Enhancement: Edit line list metadata in place

app/components/samples/editable_cell.rb

@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+
+module Samples
+  # Component for rendering an editable cell
+  class EditableCell < Component
+    with_collection_parameter :field
+
+    erb_template <<~ERB
+      <td id="<%= dom_id(@sample, @field) %>">
+        <%= form_with(url: editable_namespace_project_sample_metadata_field_path(@sample.project.namespace.parent, @sample.project, @sample), method: :get) do |form| %>
+          <%= form.hidden_field :field, value: @field %>
+          <%= form.hidden_field :format, value: "turbo_stream" %>
+          <%= form.submit @sample.metadata[@field], class: "cursor-pointer p-4 hover:bg-slate-50 dark:hover:bg-slate-600 w-full text-left" %>
+        <% end %>
+      </td>
+    ERB
+
+    def initialize(field:, sample:)
+      @sample = sample
+      @field = field
+    end
+  end
+end

app/components/samples/table_component.html.erb

@@ -132,14 +132,7 @@
                   <% end %>
                 <% end %>
               <% end %>
-              <% @metadata_fields.each do |field| %>
-                <%= render_cell(
-                tag: 'td',
-                classes: class_names('px-3 py-3')
-              ) do %>
-                  <%= sample.metadata[field] %>
-                <% end %>
-              <% end %>
+              <%= render Samples::EditableCell.with_collection(@metadata_fields, sample: sample) %>
               <% if @renders_row_actions %>
                 <%= render_cell(
                 tag: 'td',
@@ -199,7 +192,7 @@
                   >0</strong>
                 </span>
               </td>
-              <td colspan="100%" class="px-3 py-3 bg-slate-50 dark:bg-slate-700"></td>
+              <td colspan="100%" class="p-3 bg-slate-50 dark:bg-slate-700"></td>
             </tr>
           </tfoot>
         <% end %>

app/controllers/projects/samples/metadata/fields_controller.rb

@@ -4,7 +4,7 @@
   module Samples
     module Metadata
       # Controller actions for Project Samples Metadata Fields Controller
       class FieldsController < Projects::Samples::ApplicationController
         respond_to :turbo_stream
 
         # Param received as:
@@ -42,6 +42,36 @@
           end
         end
 
+        def editable
+          authorize! @project, to: :update_sample?
+          @field = params[:field]
+          @value = @sample.metadata[@field]
+          if @sample.can_update_field?(params[:field])
+            render status: :partial_content, turbo_stream: turbo_stream.replace(
+              helpers.dom_id(@sample, @field),
+              partial: 'shared/samples/metadata/fields/editing_field_cell',
+              locals: { sample: @sample, field: @field, value: @value }
+            )
+          else
+            render status: :unprocessable_entity, turbo_stream: turbo_stream.append('flashes', partial: 'shared/flash',
+                                                                                               locals: { type: 'error', message: 'This field is not editable' })
+          end
+        end
+
+        def update_value
+          authorize! @project, to: :update_sample?
+
+          @field = params[:field]
+          value = params[:value]
+          original_value = params[:original_value]
+
+          if value == original_value
+            render_unchanged_field
+          else
+            update_field_value(original_value, value)
+          end
+        end
+
         private
 
         def create_field_params
@@ -99,6 +129,55 @@
           end
           update_render_params
         end
+
+        def render_unchanged_field
+          render turbo_stream: turbo_stream.replace(
+            helpers.dom_id(@sample, @field),
+            partial: 'shared/samples/metadata/fields/editable_field_cell',
+            locals: { sample: @sample, field: @field }
+          )
+        end
+
+        def update_field_value(original_value, new_value)
+          perform_field_update(original_value, new_value)
+
+          if @sample.errors.any?
+            render_update_error
+          else
+            render_update_success
+          end
+        end
+
+        def perform_field_update(original_value, new_value)
+          ::Samples::Metadata::Fields::UpdateService.new(
+            @project,
+            @sample,
+            current_user,
+            build_update_params(original_value, new_value)
+          ).execute
+        end
+
+        def build_update_params(original_value, new_value)
+          {
+            'update_field' => {
+              'key' => { @field => @field },
+              'value' => { original_value => new_value }
+            }
+          }
+        end
+
+        def render_update_error
+          render status: :unprocessable_entity,
+                 locals: { type: 'error', message: @sample.errors.full_messages.first }
+        end
+
+        def render_update_success
+          render turbo_stream: turbo_stream.replace(
+            helpers.dom_id(@sample, @field),
+            partial: 'shared/samples/metadata/fields/editable_field_cell',
+            locals: { sample: @sample, field: @field }
+          )
+        end
       end
     end
   end

app/javascript/controllers/inline_edit_controller.js

@@ -0,0 +1,28 @@
+import { Controller } from "@hotwired/stimulus";
+
+export default class extends Controller {
+  static targets = ["input"];
+  static values = {
+    original: String,
+  };
+
+  connect() {
+    this.inputTarget.focus();
+    this.inputTarget.select();
+  }
+
+  submit() {
+    if (!this.submitted) {
+      this.element.requestSubmit();
+    }
+  }
+
+  cancel(event) {
+    if (event.key === "Escape") {
+      this.inputTarget.value = this.originalValue;
+      this.inputTarget.blur();
+    } else if (event.key === "Enter") {
+      this.submitted = true;
+    }
+  }
+}

app/models/sample.rb

@@ -98,6 +98,10 @@ def search_data
     }
   end
 
+  def can_update_field?(field)
+    metadata_provenance.key?(field) && metadata_provenance[field]['source'] == 'user'
+  end
+
   def should_index?
     !deleted?
   end

app/views/shared/_flash.html.erb

@@ -0,0 +1,3 @@
+<%= turbo_stream.prepend 'flashes' do %>
+  <%= viral_flash(type: type, data: message) %>
+<% end %>

app/views/shared/samples/metadata/fields/_editable_field_cell.html.erb

@@ -0,0 +1 @@
+<%= render Samples::EditableCell.new(field: @field, sample: @sample) %>

app/views/shared/samples/metadata/fields/_editing_field_cell.html.erb

@@ -0,0 +1,16 @@
+<td id="<%= dom_id(@sample, @field) %>">
+  <%= form_with(url: update_value_namespace_project_sample_metadata_field_path(sample_id: @sample.id), method: :patch,
+  data: { controller: "inline-edit", "inline-edit-original-value": @value  }) do |f| %>
+    <%= f.hidden_field :field, value: @field %>
+    <%= f.hidden_field :original_value, value: @value %>
+    <%= f.hidden_field :format, value: "turbo_stream" %>
+    <%= f.text_field :value,
+                 value: @value,
+                 class:
+                   "w-full m-0 border-slate-300 text-slate-900 text-sm focus:ring-primary-500 focus:border-primary-500 block w-full p-2.5 dark:bg-slate-700 dark:border-slate-600 dark:text-white dark:focus:ring-primary-500 dark:focus:border-primary-500",
+                 data: {
+                   "inline-edit-target": "input",
+                   action: "blur->inline-edit#submit keydown->inline-edit#cancel",
+                 } %>
+  <% end %>
+</td>

config/routes/project.rb

@@ -74,7 +74,10 @@
         resource :metadata, module: :samples, only: %i[new edit destroy] do
           scope module: :metadata, as: :metadata do
             collection do
-              resource :field, only: %i[update create]
+              resource :field, only: %i[update create] do
+                get :editable
+                patch :update_value
+              end
             end
             collection do
               resource :deletion, only: %i[new destroy]

test/controllers/projects/samples/metadata/fields/fields_controller_test.rb

@@ -156,6 +156,70 @@ class FieldsControllerTest < ActionDispatch::IntegrationTest
                   } }, format: :turbo_stream }
             assert_response :unprocessable_entity
           end
+
+          test 'check to edit a metadata field' do
+            get editable_namespace_project_sample_metadata_field_path(
+              @namespace, @project29, @sample32
+            ), params: {
+              'field' => 'metadatafield1',
+              'format' => :turbo_stream
+            }
+            assert_response :partial_content
+          end
+
+          test 'checking to see if a field can be edited fails if it belongs to an analysis' do
+            sample34 = samples(:sample34)
+            project31 = projects(:project31)
+            namespace = groups(:subgroup_twelve_a_a)
+            get editable_namespace_project_sample_metadata_field_path(
+              namespace, project31, sample34
+            ), params: {
+              'field' => 'metadatafield1',
+              'format' => :turbo_stream
+            }
+            assert_response :unprocessable_entity
+          end
+
+          test 'builds correct update params for updating a value' do
+            controller = FieldsController.new
+            controller.instance_variable_set(:@field, @field)
+
+            expected_params = {
+              'update_field' => {
+                'key' => { @field => @field },
+                'value' => { 'old_value' => 'new_value' }
+              }
+            }
+
+            assert_equal expected_params,
+                         controller.send(:build_update_params, 'old_value', 'new_value')
+          end
+
+          test 'renders unchanged field when value does not change' do
+            patch update_value_namespace_project_sample_metadata_field_path(
+              @namespace, @project29, @sample32
+            ),
+                  params: {
+                    'field' => 'metadatafield1',
+                    'value' => 'old_value',
+                    'original_value' => 'old_value',
+                    'format' => :turbo_stream
+                  }
+            assert_response :ok
+          end
+
+          test 'updates sample metadata with new value' do
+            patch update_value_namespace_project_sample_metadata_field_path(
+              @namespace, @project29, @sample32
+            ),
+                  params: {
+                    'field' => 'metadatafield1',
+                    'value' => 'new_value',
+                    'original_value' => 'old_value',
+                    'format' => :turbo_stream
+                  }
+            assert_response :ok
+          end
         end
       end
     end

test/system/groups/samples_test.rb

@@ -391,16 +391,16 @@ def retrieve_puids
       assert_selector 'table thead tr th', count: 9
       within('table tbody tr:first-child') do
         assert_text @sample30.name
-        assert_selector 'td:nth-child(7)', text: 'value1'
-        assert_selector 'td:nth-child(8)', text: 'value2'
-        assert_selector 'td:nth-child(9)', text: ''
+        assert_selector 'td:nth-child(7) input[value="value1"]'
+        assert_selector 'td:nth-child(8) input[value="value2"]'
+        assert_selector 'td:nth-child(9) input[type="submit"]'
       end
 
       within('table tbody tr:nth-child(3)') do
         assert_text @sample28.name
-        assert_selector 'td:nth-child(7)', text: ''
-        assert_selector 'td:nth-child(8)', text: ''
-        assert_selector 'td:nth-child(9)', text: 'unique_value'
+        assert_selector 'td:nth-child(7) input[type="submit"]'
+        assert_selector 'td:nth-child(8) input[type="submit"]'
+        assert_selector 'td:nth-child(9) input[value="unique_value"]'
       end
 
       find('label', text: I18n.t('projects.samples.shared.metadata_toggle.label')).click
@@ -767,5 +767,28 @@ def retrieve_puids
         click_on I18n.t('shared.samples.metadata.file_imports.errors.ok_button')
       end
     end
+
+    test 'can update metadata value that is not from an analysis' do
+      visit group_samples_url(@group)
+      assert_selector 'table thead tr th', count: 6
+
+      click_on 'Last Updated'
+      assert_selector 'table thead th:nth-child(5) svg.icon-arrow_up'
+
+      assert_selector 'label', text: I18n.t('projects.samples.shared.metadata_toggle.label'), count: 1
+      find('label', text: I18n.t('projects.samples.shared.metadata_toggle.label')).click
+
+      within 'div.overflow-auto.scrollbar' do |div|
+        div.scroll_to div.find('table thead th:nth-child(7)')
+      end
+
+      assert_selector 'table thead tr th', count: 9
+      within('table tbody tr:first-child') do
+        assert_text @sample30.name
+        assert_selector 'td:nth-child(7) input[type="submit"][value="value1"]'
+        click_button 'input[type="submit"][value="value1"]'
+        assert_selector 'input[type="text"][value="value1"]'
+      end
+    end
   end
 end

test/system/projects/samples_test.rb

@@ -827,8 +827,8 @@ class SamplesTest < ApplicationSystemTestCase
       assert_selector '#samples-table table thead tr th', count: 8
       within('#samples-table table tbody tr:first-child') do
         assert_text @sample3.name
-        assert_selector 'td:nth-child(6)', text: 'value1'
-        assert_selector 'td:nth-child(7)', text: 'value2'
+        assert_selector 'td:nth-child(6) button', text: 'value1'
+        assert_selector 'td:nth-child(7) button', text: 'value2'
       end
       find('label', text: I18n.t('projects.samples.shared.metadata_toggle.label')).click
       assert_selector '#samples-table table thead tr th', count: 6
@@ -1548,6 +1548,20 @@ def retrieve_puids
       end
     end
 
+    test 'can inline edit a sample metadata field' do
+      visit namespace_project_samples_url(@namespace, @project)
+
+      assert_selector 'label', text: I18n.t(:'projects.samples.shared.metadata_toggle.label'), count: 1
+      find('label', text: I18n.t('projects.samples.shared.metadata_toggle.label')).click
+
+      assert_selector '#samples-table table thead tr th', count: 8
+      within('#samples-table table tbody tr:first-child') do
+        assert_text @sample3.name
+        assert_selector 'td:nth-child(6) button', text: 'value1'
+        assert_selector 'td:nth-child(7) button', text: 'value2'
+      end
+    end
+
     def long_filter_text
       text = (1..500).map { |n| "sample#{n}" }.join(', ')
       "#{text}, #{@sample1.name}" # Need to comma to force the tag to be created