File import controller enhancements (#714)

* starting to create the group metadata file import controller

* adding translations

* trying to move action into the new file import concern

app/controllers/concerns/file_import_actions.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+# Common file import actions
+module FileImportActions
+  extend ActiveSupport::Concern
+
+  included do
+    before_action proc { namespace }
+  end
+
+  def create
+    authorize! @namespace, to: :update_sample_metadata?
+    @imported_metadata = ::Samples::Metadata::FileImportService.new(@namespace, current_user,
+                                                                    file_import_params).execute
+    if @namespace.errors.empty?
+      render status: :ok, locals: { type: :success, message: t('.success') }
+    elsif @namespace.errors.include?(:sample)
+      errors = @namespace.errors.messages_for(:sample)
+      render status: :partial_content, locals: { type: :alert, message: t('.error'), errors: }
+    else
+      error = @namespace.errors.full_messages_for(:base).first
+      render status: :unprocessable_entity, locals: { type: :danger, message: error }
+    end
+  end
+
+  private
+
+  def file_import_params
+    params.require(:file_import).permit(:file, :sample_id_column, :ignore_empty_values)
+  end
+end

app/controllers/groups/samples/metadata/file_imports_controller.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+module Groups
+  module Samples
+    module Metadata
+      # Controller actions for Group Samples Metadata File Import Controller
+      class FileImportsController < Groups::ApplicationController
+        include FileImportActions
+
+        respond_to :turbo_stream
+
+        private
+
+        def namespace
+          @namespace = group
+        end
+
+        def group
+          @group = Group.find_by_full_path(params[:group_id]) # rubocop:disable Rails/DynamicFindBy
+        end
+      end
+    end
+  end
+end

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

@@ -5,28 +5,14 @@ module Samples
     module Metadata
       # Controller actions for Project Samples Metadata File Import Controller
       class FileImportsController < Projects::ApplicationController
-        respond_to :turbo_stream
+        include FileImportActions
 
-        def create # rubocop:disable Metrics/AbcSize
-          @namespace = @project.namespace
-          authorize! @namespace, to: :update_sample_metadata?
-          @imported_metadata = ::Samples::Metadata::FileImportService.new(@namespace, current_user,
-                                                                          file_import_params).execute
-          if @namespace.errors.empty?
-            render status: :ok, locals: { type: :success, message: t('.success') }
-          elsif @namespace.errors.include?(:sample)
-            errors = @namespace.errors.messages_for(:sample)
-            render status: :partial_content, locals: { type: :alert, message: t('.error'), errors: }
-          else
-            error = @namespace.errors.full_messages_for(:base).first
-            render status: :unprocessable_entity, locals: { type: :danger, message: error }
-          end
-        end
+        respond_to :turbo_stream
 
         private
 
-        def file_import_params
-          params.require(:file_import).permit(:file, :sample_id_column, :ignore_empty_values)
+        def namespace
+          @namespace = @project.namespace
         end
       end
     end

config/locales/en.yml

@@ -799,6 +799,11 @@ en:
           selected: Selected
         no_samples: No Samples
         no_associated_samples: There are no samples associated with this group.
+      metadata:
+        file_imports:
+          create:
+            success: Sample metadata was successfully imported.
+            error: "Metadata was not successfully imported for the following samples:"
   models:
     sample:
       analysis: Analysis

config/locales/fr.yml

@@ -799,6 +799,11 @@ fr:
           selected: Selected
         no_samples: No Samples
         no_associated_samples: There are no samples associated with this group.
+      metadata:
+        file_imports:
+          create:
+            success: Sample metadata was successfully imported.
+            error: "Metadata was not successfully imported for the following samples:"
   models:
     sample:
       analysis: Analysis

config/routes/group.rb

@@ -27,6 +27,11 @@
 
     resources :group_links, only: %i[create destroy update index new]
     resources :samples, only: %i[index] do
+      scope module: :samples, as: :samples do
+        collection do
+          resource :file_import, module: :metadata, only: %i[create new]
+        end
+      end
       collection do
         get :select
         post :search

test/controllers/groups/samples/metadata/file_import_controller_test.rb

@@ -0,0 +1,113 @@
+# frozen_string_literal: true
+
+require 'test_helper'
+
+module Groups
+  module Samples
+    module Metadata
+      class FileImportControllerTest < ActionDispatch::IntegrationTest
+        setup do
+          sign_in users(:john_doe)
+          @group = groups(:group_one)
+          @csv = fixture_file_upload('test/fixtures/files/metadata/valid.csv')
+        end
+
+        test 'import sample metadata with permission' do
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: {
+                   file: @csv,
+                   sample_id_column: 'sample_name'
+                 }
+               }
+
+          assert_response :success
+        end
+
+        test 'import sample metadata without permission' do
+          login_as users(:micha_doe)
+
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: {
+                   file: @csv,
+                   sample_id_column: 'sample_name'
+                 }
+               }
+
+          assert_response :unauthorized
+        end
+
+        test 'import sample metadata with no file' do
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: { sample_id_column: 'sample_name' }
+               }
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with no sample_id_column' do
+          csv = File.new('test/fixtures/files/metadata/missing_sample_id_column.csv', 'r')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: { file: csv, sample_id_column: 'sample_name' }
+               }
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with duplicate column names' do
+          csv = File.new('test/fixtures/files/metadata/duplicate_headers.csv', 'r')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: { file: csv, sample_id_column: 'sample_name' }
+               }
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with no metadata columns' do
+          csv = File.new('test/fixtures/files/metadata/missing_metadata_columns.csv', 'r')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: { file: csv, sample_id_column: 'sample_name' }
+               }
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with no metadata rows' do
+          csv = File.new('test/fixtures/files/metadata/missing_metadata_rows.csv', 'r')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: { file: csv, sample_id_column: 'sample_name' }
+               }
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with invalid file' do
+          other = fixture_file_upload('test/fixtures/files/metadata/invalid.txt')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: {
+                   file: other,
+                   sample_id_column: 'sample_name'
+                 }
+               }
+
+          assert_response :unprocessable_entity
+        end
+
+        test 'import sample metadata with a sample that does not belong to group' do
+          csv = fixture_file_upload('test/fixtures/files/metadata/mixed_project_samples.csv')
+          post group_samples_file_import_path(@group, format: :turbo_stream),
+               params: {
+                 file_import: {
+                   file: csv,
+                   sample_id_column: 'sample_name'
+                 }
+               }
+
+          assert_response :partial_content
+        end
+      end
+    end
+  end
+end