Batch tutorial tests

test/models/tutorial_test.rb

@@ -1,7 +1,80 @@
 require 'test_helper'
 
 class TutorialTest < ActiveSupport::TestCase
-  # test "the truth" do
-  #   assert true
-  # end
+  test 'batch parses a name from a spreadsheet' do
+    tutorial = upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+
+    assert_equal 1, tutorial.step
+    assert_empty tutorial.value(:genomes)
+    assert_equal 1, tutorial.value(:names).size
+    assert_equal 'Nanoclepta', tutorial.value(:names).first['name']
+    assert_equal 'Nanobdellaceae', tutorial.value(:names).first['parent']
+  end
+
+  test 'batch parses an incertae sedis name from a spreadsheet' do
+    tutorial = upload_batch_spreadsheet(
+      'SCR_UploadBatch-Luteria-Incertae_sedis.xlsx'
+    )
+
+    assert_equal 1, tutorial.step
+    assert_empty tutorial.value(:genomes)
+    assert_equal 1, tutorial.value(:names).size
+    assert_equal 'Luteria', tutorial.value(:names).first['name']
+    assert_equal(
+      'incertae sedis (Bacteria)', tutorial.value(:names).first['parent']
+    )
+  end
+
+  test 'batch creates a parent placement' do
+    parent = Name.create!(
+      name: 'Nanobdellaceae', rank: 'family', status: 15
+    )
+    placement = create_batch_placement(
+      name: 'Nanoclepta', rank: 'genus',
+      description: 'A genus of ectosymbiotic archaea.', parent: parent.name
+    )
+
+    assert_equal parent, placement.parent
+    assert_nil placement.incertae_sedis
+  end
+
+  test 'batch creates an incertae sedis placement' do
+    explanation = 'The genus cannot currently be assigned to a family.'
+    placement = create_batch_placement(
+      name: 'Luteria', rank: 'genus', description: explanation,
+      parent: 'incertae sedis (Bacteria)'
+    )
+
+    assert_nil placement.parent
+    assert_equal 'incertae sedis (Bacteria)', placement.incertae_sedis
+    assert_equal explanation, placement.incertae_sedis_text.to_plain_text
+  end
+
+  private
+
+  def create_batch_placement(name:, **attributes)
+    tutorial = Tutorial.create!(
+      pipeline: 'batch', user: users(:contributor), step: 1,
+      data: {
+        names: [attributes.merge(name: name)], genomes: []
+      }.to_json
+    )
+
+    assert tutorial.batch_step_01({}, users(:contributor))
+
+    placement = Name.find_by!(name: name).placement
+    assert_not_nil placement
+    assert_predicate placement, :preferred?
+    placement
+  end
+
+  def upload_batch_spreadsheet(filename)
+    tutorial = Tutorial.create!(
+      pipeline: 'batch', user: users(:contributor), step: 0, ongoing: true
+    )
+    File.open(Rails.root.join('test/fixtures/files', filename)) do |file|
+      assert tutorial.batch_step_00({ file: file }, users(:contributor))
+    end
+    tutorial
+  end
 end

test/system/tutorials_test.rb

@@ -1,8 +1,104 @@
+# frozen_string_literal: true
+
 require 'application_system_test_case'
 
 class TutorialsTest < ApplicationSystemTestCase
+  include Warden::Test::Helpers
+
   setup do
-    @tutorial = tutorials(:one)
+    @user = users(:contributor)
+    @tutorial = Tutorial.create!(
+      pipeline: 'batch', user: @user, step: 0, ongoing: true
+    )
+
+    login_as(@user, scope: :user)
+  end
+
+  teardown { Warden.test_reset! }
+
+  test 'batch uploading a single genus' do
+    family = Name.create!(name: 'Nanobdellaceae', rank: 'family', status: 15)
+    type_species = Name.create!(
+      name: 'Nanoclepta minutus', rank: 'species', status: 15
+    )
+    visit tutorial_url(@tutorial)
+
+    assert_text 'Step 0: Upload spreadsheet'
+
+    upload_batch_spreadsheet('SCR_UploadBatch-Nanoclepta.xlsx')
+    assert_batch_review(name: 'Nanoclepta', parent: 'Nanobdellaceae')
+    create_batch_entries
+
+    genus = Name.find_by!(name: 'Nanoclepta')
+    @tutorial.reload
+
+    assert_equal 'genus', genus.rank
+    assert_equal family, genus.parent
+    assert_equal type_species, genus.nomenclatural_type
+    assert_equal @tutorial, genus.tutorial
+    assert_equal ['Nanoclepta'], @tutorial.names.pluck(:name)
+
+    complete_batch_tutorial
   end
 
+  test 'batch uploading a single incertae sedis genus' do
+    type_species = Name.create!(
+      name: 'Luteria ianthellae', rank: 'species', status: 15
+    )
+    visit tutorial_url(@tutorial)
+
+    upload_batch_spreadsheet('SCR_UploadBatch-Luteria-Incertae_sedis.xlsx')
+    assert_batch_review(name: 'Luteria', parent: 'unknown')
+    create_batch_entries
+
+    genus = Name.find_by!(name: 'Luteria')
+    @tutorial.reload
+
+    assert_equal 'genus', genus.rank
+    assert_nil genus.parent
+    assert_equal 'incertae sedis (Bacteria)', genus.incertae_sedis
+    assert_equal type_species, genus.nomenclatural_type
+    assert_equal @tutorial, genus.tutorial
+    assert_equal ['Luteria'], @tutorial.names.pluck(:name)
+
+    complete_batch_tutorial
+  end
+
+  private
+
+  def complete_batch_tutorial
+    click_button 'Continue'
+
+    assert_current_path new_register_path(tutorial: @tutorial)
+    assert_not @tutorial.reload.ongoing?
+  end
+
+  def upload_batch_spreadsheet(filename)
+    attach_file(
+      'Batch spreadsheet',
+      Rails.root.join('test/fixtures/files', filename)
+    )
+    click_button 'Continue'
+  end
+
+  def assert_batch_review(name:, parent:)
+    assert_text 'Step 1: Review parsed data'
+    within '#batch-names-0-h' do
+      assert_text name
+      assert_text 'genus of'
+      assert_text parent
+    end
+    assert_no_selector '#batch-names-1-h'
+
+    assert_no_selector '#batch-genomes-0-h'
+  end
+
+  def create_batch_entries
+    assert_difference('Name.count', 1) do
+      assert_no_difference('Genome.count') do
+        click_button 'Continue'
+        assert_text 'Step 2: Validation list'
+      end
+    end
+  end
 end