excel_form" action="<%= upload_samples_single_page_url() %>" method="post" enctype="multipart/form-data">
+    <div class="mb-3">
+      <label for="file" class="form-label">Upload excel file:</label>
+    </div>
+    <div class="mb-3">
+      <input id="fileUpload" name="fileUpload" type="file" class="form-control form-control-lg"/>
+    </div>
+    <div class="mb-3">
+      <button class="btn btn-default">Upload</button>
+    </div>
+  </form>
 </div>
 
 <script>
@@ -30,7 +37,7 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
       method: "GET",
       url: "<%= batch_sharing_permission_preview_single_pages_path %>",
       data: { sample_ids, single_page: true },
-      success: (res) => { 
+      success: (res) => {
         if (res?.status == "unprocessable_entity"){
           alert(res?.error)
         } else {
@@ -39,11 +46,39 @@ permissions||="loadBatchPermission('sampleDynamicTable',this)"
           ObjectsInput.init();
         }
       },
-      error: (e) => { 
+      error: (e) => {
         console.log(e);
         alert("An error occurred while fetching data from the server.")
       }
     });
-  
+
   }
-</script>
\ No newline at end of file
+
+async function handleUploadSubmit(e){
+  const form = e.target;
+  const url = new URL(form.action);
+  let formData = new FormData();
+  formData.append('file', fileUpload.files[0]);
+
+
+  $j.ajax({
+    type: 'POST',
+    url: url,
+    data: formData,
+    dataType: 'html',
+    processData: false,
+    contentType: false,
+    enctype: 'multipart/form-data',
+    success: function(response){
+      $j('#upload-excel-modal').modal('show').focus();
+      $j('#upload-excel').html(response);
+    },
+    error: function(err){
+      alert(`The following error occurred!\n${err}`);
+    }
+  });
+  e.preventDefault();
+}
+  const uploadExcelForm = document.getElementById("upload_excel_form");
+  uploadExcelForm.addEventListener('submit', handleUploadSubmit);
+</script>

From d851c6188ad962871c0b96afde059f581d106768 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 16 Jun 2023 17:41:46 +0200
Subject: [PATCH 15/54] Added a modal form for the overview  of the upload
 actions

---
 .../sample_upload_content.html.erb            | 134 ++++++++++++++++++
 app/views/single_pages/show.html.erb          |   7 +
 2 files changed, 141 insertions(+)
 create mode 100644 app/views/single_pages/sample_upload_content.html.erb

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
new file mode 100644
index 0000000000..572a3637a5
--- /dev/null
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -0,0 +1,134 @@
+<div id="upload-summary">
+  <%= folding_panel("General Inforamtion", true, :id => "general-information-panel") do %>
+    <% [@study, @sample_type, @template]. map do | entity | %>
+      <h4> <%= entity.class.to_s.singularize %> </h4>
+      <p><b>ID: </b><span><%= entity.id%></span></p>
+      <p><b>UUID: </b><span><%= entity.uuid %></span></p>
+      <p><b>Title: </b><span><%= entity.title %></span></p>
+      <hr>
+    <% end %>
+  <% end %>
+
+  <% unless @new_samples.nil? or @new_samples.compact == [] %>
+  <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
+  :help_text => "These samples have been detected as new samples and will be created.") do %>
+    <div class="table-responsive">
+      <table id="create-sample-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @new_samples[0].keys %>
+            <th><%= key unless %w[uuid].include?(key) %></th>
+          <% end %>
+        </tr>
+        <% for new_sample in @new_samples %>
+          <% new_sample_id = UUID.generate %>
+          <tr id='<%= "new-sample-#{new_sample_id}" %>'>
+            <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+              <% new_sample.map do |key, val| %>
+                <% val = '<new>' if key =='id' %>
+                <td><%= val unless %w[uuid].include?(key) %></td>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
+
+ <% unless @update_samples.nil? or @update_samples.compact == [] %>
+  <%= folding_panel("Samples to Update <span class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+  :help_text => "These samples were detected existing samples and will be updated.") do %>
+    <div class="table-responsive">
+      <table id="update-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @update_samples[0].keys %>
+            <th><%= key unless key == 'uuid' %></th>
+          <% end %>
+        </tr>
+        <% for update_sample in @update_samples %>
+          <tr id='<%= "update-sample-#{update_sample['id']}-1" %>' >
+            <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
+            <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
+            <% update_sample.map do |key, val| %>
+              <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' >
+                <%= val unless key == 'uuid' %>
+              </td>
+            <% end %>
+          </tr>
+          <tr id='<%= "update-sample-#{update_sample['id']}-2" %>' >
+            <% db_sample.map do |key, val| %>
+              <td>
+                <%= val unless key == 'uuid' %>
+              </td>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
+
+<% unless @possible_duplicates.nil? or @possible_duplicates.compact == [] %>
+  <%= folding_panel("Possible Duplicates <span class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+                  :help_text => "These new samples have been matched to already existing samples.") do %>
+    <div class="table-responsive">
+      <table id="duplicate-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @possible_duplicates[0].keys %>
+            <th>
+              <%= key unless %w[uuid duplicate].include?(key) %>
+            </th>
+          <% end %>
+        </tr>
+        <% for dupl_sample in @possible_duplicates %>
+          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
+            <td rowspan=2>
+              <button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button>
+          </td>
+        <% dupl_sample.map do |key, val| %>
+          <% val = '<new>' if key =='id' %>
+          <td rowspan=1 class="table-danger">
+            <%= val unless %w[uuid duplicate].include?(key) %>
+          </td>
+        <% end %>
+            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
+              <% dupl_sample['duplicate'].map do |key, val| %>
+                <td rowspan=1>
+                  <%= val unless %w[uuid duplicate].include?(key) %>
+                </td>
+              <% end %>
+            </tr>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+  <% end %>
+
+
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
+</div>
+<script type="text/javascript">
+  function removeSample(elementName){
+    console.log("elementName", elementName);
+    $j(`tr[id*='${elementName}']`).remove();
+  }
+
+  function submitUpload(){
+    $j.ajax({
+      method: "POST",
+      url: '<%= batch_change_permission_for_selected_items_single_pages_path -%>?single_page=true',
+      data: $j("#change-permission-preview-form").serialize(),
+      success: (res) => {
+        $j('#change-batch-permission').html(res);
+        // Handling 'remaining backdrop' issue when multiple modals
+        $j('#add-person-permission-modal').data("backdrop", "");
+        $j('#add-project-permission-modal').data("backdrop", "");
+        ObjectsInput.init();
+      },
+      error: (e) => { console.log(e) }
+    });
+  }
+</script>
diff --git a/app/views/single_pages/show.html.erb b/app/views/single_pages/show.html.erb
index 327d96e652..29c6185021 100644
--- a/app/views/single_pages/show.html.erb
+++ b/app/views/single_pages/show.html.erb
@@ -56,6 +56,13 @@
       <% end %>
     <% end %>
 
+    <%= modal(id: 'upload-excel-modal', size: 'xl') do %>
+      <%= modal_header("Upload from spreadsheet") %>
+      <%= modal_body do %>
+        <div id="upload-excel">...</div>
+      <% end %>
+    <% end %>
+
 </div>
 
 <script type="text/javascript">

From 4db4ab2ff4b5993c7e315f7a20a83eb665993b51 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:15:42 +0200
Subject: [PATCH 16/54] Added `project` and changed `db_samples` to match the
 samples from the database the current user has at least editing authorization
 for.

---
 app/controllers/single_pages_controller.rb | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index f67affdd27..f4ee217e22 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -74,6 +74,7 @@ def upload_samples
     @study = Study.find(study_id)
     @sample_type = SampleType.find(sample_type_id)
     @template = Template.find(template_id)
+    @project = @study.projects.first # In Single Page a study can only belong to one project
 
     sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
@@ -89,11 +90,10 @@ def upload_samples
     @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
     @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
-    @db_samples = @existing_excel_samples.map do |sample|
-      raw_sample = Sample.find(sample['id'])
-      attributes = JSON.parse(raw_sample[:json_metadata])
-      { 'id' => raw_sample.id,
-        'uuid' => raw_sample.uuid }.merge(attributes)
+    @db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
+      attributes = JSON.parse(sample[:json_metadata])
+      { 'id' => sample.id,
+        'uuid' => sample.uuid }.merge(attributes)
     end
 
     # Determine whether samples have been modified or not
@@ -121,15 +121,15 @@ def upload_samples
     @new_excel_samples.map do |nes|
       is_duplicate = true
 
-      @existing_excel_samples.map do |ees|
-        ees.map do |k, v|
+      @db_samples.map do |dbs|
+        dbs.map do |k, v|
           unless %w[id uuid].include?(k)
             is_duplicate = (nes[k] == v)
             break unless is_duplicate
           end
         end
         if is_duplicate
-          @possible_duplicates.append(nes.merge({ 'duplicate' => ees }))
+          @possible_duplicates.append(nes.merge({ 'duplicate' => dbs }))
           break
         end
       end

From d1efb55f994b262e4dbe10bed945a22b125a1235 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:17:09 +0200
Subject: [PATCH 17/54] Implemented javascript functions to submit samples to
 update and samples to create.

---
 .../sample_upload_content.html.erb            | 138 ++++++++++++++++--
 1 file changed, 126 insertions(+), 12 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 572a3637a5..2ead616ef0 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -110,6 +110,7 @@
 
   <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
 </div>
+
 <script type="text/javascript">
   function removeSample(elementName){
     console.log("elementName", elementName);
@@ -117,18 +118,131 @@
   }
 
   function submitUpload(){
-    $j.ajax({
-      method: "POST",
-      url: '<%= batch_change_permission_for_selected_items_single_pages_path -%>?single_page=true',
-      data: $j("#change-permission-preview-form").serialize(),
-      success: (res) => {
-        $j('#change-batch-permission').html(res);
-        // Handling 'remaining backdrop' issue when multiple modals
-        $j('#add-person-permission-modal').data("backdrop", "");
-        $j('#add-project-permission-modal').data("backdrop", "");
-        ObjectsInput.init();
-      },
-      error: (e) => { console.log(e) }
+    const newSamples = { data: getNewSamples() };
+    const updatedSamples= { data: getUpdateSamples() };
+
+    console.log('newSamples', newSamples);
+    console.log('updatedSamples', updatedSamples);
+
+    if(true){
+      uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
+      uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
+    }
+
+    closeModalForm();
+    location.reload();
+  }
+
+  // Retrieves the samples from the create-samples-table and the duplicate-samples-table
+  function getNewSamples(){
+    const newRows = $j('#create-samples-table tr:not(:has(th))').toArray();
+    const duplicatedRows = $j('#duplicate-samples-table tr:not([class="danger"]):not(:has(th))').toArray();
+    let createRows = newRows;
+
+    if (duplicatedRows.length > 0 && confirm("Are you sure you want to add potentially duplicated rows?")) {
+      createRows = createRows.concat(duplicatedRows);
+    }
+    console.log('createRows', createRows);
+    const sampleObjects = createRows.map((cr, index) => createSampleObject(cr, "new", index));
+
+   return sampleObjects
+  }
+
+  function getUpdateSamples(){
+    const updateRows = $j('#update-samples-table [id*="updated"]').toArray();
+
+    const sampleObjects = updateRows.map((ur, index) => createSampleObject(ur, "update", index));
+
+    return sampleObjects
+  }
+
+  function createSampleObject(row, action, index){
+
+    cells = $j(row).find('td:not(:has(".danger"))').toArray();
+    samplesObj = {};
+    cells.map(function(cell){
+      val = cell.textContent;
+      key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
+      samplesObj[key] = val;
     });
+
+    const {id: objId, ...attrMap} = samplesObj;
+
+    attrMap["status"] = action;
+
+    if (action === "update"){
+      return {
+        id: objId,
+        ex_id: `update-${index}-<%= @sample_type.id %>`,
+        data: {
+          type: "samples",
+          attributes: {
+            attribute_map: attrMap
+          }
+        }
+      };
+    } else {
+        return {
+          ex_id: `new-${index}-<%= @sample_type.id %>`,
+            data:{
+              type: "samples",
+              tags: null,
+              attributes: {
+              policy: {
+                access: getAccess(projectDefaultPolicy),
+                permissions: [
+                  {
+                    resource: { type: "Project", id: <%= @project.id %> },
+                    access: getPermission(projectDefaultPolicy, <%= @project.id %>)
+                  }
+                ]
+              },
+              attribute_map: attrMap
+              },
+              relationships: {
+                projects: {
+                  data: [
+                    {type: "projects", id: <%= @project.id %>}
+                  ]
+                },
+                sample_type: {
+                  data: {
+                    type: "sample_types",
+                    id: <%= @sample_type.id %>
+                  }
+                }
+              }
+            }
+        };
+    }
+  }
+  function closeModalForm(){
+    $j('#upload-excel-modal').modal('hide');
   }
+
+  const uploadAjaxCall = (url, method, params) => {
+    const { data, cache, dataType } = params;
+    if (!url || !method) throw new Error("Parameter(s) missing");
+    return $j.ajax({
+      method,
+      url,
+      data,
+      dataType,
+      cache: cache || false,
+      headers: {
+        "Content-Type": "application/json",
+        Accept: "application/json"
+      },
+      beforeSend: function () {
+        $j('#check-excel-upload-result').html('<h2>Updating Samples...</h2>');
+      },
+      success: function(res) {
+        console.log("res", res);
+      },
+      error: function(err) {
+        console.log("err", err);
+      }
+    });
+  };
+
 </script>

From ddaba00e1cf6b967b0654298c2b00367e830a673 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:20:00 +0200
Subject: [PATCH 18/54] Changed the sample upload modal:

- Removed trailing `\n` from cells
- Added more information to 'General Information' pane
---
 .../sample_upload_content.html.erb            | 90 +++++++++++--------
 1 file changed, 55 insertions(+), 35 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 2ead616ef0..48636bebc9 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,10 +1,24 @@
 <div id="upload-summary">
-  <%= folding_panel("General Inforamtion", true, :id => "general-information-panel") do %>
-    <% [@study, @sample_type, @template]. map do | entity | %>
-      <h4> <%= entity.class.to_s.singularize %> </h4>
-      <p><b>ID: </b><span><%= entity.id%></span></p>
-      <p><b>UUID: </b><span><%= entity.uuid %></span></p>
-      <p><b>Title: </b><span><%= entity.title %></span></p>
+  <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
+    <% [@project, @study, @sample_type, @template]. map do | asset | %>
+      <% asset_name = asset.class.to_s.singularize %>
+      <h4> <%= asset_name %> </h4>
+      <p><b>ID: </b><span><%= asset.id%></span></p>
+      <p><b>UUID: </b><span><%= asset.uuid %></span></p>
+      <p><b>Title: </b><span><%= asset.title %></span></p>
+      <% if asset_name == "Project"%>
+        <% if current_user.person.member_of?(asset)%>
+          <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% else %>
+          <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% end %>
+      <% else %>
+        <% if asset.can_manage?%>
+          <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% else %>
+          <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% end %>
+      <% end %>
       <hr>
     <% end %>
   <% end %>
@@ -13,11 +27,13 @@
   <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
   :help_text => "These samples have been detected as new samples and will be created.") do %>
     <div class="table-responsive">
-      <table id="create-sample-table" class="table">
+      <table id="create-samples-table" class="table">
         <tr>
           <th></th>
           <% for key in @new_samples[0].keys %>
-            <th><%= key unless %w[uuid].include?(key) %></th>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for new_sample in @new_samples %>
@@ -26,7 +42,9 @@
             <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
               <% new_sample.map do |key, val| %>
                 <% val = '<new>' if key =='id' %>
-                <td><%= val unless %w[uuid].include?(key) %></td>
+              <% unless key == 'uuid' %>
+                <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
         <% end %>
@@ -43,24 +61,26 @@
         <tr>
           <th></th>
           <% for key in @update_samples[0].keys %>
-            <th><%= key unless key == 'uuid' %></th>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for update_sample in @update_samples %>
-          <tr id='<%= "update-sample-#{update_sample['id']}-1" %>' >
+          <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
             <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
             <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
             <% update_sample.map do |key, val| %>
-              <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' >
-                <%= val unless key == 'uuid' %>
-              </td>
+              <% unless key == 'uuid' %>
+                <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
-          <tr id='<%= "update-sample-#{update_sample['id']}-2" %>' >
+          <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
             <% db_sample.map do |key, val| %>
-              <td>
-                <%= val unless key == 'uuid' %>
-              </td>
+              <% unless key == 'uuid' %>
+                <td><%= val %></td>
+              <% end %>
             <% end %>
           </tr>
         <% end %>
@@ -77,27 +97,25 @@
         <tr>
           <th></th>
           <% for key in @possible_duplicates[0].keys %>
-            <th>
-              <%= key unless %w[uuid duplicate].include?(key) %>
-            </th>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <th><%= key %></th>
+            <% end %>
           <% end %>
         </tr>
         <% for dupl_sample in @possible_duplicates %>
           <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-            <td rowspan=2>
-              <button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button>
-          </td>
-        <% dupl_sample.map do |key, val| %>
-          <% val = '<new>' if key =='id' %>
-          <td rowspan=1 class="table-danger">
-            <%= val unless %w[uuid duplicate].include?(key) %>
-          </td>
-        <% end %>
+            <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+          <% dupl_sample.map do |key, val| %>
+            <% val = '<new>' if key =='id' %>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+            <% end %>
+          <% end %>
             <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
               <% dupl_sample['duplicate'].map do |key, val| %>
-                <td rowspan=1>
-                  <%= val unless %w[uuid duplicate].include?(key) %>
-                </td>
+                <% unless %w[uuid duplicate].include?(key) %>
+                  <td><%= val %></td>
+                <% end %>
               <% end %>
             </tr>
           </tr>
@@ -105,10 +123,12 @@
       </table>
     </div>
   <% end %>
-  <% end %>
+<% end %>
 
+<div id='check-excel-upload-result'></div>
 
-  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "" %>
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" %>
+  <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 
 <script type="text/javascript">

From 5ed71386b70328791b25068d38d3a234f3ae60e8 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 26 Jun 2023 21:37:00 +0200
Subject: [PATCH 19/54] Added error message to the bottom of the form.

---
 .../sample_upload_content.html.erb             | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 48636bebc9..7674c4c627 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,3 +1,4 @@
+<% can_upload = true %>
 <div id="upload-summary">
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
     <% [@project, @study, @sample_type, @template]. map do | asset | %>
@@ -11,12 +12,19 @@
           <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
           <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+          <% can_upload = false %>
         <% end %>
       <% else %>
         <% if asset.can_manage?%>
           <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
           <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+ <%
+=begin%>
+ <% can_upload = false %>
+<%
+=end%>
+ <% can_upload = false unless asset_name == "Template" %>
         <% end %>
       <% end %>
       <hr>
@@ -126,8 +134,16 @@
 <% end %>
 
 <div id='check-excel-upload-result'></div>
+<% unless can_upload %>
+  <div class="alert alert-danger alert-dismissible" role="alert">
+      <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+      <h3>Error</h3>
+      <strong>Unable to upload the current set of samples!</strong>
+      <p>Please expand the 'General Information' pane for more information.</p>
+  </div>
+<% end %>
 
-  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" %>
+  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 

From 84f01e68d1ec01f5f696d674a36fac8850a8fae7 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 27 Jun 2023 09:40:43 +0200
Subject: [PATCH 20/54] Change `can_manage?` to `can_edit?` and removed the
 template from the general information.

---
 .../single_pages/sample_upload_content.html.erb   | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 7674c4c627..557ab82d94 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,7 +1,7 @@
 <% can_upload = true %>
 <div id="upload-summary">
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
-    <% [@project, @study, @sample_type, @template]. map do | asset | %>
+    <% [@project, @study, @sample_type]. map do | asset | %>
       <% asset_name = asset.class.to_s.singularize %>
       <h4> <%= asset_name %> </h4>
       <p><b>ID: </b><span><%= asset.id%></span></p>
@@ -15,16 +15,11 @@
           <% can_upload = false %>
         <% end %>
       <% else %>
-        <% if asset.can_manage?%>
-          <p><b><%= current_user.person.name %> can manage: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% if asset.can_edit?%>
+          <p><b><%= current_user.person.name %> can edit: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
-          <p><b><%= current_user.person.name %> can manage: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
- <%
-=begin%>
- <% can_upload = false %>
-<%
-=end%>
- <% can_upload = false unless asset_name == "Template" %>
+          <p><b><%= current_user.person.name %> can edit: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% can_upload = false %>
         <% end %>
       <% end %>
       <hr>

From b9c40e880b85abf9ecec644d06e76b6d5d213bdf Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 4 Jul 2023 10:30:40 +0200
Subject: [PATCH 21/54] Remove duplicated gems

---
 Gemfile | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Gemfile b/Gemfile
index efce9dea63..f4ce9f873a 100644
--- a/Gemfile
+++ b/Gemfile
@@ -162,10 +162,6 @@ gem 'net-ftp'
 gem "roo", "~> 2.10.0"
 gem 'roo-xls', '~> 1.1'
 
-# Reading excel spreadsheets
-gem "roo", "~> 2.10.0"
-gem 'roo-xls', '~> 1.1'
-
 group :production do
   gem 'passenger'
 end

From 961bbdf6982383c3e972e58ecd952da6a21c98d1 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Thu, 6 Jul 2023 15:09:10 +0200
Subject: [PATCH 22/54] Updated the sample upload view: - Cancel button should
 close modal form - Clean-up and simplification

---
 .../sample_upload_content.html.erb            | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 557ab82d94..3aec638b0f 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,7 +1,8 @@
 <% can_upload = true %>
 <div id="upload-summary">
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
-    <% [@project, @study, @sample_type]. map do | asset | %>
+    <% [@project, @study, @assay, @sample_type]. map do | asset | %>
+      <% next if asset.nil? %>
       <% asset_name = asset.class.to_s.singularize %>
       <h4> <%= asset_name %> </h4>
       <p><b>ID: </b><span><%= asset.id%></span></p>
@@ -26,7 +27,7 @@
     <% end %>
   <% end %>
 
-  <% unless @new_samples.nil? or @new_samples.compact == [] %>
+  <% unless @new_samples.nil? or @new_samples.compact.none? %>
   <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
   :help_text => "These samples have been detected as new samples and will be created.") do %>
     <div class="table-responsive">
@@ -56,7 +57,7 @@
   <% end %>
 <% end %>
 
- <% unless @update_samples.nil? or @update_samples.compact == [] %>
+ <% unless @update_samples.nil? or @update_samples.compact.none? %>
   <%= folding_panel("Samples to Update <span class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
   :help_text => "These samples were detected existing samples and will be updated.") do %>
     <div class="table-responsive">
@@ -92,7 +93,7 @@
   <% end %>
 <% end %>
 
-<% unless @possible_duplicates.nil? or @possible_duplicates.compact == [] %>
+<% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
   <%= folding_panel("Possible Duplicates <span class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
                   :help_text => "These new samples have been matched to already existing samples.") do %>
     <div class="table-responsive">
@@ -138,13 +139,12 @@
   </div>
 <% end %>
 
-  <%= submit_tag "Next", data: {disable_with: 'Next'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
+  <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 
 <script type="text/javascript">
   function removeSample(elementName){
-    console.log("elementName", elementName);
     $j(`tr[id*='${elementName}']`).remove();
   }
 
@@ -152,9 +152,6 @@
     const newSamples = { data: getNewSamples() };
     const updatedSamples= { data: getUpdateSamples() };
 
-    console.log('newSamples', newSamples);
-    console.log('updatedSamples', updatedSamples);
-
     if(true){
       uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
       uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
@@ -170,13 +167,18 @@
     const duplicatedRows = $j('#duplicate-samples-table tr:not([class="danger"]):not(:has(th))').toArray();
     let createRows = newRows;
 
-    if (duplicatedRows.length > 0 && confirm("Are you sure you want to add potentially duplicated rows?")) {
-      createRows = createRows.concat(duplicatedRows);
+    if (duplicatedRows.length > 0 ) {
+      if (confirm("Are you sure you want to add potentially duplicated rows?")) {
+        createRows = createRows.concat(duplicatedRows);
+      } else {
+        closeModalForm();
+        return;
+      }
     }
-    console.log('createRows', createRows);
+
     const sampleObjects = createRows.map((cr, index) => createSampleObject(cr, "new", index));
 
-   return sampleObjects
+    return sampleObjects;
   }
 
   function getUpdateSamples(){
@@ -255,6 +257,7 @@
     const { data, cache, dataType } = params;
     if (!url || !method) throw new Error("Parameter(s) missing");
     return $j.ajax({
+      async: false,
       method,
       url,
       data,
@@ -264,9 +267,6 @@
         "Content-Type": "application/json",
         Accept: "application/json"
       },
-      beforeSend: function () {
-        $j('#check-excel-upload-result').html('<h2>Updating Samples...</h2>');
-      },
       success: function(res) {
         console.log("res", res);
       },

From 74742f74afa89998e14247a0c5bd254e69a47a0a Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Thu, 6 Jul 2023 15:12:06 +0200
Subject: [PATCH 23/54] Extrapolate upload functionality to other dynamic
 tables: - Changed upload route from member to collection - Move Ajax call to
 the index.js file - Add function to the different tables

---
 .../javascripts/single_page/index.js.erb      | 19 ++++++++
 app/views/isa_assays/_assay_samples.html.erb  | 10 +++-
 app/views/isa_studies/_buttons.html.erb       | 48 ++++---------------
 .../isa_studies/_source_material.html.erb     | 11 ++++-
 app/views/isa_studies/_study_samples.html.erb | 10 +++-
 config/routes.rb                              |  2 +-
 6 files changed, 58 insertions(+), 42 deletions(-)

diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
index f9beb902db..c17e1b238d 100644
--- a/app/assets/javascripts/single_page/index.js.erb
+++ b/app/assets/javascripts/single_page/index.js.erb
@@ -282,6 +282,25 @@ async function batchUpdateSample(sampleTypes) {
   }
 }
 
+async function handleUploadSubmit(formData){
+  $j.ajax({
+    type: 'POST',
+    url: "<%= upload_samples_single_pages_path %>",
+    data: formData,
+    dataType: 'html',
+    processData: false,
+    contentType: false,
+    enctype: 'multipart/form-data',
+    success: function(response){
+      $j('#upload-excel-modal').modal('show').focus();
+      $j('#upload-excel').html(response);
+    },
+    error: function(err){
+      alert(`The following error occurred!\n${err}`);
+    }
+  });
+}
+
 function isMobile() {
 	/Android|webOS|iPhone|iPad|iPod|BlackBerry|IEMobile|Opera Mini/i.test(navigator.userAgent)
 }
diff --git a/app/views/isa_assays/_assay_samples.html.erb b/app/views/isa_assays/_assay_samples.html.erb
index e6aa9aad0a..4712ea8e9d 100644
--- a/app/views/isa_assays/_assay_samples.html.erb
+++ b/app/views/isa_assays/_assay_samples.html.erb
@@ -10,7 +10,7 @@
     </div>
 </div>
 
-<%= render partial: 'isa_studies/buttons' %>
+<%= render partial: 'isa_studies/buttons', locals: {uploadExcel: "assaySampleUploadExcel()", sample_type_id: sample_type&.id} %>
 
 <% if valid_assay %>
     <script>
@@ -62,5 +62,13 @@
             exportToExcel("assay-samples-table", '<%=assay.study_id%>', '<%=assay.id%>', '<%=sample_type.id%>');
         }
 
+        function assaySampleUploadExcel(){
+          const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          let formData = new FormData();
+          formData.append('file', file);
+          formData.append('sample_type_id', <%=sample_type.id%>);
+          handleUploadSubmit(formData);
+        }
+
     </script>
 <% end %>
diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 350bf0ffc4..61a928c0b9 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -6,6 +6,7 @@ delete||="SampleSetAsDeleted()"
 save||="SampleSave()"
 permissions||="loadBatchPermission('sampleDynamicTable',this)"
 exportToExcel||="sampleExportExcel()"
+uploadExcel||="studySampleUploadExcel()"
 %>
 
 <div class="btn-group">
@@ -18,17 +19,15 @@ exportToExcel||="sampleExportExcel()"
 </div>
 
 <div class="container-sm">
-  <form id="upload_excel_form" action="<%= upload_samples_single_page_url() %>" method="post" enctype="multipart/form-data">
-    <div class="mb-3">
-      <label for="file" class="form-label">Upload excel file:</label>
-    </div>
-    <div class="mb-3">
-      <input id="fileUpload" name="fileUpload" type="file" class="form-control form-control-lg"/>
-    </div>
-    <div class="mb-3">
-      <button class="btn btn-default">Upload</button>
-    </div>
-  </form>
+  <div class="mb-3">
+    <label for="file-<%= sample_type_id %>" class="form-label">Upload excel file:</label>
+  </div>
+  <div class="mb-3">
+    <input id="file-<%= sample_type_id %>" name="file-<%= sample_type_id %>" type="file" class="form-control form-control-lg"/>
+  </div>
+  <div class="mb-3">
+    <button class="btn btn-default" onClick=<%= uploadExcel %>>Upload</button>
+  </div>
 </div>
 
 <script>
@@ -56,31 +55,4 @@ exportToExcel||="sampleExportExcel()"
 
   }
 
-async function handleUploadSubmit(e){
-  const form = e.target;
-  const url = new URL(form.action);
-  let formData = new FormData();
-  formData.append('file', fileUpload.files[0]);
-
-
-  $j.ajax({
-    type: 'POST',
-    url: url,
-    data: formData,
-    dataType: 'html',
-    processData: false,
-    contentType: false,
-    enctype: 'multipart/form-data',
-    success: function(response){
-      $j('#upload-excel-modal').modal('show').focus();
-      $j('#upload-excel').html(response);
-    },
-    error: function(err){
-      alert(`The following error occurred!\n${err}`);
-    }
-  });
-  e.preventDefault();
-}
-  const uploadExcelForm = document.getElementById("upload_excel_form");
-  uploadExcelForm.addEventListener('submit', handleUploadSubmit);
 </script>
diff --git a/app/views/isa_studies/_source_material.html.erb b/app/views/isa_studies/_source_material.html.erb
index f534cba03f..7a2ecb74bc 100644
--- a/app/views/isa_studies/_source_material.html.erb
+++ b/app/views/isa_studies/_source_material.html.erb
@@ -11,7 +11,8 @@
 
 <%= render partial: 'isa_studies/buttons', locals:{ add_row: "SourceAddNewRow()", paste_cb:
 "SourcePasteFromClipboard()", delete: "SourceSetAsDeleted()", save: "SourceSave()",
-permissions: "loadBatchPermission('sourceDynamicTable',this)", exportToExcel: "sourceExportExcel()" } %>
+permissions: "loadBatchPermission('sourceDynamicTable',this)", exportToExcel: "sourceExportExcel()",
+uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>
 
 <% if sample_type %>
     <script>
@@ -75,5 +76,13 @@ permissions: "loadBatchPermission('sourceDynamicTable',this)", exportToExcel: "s
             exportToExcel("source-material-table", '<%=study.id%>', null, '<%=sample_type.id%>');
         }
 
+        function sourceUploadExcel(){
+          const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          let formData = new FormData();
+          formData.append('file', file);
+          formData.append('sample_type_id', <%=sample_type.id%>);
+          handleUploadSubmit(formData);
+        }
+
     </script>
 <% end %>
diff --git a/app/views/isa_studies/_study_samples.html.erb b/app/views/isa_studies/_study_samples.html.erb
index 4b206980c1..3c339dac57 100644
--- a/app/views/isa_studies/_study_samples.html.erb
+++ b/app/views/isa_studies/_study_samples.html.erb
@@ -9,7 +9,7 @@
     </div>
 </div>
 
-<%= render partial: 'isa_studies/buttons' %>
+<%= render partial: 'isa_studies/buttons', locals: {uploadExcel: "studySampleUploadExcel()", sample_type_id: sample_type&.id} %>
 
 <% if sample_type %>
     <script>
@@ -68,5 +68,13 @@
             exportToExcel("study-samples-table", '<%=study.id%>', null, '<%=sample_type.id%>');
         }
 
+        function studySampleUploadExcel(){
+          const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          let formData = new FormData();
+          formData.append('file', file);
+          formData.append('sample_type_id', <%=sample_type.id%>);
+          handleUploadSubmit(formData);
+        }
+
     </script>
 <% end %>
diff --git a/config/routes.rb b/config/routes.rb
index afdc8e184c..3e65e18022 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -750,7 +750,6 @@
     member do
       get :dynamic_table_data
       get :export_isa, action: :export_isa
-      post :upload_samples, action: :upload_samples
     end
     collection do
       get :batch_sharing_permission_preview
@@ -758,6 +757,7 @@
       post :batch_sharing_permission_changed
       post :export_to_excel, action: :export_to_excel
       get :download_samples_excel, action: :download_samples_excel
+      post :upload_samples, action: :upload_samples
     end
   end
 

From d0598ced10252ebb42a27b1428f66833815c1bb5 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 09:25:05 +0200
Subject: [PATCH 24/54] Fixed notice when error occurs

---
 app/assets/javascripts/single_page/index.js.erb | 2 +-
 app/controllers/single_pages_controller.rb      | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
index c17e1b238d..ee554f2d3b 100644
--- a/app/assets/javascripts/single_page/index.js.erb
+++ b/app/assets/javascripts/single_page/index.js.erb
@@ -296,7 +296,7 @@ async function handleUploadSubmit(formData){
       $j('#upload-excel').html(response);
     },
     error: function(err){
-      alert(`The following error occurred!\n${err}`);
+      location.reload(); // Page needs reloading for the notice message to appear
     }
   });
 }
diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 49351bcf17..ecd63eb84f 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -213,7 +213,10 @@ def upload_samples
       format.json { render json: { uploadData: upload_data } }
       format.html { render 'single_pages/sample_upload_content', { layout: false } }
     end
-  end
+  rescue StandardError => e
+    flash[:error] = e.message
+    redirect_to single_page_path(@study.project_ids.first), status: :bad_request
+end
 
   private
 

From 546c861a6d11f555453583725e73892c8e215f03 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 13:14:01 +0200
Subject: [PATCH 25/54] Update counter when a sample is removed.

---
 .../sample_upload_content.html.erb            | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 3aec638b0f..5a459ad02d 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -28,7 +28,7 @@
   <% end %>
 
   <% unless @new_samples.nil? or @new_samples.compact.none? %>
-  <%= folding_panel("New Samples <span class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
+  <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
   :help_text => "These samples have been detected as new samples and will be created.") do %>
     <div class="table-responsive">
       <table id="create-samples-table" class="table">
@@ -58,7 +58,7 @@
 <% end %>
 
  <% unless @update_samples.nil? or @update_samples.compact.none? %>
-  <%= folding_panel("Samples to Update <span class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+  <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
   :help_text => "These samples were detected existing samples and will be updated.") do %>
     <div class="table-responsive">
       <table id="update-samples-table" class="table">
@@ -94,7 +94,7 @@
 <% end %>
 
 <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
-  <%= folding_panel("Possible Duplicates <span class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+  <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
                   :help_text => "These new samples have been matched to already existing samples.") do %>
     <div class="table-responsive">
       <table id="duplicate-samples-table" class="table">
@@ -145,7 +145,20 @@
 
 <script type="text/javascript">
   function removeSample(elementName){
+    let counterName = ''
+    if (/duplicate-sample/.test(elementName)){
+      counterName = 'duplicate-samples-counter'
+    } else if (/new-sample/.test(elementName)){
+      counterName = 'new-samples-counter'
+    } else if(/update-sample/.test(elementName)){
+      counterName = 'update-samples-counter'
+    }
+
     $j(`tr[id*='${elementName}']`).remove();
+    debugger;
+    const counter = parseInt($j(`span[id='${counterName}']`)[0].textContent);
+    const newCounter = (counter > 0) ? (counter - 1) : counter;
+    $j(`span[id='${counterName}']`).text(newCounter);
   }
 
   function submitUpload(){

From 4c4c8c0be2bfdd9c6c7a594e7bd10b76851ff0b4 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 13:29:32 +0200
Subject: [PATCH 26/54] Modified controller to handle multi-sample inputs

---
 app/controllers/single_pages_controller.rb    | 59 +++++++++++++++++--
 .../sample_upload_content.html.erb            |  1 -
 2 files changed, 53 insertions(+), 7 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index ecd63eb84f..941163cb7c 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -126,24 +126,69 @@ def export_to_excel
 
   def upload_samples
     wb = Roo::Excelx.new(params[:file].path)
-    puts params
-    # Extract Samples metadata
-    study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
-    sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
-    template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+    sample_type_id_ui = params[:sample_type_id].to_i
 
+    # Extract Samples metadata from spreadsheet
+    study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
     @study = Study.find(study_id)
+    sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
     @sample_type = SampleType.find(sample_type_id)
+
+    # Sample Type validation rules
+    unless sample_type_id_ui == @sample_type&.id
+      raise "Sample Type #{@sample_type&.id} from spreadsheet doesn't match Sample Type #{sample_type_id_ui} from the table. Please upload in the correct table."
+    end
+    unless @study.sample_types.include?(@sample_type)
+      raise "Sample Type '#{@sample_type.id}' doesn't belong to Study #{@study.id}. Sample Upload aborted."
+    end
+
+    is_assay = @sample_type.assays.any?
+    @assay = @sample_type.assays.first
+
+    multiple_input_fields = @sample_type.sample_attributes.map do |sa_attr|
+      sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
+    end
+
+    if is_assay
+      assay_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+      template_id = wb.cell(11, 2, sheet = 'Metadata').to_i
+    else
+      template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+    end
+
+    @assay = Assay.find(assay_id) unless assay_id.nil?
     @template = Template.find(template_id)
     @project = @study.projects.first # In Single Page a study can only belong to one project
 
+
     sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
 
+    # Compare Excel header row to Sample Type Sample Attributes
+    # Should raise an error if they don't match
+    sample_type_attributes = %w[id uuid].concat(@sample_type.sample_attributes.map(&:title))
+    has_unmapped_sample_attributes = sample_type_attributes.map { |sa| sample_fields.include?(sa) }.include?(false)
+    if has_unmapped_sample_attributes
+      raise "The Sample Attributes from the excel sheet don't match those of the Sample Type in the database. Sample upload was aborted!"
+    end
+
+    # Construct Samples objects from Excel data
     @excel_samples = samples_data.map do |excel_sample|
       obj = {}
       (0..sample_fields.size - 1).map do |i|
-        obj.merge!(sample_fields[i] => excel_sample[i])
+        if multiple_input_fields.include?(sample_fields[i])
+          parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub('=>', ':')).map do |subsample|
+            # Uploader should at least have viewing permissions for the inputs he's using
+            unless Sample.find(subsample['id'])&.authorized_for_view?
+              raise "Unauthorized Sample was detected in spreadsheet: #{subsample.inspect}"
+            end
+
+            subsample
+          end
+          obj.merge!(sample_fields[i] => parsed_excel_input_samples)
+        else
+          obj.merge!(sample_fields[i] => excel_sample[i])
+        end
       end
       obj
     end
@@ -162,6 +207,7 @@ def upload_samples
       db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
       # An exception is raised if the ID of an existing Sample cannot be found in the DB
       raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
+
       is_changed = false
 
       db_sample.map do |k, v|
@@ -198,6 +244,7 @@ def upload_samples
     end
 
     upload_data = { study: @study,
+                    assay: @assay,
                     sampleType: @sample_type,
                     template: @template,
                     excelSamples: @excel_samples,
diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 5a459ad02d..e6f00f5fab 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -155,7 +155,6 @@
     }
 
     $j(`tr[id*='${elementName}']`).remove();
-    debugger;
     const counter = parseInt($j(`span[id='${counterName}']`)[0].textContent);
     const newCounter = (counter > 0) ? (counter - 1) : counter;
     $j(`span[id='${counterName}']`).text(newCounter);

From e447c1f639d7173152de958df9882b40fe2ce2db Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 13:44:06 +0200
Subject: [PATCH 27/54] Format upload summary

---
 .../sample_upload_content.html.erb            | 187 +++++++++---------
 1 file changed, 96 insertions(+), 91 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index e6f00f5fab..3459e04af9 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,5 +1,7 @@
 <% can_upload = true %>
 <div id="upload-summary">
+
+  <% # General information panel %>
   <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
     <% [@project, @study, @assay, @sample_type]. map do | asset | %>
       <% next if asset.nil? %>
@@ -27,117 +29,120 @@
     <% end %>
   <% end %>
 
+  <% # New Samples panel %>
   <% unless @new_samples.nil? or @new_samples.compact.none? %>
-  <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
-  :help_text => "These samples have been detected as new samples and will be created.") do %>
-    <div class="table-responsive">
-      <table id="create-samples-table" class="table">
-        <tr>
-          <th></th>
-          <% for key in @new_samples[0].keys %>
-            <% unless key == 'uuid' %>
-              <th><%= key %></th>
-            <% end %>
-          <% end %>
-        </tr>
-        <% for new_sample in @new_samples %>
-          <% new_sample_id = UUID.generate %>
-          <tr id='<%= "new-sample-#{new_sample_id}" %>'>
-            <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
-              <% new_sample.map do |key, val| %>
-                <% val = '<new>' if key =='id' %>
+    <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
+    :help_text => "These samples have been detected as new samples and will be created.") do %>
+      <div class="table-responsive">
+        <table id="create-samples-table" class="table">
+          <tr>
+            <th></th>
+            <% for key in @new_samples[0].keys %>
               <% unless key == 'uuid' %>
-                <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                <th><%= key %></th>
               <% end %>
             <% end %>
           </tr>
-        <% end %>
-      </table>
-    </div>
+          <% for new_sample in @new_samples %>
+            <% new_sample_id = UUID.generate %>
+            <tr id='<%= "new-sample-#{new_sample_id}" %>'>
+              <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+                <% new_sample.map do |key, val| %>
+                  <% val = '<new>' if key =='id' %>
+                <% unless key == 'uuid' %>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                <% end %>
+              <% end %>
+            </tr>
+          <% end %>
+        </table>
+      </div>
+    <% end %>
   <% end %>
-<% end %>
 
- <% unless @update_samples.nil? or @update_samples.compact.none? %>
-  <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
-  :help_text => "These samples were detected existing samples and will be updated.") do %>
-    <div class="table-responsive">
-      <table id="update-samples-table" class="table">
-        <tr>
-          <th></th>
-          <% for key in @update_samples[0].keys %>
-            <% unless key == 'uuid' %>
-              <th><%= key %></th>
-            <% end %>
-          <% end %>
-        </tr>
-        <% for update_sample in @update_samples %>
-          <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
-            <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
-            <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
-            <% update_sample.map do |key, val| %>
+  <% # Update Samples panel %>
+  <% unless @update_samples.nil? or @update_samples.compact.none? %>
+    <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+    :help_text => "These samples were detected existing samples and will be updated.") do %>
+      <div class="table-responsive">
+        <table id="update-samples-table" class="table">
+          <tr>
+            <th></th>
+            <% for key in @update_samples[0].keys %>
               <% unless key == 'uuid' %>
-                <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+                <th><%= key %></th>
               <% end %>
             <% end %>
           </tr>
-          <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
-            <% db_sample.map do |key, val| %>
-              <% unless key == 'uuid' %>
-                <td><%= val %></td>
+          <% for update_sample in @update_samples %>
+            <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
+              <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
+              <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
+              <% update_sample.map do |key, val| %>
+                <% unless key == 'uuid' %>
+                  <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+                <% end %>
               <% end %>
-            <% end %>
-          </tr>
-        <% end %>
-      </table>
-    </div>
+            </tr>
+            <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
+              <% db_sample.map do |key, val| %>
+                <% unless key == 'uuid' %>
+                  <td><%= val %></td>
+                <% end %>
+              <% end %>
+            </tr>
+          <% end %>
+        </table>
+      </div>
+    <% end %>
   <% end %>
-<% end %>
 
-<% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
-  <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
-                  :help_text => "These new samples have been matched to already existing samples.") do %>
-    <div class="table-responsive">
-      <table id="duplicate-samples-table" class="table">
-        <tr>
-          <th></th>
-          <% for key in @possible_duplicates[0].keys %>
-            <% unless %w[uuid duplicate].include?(key) %>
-              <th><%= key %></th>
+  <% # Possible Duplicate Samples panel %>
+  <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
+    <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+                    :help_text => "These new samples have been matched to already existing samples.") do %>
+      <div class="table-responsive">
+        <table id="duplicate-samples-table" class="table">
+          <tr>
+            <th></th>
+            <% for key in @possible_duplicates[0].keys %>
+              <% unless %w[uuid duplicate].include?(key) %>
+                <th><%= key %></th>
+              <% end %>
             <% end %>
-          <% end %>
-        </tr>
-        <% for dupl_sample in @possible_duplicates %>
-          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-            <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
-          <% dupl_sample.map do |key, val| %>
-            <% val = '<new>' if key =='id' %>
-            <% unless %w[uuid duplicate].include?(key) %>
-              <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+          </tr>
+          <% for dupl_sample in @possible_duplicates %>
+            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
+              <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+            <% dupl_sample.map do |key, val| %>
+              <% val = '<new>' if key =='id' %>
+              <% unless %w[uuid duplicate].include?(key) %>
+                <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+              <% end %>
             <% end %>
-          <% end %>
-            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
-              <% dupl_sample['duplicate'].map do |key, val| %>
-                <% unless %w[uuid duplicate].include?(key) %>
-                  <td><%= val %></td>
+              <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
+                <% dupl_sample['duplicate'].map do |key, val| %>
+                  <% unless %w[uuid duplicate].include?(key) %>
+                    <td><%= val %></td>
+                  <% end %>
                 <% end %>
-              <% end %>
+              </tr>
             </tr>
-          </tr>
-        <% end %>
-      </table>
-    </div>
+          <% end %>
+        </table>
+      </div>
+    <% end %>
   <% end %>
-<% end %>
 
-<div id='check-excel-upload-result'></div>
-<% unless can_upload %>
-  <div class="alert alert-danger alert-dismissible" role="alert">
-      <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-      <h3>Error</h3>
-      <strong>Unable to upload the current set of samples!</strong>
-      <p>Please expand the 'General Information' pane for more information.</p>
-  </div>
-<% end %>
+  <div id='check-excel-upload-result'></div>
+  <% unless can_upload %>
+    <div class="alert alert-danger alert-dismissible" role="alert">
+        <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h3>Error</h3>
+        <strong>Unable to upload the current set of samples!</strong>
+        <p>Please expand the 'General Information' pane for more information.</p>
+    </div>
+  <% end %>
 
   <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>

From c7fa56716828a16b901fed2a9d5c13f4c99ae96e Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 16:41:28 +0200
Subject: [PATCH 28/54] Make table in modal form render multiple inputs as
 badges

---
 .../sample_upload_content.html.erb            | 62 ++++++++++++++++---
 1 file changed, 52 insertions(+), 10 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 3459e04af9..d4eb9ca873 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -50,7 +50,15 @@
                 <% new_sample.map do |key, val| %>
                   <% val = '<new>' if key =='id' %>
                 <% unless key == 'uuid' %>
-                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                  <% if @multiple_input_fields.include?(key)%>
+                    <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
+                      <% val.each do |sub_sample| %>
+                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <% end %>
+                    </td>
+                  <% else %>
+                    <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                  <% end %>
                 <% end %>
               <% end %>
             </tr>
@@ -80,14 +88,30 @@
               <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
               <% update_sample.map do |key, val| %>
                 <% unless key == 'uuid' %>
-                  <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+                  <% if @multiple_input_fields.include?(key)%>
+                    <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' >
+                      <% val.each do |sub_sample| %>
+                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <% end %>
+                    </td>
+                  <% else %>
+                    <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+                  <% end %>
                 <% end %>
               <% end %>
             </tr>
             <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
               <% db_sample.map do |key, val| %>
                 <% unless key == 'uuid' %>
-                  <td><%= val %></td>
+                  <% if @multiple_input_fields.include?(key)%>
+                    <td>
+                      <% val.each do |sub_sample| %>
+                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <% end %>
+                    </td>
+                  <% else %>
+                    <td><%= val %></td>
+                  <% end %>
                 <% end %>
               <% end %>
             </tr>
@@ -117,13 +141,29 @@
             <% dupl_sample.map do |key, val| %>
               <% val = '<new>' if key =='id' %>
               <% unless %w[uuid duplicate].include?(key) %>
-                <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+                <% if @multiple_input_fields.include?(key)%>
+                  <td>
+                    <% val.each do |sub_sample| %>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% else %>
+                  <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+                <% end %>
               <% end %>
             <% end %>
               <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
                 <% dupl_sample['duplicate'].map do |key, val| %>
                   <% unless %w[uuid duplicate].include?(key) %>
-                    <td><%= val %></td>
+                    <% if @multiple_input_fields.include?(key)%>
+                      <td>
+                        <% val.each do |sub_sample| %>
+                          <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                        <% end %>
+                      </td>
+                    <% else %>
+                      <td><%= val%></td>
+                    <% end %>
                   <% end %>
                 <% end %>
               </tr>
@@ -169,10 +209,8 @@
     const newSamples = { data: getNewSamples() };
     const updatedSamples= { data: getUpdateSamples() };
 
-    if(true){
       uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
       uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
-    }
 
     closeModalForm();
     location.reload();
@@ -194,7 +232,6 @@
     }
 
     const sampleObjects = createRows.map((cr, index) => createSampleObject(cr, "new", index));
-
     return sampleObjects;
   }
 
@@ -202,7 +239,6 @@
     const updateRows = $j('#update-samples-table [id*="updated"]').toArray();
 
     const sampleObjects = updateRows.map((ur, index) => createSampleObject(ur, "update", index));
-
     return sampleObjects
   }
 
@@ -213,7 +249,13 @@
     cells.map(function(cell){
       val = cell.textContent;
       key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
-      samplesObj[key] = val;
+      const multiInputfields = $j(cell).find('span[class*="label"]').toArray();
+      if (multiInputfields.length > 0 ){
+        const inputIds = multiInputfields.map(is => is.title).join(',');
+        samplesObj[key] = inputIds;
+      } else {
+        samplesObj[key] = val;
+      }
     });
 
     const {id: objId, ...attrMap} = samplesObj;

From c19521fdba4f36d112cbd0e787e882cf8dfea9fd Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 16:42:00 +0200
Subject: [PATCH 29/54] Moving the assay information down to avoid problems
 when uploading it back.

---
 app/views/single_pages/download_samples_excel.axlsx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/app/views/single_pages/download_samples_excel.axlsx b/app/views/single_pages/download_samples_excel.axlsx
index 82b8837615..800b4a4d09 100644
--- a/app/views/single_pages/download_samples_excel.axlsx
+++ b/app/views/single_pages/download_samples_excel.axlsx
@@ -41,12 +41,6 @@ workbook.add_worksheet(name: 'Metadata') do |sheet|
   sheet.add_row ['Fairdom ID:', @study.id]
   sheet.add_row ['UUID:', @study.uuid]
 
-  if @assay
-    sheet.add_row ['Assay:'], style: title_style
-    sheet.add_row ['Fairdom ID:', @assay.id]
-    sheet.add_row ['UUID:', @assay.uuid]
-  end
-
   sheet.add_row ['Sample Type:'], style: title_style
   sheet.add_row ['Fairdom ID:', @sample_type.id]
   sheet.add_row ['UUID:', @sample_type.uuid]
@@ -55,6 +49,12 @@ workbook.add_worksheet(name: 'Metadata') do |sheet|
   sheet.add_row ['Fairdom ID:', @template.id]
   sheet.add_row ['UUID:', @template.uuid]
 
+  if @assay
+    sheet.add_row ['Assay:'], style: title_style
+    sheet.add_row ['Fairdom ID:', @assay.id]
+    sheet.add_row ['UUID:', @assay.uuid]
+  end
+
   sheet.sheet_protection.password = secret_pwd
 end
 

From 3b3ed8eac33987128ffa0f72a2c3e12ea07e461a Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 16:45:57 +0200
Subject: [PATCH 30/54] Made changes to cope with assay data

---
 app/controllers/single_pages_controller.rb | 29 ++++++++--------------
 1 file changed, 11 insertions(+), 18 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 941163cb7c..d505c22000 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -133,34 +133,27 @@ def upload_samples
     @study = Study.find(study_id)
     sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
     @sample_type = SampleType.find(sample_type_id)
+    template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+    @template = Template.find(template_id)
+    is_assay = @sample_type.assays.any?
+    @assay = @sample_type.assays.first
+    @project = @study.projects.first # In Single Page a study can only belong to one project
 
     # Sample Type validation rules
     unless sample_type_id_ui == @sample_type&.id
       raise "Sample Type #{@sample_type&.id} from spreadsheet doesn't match Sample Type #{sample_type_id_ui} from the table. Please upload in the correct table."
     end
-    unless @study.sample_types.include?(@sample_type)
+    unless @study.sample_types.include?(@sample_type) || is_assay
       raise "Sample Type '#{@sample_type.id}' doesn't belong to Study #{@study.id}. Sample Upload aborted."
     end
-
-    is_assay = @sample_type.assays.any?
-    @assay = @sample_type.assays.first
-
-    multiple_input_fields = @sample_type.sample_attributes.map do |sa_attr|
-      sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
+    unless (@assay&.sample_type == @sample_type) || !is_assay
+      raise "Sample Type '#{@sample_type.id}' doesn't belong to Assay #{@assay.id}. Sample Upload aborted."
     end
 
-    if is_assay
-      assay_id = wb.cell(8, 2, sheet = 'Metadata').to_i
-      template_id = wb.cell(11, 2, sheet = 'Metadata').to_i
-    else
-      template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+    @multiple_input_fields = @sample_type.sample_attributes.map do |sa_attr|
+      sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
     end
 
-    @assay = Assay.find(assay_id) unless assay_id.nil?
-    @template = Template.find(template_id)
-    @project = @study.projects.first # In Single Page a study can only belong to one project
-
-
     sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
     samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
 
@@ -176,7 +169,7 @@ def upload_samples
     @excel_samples = samples_data.map do |excel_sample|
       obj = {}
       (0..sample_fields.size - 1).map do |i|
-        if multiple_input_fields.include?(sample_fields[i])
+        if @multiple_input_fields.include?(sample_fields[i])
           parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub('=>', ':')).map do |subsample|
             # Uploader should at least have viewing permissions for the inputs he's using
             unless Sample.find(subsample['id'])&.authorized_for_view?

From 78cc293951bfe3032419dd22bbeacb2449077d62 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 7 Jul 2023 17:09:43 +0200
Subject: [PATCH 31/54] Making sure the user selects a file to upload

---
 app/views/isa_assays/_assay_samples.html.erb    | 4 ++++
 app/views/isa_studies/_source_material.html.erb | 4 ++++
 app/views/isa_studies/_study_samples.html.erb   | 4 ++++
 3 files changed, 12 insertions(+)

diff --git a/app/views/isa_assays/_assay_samples.html.erb b/app/views/isa_assays/_assay_samples.html.erb
index 4712ea8e9d..e6f86a3279 100644
--- a/app/views/isa_assays/_assay_samples.html.erb
+++ b/app/views/isa_assays/_assay_samples.html.erb
@@ -64,6 +64,10 @@
 
         function assaySampleUploadExcel(){
           const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          if (!file) {
+            alert("File not found! Please select a file to upload.");
+            return
+          }
           let formData = new FormData();
           formData.append('file', file);
           formData.append('sample_type_id', <%=sample_type.id%>);
diff --git a/app/views/isa_studies/_source_material.html.erb b/app/views/isa_studies/_source_material.html.erb
index 7a2ecb74bc..a166f89df8 100644
--- a/app/views/isa_studies/_source_material.html.erb
+++ b/app/views/isa_studies/_source_material.html.erb
@@ -78,6 +78,10 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>
 
         function sourceUploadExcel(){
           const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          if (!file) {
+            alert("File not found! Please select a file to upload.");
+            return
+          }
           let formData = new FormData();
           formData.append('file', file);
           formData.append('sample_type_id', <%=sample_type.id%>);
diff --git a/app/views/isa_studies/_study_samples.html.erb b/app/views/isa_studies/_study_samples.html.erb
index 3c339dac57..9ba12968a8 100644
--- a/app/views/isa_studies/_study_samples.html.erb
+++ b/app/views/isa_studies/_study_samples.html.erb
@@ -70,6 +70,10 @@
 
         function studySampleUploadExcel(){
           const file = $j('input[type="file"][id="file-<%=sample_type.id%>"]').toArray()[0].files[0];
+          if (!file) {
+            alert("File not found! Please select a file to upload.");
+            return
+          }
           let formData = new FormData();
           formData.append('file', file);
           formData.append('sample_type_id', <%=sample_type.id%>);

From c130c2a12f0673124968ece446979d89da46d3fe Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 10 Jul 2023 15:07:19 +0200
Subject: [PATCH 32/54] Validation on the Excel spreadsheet: - Test for file
 extension - Test for spreadsheet structure

---
 app/controllers/single_pages_controller.rb    | 26 ++++++++++++++++---
 app/views/isa_assays/_assay_samples.html.erb  | 12 ++++++---
 app/views/isa_studies/_buttons.html.erb       |  2 +-
 .../isa_studies/_source_material.html.erb     | 10 ++++---
 app/views/isa_studies/_study_samples.html.erb | 10 ++++---
 5 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index d505c22000..fe74d5e907 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -125,9 +125,26 @@ def export_to_excel
   end
 
   def upload_samples
-    wb = Roo::Excelx.new(params[:file].path)
+    uploaded_file = params[:file]
+    project_id = params[:project_id]
+    @project = Project.find(project_id)
+
+    # Check file type if is xls or xlsx
+    case uploaded_file.content_type
+    when 'application/vnd.ms-excel'
+      wb = Roo::Spreadsheet.open(uploaded_file.path)
+    when 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
+      wb = Roo::Excelx.new(uploaded_file.path)
+    else
+      raise "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx"
+    end
+
     sample_type_id_ui = params[:sample_type_id].to_i
 
+    unless is_valid_workbook?(wb)
+      raise "Invalid workbook! Cannot process this spreadsheet. Consider first exporting the table as a spreadsheet for the proper format."
+    end
+
     # Extract Samples metadata from spreadsheet
     study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
     @study = Study.find(study_id)
@@ -137,7 +154,6 @@ def upload_samples
     @template = Template.find(template_id)
     is_assay = @sample_type.assays.any?
     @assay = @sample_type.assays.first
-    @project = @study.projects.first # In Single Page a study can only belong to one project
 
     # Sample Type validation rules
     unless sample_type_id_ui == @sample_type&.id
@@ -255,11 +271,15 @@ def upload_samples
     end
   rescue StandardError => e
     flash[:error] = e.message
-    redirect_to single_page_path(@study.project_ids.first), status: :bad_request
+    redirect_to single_page_path(@project), status: :bad_request
 end
 
   private
 
+  def is_valid_workbook?(wb)
+    !(wb.sheets.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false && wb.sheets.size != 3)
+  end
+
   def set_up_instance_variable
     @single_page = true
   end
diff --git a/app/views/isa_assays/_assay_samples.html.erb b/app/views/isa_assays/_assay_samples.html.erb
index e6f86a3279..1d1b58ea89 100644
--- a/app/views/isa_assays/_assay_samples.html.erb
+++ b/app/views/isa_assays/_assay_samples.html.erb
@@ -1,6 +1,9 @@
-<% assay ||= nil %>
-<% valid_assay = assay&.sample_type.present? %>
-<% sample_type = assay&.sample_type %>
+<%
+  assay ||= nil
+  valid_assay = assay&.sample_type.present?
+  sample_type = assay&.sample_type
+  project = assay&.projects&.first
+%>
 
 <div style="padding:0 20px 20px 20px;">
     <div class="row">
@@ -70,7 +73,8 @@
           }
           let formData = new FormData();
           formData.append('file', file);
-          formData.append('sample_type_id', <%=sample_type.id%>);
+          formData.append('sample_type_id', <%=sample_type&.id%>);
+          formData.append('project_id', <%=project&.id%>);
           handleUploadSubmit(formData);
         }
 
diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 61a928c0b9..5f5a2eaff8 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -23,7 +23,7 @@ uploadExcel||="studySampleUploadExcel()"
     <label for="file-<%= sample_type_id %>" class="form-label">Upload excel file:</label>
   </div>
   <div class="mb-3">
-    <input id="file-<%= sample_type_id %>" name="file-<%= sample_type_id %>" type="file" class="form-control form-control-lg"/>
+    <input id="file-<%= sample_type_id %>" name="file-<%= sample_type_id %>" type="file" accept=".xlsx, .xls" class="form-control form-control-lg"/>
   </div>
   <div class="mb-3">
     <button class="btn btn-default" onClick=<%= uploadExcel %>>Upload</button>
diff --git a/app/views/isa_studies/_source_material.html.erb b/app/views/isa_studies/_source_material.html.erb
index a166f89df8..3d4007ab5e 100644
--- a/app/views/isa_studies/_source_material.html.erb
+++ b/app/views/isa_studies/_source_material.html.erb
@@ -1,5 +1,8 @@
-<% study ||= nil %>
-<% sample_type = study&.sample_types&.first %>
+<%
+  study ||= nil
+  sample_type = study&.sample_types&.first
+  project = study&.projects&.first
+%>
 
 <div style="padding:0 20px 20px 20px;">
     <div class="row">
@@ -84,7 +87,8 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>
           }
           let formData = new FormData();
           formData.append('file', file);
-          formData.append('sample_type_id', <%=sample_type.id%>);
+          formData.append('sample_type_id', <%=sample_type&.id%>);
+          formData.append('project_id', <%=project&.id%>);
           handleUploadSubmit(formData);
         }
 
diff --git a/app/views/isa_studies/_study_samples.html.erb b/app/views/isa_studies/_study_samples.html.erb
index 9ba12968a8..20105bc00b 100644
--- a/app/views/isa_studies/_study_samples.html.erb
+++ b/app/views/isa_studies/_study_samples.html.erb
@@ -1,5 +1,8 @@
-<% study ||= nil %>
-<% sample_type = study&.sample_types&.second %>
+<%
+  study ||= nil
+  sample_type = study&.sample_types&.second
+  project = study&.projects&.first
+%>
 
 <div style="padding:0 20px 20px 20px;">
     <div class="row">
@@ -76,7 +79,8 @@
           }
           let formData = new FormData();
           formData.append('file', file);
-          formData.append('sample_type_id', <%=sample_type.id%>);
+          formData.append('sample_type_id', <%=sample_type&.id%>);
+          formData.append('project_id', <%=project&.id%>);
           handleUploadSubmit(formData);
         }
 

From 4d40b72147566205318af86e8564371f330e1139 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 10 Jul 2023 17:34:40 +0200
Subject: [PATCH 33/54] Written a test for uploading a spreadsheet

---
 app/controllers/single_pages_controller.rb    |   2 +-
 test/fixtures/files/ods_test_spreadsheet.ods  | Bin 0 -> 6943 bytes
 .../single_pages_controller_test.rb           |  18 ++++++++++++++++++
 3 files changed, 19 insertions(+), 1 deletion(-)
 create mode 100644 test/fixtures/files/ods_test_spreadsheet.ods

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index fe74d5e907..7d4fcc7f13 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -136,7 +136,7 @@ def upload_samples
     when 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
       wb = Roo::Excelx.new(uploaded_file.path)
     else
-      raise "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx"
+      raise "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx'"
     end
 
     sample_type_id_ui = params[:sample_type_id].to_i
diff --git a/test/fixtures/files/ods_test_spreadsheet.ods b/test/fixtures/files/ods_test_spreadsheet.ods
new file mode 100644
index 0000000000000000000000000000000000000000..1fbacaba088fe7b632b46c464646998144e8c2ea
GIT binary patch
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diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb
index d31df57204..2334b49186 100644
--- a/test/functional/single_pages_controller_test.rb
+++ b/test/functional/single_pages_controller_test.rb
@@ -188,4 +188,22 @@ def setup
       assert_response :ok, msg = 'Unable to generate the excel'
     end
   end
+
+  test 'invalid file extension should raise exception' do
+    with_config_value(:project_single_page_enabled, true) do
+      file_path = Rails.root.join('test/fixtures/files/ods_test_spreadsheet.ods')
+      file = fixture_file_upload(file_path, 'application/vnd.oasis.opendocument.spreadsheet')
+
+      person, project, study, assay, source_sample_type, sample_collection_sample_type, assay_sample_type = setup_file_upload.values_at(
+        :person, :project, :study, :assay, :source_sample_type, :sample_collection_sample_type, :assay_sample_type
+      )
+
+      post :upload_samples, params: { file: file, project_id: project.id,
+                                      sample_type_id: source_sample_type.id }
+
+      assert_response :bad_request
+      assert_equal flash[:error], "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx'"
+    end
+  end
+
 end

From f62d7738199ffadab23a030d894e020bf79013ee Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 10 Jul 2023 17:35:27 +0200
Subject: [PATCH 34/54] Refactored Single Pages tests

---
 .../single_pages_controller_test.rb           | 71 ++++++++++---------
 1 file changed, 39 insertions(+), 32 deletions(-)

diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb
index 2334b49186..f6865063fe 100644
--- a/test/functional/single_pages_controller_test.rb
+++ b/test/functional/single_pages_controller_test.rb
@@ -50,16 +50,9 @@ def setup
   test 'generates a valid export of sources in single page' do
     with_config_value(:project_single_page_enabled, true) do
       # Generate the excel data
-      person = @member.person
-      project = FactoryBot.create(:project)
-      study = FactoryBot.create(:study)
-      id_label = "#{Seek::Config::instance_name} id"
-
-      source_sample_type = FactoryBot.create(:isa_source_sample_type,
-                                             contributor: person,
-                                             project_ids: [project.id],
-                                             isa_template: Template.find_by_title('ISA Source'),
-                                             studies: [study])
+      id_label, person, project, study, source_sample_type = setup_file_upload.values_at(
+        :id_label, :person, :project, :study, :source_sample_type
+      )
 
       sources = (1..5).map do |n|
         FactoryBot.create(
@@ -108,24 +101,9 @@ def setup
 
   test 'generates a valid export of source samples in single page' do
     with_config_value(:project_single_page_enabled, true) do
-      person = @member.person
-      project = FactoryBot.create(:project)
-      study = FactoryBot.create(:study)
-      assay = FactoryBot.create(:assay)
-      id_label = "#{Seek::Config::instance_name} id"
-
-      source_sample_type = FactoryBot.create(:isa_source_sample_type,
-                                             contributor: person,
-                                             project_ids: [project.id],
-                                             isa_template: Template.find_by_title('ISA Source'),
-                                             studies: [study])
-
-      sample_collection_sample_type = FactoryBot.create(:isa_sample_collection_sample_type,
-                                                        contributor: person,
-                                                        project_ids: [project.id],
-                                                        isa_template: Template.find_by_title('ISA sample collection'),
-                                                        studies: [study],
-                                                        linked_sample_type: source_sample_type)
+      id_label, person, project, study, assay, source_sample_type, sample_collection_sample_type = setup_file_upload.values_at(
+        :id_label, :person, :project, :study, :assay, :source_sample_type, :sample_collection_sample_type
+      )
 
       sources = (1..5).map do |n|
         FactoryBot.create(
@@ -181,8 +159,8 @@ def setup
       assert_response :ok, msg = "Couldn't reach the server"
 
       response_body = JSON.parse(response.body)
-      assert response_body.key?("uuid"), msg = "Response body is expected to have a 'uuid' key"
-      cache_uuid = response_body["uuid"]
+      assert response_body.key?('uuid'), msg = "Response body is expected to have a 'uuid' key"
+      cache_uuid = response_body['uuid']
 
       get :download_samples_excel, params: { uuid: cache_uuid }
       assert_response :ok, msg = 'Unable to generate the excel'
@@ -194,8 +172,8 @@ def setup
       file_path = Rails.root.join('test/fixtures/files/ods_test_spreadsheet.ods')
       file = fixture_file_upload(file_path, 'application/vnd.oasis.opendocument.spreadsheet')
 
-      person, project, study, assay, source_sample_type, sample_collection_sample_type, assay_sample_type = setup_file_upload.values_at(
-        :person, :project, :study, :assay, :source_sample_type, :sample_collection_sample_type, :assay_sample_type
+      project, source_sample_type = setup_file_upload.values_at(
+        :project, :source_sample_type
       )
 
       post :upload_samples, params: { file: file, project_id: project.id,
@@ -206,4 +184,33 @@ def setup
     end
   end
 
+  def setup_file_upload
+    id_label = "#{Seek::Config::instance_name} id"
+    person = @member.person
+    project = FactoryBot.create(:project)
+    study = FactoryBot.create(:study)
+    assay = FactoryBot.create(:assay)
+    source_sample_type = FactoryBot.create(:isa_source_sample_type,
+                                           contributor: person,
+                                           project_ids: [project.id],
+                                           isa_template: Template.find_by_title('ISA Source'),
+                                           studies: [study])
+
+    sample_collection_sample_type = FactoryBot.create(:isa_sample_collection_sample_type,
+                                                      contributor: person,
+                                                      project_ids: [project.id],
+                                                      isa_template: Template.find_by_title('ISA sample collection'),
+                                                      studies: [study],
+                                                      linked_sample_type: source_sample_type)
+
+    assay_sample_type = FactoryBot.create(:isa_assay_sample_type,
+                                          contributor: person,
+                                          projects: [project],
+                                          linked_sample_type: sample_collection_sample_type
+                  )
+
+    { "id_label": id_label, "person": person, "project": project, "study": study, "assay": assay,
+      "source_sample_type": source_sample_type, "sample_collection_sample_type": sample_collection_sample_type,
+      "assay_sample_type": assay_sample_type }
+  end
 end

From ac27f257c2877848acd6501fc13957e235909311 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Thu, 13 Jul 2023 14:17:03 +0200
Subject: [PATCH 35/54] clean up the controller

---
 app/controllers/single_pages_controller.rb | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 7d4fcc7f13..a4a12e1c66 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -151,7 +151,7 @@ def upload_samples
     sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
     @sample_type = SampleType.find(sample_type_id)
     template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
-    @template = Template.find(template_id)
+    template = Template.find(template_id)
     is_assay = @sample_type.assays.any?
     @assay = @sample_type.assays.first
 
@@ -182,7 +182,7 @@ def upload_samples
     end
 
     # Construct Samples objects from Excel data
-    @excel_samples = samples_data.map do |excel_sample|
+    excel_samples = samples_data.map do |excel_sample|
       obj = {}
       (0..sample_fields.size - 1).map do |i|
         if @multiple_input_fields.include?(sample_fields[i])
@@ -202,8 +202,8 @@ def upload_samples
       obj
     end
 
-    @existing_excel_samples = @excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
-    @new_excel_samples = @excel_samples.map { |sample| sample if sample['id'].nil? }.compact
+    existing_excel_samples = excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
+    new_excel_samples = excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
     @db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
       attributes = JSON.parse(sample[:json_metadata])
@@ -212,7 +212,7 @@ def upload_samples
     end
 
     # Determine whether samples have been modified or not
-    @update_samples = @existing_excel_samples.map do |ees|
+    @update_samples = existing_excel_samples.map do |ees|
       db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
       # An exception is raised if the ID of an existing Sample cannot be found in the DB
       raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
@@ -234,7 +234,7 @@ def upload_samples
     # based on the attribute values
     @possible_duplicates = []
     @new_samples = []
-    @new_excel_samples.map do |nes|
+    new_excel_samples.map do |nes|
       is_duplicate = true
 
       @db_samples.map do |dbs|
@@ -255,10 +255,6 @@ def upload_samples
     upload_data = { study: @study,
                     assay: @assay,
                     sampleType: @sample_type,
-                    template: @template,
-                    excelSamples: @excel_samples,
-                    existingExcelSamples: @existing_excel_samples,
-                    newExcelSamples: @new_excel_samples,
                     updateSamples: @update_samples,
                     newSamples: @new_samples,
                     possibleDuplicates: @possible_duplicates,
@@ -277,7 +273,7 @@ def upload_samples
   private
 
   def is_valid_workbook?(wb)
-    !(wb.sheets.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false && wb.sheets.size != 3)
+    !((wb.sheets.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false) && (wb.sheets.size != 3))
   end
 
   def set_up_instance_variable

From 870719cff64d46b82d1ebc402577d8599e896e3a Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Thu, 13 Jul 2023 18:35:41 +0200
Subject: [PATCH 36/54] Tests for upload functionality in different Sample
 Types

---
 app/controllers/single_pages_controller.rb    |  15 +-
 .../00_wrong_format_spreadsheet.ods}          | Bin
 .../01_combo_update_sources_spreadsheet.xlsx  | Bin 0 -> 24765 bytes
 .../02_invalid_workbook.xlsx                  | Bin 0 -> 24538 bytes
 .../03_combo_update_samples_spreadsheet.xlsx  | Bin 0 -> 27970 bytes
 ...ombo_update_assay_samples_spreadsheet.xlsx | Bin 0 -> 27917 bytes
 .../single_pages_controller_test.rb           | 267 +++++++++++++-----
 7 files changed, 206 insertions(+), 76 deletions(-)
 rename test/fixtures/files/{ods_test_spreadsheet.ods => upload_single_page/00_wrong_format_spreadsheet.ods} (100%)
 create mode 100644 test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx
 create mode 100644 test/fixtures/files/upload_single_page/02_invalid_workbook.xlsx
 create mode 100644 test/fixtures/files/upload_single_page/03_combo_update_samples_spreadsheet.xlsx
 create mode 100644 test/fixtures/files/upload_single_page/04_combo_update_assay_samples_spreadsheet.xlsx

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index a4a12e1c66..6bd7665ec4 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -249,12 +249,19 @@ def upload_samples
           break
         end
       end
-      @new_samples.append(nes) unless is_duplicate
+      if @db_samples.none?
+        @new_samples.append(nes)
+      else
+        @new_samples.append(nes) unless is_duplicate
+      end
     end
 
     upload_data = { study: @study,
                     assay: @assay,
                     sampleType: @sample_type,
+                    excel_samples: excel_samples,
+                    existingExcelSamples: existing_excel_samples,
+                    newExcelSamples: new_excel_samples,
                     updateSamples: @update_samples,
                     newSamples: @new_samples,
                     possibleDuplicates: @possible_duplicates,
@@ -267,7 +274,11 @@ def upload_samples
     end
   rescue StandardError => e
     flash[:error] = e.message
-    redirect_to single_page_path(@project), status: :bad_request
+    respond_to do |format|
+      format.html { redirect_to single_page_path(@project), status: :bad_request }
+      format.json { render json: { error: e }, status: :bad_request }
+    end
+
 end
 
   private
diff --git a/test/fixtures/files/ods_test_spreadsheet.ods b/test/fixtures/files/upload_single_page/00_wrong_format_spreadsheet.ods
similarity index 100%
rename from test/fixtures/files/ods_test_spreadsheet.ods
rename to test/fixtures/files/upload_single_page/00_wrong_format_spreadsheet.ods
diff --git a/test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx b/test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..026a2c5946675578ce8535ebd58baeddf84342be
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diff --git a/test/fixtures/files/upload_single_page/02_invalid_workbook.xlsx b/test/fixtures/files/upload_single_page/02_invalid_workbook.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..e05a7d4c6defa011e7355ff3b3b1a68e47160738
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diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb
index f6865063fe..e9b7b81f96 100644
--- a/test/functional/single_pages_controller_test.rb
+++ b/test/functional/single_pages_controller_test.rb
@@ -50,32 +50,10 @@ def setup
   test 'generates a valid export of sources in single page' do
     with_config_value(:project_single_page_enabled, true) do
       # Generate the excel data
-      id_label, person, project, study, source_sample_type = setup_file_upload.values_at(
-        :id_label, :person, :project, :study, :source_sample_type
+      id_label, person, project, study, source_sample_type, sources = setup_file_upload.values_at(
+        :id_label, :person, :project, :study, :source_sample_type, :sources
       )
 
-      sources = (1..5).map do |n|
-        FactoryBot.create(
-          :sample,
-          title: "source#{n}",
-          sample_type: source_sample_type,
-          project_ids: [project.id],
-          contributor: person,
-          data: {
-            'Source Name': 'Source Name',
-            'Source Characteristic 1': 'Source Characteristic 1',
-            'Source Characteristic 2':
-              source_sample_type
-                .sample_attributes
-                .find_by_title('Source Characteristic 2')
-                .sample_controlled_vocab
-                .sample_controlled_vocab_terms
-                .first
-                .label
-          }
-        )
-      end
-
       source_ids = sources.map { |s| { id_label => s.id } }
       sample_type_id = source_sample_type.id
       study_id = study.id
@@ -101,49 +79,10 @@ def setup
 
   test 'generates a valid export of source samples in single page' do
     with_config_value(:project_single_page_enabled, true) do
-      id_label, person, project, study, assay, source_sample_type, sample_collection_sample_type = setup_file_upload.values_at(
-        :id_label, :person, :project, :study, :assay, :source_sample_type, :sample_collection_sample_type
+      id_label, study, assay, sample_collection_sample_type, source_samples = setup_file_upload.values_at(
+        :id_label, :study, :assay, :sample_collection_sample_type, :source_samples
       )
 
-      sources = (1..5).map do |n|
-        FactoryBot.create(
-          :sample,
-          title: "source #{n}",
-          sample_type: source_sample_type,
-          project_ids: [project.id],
-          contributor: person,
-          data: {
-            'Source Name': 'Source Name',
-            'Source Characteristic 1': 'Source Characteristic 1',
-            'Source Characteristic 2':
-              source_sample_type
-                .sample_attributes
-                .find_by_title('Source Characteristic 2')
-                .sample_controlled_vocab
-                .sample_controlled_vocab_terms
-                .first
-                .label
-          }
-        )
-      end
-
-      source_samples = (1..4).map do |n|
-        FactoryBot.create(
-          :sample,
-          title: "Sample collection #{n}",
-          sample_type: sample_collection_sample_type,
-          project_ids: [project.id],
-          contributor: person,
-          data: {
-            Input: [sources[n - 1].id, sources[n].id],
-            'sample collection': 'sample collection',
-            'sample collection parameter value 1': 'sample collection parameter value 1',
-            'Sample Name': 'sample name',
-            'sample characteristic 1': 'sample characteristic 1'
-          }
-        )
-      end
-
       source_sample_ids = source_samples.map { |ss| { id_label => ss.id } }
       sample_type_id = sample_collection_sample_type.id
       study_id = study.id
@@ -169,7 +108,7 @@ def setup
 
   test 'invalid file extension should raise exception' do
     with_config_value(:project_single_page_enabled, true) do
-      file_path = Rails.root.join('test/fixtures/files/ods_test_spreadsheet.ods')
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/00_wrong_format_spreadsheet.ods')
       file = fixture_file_upload(file_path, 'application/vnd.oasis.opendocument.spreadsheet')
 
       project, source_sample_type = setup_file_upload.values_at(
@@ -184,33 +123,213 @@ def setup
     end
   end
 
+  test 'Should prevent to upload to the wrong Sample Type' do
+    with_config_value(:project_single_page_enabled, true) do
+      project, sample_collection_sample_type = setup_file_upload.values_at(
+        :project, :sample_collection_sample_type
+      )
+
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx')
+      file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+      post :upload_samples, as: :json, params: { file:, project_id: project.id,
+                                                 sample_type_id: sample_collection_sample_type.id }
+
+      assert_response :bad_request
+    end
+  end
+
+  test 'Should not process invalid workbooks' do
+    with_config_value(:project_single_page_enabled, true) do
+      project, source_sample_type = setup_file_upload.values_at(
+        :project, :source_sample_type
+      )
+
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/02_invalid_workbook.xlsx')
+      file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+      post :upload_samples, as: :json, params: { file:, project_id: project.id,
+                                                 sample_type_id: source_sample_type.id }
+
+      assert_response :bad_request
+    end
+  end
+
+  test 'Should update, create and detect duplicate sources when uploading to a source Sample Type' do
+    with_config_value(:project_single_page_enabled, true) do
+      project, source_sample_type = setup_file_upload.values_at(
+        :project, :source_sample_type
+      )
+
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx')
+      file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+      post :upload_samples, as: :json, params: { file:, project_id: project.id,
+      sample_type_id: source_sample_type.id }
+
+      response_data = JSON.parse(response.body)['uploadData']
+      assert_response :success
+
+      updated_samples = response_data['updateSamples']
+      assert(updated_samples.size, 2)
+
+      new_samples = response_data['newSamples']
+      assert(new_samples.size, 2)
+
+      possible_duplicates = response_data['possibleDuplicates']
+      assert(possible_duplicates.size, 1)
+    end
+  end
+
+  test 'Should update, create and detect duplicate samples when uploading to a source sample Sample Type' do
+    with_config_value(:project_single_page_enabled, true) do
+      project, sample_collection_sample_type = setup_file_upload.values_at(
+        :project, :sample_collection_sample_type
+      )
+
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/03_combo_update_samples_spreadsheet.xlsx')
+      file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+      post :upload_samples, as: :json, params: { file:, project_id: project.id,
+                                                 sample_type_id: sample_collection_sample_type.id }
+
+      response_data = JSON.parse(response.body)['uploadData']
+      assert_response :success
+
+      updated_samples = response_data['updateSamples']
+      assert(updated_samples.size, 2)
+
+      new_samples = response_data['newSamples']
+      assert(new_samples.size, 2)
+
+      possible_duplicates = response_data['possibleDuplicates']
+      assert(possible_duplicates.size, 1)
+    end
+  end
+
+  test 'Should update, create and detect duplicate samples when uploading to a assay Sample Type' do
+    with_config_value(:project_single_page_enabled, true) do
+      project, assay_sample_type = setup_file_upload.values_at(
+        :project, :assay_sample_type
+      )
+
+      file_path = Rails.root.join('test/fixtures/files/upload_single_page/04_combo_update_assay_samples_spreadsheet.xlsx')
+      file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
+
+      post :upload_samples, as: :json, params: { file:, project_id: project.id,
+                                                 sample_type_id: assay_sample_type.id }
+
+      response_data = JSON.parse(response.body)['uploadData']
+      assert_response :success
+
+      updated_samples = response_data['updateSamples']
+      assert(updated_samples.size, 2)
+
+      new_samples = response_data['newSamples']
+      assert(new_samples.size, 1)
+
+      possible_duplicates = response_data['possibleDuplicates']
+      assert(possible_duplicates.size, 1)
+    end
+  end
+
   def setup_file_upload
     id_label = "#{Seek::Config::instance_name} id"
     person = @member.person
-    project = FactoryBot.create(:project)
-    study = FactoryBot.create(:study)
-    assay = FactoryBot.create(:assay)
+    project = FactoryBot.create(:project, id: 10000)
+    study = FactoryBot.create(:study, id: 10001)
+    assay = FactoryBot.create(:assay, id: 10002, study: study)
+
+    source_sample_type_template = FactoryBot.create(:isa_source_template, id: 10006)
     source_sample_type = FactoryBot.create(:isa_source_sample_type,
+                                           id: 10003,
                                            contributor: person,
                                            project_ids: [project.id],
-                                           isa_template: Template.find_by_title('ISA Source'),
+                                           isa_template: source_sample_type_template,
                                            studies: [study])
 
+
+    sample_collection_sample_type_template = FactoryBot.create(:isa_sample_collection_template, id: 10007)
     sample_collection_sample_type = FactoryBot.create(:isa_sample_collection_sample_type,
+                                                      id: 10004,
                                                       contributor: person,
                                                       project_ids: [project.id],
-                                                      isa_template: Template.find_by_title('ISA sample collection'),
+                                                      isa_template: sample_collection_sample_type_template,
                                                       studies: [study],
                                                       linked_sample_type: source_sample_type)
 
+    assay_sample_type_template = FactoryBot.create(:isa_assay_template, id: 10008)
     assay_sample_type = FactoryBot.create(:isa_assay_sample_type,
+                                          id: 10005,
                                           contributor: person,
+                                          isa_template: assay_sample_type_template,
                                           projects: [project],
-                                          linked_sample_type: sample_collection_sample_type
-                  )
+                                          studies: [study],
+                                          linked_sample_type: sample_collection_sample_type)
+
+    sources = (1..5).map do |n|
+      FactoryBot.create(
+        :sample,
+        id: 10010 + n,
+        title: "source#{n}",
+        sample_type: source_sample_type,
+        project_ids: [project.id],
+        contributor: person,
+        data: {
+          'Source Name': 'Source Name',
+          'Source Characteristic 1': 'Source Characteristic 1',
+          'Source Characteristic 2':
+            source_sample_type
+              .sample_attributes
+              .find_by_title('Source Characteristic 2')
+              .sample_controlled_vocab
+              .sample_controlled_vocab_terms
+              .first
+              .label
+        }
+      )
+    end
+
+    source_samples = (1..4).map do |n|
+      FactoryBot.create(
+        :sample,
+        id: 10020 + n,
+        title: "Sample collection #{n}",
+        sample_type: sample_collection_sample_type,
+        project_ids: [project.id],
+        contributor: person,
+        data: {
+          Input: [sources[n - 1].id, sources[n].id],
+          'sample collection': 'sample collection',
+          'sample collection parameter value 1': 'sample collection parameter value 1',
+          'Sample Name': "sample nr. #{n}",
+          'sample characteristic 1': 'sample characteristic 1'
+        }
+      )
+    end
+
+    assay_samples = (1..3).map do |n|
+      FactoryBot.create(
+        :sample,
+        id: 10030 + n,
+        title: "Assay Sample #{n}",
+        sample_type: assay_sample_type,
+        project_ids: [project.id],
+        contributor: person,
+        data: {
+          Input: [source_samples[n - 1].id, source_samples[n].id],
+          'Protocol Assay 1': 'How to make concentrated dark matter',
+          'Assay 1 parameter value 1': 'Assay 1 parameter value 1',
+          'Extract Name': "Extract nr. #{n}",
+          'other material characteristic 1': 'other material characteristic 1'
+        }
+      )
+    end
 
     { "id_label": id_label, "person": person, "project": project, "study": study, "assay": assay,
       "source_sample_type": source_sample_type, "sample_collection_sample_type": sample_collection_sample_type,
-      "assay_sample_type": assay_sample_type }
+      "assay_sample_type": assay_sample_type, "sources": sources, "source_samples": source_samples,
+      "assay_samples": assay_samples }
+
   end
 end

From 865aaf3e947bcd4dee6d220e13c190a79d919f43 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 14 Jul 2023 11:10:35 +0200
Subject: [PATCH 37/54] Cleaned up the upload area in the UI

---
 app/views/isa_studies/_buttons.html.erb | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/app/views/isa_studies/_buttons.html.erb b/app/views/isa_studies/_buttons.html.erb
index 5f5a2eaff8..e9a15091ed 100644
--- a/app/views/isa_studies/_buttons.html.erb
+++ b/app/views/isa_studies/_buttons.html.erb
@@ -18,15 +18,15 @@ uploadExcel||="studySampleUploadExcel()"
   <button class="btn btn-primary dt-action" id="btn_save_assay_sample" onClick=<%=save%>>Save</button>
 </div>
 
-<div class="container-sm">
-  <div class="mb-3">
-    <label for="file-<%= sample_type_id %>" class="form-label">Upload excel file:</label>
-  </div>
-  <div class="mb-3">
-    <input id="file-<%= sample_type_id %>" name="file-<%= sample_type_id %>" type="file" accept=".xlsx, .xls" class="form-control form-control-lg"/>
-  </div>
-  <div class="mb-3">
-    <button class="btn btn-default" onClick=<%= uploadExcel %>>Upload</button>
+<div class="container-sm" style="max-width: 780px; margin-top:25px;">
+  <label for="file-<%= sample_type_id %>" class="form-label">Upload excel spreadsheet:</label>
+  <div class="input-group">
+    <div class="mb-3">
+      <input id="file-<%= sample_type_id %>" name="file-<%= sample_type_id %>" type="file" accept=".xlsx, .xls" class="form-control form-control-lg"/>
+    </div>
+    <div class="input-group-btn">
+      <button class="btn btn-primary" onClick=<%= uploadExcel %>>Upload</button>
+    </div>
   </div>
 </div>
 

From 06a210c3b0b939492d3964b93457e8c3e97b2687 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 14 Jul 2023 17:17:38 +0200
Subject: [PATCH 38/54] Implement the SpreadsheetExplorerRepresentation instead
 of roo for spreadsheet extraction.

---
 Gemfile                                       |  4 ---
 app/controllers/single_pages_controller.rb    | 36 ++++++++++++-------
 .../spreadsheet_explorer_representation.rb    |  4 +++
 3 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/Gemfile b/Gemfile
index 13ece2a2b6..1baa2b4cc2 100644
--- a/Gemfile
+++ b/Gemfile
@@ -158,10 +158,6 @@ gem 'caxlsx_rails', '~> 0.6.2'
 
 gem 'net-ftp'
 
-# Reading excel spreadsheets
-gem "roo", "~> 2.10.0"
-gem 'roo-xls', '~> 1.1'
-
 gem 'licensee'
 
 group :production do
diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 6bd7665ec4..b94402f0f9 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -1,10 +1,9 @@
 require 'isatab_converter'
-require 'roo'
-require 'roo-xls'
 
 class SinglePagesController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Sharing::SharingCommon
+  include Seek::Data::SpreadsheetExplorerRepresentation
 
   before_action :set_up_instance_variable
   before_action :project_single_page_enabled?
@@ -131,12 +130,13 @@ def upload_samples
 
     # Check file type if is xls or xlsx
     case uploaded_file.content_type
-    when 'application/vnd.ms-excel'
-      wb = Roo::Spreadsheet.open(uploaded_file.path)
     when 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
-      wb = Roo::Excelx.new(uploaded_file.path)
+      spreadsheet_xml = spreadsheet_to_xml(uploaded_file.path, Seek::Config.jvm_memory_allocation)
+      wb = parse_spreadsheet_xml(spreadsheet_xml)
+      metadata_sheet = wb.sheet('Metadata')
+      samples_sheet = wb.sheet('Samples')
     else
-      raise "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx'"
+      raise "Please upload a valid spreadsheet file with extension '.xlsx'"
     end
 
     sample_type_id_ui = params[:sample_type_id].to_i
@@ -146,11 +146,11 @@ def upload_samples
     end
 
     # Extract Samples metadata from spreadsheet
-    study_id = wb.cell(2, 2, sheet = 'Metadata').to_i
+    study_id = metadata_sheet.cell(2, 2).value.to_i
     @study = Study.find(study_id)
-    sample_type_id = wb.cell(5, 2, sheet = 'Metadata').to_i
+    sample_type_id = metadata_sheet.cell(5, 2).value.to_i
     @sample_type = SampleType.find(sample_type_id)
-    template_id = wb.cell(8, 2, sheet = 'Metadata').to_i
+    template_id = metadata_sheet.cell(8, 2).value.to_i
     template = Template.find(template_id)
     is_assay = @sample_type.assays.any?
     @assay = @sample_type.assays.first
@@ -170,8 +170,14 @@ def upload_samples
       sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
     end
 
-    sample_fields = wb.row(1, sheet = 'Samples').map { |field| field.sub(' *', '') }
-    samples_data = (2..wb.last_row(sheet = 'Samples')).map { |i| wb.row(i, sheet = 'Samples') }
+    sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }
+    samples_data = (2..samples_sheet.actual_rows.size).map do |i|
+      act_cells = samples_sheet.row(i).actual_cells
+      act_cells.map { |cell| cell&.value } unless act_cells.all? { |cell| cell&.value&.empty? }
+    end
+
+    samples_data.compact!
+
 
     # Compare Excel header row to Sample Type Sample Attributes
     # Should raise an error if they don't match
@@ -195,6 +201,12 @@ def upload_samples
             subsample
           end
           obj.merge!(sample_fields[i] => parsed_excel_input_samples)
+        elsif sample_fields[i] == 'id'
+          if excel_sample[i] == ''
+            obj.merge!(sample_fields[i] => nil)
+          else
+            obj.merge!(sample_fields[i] => excel_sample[i]&.to_i)
+          end
         else
           obj.merge!(sample_fields[i] => excel_sample[i])
         end
@@ -284,7 +296,7 @@ def upload_samples
   private
 
   def is_valid_workbook?(wb)
-    !((wb.sheets.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false) && (wb.sheets.size != 3))
+    !((wb.sheet_names.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false) && (wb.sheets.size != 3))
   end
 
   def set_up_instance_variable
diff --git a/lib/seek/data/spreadsheet_explorer_representation.rb b/lib/seek/data/spreadsheet_explorer_representation.rb
index bcaac17688..273f286fee 100644
--- a/lib/seek/data/spreadsheet_explorer_representation.rb
+++ b/lib/seek/data/spreadsheet_explorer_representation.rb
@@ -255,6 +255,10 @@ def sheet(x)
             @sheets[x]
           end
         end
+
+        def sheet_names
+          @sheets.map(&:name)
+        end
       end
 
       class Style

From 20c8035f42bacceca82abfc8e5e41d0d389370f5 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 7 Aug 2023 12:23:49 +0200
Subject: [PATCH 39/54] Fixes for multiinput tables

---
 .../single_pages/sample_upload_content.html.erb      | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index d4eb9ca873..2bad6626a6 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -209,8 +209,10 @@
     const newSamples = { data: getNewSamples() };
     const updatedSamples= { data: getUpdateSamples() };
 
-      uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
-      uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
+    if (newSamples.data === "abort") return;
+
+    uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
+    uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
 
     closeModalForm();
     location.reload();
@@ -227,7 +229,7 @@
         createRows = createRows.concat(duplicatedRows);
       } else {
         closeModalForm();
-        return;
+        return "abort";
       }
     }
 
@@ -249,9 +251,9 @@
     cells.map(function(cell){
       val = cell.textContent;
       key = cell.id.match(/\[.*\]/)[0].replace('[', "").replace("]", '');
-      const multiInputfields = $j(cell).find('span[class*="label"]').toArray();
+      const multiInputfields = $j(cell).find('span[class*="badge"]').toArray();
       if (multiInputfields.length > 0 ){
-        const inputIds = multiInputfields.map(is => is.title).join(',');
+        const inputIds = multiInputfields.map(is => is.title.split(" ").pop()).join(',');
         samplesObj[key] = inputIds;
       } else {
         samplesObj[key] = val;

From e0dd9e28ee0fa00d9fbc539ea52ca42e7df0494e Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 7 Aug 2023 12:35:18 +0200
Subject: [PATCH 40/54] Removed roo from Gemfile.lock

---
 Gemfile.lock | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/Gemfile.lock b/Gemfile.lock
index 87663aab74..3b608cde84 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -734,13 +734,6 @@ GEM
     ro-crate (0.5.1)
       addressable (>= 2.7, < 2.9)
       rubyzip (~> 2.0.0)
-    roo (2.10.0)
-      nokogiri (~> 1)
-      rubyzip (>= 1.3.0, < 3.0.0)
-    roo-xls (1.2.0)
-      nokogiri
-      roo (>= 2.0.0, < 3)
-      spreadsheet (> 0.9.0)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -772,7 +765,6 @@ GEM
       unicode-display_width (>= 1.4.0, < 3.0)
     rubocop-ast (1.15.1)
       parser (>= 3.0.1.1)
-    ruby-ole (1.2.12.2)
     ruby-prof (1.4.3)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
@@ -851,8 +843,6 @@ GEM
     sparql-client (3.2.0)
       net-http-persistent (~> 4.0, >= 4.0.1)
       rdf (~> 3.2)
-    spreadsheet (1.3.0)
-      ruby-ole
     sprockets (4.2.0)
       concurrent-ruby (~> 1.0)
       rack (>= 2.2.4, < 4)
@@ -1071,8 +1061,6 @@ DEPENDENCIES
   rmagick (= 4.2.5)
   ro-bundle (~> 0.3.0)
   ro-crate (~> 0.5.1)
-  roo (~> 2.10.0)
-  roo-xls (~> 1.1)
   rspec-rails (~> 5.1)
   rubocop
   ruby-prof

From b3c0cb455a3520ac39521aca19576329f4734f14 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 7 Aug 2023 13:30:19 +0200
Subject: [PATCH 41/54] Fix failing test

---
 test/functional/single_pages_controller_test.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb
index e9b7b81f96..4014b03991 100644
--- a/test/functional/single_pages_controller_test.rb
+++ b/test/functional/single_pages_controller_test.rb
@@ -119,7 +119,7 @@ def setup
                                       sample_type_id: source_sample_type.id }
 
       assert_response :bad_request
-      assert_equal flash[:error], "Please upload a valid spreadsheet file with extension '.xls' or '.xlsx'"
+      assert_equal flash[:error], "Please upload a valid spreadsheet file with extension '.xlsx'"
     end
   end
 

From 92a4edc531978cfcb4dfa609081a049ce5a3f347 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 8 Aug 2023 16:29:37 +0200
Subject: [PATCH 42/54] Added regex to exclude '=>' in values.

---
 app/controllers/single_pages_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index b94402f0f9..673617bba5 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -192,7 +192,7 @@ def upload_samples
       obj = {}
       (0..sample_fields.size - 1).map do |i|
         if @multiple_input_fields.include?(sample_fields[i])
-          parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub('=>', ':')).map do |subsample|
+          parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub(/\"=>/x, "\":")).map do |subsample|
             # Uploader should at least have viewing permissions for the inputs he's using
             unless Sample.find(subsample['id'])&.authorized_for_view?
               raise "Unauthorized Sample was detected in spreadsheet: #{subsample.inspect}"

From f2c9fd046390edeec92e398a03e2214ca7d31663 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Wed, 9 Aug 2023 15:23:54 +0200
Subject: [PATCH 43/54] Modified the upload preview table to: - Hide the button
 if no sample are added - Summarize samples the user does not have editing
 permissions for.

---
 app/controllers/single_pages_controller.rb    | 46 +++++++++-------
 .../sample_upload_content.html.erb            | 53 +++++++++++++++++--
 2 files changed, 76 insertions(+), 23 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 673617bba5..5f576cc1fb 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -178,7 +178,6 @@ def upload_samples
 
     samples_data.compact!
 
-
     # Compare Excel header row to Sample Type Sample Attributes
     # Should raise an error if they don't match
     sample_type_attributes = %w[id uuid].concat(@sample_type.sample_attributes.map(&:title))
@@ -217,18 +216,30 @@ def upload_samples
     existing_excel_samples = excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
     new_excel_samples = excel_samples.map { |sample| sample if sample['id'].nil? }.compact
 
-    @db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
+    @db_samples = @sample_type.samples&.map do |sample|
+      attributes = JSON.parse(sample[:json_metadata])
+      { 'id' => sample.id,
+        'uuid' => sample.uuid }.merge(attributes)
+    end
+
+    @authorized_db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
       attributes = JSON.parse(sample[:json_metadata])
       { 'id' => sample.id,
         'uuid' => sample.uuid }.merge(attributes)
     end
 
-    # Determine whether samples have been modified or not
-    @update_samples = existing_excel_samples.map do |ees|
+    # Determine whether samples have been modified or not,
+    # and checking whether the user is permitted to edit them
+    @unauthorized_samples = []
+    @update_samples = []
+    existing_excel_samples.map do |ees|
       db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
+
       # An exception is raised if the ID of an existing Sample cannot be found in the DB
       raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
 
+      is_authorized_for_update = @authorized_db_samples.select { |s| s['id'] == ees['id'] }.any?
+
       is_changed = false
 
       db_sample.map do |k, v|
@@ -238,9 +249,14 @@ def upload_samples
         end
       end
 
-      ees if is_changed
+      if is_changed
+        if is_authorized_for_update
+          @update_samples.append(ees)
+        else
+          @unauthorized_samples.append(ees)
+        end
+      end
     end
-    @update_samples.compact!
 
     # Determine if the new samples are no duplicates of existing ones,
     # based on the attribute values
@@ -249,37 +265,27 @@ def upload_samples
     new_excel_samples.map do |nes|
       is_duplicate = true
 
-      @db_samples.map do |dbs|
+      @authorized_db_samples.map do |dbs|
         dbs.map do |k, v|
           unless %w[id uuid].include?(k)
             is_duplicate = (nes[k] == v)
             break unless is_duplicate
           end
         end
+
         if is_duplicate
           @possible_duplicates.append(nes.merge({ 'duplicate' => dbs }))
           break
         end
       end
-      if @db_samples.none?
+
+      if @authorized_db_samples.none?
         @new_samples.append(nes)
       else
         @new_samples.append(nes) unless is_duplicate
       end
     end
 
-    upload_data = { study: @study,
-                    assay: @assay,
-                    sampleType: @sample_type,
-                    excel_samples: excel_samples,
-                    existingExcelSamples: existing_excel_samples,
-                    newExcelSamples: new_excel_samples,
-                    updateSamples: @update_samples,
-                    newSamples: @new_samples,
-                    possibleDuplicates: @possible_duplicates,
-                    dbSamples: @db_samples }
-
-
     respond_to do |format|
       format.json { render json: { uploadData: upload_data } }
       format.html { render 'single_pages/sample_upload_content', { layout: false } }
diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 2bad6626a6..36c5aff131 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -1,3 +1,9 @@
+<%
+  def any_samples_to_upload?
+    !((@new_samples.nil? or @new_samples.compact.none?) and (@update_samples.nil? or @update_samples.compact.none?) and (@possible_duplicates.nil? or @possible_duplicates.compact.none?))
+  end
+%>
+
 <% can_upload = true %>
 <div id="upload-summary">
 
@@ -84,7 +90,7 @@
           </tr>
           <% for update_sample in @update_samples %>
             <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
-              <% db_sample = @db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
+              <% db_sample = @authorized_db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
               <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
               <% update_sample.map do |key, val| %>
                 <% unless key == 'uuid' %>
@@ -123,7 +129,7 @@
 
   <% # Possible Duplicate Samples panel %>
   <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
-    <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+    <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"},
                     :help_text => "These new samples have been matched to already existing samples.") do %>
       <div class="table-responsive">
         <table id="duplicate-samples-table" class="table">
@@ -174,6 +180,47 @@
     <% end %>
   <% end %>
 
+  <% # Panel for Sample with wrong permissions %>
+  <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
+    <% can_upload = false %>
+    <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"},
+                  :help_text => "Sample the current user does not have permission to edit them.") do %>
+      <div>
+        <p>
+          <b>You don't have permission to edit the samples listed below. Please contact the submitter of these samples or revert the changes in the spreadsheet to its original values.</b>
+        </p>
+      </div>
+      <div class="table-responsive">
+        <table id="unauthorized-samples-table" class="table">
+          <tr>
+            <% for key in @unauthorized_samples[0].keys %>
+              <% unless key == 'uuid' %>
+                <th><%= key %></th>
+              <% end %>
+            <% end %>
+          </tr>
+          <% for unauthorized_sample in @unauthorized_samples %>
+            <tr id='<%= "unauthorized-sample-#{unauthorized_sample['id']}" %>' class="">
+              <% unauthorized_sample.map do |key, val| %>
+                <% unless key == 'uuid' %>
+                  <% if @multiple_input_fields.include?(key) %>
+                    <td>
+                      <% val.each do |sub_sample| %>
+                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <% end %>
+                    </td>
+                  <% else %>
+                    <td><%= val %></td>
+                  <% end %>
+                <% end %>
+              <% end %>
+            </tr>
+          <% end %>
+        </table>
+      </div>
+    <% end %>
+  <% end %>
+
   <div id='check-excel-upload-result'></div>
   <% unless can_upload %>
     <div class="alert alert-danger alert-dismissible" role="alert">
@@ -184,7 +231,7 @@
     </div>
   <% end %>
 
-  <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if can_upload%>
+  <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if (can_upload and any_samples_to_upload?)%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 

From f0990f4bb7c31508df09af473d38f5ae7d4a50fc Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Wed, 9 Aug 2023 16:10:09 +0200
Subject: [PATCH 44/54] Fixed failing test

---
 app/controllers/single_pages_controller.rb | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 5f576cc1fb..bb76cbb84c 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -286,6 +286,19 @@ def upload_samples
       end
     end
 
+    upload_data = { study: @study,
+                    assay: @assay,
+                    sampleType: @sample_type,
+                    excel_samples: excel_samples,
+                    existingExcelSamples: existing_excel_samples,
+                    newExcelSamples: new_excel_samples,
+                    updateSamples: @update_samples,
+                    newSamples: @new_samples,
+                    possibleDuplicates: @possible_duplicates,
+                    dbSamples: @db_samples,
+                    authorized_db_samples: @authorized_db_samples,
+                    unauthorized_samples: @unauthorized_samples }
+
     respond_to do |format|
       format.json { render json: { uploadData: upload_data } }
       format.html { render 'single_pages/sample_upload_content', { layout: false } }

From 6b108fb7ee635acd9f11900264f9c2491dbe1e1e Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Fri, 11 Aug 2023 15:47:31 +0200
Subject: [PATCH 45/54] Fixing the upload summary popup

---
 app/controllers/single_pages_controller.rb    |  4 +-
 .../sample_upload_content.html.erb            | 38 +++++++++++++++----
 2 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index bb76cbb84c..98ae23d4f5 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -265,7 +265,7 @@ def upload_samples
     new_excel_samples.map do |nes|
       is_duplicate = true
 
-      @authorized_db_samples.map do |dbs|
+      @db_samples.map do |dbs|
         dbs.map do |k, v|
           unless %w[id uuid].include?(k)
             is_duplicate = (nes[k] == v)
@@ -279,7 +279,7 @@ def upload_samples
         end
       end
 
-      if @authorized_db_samples.none?
+      if @db_samples.none?
         @new_samples.append(nes)
       else
         @new_samples.append(nes) unless is_duplicate
diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 36c5aff131..82c5949a76 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -2,14 +2,16 @@
   def any_samples_to_upload?
     !((@new_samples.nil? or @new_samples.compact.none?) and (@update_samples.nil? or @update_samples.compact.none?) and (@possible_duplicates.nil? or @possible_duplicates.compact.none?))
   end
+  errors = []
 %>
 
 <% can_upload = true %>
 <div id="upload-summary">
 
   <% # General information panel %>
-  <%= folding_panel("General Information", true, :id => "general-information-panel") do %>
-    <% [@project, @study, @assay, @sample_type]. map do | asset | %>
+  <%= folding_panel("General Information", true, :id => "general-information-panel",
+  :help_text => "This pane contains an overview of the permissions needed to upload.") do %>
+    <% [@project, @study, @assay]. map do | asset | %>
       <% next if asset.nil? %>
       <% asset_name = asset.class.to_s.singularize %>
       <h4> <%= asset_name %> </h4>
@@ -22,13 +24,15 @@
         <% else %>
           <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
           <% can_upload = false %>
+          <% errors.append("You must be a member of this project!") %>
         <% end %>
       <% else %>
-        <% if asset.can_edit?%>
-          <p><b><%= current_user.person.name %> can edit: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+        <% if asset.can_view?%>
+          <p><b><%= current_user.person.name %> can view: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
         <% else %>
-          <p><b><%= current_user.person.name %> can edit: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+          <p><b><%= current_user.person.name %> can view: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
         <% can_upload = false %>
+        <% errors.append("You must have at least viewing permission for the #{asset_name} '#{asset.title}'.") %>
         <% end %>
       <% end %>
       <hr>
@@ -183,6 +187,7 @@
   <% # Panel for Sample with wrong permissions %>
   <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
     <% can_upload = false %>
+    <% errors.append("There are unauthorized samples present in the spreadsheet.") %>
     <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"},
                   :help_text => "Sample the current user does not have permission to edit them.") do %>
       <div>
@@ -225,9 +230,24 @@
   <% unless can_upload %>
     <div class="alert alert-danger alert-dismissible" role="alert">
         <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-        <h3>Error</h3>
+        <h3>Permissions conflict</h3>
         <strong>Unable to upload the current set of samples!</strong>
-        <p>Please expand the 'General Information' pane for more information.</p>
+        <p>Please expand the 'General Information' and/or 'Unauthorized Samples' pane for more information.</p>
+        <p>Correct the following errors:</p>
+        <ul>
+          <% for error in errors %>
+            <li><%= error %></li>
+          <% end %>
+        </ul>
+    </div>
+  <% end %>
+
+  <% if (can_upload and !any_samples_to_upload?) %>
+    <div class="alert alert-info alert-dismissible" role="alert">
+        <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h3>No changes detected</h3>
+        <strong>The provided spreadsheet did not include any new samples or changes to already existing ones!</strong>
+        <p>Please click the cancel button to dismiss this window.</p>
     </div>
   <% end %>
 
@@ -376,10 +396,12 @@
         Accept: "application/json"
       },
       success: function(res) {
-        console.log("res", res);
+        location.reload();
       },
       error: function(err) {
         console.log("err", err);
+        alert(json.stringify(err));
+        location.reload();
       }
     });
   };

From 635d726ed44f7c494563ba4fdaf7eb607545ffa7 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Wed, 16 Aug 2023 09:38:24 +0200
Subject: [PATCH 46/54] Clean up the uploadAjaxCall

---
 app/views/single_pages/sample_upload_content.html.erb | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 82c5949a76..4cb22b28ea 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -395,13 +395,9 @@
         "Content-Type": "application/json",
         Accept: "application/json"
       },
-      success: function(res) {
-        location.reload();
-      },
       error: function(err) {
         console.log("err", err);
         alert(json.stringify(err));
-        location.reload();
       }
     });
   };

From 31a01b0040ad958877bebff9a3e33d7aec15377d Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Wed, 16 Aug 2023 14:50:20 +0200
Subject: [PATCH 47/54] Fixing the empty cells issue for MS Excel spreadsheets

---
 app/controllers/single_pages_controller.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 98ae23d4f5..fb6e42d165 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -170,10 +170,10 @@ def upload_samples
       sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
     end
 
-    sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }
+    sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }.compact
     samples_data = (2..samples_sheet.actual_rows.size).map do |i|
-      act_cells = samples_sheet.row(i).actual_cells
-      act_cells.map { |cell| cell&.value } unless act_cells.all? { |cell| cell&.value&.empty? }
+      sample_cells = samples_sheet.row(i).cells
+      sample_cells.map { |cell| cell&.value }.drop(1) unless act_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
     end
 
     samples_data.compact!

From 451af953b0666bbbe95c4e7df402b87e1e337b5b Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Wed, 16 Aug 2023 15:34:00 +0200
Subject: [PATCH 48/54] Fixed typo

---
 app/controllers/single_pages_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index fb6e42d165..510593e00c 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -173,7 +173,7 @@ def upload_samples
     sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }.compact
     samples_data = (2..samples_sheet.actual_rows.size).map do |i|
       sample_cells = samples_sheet.row(i).cells
-      sample_cells.map { |cell| cell&.value }.drop(1) unless act_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
+      sample_cells.map { |cell| cell&.value }.drop(1) unless sample_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
     end
 
     samples_data.compact!

From 079a5a565f6b46091d9305be0751eef15982d8ab Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 18 Sep 2023 15:03:30 +0200
Subject: [PATCH 49/54] Simplify the relative path of the testing files

---
 .../single_pages_controller_test.rb           | 50 +++++++++----------
 1 file changed, 24 insertions(+), 26 deletions(-)

diff --git a/test/functional/single_pages_controller_test.rb b/test/functional/single_pages_controller_test.rb
index 4014b03991..9e96bba7a6 100644
--- a/test/functional/single_pages_controller_test.rb
+++ b/test/functional/single_pages_controller_test.rb
@@ -6,7 +6,7 @@ class SinglePagesControllerTest < ActionController::TestCase
   fixtures :isa_tags, :templates
 
   def setup
-    @instance_name = Seek::Config::instance_name
+    @instance_name = Seek::Config.instance_name
     @member = FactoryBot.create :user
     login_as @member
   end
@@ -22,11 +22,11 @@ def setup
   test 'should hide inaccessible items in treeview' do
     project = FactoryBot.create(:project)
     FactoryBot.create(:investigation, contributor: @member.person, policy: FactoryBot.create(:private_policy),
-                            projects: [project])
+                                      projects: [project])
 
     login_as(FactoryBot.create(:user))
     inv_two = FactoryBot.create(:investigation, contributor: User.current_user.person, policy: FactoryBot.create(:private_policy),
-                                      projects: [project])
+                                                projects: [project])
 
     controller = TreeviewBuilder.new project, nil
     result = controller.send(:build_tree_data)
@@ -108,14 +108,14 @@ def setup
 
   test 'invalid file extension should raise exception' do
     with_config_value(:project_single_page_enabled, true) do
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/00_wrong_format_spreadsheet.ods')
+      file_path = 'upload_single_page/00_wrong_format_spreadsheet.ods'
       file = fixture_file_upload(file_path, 'application/vnd.oasis.opendocument.spreadsheet')
 
       project, source_sample_type = setup_file_upload.values_at(
         :project, :source_sample_type
       )
 
-      post :upload_samples, params: { file: file, project_id: project.id,
+      post :upload_samples, params: { file:, project_id: project.id,
                                       sample_type_id: source_sample_type.id }
 
       assert_response :bad_request
@@ -129,7 +129,7 @@ def setup
         :project, :sample_collection_sample_type
       )
 
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx')
+      file_path = 'upload_single_page/01_combo_update_sources_spreadsheet.xlsx'
       file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
 
       post :upload_samples, as: :json, params: { file:, project_id: project.id,
@@ -145,7 +145,7 @@ def setup
         :project, :source_sample_type
       )
 
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/02_invalid_workbook.xlsx')
+      file_path = 'upload_single_page/02_invalid_workbook.xlsx'
       file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
 
       post :upload_samples, as: :json, params: { file:, project_id: project.id,
@@ -161,11 +161,11 @@ def setup
         :project, :source_sample_type
       )
 
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/01_combo_update_sources_spreadsheet.xlsx')
+      file_path = 'upload_single_page/01_combo_update_sources_spreadsheet.xlsx'
       file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
 
       post :upload_samples, as: :json, params: { file:, project_id: project.id,
-      sample_type_id: source_sample_type.id }
+                                                 sample_type_id: source_sample_type.id }
 
       response_data = JSON.parse(response.body)['uploadData']
       assert_response :success
@@ -187,7 +187,7 @@ def setup
         :project, :sample_collection_sample_type
       )
 
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/03_combo_update_samples_spreadsheet.xlsx')
+      file_path = 'upload_single_page/03_combo_update_samples_spreadsheet.xlsx'
       file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
 
       post :upload_samples, as: :json, params: { file:, project_id: project.id,
@@ -213,7 +213,7 @@ def setup
         :project, :assay_sample_type
       )
 
-      file_path = Rails.root.join('test/fixtures/files/upload_single_page/04_combo_update_assay_samples_spreadsheet.xlsx')
+      file_path = 'upload_single_page/04_combo_update_assay_samples_spreadsheet.xlsx'
       file = fixture_file_upload(file_path, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
 
       post :upload_samples, as: :json, params: { file:, project_id: project.id,
@@ -234,33 +234,32 @@ def setup
   end
 
   def setup_file_upload
-    id_label = "#{Seek::Config::instance_name} id"
+    id_label = "#{Seek::Config.instance_name} id"
     person = @member.person
-    project = FactoryBot.create(:project, id: 10000)
-    study = FactoryBot.create(:study, id: 10001)
-    assay = FactoryBot.create(:assay, id: 10002, study: study)
+    project = FactoryBot.create(:project, id: 10_000)
+    study = FactoryBot.create(:study, id: 10_001)
+    assay = FactoryBot.create(:assay, id: 10_002, study:)
 
-    source_sample_type_template = FactoryBot.create(:isa_source_template, id: 10006)
+    source_sample_type_template = FactoryBot.create(:isa_source_template, id: 10_006)
     source_sample_type = FactoryBot.create(:isa_source_sample_type,
-                                           id: 10003,
+                                           id: 10_003,
                                            contributor: person,
                                            project_ids: [project.id],
                                            isa_template: source_sample_type_template,
                                            studies: [study])
 
-
-    sample_collection_sample_type_template = FactoryBot.create(:isa_sample_collection_template, id: 10007)
+    sample_collection_sample_type_template = FactoryBot.create(:isa_sample_collection_template, id: 10_007)
     sample_collection_sample_type = FactoryBot.create(:isa_sample_collection_sample_type,
-                                                      id: 10004,
+                                                      id: 10_004,
                                                       contributor: person,
                                                       project_ids: [project.id],
                                                       isa_template: sample_collection_sample_type_template,
                                                       studies: [study],
                                                       linked_sample_type: source_sample_type)
 
-    assay_sample_type_template = FactoryBot.create(:isa_assay_template, id: 10008)
+    assay_sample_type_template = FactoryBot.create(:isa_assay_template, id: 10_008)
     assay_sample_type = FactoryBot.create(:isa_assay_sample_type,
-                                          id: 10005,
+                                          id: 10_005,
                                           contributor: person,
                                           isa_template: assay_sample_type_template,
                                           projects: [project],
@@ -270,7 +269,7 @@ def setup_file_upload
     sources = (1..5).map do |n|
       FactoryBot.create(
         :sample,
-        id: 10010 + n,
+        id: 10_010 + n,
         title: "source#{n}",
         sample_type: source_sample_type,
         project_ids: [project.id],
@@ -293,7 +292,7 @@ def setup_file_upload
     source_samples = (1..4).map do |n|
       FactoryBot.create(
         :sample,
-        id: 10020 + n,
+        id: 10_020 + n,
         title: "Sample collection #{n}",
         sample_type: sample_collection_sample_type,
         project_ids: [project.id],
@@ -311,7 +310,7 @@ def setup_file_upload
     assay_samples = (1..3).map do |n|
       FactoryBot.create(
         :sample,
-        id: 10030 + n,
+        id: 10_030 + n,
         title: "Assay Sample #{n}",
         sample_type: assay_sample_type,
         project_ids: [project.id],
@@ -330,6 +329,5 @@ def setup_file_upload
       "source_sample_type": source_sample_type, "sample_collection_sample_type": sample_collection_sample_type,
       "assay_sample_type": assay_sample_type, "sources": sources, "source_samples": source_samples,
       "assay_samples": assay_samples }
-
   end
 end

From b221684c9686ddceec585ce53f7bfcf9454fea7f Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Mon, 18 Sep 2023 15:22:08 +0200
Subject: [PATCH 50/54] Remove spaces in comment lines of ERB files and add btn
 bootstrap class

---
 .../single_pages/sample_upload_content.html.erb  | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 4cb22b28ea..a628417871 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -8,7 +8,7 @@
 <% can_upload = true %>
 <div id="upload-summary">
 
-  <% # General information panel %>
+  <%# General information panel %>
   <%= folding_panel("General Information", true, :id => "general-information-panel",
   :help_text => "This pane contains an overview of the permissions needed to upload.") do %>
     <% [@project, @study, @assay]. map do | asset | %>
@@ -39,7 +39,7 @@
     <% end %>
   <% end %>
 
-  <% # New Samples panel %>
+  <%# New Samples panel %>
   <% unless @new_samples.nil? or @new_samples.compact.none? %>
     <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
     :help_text => "These samples have been detected as new samples and will be created.") do %>
@@ -56,7 +56,7 @@
           <% for new_sample in @new_samples %>
             <% new_sample_id = UUID.generate %>
             <tr id='<%= "new-sample-#{new_sample_id}" %>'>
-              <td><button id=<%= "remove-#{new_sample_id}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+              <td><button id=<%= "remove-#{new_sample_id}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
                 <% new_sample.map do |key, val| %>
                   <% val = '<new>' if key =='id' %>
                 <% unless key == 'uuid' %>
@@ -78,7 +78,7 @@
     <% end %>
   <% end %>
 
-  <% # Update Samples panel %>
+  <%# Update Samples panel %>
   <% unless @update_samples.nil? or @update_samples.compact.none? %>
     <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
     :help_text => "These samples were detected existing samples and will be updated.") do %>
@@ -95,7 +95,7 @@
           <% for update_sample in @update_samples %>
             <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
               <% db_sample = @authorized_db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
-              <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
+              <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
               <% update_sample.map do |key, val| %>
                 <% unless key == 'uuid' %>
                   <% if @multiple_input_fields.include?(key)%>
@@ -131,7 +131,7 @@
     <% end %>
   <% end %>
 
-  <% # Possible Duplicate Samples panel %>
+  <%# Possible Duplicate Samples panel %>
   <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
     <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"},
                     :help_text => "These new samples have been matched to already existing samples.") do %>
@@ -147,7 +147,7 @@
           </tr>
           <% for dupl_sample in @possible_duplicates %>
             <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-              <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+              <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
             <% dupl_sample.map do |key, val| %>
               <% val = '<new>' if key =='id' %>
               <% unless %w[uuid duplicate].include?(key) %>
@@ -184,7 +184,7 @@
     <% end %>
   <% end %>
 
-  <% # Panel for Sample with wrong permissions %>
+  <%# Panel for Sample with wrong permissions %>
   <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
     <% can_upload = false %>
     <% errors.append("There are unauthorized samples present in the spreadsheet.") %>

From c58afdb651cd019064caa4ac0de79d8d577b915b Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 19 Sep 2023 10:52:30 +0200
Subject: [PATCH 51/54] Refactor the upload_samples function

---
 app/controllers/single_pages_controller.rb | 224 ++++++++++++---------
 1 file changed, 129 insertions(+), 95 deletions(-)

diff --git a/app/controllers/single_pages_controller.rb b/app/controllers/single_pages_controller.rb
index 510593e00c..a16e525ce7 100644
--- a/app/controllers/single_pages_controller.rb
+++ b/app/controllers/single_pages_controller.rb
@@ -1,5 +1,6 @@
 require 'isatab_converter'
 
+# Controller for the Single Page view
 class SinglePagesController < ApplicationController
   include Seek::AssetsCommon
   include Seek::Sharing::SharingCommon
@@ -15,9 +16,7 @@ class SinglePagesController < ApplicationController
   def show
     @project = Project.find(params[:id])
     @folders = project_folders
-    respond_to do |format|
-      format.html
-    end
+    respond_to(&:html)
   end
 
   def index; end
@@ -62,21 +61,20 @@ def export_isa
   end
 
   def download_samples_excel
-
     sample_ids, sample_type_id, study_id, assay_id = Rails.cache.read(params[:uuid]).values_at(:sample_ids, :sample_type_id,
-                                                                                     :study_id, :assay_id)
+                                                                                               :study_id, :assay_id)
 
     @study = Study.find(study_id)
     @assay = Assay.find(assay_id) unless assay_id.nil?
     @project = @study.projects.first
-    @samples = Sample.where(id: sample_ids)&.authorized_for(:view).sort_by(&:id)
+    @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?
+    raise 'Nothing to export to Excel.' if @samples.nil? || @samples == [] || sample_type_id.nil?
 
     @sample_type = SampleType.find(sample_type_id)
 
     sample_attributes = @sample_type.sample_attributes.map do |sa|
-      obj = if (sa.sample_controlled_vocab_id.nil?)
+      obj = if sa.sample_controlled_vocab_id.nil?
               { sa_cv_title: sa.title, sa_cv_id: nil }
             else
               { sa_cv_title: sa.title, sa_cv_id: sa.sample_controlled_vocab_id }
@@ -84,17 +82,20 @@ def download_samples_excel
       obj.merge({ required: sa.required })
     end
 
-    @sa_cv_terms = [{ "name" => "id", "has_cv" => false, "data" => nil, "allows_custom_input" => nil, "required" => nil },
-                    { "name" => "uuid", "has_cv" => false, "data" => nil, "allows_custom_input" => nil, "required" => nil }]
+    @sa_cv_terms = [{ 'name' => 'id', 'has_cv' => false, 'data' => nil, 'allows_custom_input' => nil, 'required' => nil },
+                    { 'name' => 'uuid', 'has_cv' => false, 'data' => nil, 'allows_custom_input' => nil,
+                      'required' => nil }]
 
     sample_attributes.map do |sa|
-        if sa[:sa_cv_id].nil?
-          @sa_cv_terms.push({ "name" => sa[:sa_cv_title], "has_cv" => false, "data" => nil, "allows_custom_input" => nil, "required" => sa[:required] })
-        else
-          allows_custom_input = SampleControlledVocab.find(sa[:sa_cv_id])&.custom_input
-          sa_terms = SampleControlledVocabTerm.where(sample_controlled_vocab_id: sa[:sa_cv_id]).map(&:label)
-          @sa_cv_terms.push({ "name" => sa[:sa_cv_title], "has_cv" => true, "data" => sa_terms, "allows_custom_input" => allows_custom_input, "required" => sa[:required] })
-        end
+      if sa[:sa_cv_id].nil?
+        @sa_cv_terms.push({ 'name' => sa[:sa_cv_title], 'has_cv' => false, 'data' => nil,
+                            'allows_custom_input' => nil, 'required' => sa[:required] })
+      else
+        allows_custom_input = SampleControlledVocab.find(sa[:sa_cv_id])&.custom_input
+        sa_terms = SampleControlledVocabTerm.where(sample_controlled_vocab_id: sa[:sa_cv_id]).map(&:label)
+        @sa_cv_terms.push({ 'name' => sa[:sa_cv_title], 'has_cv' => true, 'data' => sa_terms,
+                            'allows_custom_input' => allows_custom_input, 'required' => sa[:required] })
+      end
     end
     @template = Template.find(@sample_type.template_id)
 
@@ -103,13 +104,15 @@ def download_samples_excel
     flash[:error] = e.message
     respond_to do |format|
       format.html { redirect_to single_page_path(@project.id) }
-      format.json { render json: { parameters: { sample_ids: sample_ids, sample_type_id: sample_type_id, study_id: study_id } } }
+      format.json do
+        render json: { parameters: { sample_ids:, sample_type_id:, study_id: } }
+      end
     end
   end
 
   def export_to_excel
     cache_uuid = UUID.new.generate
-    id_label = "#{Seek::Config::instance_name} id"
+    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_type_id = JSON.parse(params[:sample_type_id])
     study_id = JSON.parse(params[:study_id])
@@ -141,8 +144,8 @@ def upload_samples
 
     sample_type_id_ui = params[:sample_type_id].to_i
 
-    unless is_valid_workbook?(wb)
-      raise "Invalid workbook! Cannot process this spreadsheet. Consider first exporting the table as a spreadsheet for the proper format."
+    unless valid_workbook?(wb)
+      raise 'Invalid workbook! Cannot process this spreadsheet. Consider first exporting the table as a spreadsheet for the proper format.'
     end
 
     # Extract Samples metadata from spreadsheet
@@ -150,8 +153,6 @@ def upload_samples
     @study = Study.find(study_id)
     sample_type_id = metadata_sheet.cell(5, 2).value.to_i
     @sample_type = SampleType.find(sample_type_id)
-    template_id = metadata_sheet.cell(8, 2).value.to_i
-    template = Template.find(template_id)
     is_assay = @sample_type.assays.any?
     @assay = @sample_type.assays.first
 
@@ -170,13 +171,7 @@ def upload_samples
       sa_attr.title if sa_attr.sample_attribute_type.base_type == 'SeekSampleMulti'
     end
 
-    sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }.compact
-    samples_data = (2..samples_sheet.actual_rows.size).map do |i|
-      sample_cells = samples_sheet.row(i).cells
-      sample_cells.map { |cell| cell&.value }.drop(1) unless sample_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
-    end
-
-    samples_data.compact!
+    sample_fields, samples_data = get_spreadsheet_data(samples_sheet)
 
     # Compare Excel header row to Sample Type Sample Attributes
     # Should raise an error if they don't match
@@ -187,11 +182,72 @@ def upload_samples
     end
 
     # Construct Samples objects from Excel data
-    excel_samples = samples_data.map do |excel_sample|
+    excel_samples = generate_excel_samples(samples_data, sample_fields)
+
+    existing_excel_samples = excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
+    new_excel_samples = excel_samples.map { |sample| sample if sample['id'].nil? }.compact
+
+    # Retrieve all samples of the Sample Type, also the unauthorized ones
+    @db_samples = sample_type_samples(@sample_type)
+    # Retrieve the Sample Types samples wich are authorized for editing
+    @authorized_db_samples = sample_type_samples(@sample_type, :edit)
+
+    # Determine whether samples have been modified or not,
+    # and checking whether the user is permitted to edit them
+    @unauthorized_samples, @update_samples = separate_unauthorized_samples(existing_excel_samples, @db_samples,
+                                                                           @authorized_db_samples)
+
+    # Determine if the new samples are no duplicates of existing ones,
+    # based on the attribute values
+    @possible_duplicates, @new_samples = separate_possible_duplicates(new_excel_samples, @db_samples)
+
+    upload_data = { study: @study,
+                    assay: @assay,
+                    sampleType: @sample_type,
+                    excel_samples:,
+                    existingExcelSamples: existing_excel_samples,
+                    newExcelSamples: new_excel_samples,
+                    updateSamples: @update_samples,
+                    newSamples: @new_samples,
+                    possibleDuplicates: @possible_duplicates,
+                    dbSamples: @db_samples,
+                    authorized_db_samples: @authorized_db_samples,
+                    unauthorized_samples: @unauthorized_samples }
+
+    respond_to do |format|
+      format.json { render json: { uploadData: upload_data } }
+      format.html { render 'single_pages/sample_upload_content', { layout: false } }
+    end
+  rescue StandardError => e
+    flash[:error] = e.message
+    respond_to do |format|
+      format.html { redirect_to single_page_path(@project), status: :bad_request }
+      format.json { render json: { error: e }, status: :bad_request }
+    end
+  end
+
+  private
+
+  def get_spreadsheet_data(samples_sheet)
+    sample_fields = samples_sheet.row(1).actual_cells.map { |field| field&.value&.sub(' *', '') }.compact
+    samples_data = (2..samples_sheet.actual_rows.size).map do |i|
+      sample_cells = samples_sheet.row(i).cells
+      next if sample_cells.all? { |cell| (cell&.value == '' || cell&.value.nil?) }
+
+      sample_cells.map do |cell|
+        cell&.value
+      end.drop(1)
+    end.compact
+
+    [sample_fields, samples_data]
+  end
+
+  def generate_excel_samples(samples_data, sample_fields)
+    samples_data.map do |excel_sample|
       obj = {}
       (0..sample_fields.size - 1).map do |i|
         if @multiple_input_fields.include?(sample_fields[i])
-          parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub(/\"=>/x, "\":")).map do |subsample|
+          parsed_excel_input_samples = JSON.parse(excel_sample[i].gsub(/"=>/x, '":')).map do |subsample|
             # Uploader should at least have viewing permissions for the inputs he's using
             unless Sample.find(subsample['id'])&.authorized_for_view?
               raise "Unauthorized Sample was detected in spreadsheet: #{subsample.inspect}"
@@ -212,33 +268,34 @@ def upload_samples
       end
       obj
     end
+  end
 
-    existing_excel_samples = excel_samples.map { |sample| sample unless sample['id'].nil? }.compact
-    new_excel_samples = excel_samples.map { |sample| sample if sample['id'].nil? }.compact
-
-    @db_samples = @sample_type.samples&.map do |sample|
-      attributes = JSON.parse(sample[:json_metadata])
-      { 'id' => sample.id,
-        'uuid' => sample.uuid }.merge(attributes)
-    end
-
-    @authorized_db_samples = @sample_type.samples&.authorized_for(:edit)&.map do |sample|
-      attributes = JSON.parse(sample[:json_metadata])
-      { 'id' => sample.id,
-        'uuid' => sample.uuid }.merge(attributes)
+  def sample_type_samples(sample_type, authorization_method = nil)
+    if authorization_method
+      sample_type.samples&.authorized_for(authorization_method)&.map do |sample|
+        attributes = JSON.parse(sample[:json_metadata])
+        { 'id' => sample.id,
+          'uuid' => sample.uuid }.merge(attributes)
+      end
+    else
+      sample_type.samples&.map do |sample|
+        attributes = JSON.parse(sample[:json_metadata])
+        { 'id' => sample.id,
+          'uuid' => sample.uuid }.merge(attributes)
+      end
     end
+  end
 
-    # Determine whether samples have been modified or not,
-    # and checking whether the user is permitted to edit them
-    @unauthorized_samples = []
-    @update_samples = []
+  def separate_unauthorized_samples(existing_excel_samples, db_samples, authorized_db_samples)
+    update_samples = []
+    unauthorized_samples = []
     existing_excel_samples.map do |ees|
-      db_sample = @db_samples.select { |s| s['id'] == ees['id'] }.first
+      db_sample = db_samples.select { |s| s['id'] == ees['id'] }.first
 
       # An exception is raised if the ID of an existing Sample cannot be found in the DB
       raise "Sample with id '#{ees['id']}' does not exist in the database. Sample upload was aborted!" if db_sample.nil?
 
-      is_authorized_for_update = @authorized_db_samples.select { |s| s['id'] == ees['id'] }.any?
+      is_authorized_for_update = authorized_db_samples.select { |s| s['id'] == ees['id'] }.any?
 
       is_changed = false
 
@@ -251,21 +308,22 @@ def upload_samples
 
       if is_changed
         if is_authorized_for_update
-          @update_samples.append(ees)
+          update_samples.append(ees)
         else
-          @unauthorized_samples.append(ees)
+          unauthorized_samples.append(ees)
         end
       end
     end
+    [unauthorized_samples, update_samples]
+  end
 
-    # Determine if the new samples are no duplicates of existing ones,
-    # based on the attribute values
-    @possible_duplicates = []
-    @new_samples = []
+  def separate_possible_duplicates(new_excel_samples, db_samples)
+    possible_duplicates = []
+    new_samples = []
     new_excel_samples.map do |nes|
       is_duplicate = true
 
-      @db_samples.map do |dbs|
+      db_samples.map do |dbs|
         dbs.map do |k, v|
           unless %w[id uuid].include?(k)
             is_duplicate = (nes[k] == v)
@@ -274,48 +332,24 @@ def upload_samples
         end
 
         if is_duplicate
-          @possible_duplicates.append(nes.merge({ 'duplicate' => dbs }))
+          possible_duplicates.append(nes.merge({ 'duplicate' => dbs }))
           break
         end
       end
 
-      if @db_samples.none?
-        @new_samples.append(nes)
+      if db_samples.none?
+        new_samples.append(nes)
       else
-        @new_samples.append(nes) unless is_duplicate
+        new_samples.append(nes) unless is_duplicate
       end
     end
+    [possible_duplicates, new_samples]
+  end
 
-    upload_data = { study: @study,
-                    assay: @assay,
-                    sampleType: @sample_type,
-                    excel_samples: excel_samples,
-                    existingExcelSamples: existing_excel_samples,
-                    newExcelSamples: new_excel_samples,
-                    updateSamples: @update_samples,
-                    newSamples: @new_samples,
-                    possibleDuplicates: @possible_duplicates,
-                    dbSamples: @db_samples,
-                    authorized_db_samples: @authorized_db_samples,
-                    unauthorized_samples: @unauthorized_samples }
-
-    respond_to do |format|
-      format.json { render json: { uploadData: upload_data } }
-      format.html { render 'single_pages/sample_upload_content', { layout: false } }
-    end
-  rescue StandardError => e
-    flash[:error] = e.message
-    respond_to do |format|
-      format.html { redirect_to single_page_path(@project), status: :bad_request }
-      format.json { render json: { error: e }, status: :bad_request }
-    end
-
-end
-
-  private
-
-  def is_valid_workbook?(wb)
-    !((wb.sheet_names.map { |sheet| %w[Metadata Samples cv_ontology].include? sheet }.include? false) && (wb.sheets.size != 3))
+  def valid_workbook?(workbook)
+    !((workbook.sheet_names.map do |sheet|
+         %w[Metadata Samples cv_ontology].include? sheet
+       end.include? false) && (workbook.sheets.size != 3))
   end
 
   def set_up_instance_variable
@@ -328,8 +362,8 @@ def find_authorized_investigation
   end
 
   def check_user_logged_in
-    unless current_user
-      render json: { status: :unprocessable_entity, error: 'You must be logged in to access batch sharing permission.' }
-    end
+    return if current_user
+
+    render json: { status: :unprocessable_entity, error: 'You must be logged in to access batch sharing permission.' }
   end
 end

From 8e5947af30b1c993bc5bae2fb2fd9270830b7884 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 19 Sep 2023 16:08:59 +0200
Subject: [PATCH 52/54] Refactor the sample_upload_content view

---
 .../_duplicate_samples_panel.html.erb         |  51 ++++
 .../single_pages/_general_panel.html.erb      |  29 +++
 .../single_pages/_new_samples_panel.html.erb  |  37 +++
 .../_unauthorized_samples_panel.html.erb      |  40 ++++
 .../_update_samples_panel.html.erb            |  51 ++++
 .../sample_upload_content.html.erb            | 221 +-----------------
 6 files changed, 217 insertions(+), 212 deletions(-)
 create mode 100644 app/views/single_pages/_duplicate_samples_panel.html.erb
 create mode 100644 app/views/single_pages/_general_panel.html.erb
 create mode 100644 app/views/single_pages/_new_samples_panel.html.erb
 create mode 100644 app/views/single_pages/_unauthorized_samples_panel.html.erb
 create mode 100644 app/views/single_pages/_update_samples_panel.html.erb

diff --git a/app/views/single_pages/_duplicate_samples_panel.html.erb b/app/views/single_pages/_duplicate_samples_panel.html.erb
new file mode 100644
index 0000000000..3e7696e7a5
--- /dev/null
+++ b/app/views/single_pages/_duplicate_samples_panel.html.erb
@@ -0,0 +1,51 @@
+<% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
+  <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"},
+                  :help_text => "These new samples have been matched to already existing samples.") do %>
+    <div class="table-responsive">
+      <table id="duplicate-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @possible_duplicates[0].keys %>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <th><%= key %></th>
+            <% end %>
+          <% end %>
+        </tr>
+        <% for dupl_sample in @possible_duplicates %>
+          <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
+            <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
+          <% dupl_sample.map do |key, val| %>
+            <% val = '<new>' if key =='id' %>
+            <% unless %w[uuid duplicate].include?(key) %>
+              <% if @multiple_input_fields.include?(key)%>
+                <td>
+                  <% val.each do |sub_sample| %>
+                    <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                  <% end %>
+                </td>
+              <% else %>
+                <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
+              <% end %>
+            <% end %>
+          <% end %>
+            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
+              <% dupl_sample['duplicate'].map do |key, val| %>
+                <% unless %w[uuid duplicate].include?(key) %>
+                  <% if @multiple_input_fields.include?(key)%>
+                    <td>
+                      <% val.each do |sub_sample| %>
+                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                      <% end %>
+                    </td>
+                  <% else %>
+                    <td><%= val%></td>
+                  <% end %>
+                <% end %>
+              <% end %>
+            </tr>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/_general_panel.html.erb b/app/views/single_pages/_general_panel.html.erb
new file mode 100644
index 0000000000..6880ad7eaf
--- /dev/null
+++ b/app/views/single_pages/_general_panel.html.erb
@@ -0,0 +1,29 @@
+<%= folding_panel("General Information", true, :id => "general-information-panel",
+:help_text => "This pane contains an overview of the permissions needed to upload.") do %>
+  <% [@project, @study, @assay]. map do | asset | %>
+    <% next if asset.nil? %>
+    <% asset_name = asset.class.to_s.singularize %>
+    <h4> <%= asset_name %> </h4>
+    <p><b>ID: </b><span><%= asset.id%></span></p>
+    <p><b>UUID: </b><span><%= asset.uuid %></span></p>
+    <p><b>Title: </b><span><%= asset.title %></span></p>
+    <% if asset_name == "Project"%>
+      <% if current_user.person.member_of?(asset)%>
+        <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+      <% else %>
+        <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+        <% can_upload = false %>
+        <% errors.append("You must be a member of this project!") %>
+      <% end %>
+    <% else %>
+      <% if asset.can_view?%>
+        <p><b><%= current_user.person.name %> can view: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
+      <% else %>
+        <p><b><%= current_user.person.name %> can view: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
+      <% can_upload = false %>
+      <% errors.append("You must have at least viewing permission for the #{asset_name} '#{asset.title}'.") %>
+      <% end %>
+    <% end %>
+    <hr>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/_new_samples_panel.html.erb b/app/views/single_pages/_new_samples_panel.html.erb
new file mode 100644
index 0000000000..cf157efaa2
--- /dev/null
+++ b/app/views/single_pages/_new_samples_panel.html.erb
@@ -0,0 +1,37 @@
+<% unless @new_samples.nil? or @new_samples.compact.none? %>
+  <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
+  :help_text => "These samples have been detected as new samples and will be created.") do %>
+    <div class="table-responsive">
+      <table id="create-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @new_samples[0].keys %>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
+          <% end %>
+        </tr>
+        <% for new_sample in @new_samples %>
+          <% new_sample_id = UUID.generate %>
+          <tr id='<%= "new-sample-#{new_sample_id}" %>'>
+            <td><button id=<%= "remove-#{new_sample_id}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
+              <% new_sample.map do |key, val| %>
+                <% val = '<new>' if key =='id' %>
+              <% unless key == 'uuid' %>
+                <% if @multiple_input_fields.include?(key)%>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
+                    <% val.each do |sub_sample| %>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% else %>
+                  <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
+                <% end %>
+              <% end %>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/_unauthorized_samples_panel.html.erb b/app/views/single_pages/_unauthorized_samples_panel.html.erb
new file mode 100644
index 0000000000..8ad35705d2
--- /dev/null
+++ b/app/views/single_pages/_unauthorized_samples_panel.html.erb
@@ -0,0 +1,40 @@
+<% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
+  <% @can_upload = false %>
+  <% errors.append("There are unauthorized samples present in the spreadsheet.") %>
+  <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"},
+                :help_text => "Sample the current user does not have permission to edit them.") do %>
+    <div>
+      <p>
+        <b>You don't have permission to edit the samples listed below. Please contact the submitter of these samples or revert the changes in the spreadsheet to its original values.</b>
+      </p>
+    </div>
+    <div class="table-responsive">
+      <table id="unauthorized-samples-table" class="table">
+        <tr>
+          <% for key in @unauthorized_samples[0].keys %>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
+          <% end %>
+        </tr>
+        <% for unauthorized_sample in @unauthorized_samples %>
+          <tr id='<%= "unauthorized-sample-#{unauthorized_sample['id']}" %>' class="">
+            <% unauthorized_sample.map do |key, val| %>
+              <% unless key == 'uuid' %>
+                <% if @multiple_input_fields.include?(key) %>
+                  <td>
+                    <% val.each do |sub_sample| %>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% else %>
+                  <td><%= val %></td>
+                <% end %>
+              <% end %>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/_update_samples_panel.html.erb b/app/views/single_pages/_update_samples_panel.html.erb
new file mode 100644
index 0000000000..b2de42c349
--- /dev/null
+++ b/app/views/single_pages/_update_samples_panel.html.erb
@@ -0,0 +1,51 @@
+<% unless @update_samples.nil? or @update_samples.compact.none? %>
+  <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
+  :help_text => "These samples were detected existing samples and will be updated.") do %>
+    <div class="table-responsive">
+      <table id="update-samples-table" class="table">
+        <tr>
+          <th></th>
+          <% for key in @update_samples[0].keys %>
+            <% unless key == 'uuid' %>
+              <th><%= key %></th>
+            <% end %>
+          <% end %>
+        </tr>
+        <% for update_sample in @update_samples %>
+          <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
+            <% db_sample = @authorized_db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
+            <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
+            <% update_sample.map do |key, val| %>
+              <% unless key == 'uuid' %>
+                <% if @multiple_input_fields.include?(key)%>
+                  <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' >
+                    <% val.each do |sub_sample| %>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% else %>
+                  <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
+                <% end %>
+              <% end %>
+            <% end %>
+          </tr>
+          <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
+            <% db_sample.map do |key, val| %>
+              <% unless key == 'uuid' %>
+                <% if @multiple_input_fields.include?(key)%>
+                  <td>
+                    <% val.each do |sub_sample| %>
+                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
+                    <% end %>
+                  </td>
+                <% else %>
+                  <td><%= val %></td>
+                <% end %>
+              <% end %>
+            <% end %>
+          </tr>
+        <% end %>
+      </table>
+    </div>
+  <% end %>
+<% end %>
diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index a628417871..474a9b0dbc 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -5,229 +5,26 @@
   errors = []
 %>
 
-<% can_upload = true %>
+<% @can_upload = true %>
 <div id="upload-summary">
 
   <%# General information panel %>
-  <%= folding_panel("General Information", true, :id => "general-information-panel",
-  :help_text => "This pane contains an overview of the permissions needed to upload.") do %>
-    <% [@project, @study, @assay]. map do | asset | %>
-      <% next if asset.nil? %>
-      <% asset_name = asset.class.to_s.singularize %>
-      <h4> <%= asset_name %> </h4>
-      <p><b>ID: </b><span><%= asset.id%></span></p>
-      <p><b>UUID: </b><span><%= asset.uuid %></span></p>
-      <p><b>Title: </b><span><%= asset.title %></span></p>
-      <% if asset_name == "Project"%>
-        <% if current_user.person.member_of?(asset)%>
-          <p><b><%= current_user.person.name %> is member of this project: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
-        <% else %>
-          <p><b><%= current_user.person.name %> is member of this project: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
-          <% can_upload = false %>
-          <% errors.append("You must be a member of this project!") %>
-        <% end %>
-      <% else %>
-        <% if asset.can_view?%>
-          <p><b><%= current_user.person.name %> can view: </b><span class="glyphicon glyphicon-ok-sign" style="color: green;"></span></p>
-        <% else %>
-          <p><b><%= current_user.person.name %> can view: </b> <span class="glyphicon glyphicon-remove-sign" style="color: red;"></span></p>
-        <% can_upload = false %>
-        <% errors.append("You must have at least viewing permission for the #{asset_name} '#{asset.title}'.") %>
-        <% end %>
-      <% end %>
-      <hr>
-    <% end %>
-  <% end %>
+  <%= render partial: 'general_panel' %>
 
   <%# New Samples panel %>
-  <% unless @new_samples.nil? or @new_samples.compact.none? %>
-    <%= folding_panel("New Samples <span id='new-samples-counter' class='label label-primary'>#{@new_samples.size}</span>", true, :id => "new-samples-panel", :body_options => {:id => "new-samples-panel-content"},
-    :help_text => "These samples have been detected as new samples and will be created.") do %>
-      <div class="table-responsive">
-        <table id="create-samples-table" class="table">
-          <tr>
-            <th></th>
-            <% for key in @new_samples[0].keys %>
-              <% unless key == 'uuid' %>
-                <th><%= key %></th>
-              <% end %>
-            <% end %>
-          </tr>
-          <% for new_sample in @new_samples %>
-            <% new_sample_id = UUID.generate %>
-            <tr id='<%= "new-sample-#{new_sample_id}" %>'>
-              <td><button id=<%= "remove-#{new_sample_id}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('new-sample-#{new_sample_id}')" %>></button></td>
-                <% new_sample.map do |key, val| %>
-                  <% val = '<new>' if key =='id' %>
-                <% unless key == 'uuid' %>
-                  <% if @multiple_input_fields.include?(key)%>
-                    <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' >
-                      <% val.each do |sub_sample| %>
-                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                      <% end %>
-                    </td>
-                  <% else %>
-                    <td id='<%= "new-sample-#{new_sample_id}[#{key}]" %>' ><%= val %></td>
-                  <% end %>
-                <% end %>
-              <% end %>
-            </tr>
-          <% end %>
-        </table>
-      </div>
-    <% end %>
-  <% end %>
+  <%= render partial: 'new_samples_panel' %>
 
   <%# Update Samples panel %>
-  <% unless @update_samples.nil? or @update_samples.compact.none? %>
-    <%= folding_panel("Samples to Update <span id='update-samples-counter' class='label label-warning'>#{@update_samples.size}</span>", true, :id => "existing-samples-panel", :body_options => {:id => "existing-samples-panel-content"},
-    :help_text => "These samples were detected existing samples and will be updated.") do %>
-      <div class="table-responsive">
-        <table id="update-samples-table" class="table">
-          <tr>
-            <th></th>
-            <% for key in @update_samples[0].keys %>
-              <% unless key == 'uuid' %>
-                <th><%= key %></th>
-              <% end %>
-            <% end %>
-          </tr>
-          <% for update_sample in @update_samples %>
-            <tr id='<%= "update-sample-#{update_sample['id']}-updated" %>' >
-              <% db_sample = @authorized_db_samples.select { |s| s['id'] == update_sample['id'] }.first %>
-              <td rowspan=2><button id=<%= "remove-#{update_sample['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('update-sample-#{update_sample['id']}')" %>></button></td>
-              <% update_sample.map do |key, val| %>
-                <% unless key == 'uuid' %>
-                  <% if @multiple_input_fields.include?(key)%>
-                    <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' >
-                      <% val.each do |sub_sample| %>
-                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                      <% end %>
-                    </td>
-                  <% else %>
-                    <td class='<%= (val != db_sample[key]) ? "warning" : "default" %>' id='<%= "update-sample-#{update_sample['id']}[#{key}]"%>' ><%= val %></td>
-                  <% end %>
-                <% end %>
-              <% end %>
-            </tr>
-            <tr id='<%= "update-sample-#{update_sample['id']}-original" %>' >
-              <% db_sample.map do |key, val| %>
-                <% unless key == 'uuid' %>
-                  <% if @multiple_input_fields.include?(key)%>
-                    <td>
-                      <% val.each do |sub_sample| %>
-                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                      <% end %>
-                    </td>
-                  <% else %>
-                    <td><%= val %></td>
-                  <% end %>
-                <% end %>
-              <% end %>
-            </tr>
-          <% end %>
-        </table>
-      </div>
-    <% end %>
-  <% end %>
+  <%= render partial: 'update_samples_panel' %>
 
   <%# Possible Duplicate Samples panel %>
-  <% unless @possible_duplicates.nil? or @possible_duplicates.compact.none? %>
-    <%= folding_panel("Possible Duplicates <span id='duplicate-samples-counter' class='label label-danger'>#{@possible_duplicates.size}</span>", true, :id => "duplicate-samples-panel", :body_options => {:id => "duplicate-samples-panel-content"},
-                    :help_text => "These new samples have been matched to already existing samples.") do %>
-      <div class="table-responsive">
-        <table id="duplicate-samples-table" class="table">
-          <tr>
-            <th></th>
-            <% for key in @possible_duplicates[0].keys %>
-              <% unless %w[uuid duplicate].include?(key) %>
-                <th><%= key %></th>
-              <% end %>
-            <% end %>
-          </tr>
-          <% for dupl_sample in @possible_duplicates %>
-            <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-1" %>' >
-              <td rowspan=2><button id=<%= "remove-#{dupl_sample['duplicate']['id']}" %> class="btn glyphicon glyphicon-trash danger" style="background-color:#d9534f;color:white;" onclick=<%= "removeSample('duplicate-sample-#{dupl_sample['duplicate']['id']}')" %>></button></td>
-            <% dupl_sample.map do |key, val| %>
-              <% val = '<new>' if key =='id' %>
-              <% unless %w[uuid duplicate].include?(key) %>
-                <% if @multiple_input_fields.include?(key)%>
-                  <td>
-                    <% val.each do |sub_sample| %>
-                      <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                    <% end %>
-                  </td>
-                <% else %>
-                  <td id='<%= "#{dupl_sample['duplicate']['id']}[#{key}]" %>' ><%= val %></td>
-                <% end %>
-              <% end %>
-            <% end %>
-              <tr id='<%= "duplicate-sample-#{dupl_sample['duplicate']['id']}-2" %>' class="danger">
-                <% dupl_sample['duplicate'].map do |key, val| %>
-                  <% unless %w[uuid duplicate].include?(key) %>
-                    <% if @multiple_input_fields.include?(key)%>
-                      <td>
-                        <% val.each do |sub_sample| %>
-                          <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                        <% end %>
-                      </td>
-                    <% else %>
-                      <td><%= val%></td>
-                    <% end %>
-                  <% end %>
-                <% end %>
-              </tr>
-            </tr>
-          <% end %>
-        </table>
-      </div>
-    <% end %>
-  <% end %>
+  <%= render partial: 'duplicate_samples_panel' %>
 
   <%# Panel for Sample with wrong permissions %>
-  <% unless @unauthorized_samples.nil? or @unauthorized_samples.compact.none? %>
-    <% can_upload = false %>
-    <% errors.append("There are unauthorized samples present in the spreadsheet.") %>
-    <%= folding_panel("Unauthorized Samples", false, :id => "unauthorized-samples-panel", :body_options => {:id => "unauthorized-samples-panel-content"},
-                  :help_text => "Sample the current user does not have permission to edit them.") do %>
-      <div>
-        <p>
-          <b>You don't have permission to edit the samples listed below. Please contact the submitter of these samples or revert the changes in the spreadsheet to its original values.</b>
-        </p>
-      </div>
-      <div class="table-responsive">
-        <table id="unauthorized-samples-table" class="table">
-          <tr>
-            <% for key in @unauthorized_samples[0].keys %>
-              <% unless key == 'uuid' %>
-                <th><%= key %></th>
-              <% end %>
-            <% end %>
-          </tr>
-          <% for unauthorized_sample in @unauthorized_samples %>
-            <tr id='<%= "unauthorized-sample-#{unauthorized_sample['id']}" %>' class="">
-              <% unauthorized_sample.map do |key, val| %>
-                <% unless key == 'uuid' %>
-                  <% if @multiple_input_fields.include?(key) %>
-                    <td>
-                      <% val.each do |sub_sample| %>
-                        <span class="badge", title='ID: <%= sub_sample['id'] %>'><%= sub_sample['title'] %></span>
-                      <% end %>
-                    </td>
-                  <% else %>
-                    <td><%= val %></td>
-                  <% end %>
-                <% end %>
-              <% end %>
-            </tr>
-          <% end %>
-        </table>
-      </div>
-    <% end %>
-  <% end %>
+  <%= render partial: 'unauthorized_samples_panel' %>
 
   <div id='check-excel-upload-result'></div>
-  <% unless can_upload %>
+  <% unless @can_upload %>
     <div class="alert alert-danger alert-dismissible" role="alert">
         <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
         <h3>Permissions conflict</h3>
@@ -242,7 +39,7 @@
     </div>
   <% end %>
 
-  <% if (can_upload and !any_samples_to_upload?) %>
+  <% if (@can_upload and !any_samples_to_upload?) %>
     <div class="alert alert-info alert-dismissible" role="alert">
         <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">&times;</span></button>
         <h3>No changes detected</h3>
@@ -251,7 +48,7 @@
     </div>
   <% end %>
 
-  <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if (can_upload and any_samples_to_upload?)%>
+  <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if (@can_upload and any_samples_to_upload?)%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
 </div>
 

From 9406e033c45d61ea1e8c04c4204a4ab721eec7f0 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 19 Sep 2023 18:17:29 +0200
Subject: [PATCH 53/54] Add static backdrop to the modal form

---
 app/assets/javascripts/single_page/index.js.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
index ee554f2d3b..85994ee285 100644
--- a/app/assets/javascripts/single_page/index.js.erb
+++ b/app/assets/javascripts/single_page/index.js.erb
@@ -292,7 +292,7 @@ async function handleUploadSubmit(formData){
     contentType: false,
     enctype: 'multipart/form-data',
     success: function(response){
-      $j('#upload-excel-modal').modal('show').focus();
+      $j('#upload-excel-modal').modal({backdrop: 'static', keyboard: false}, 'show').focus();
       $j('#upload-excel').html(response);
     },
     error: function(err){

From 430dcdaab4ea24b2b91135b69526cedf32086e76 Mon Sep 17 00:00:00 2001
From: Kevin De Pelseneer <kevin.depelseneer@psb.ugent.be>
Date: Tue, 19 Sep 2023 18:19:35 +0200
Subject: [PATCH 54/54] Make modal form stay untill Ajax call is finished

---
 .../sample_upload_content.html.erb            | 23 +++++++++++++------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/app/views/single_pages/sample_upload_content.html.erb b/app/views/single_pages/sample_upload_content.html.erb
index 474a9b0dbc..28728d8dd6 100644
--- a/app/views/single_pages/sample_upload_content.html.erb
+++ b/app/views/single_pages/sample_upload_content.html.erb
@@ -50,6 +50,7 @@
 
   <%= submit_tag "Upload", data: {disable_with: 'Uploading ...'}, :class => 'btn btn-primary', onclick: "submitUpload()" if (@can_upload and any_samples_to_upload?)%>
   <%= submit_tag "Cancel", data: {id: 'cancelModalUploadExcel'}, :class => 'btn btn-secondary', onclick: "closeModalForm()" %>
+  <%= image_tag('ajax-loader.gif', id: 'sample-upload-spinner', style: 'display: none') %>
 </div>
 
 <script type="text/javascript">
@@ -74,12 +75,20 @@
     const updatedSamples= { data: getUpdateSamples() };
 
     if (newSamples.data === "abort") return;
-
-    uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
-    uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
-
-    closeModalForm();
-    location.reload();
+    makeSampleUploadAjaxCalls(newSamples, updatedSamples);
+ }
+
+  async function makeSampleUploadAjaxCalls(newSamples, updatedSamples){
+    $j('#sample-upload-spinner').show();
+    try{
+      const postCall = await uploadAjaxCall("<%= batch_create_samples_path %>", "POST", { data: JSON.stringify(newSamples) });
+      const putCall = await uploadAjaxCall("<%= batch_update_samples_path %>", "PUT", { data: JSON.stringify(updatedSamples) });
+      $j('#sample-upload-spinner').hide();
+      closeModalForm();
+      location.reload();
+    } catch (error){
+      $j('#sample-upload-spinner').hide();
+    }
   }
 
   // Retrieves the samples from the create-samples-table and the duplicate-samples-table
@@ -182,7 +191,7 @@
     const { data, cache, dataType } = params;
     if (!url || !method) throw new Error("Parameter(s) missing");
     return $j.ajax({
-      async: false,
+      async: true,
       method,
       url,
       data,