Merge pull request #1043 from griffithlab/test-improvements

Minor test improvements

.github/workflows/build_frontend.yml

@@ -21,7 +21,7 @@ jobs:
         with:
           working-directory: ./server
           bundler-cache: true
-          ruby-version: '3.0'
+          ruby-version: '3.3'
 
       - name: Setup node
         uses: actions/setup-node@v4

.github/workflows/deploy.yml

@@ -37,7 +37,7 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           working-directory: ./server
-          ruby-version: '3.0'
+          ruby-version: '3.3'
           bundler-cache: true
 
       - name: Deploy to production

server/app/graphql/loaders/association_count_loader.rb

@@ -1,6 +1,6 @@
 module Loaders
   class AssociationCountLoader < GraphQL::Batch::Loader
-    def initialize(model, association: association)
+    def initialize(model, association: )
       @model = model
       @association = association
     end

server/app/graphql/resolvers/top_level_therapies.rb

@@ -9,12 +9,11 @@ class Resolvers::TopLevelTherapies < GraphQL::Schema::Resolver
   description 'List and filter Therapies from the NCI Thesaurus.'
 
   scope do
-    Therapy.select('therapies.id, therapies.name, therapies.ncit_id, count(distinct(assertions.id)) as assertion_count, count(distinct(evidence_items.id)) as evidence_count')
-      .left_outer_joins(:assertions)
-      .left_outer_joins(:evidence_items)
+    Therapy.select('therapies.id, therapies.name, max(therapies.ncit_id) as ncit_id, count(distinct(assertions.id)) as assertion_count, count(distinct(evidence_items.id)) as evidence_count')
+      .left_outer_joins(:assertions, :evidence_items)
       .where("evidence_items.status != 'rejected' OR assertions.status != 'rejected'")
       .where(deprecated: false)
-      .group('therapies.id, therapies.name, therapies.ncit_id')
+      .group('therapies.id, therapies.name')
       .having('COUNT(evidence_items.id) > 0 OR COUNT(assertions.id) > 0')
       .order('evidence_count DESC', :id)
   end

server/config/environments/test.rb

@@ -11,10 +11,8 @@
   config.cache_classes = false
   config.action_view.cache_template_loading = true
 
-  # Do not eager load code on boot. This avoids loading your whole application
-  # just for the purpose of running a single test. If you are using a tool that
-  # preloads Rails for running tests, you may have to set it to true.
-  config.eager_load = false
+  # Eager load when running in CI to detect any load issues
+  config.eager_load = ENV["CI"].present?
 
   # Configure public file server for tests with Cache-Control for performance.
   config.public_file_server.enabled = true
@@ -27,8 +25,7 @@
   config.action_controller.perform_caching = false
   config.cache_store = :null_store
 
-  # Raise exceptions instead of rendering exception templates.
-  config.action_dispatch.show_exceptions = false
+  config.action_dispatch.show_exceptions = true
 
   # Disable request forgery protection in test environment.
   config.action_controller.allow_forgery_protection = false
@@ -49,6 +46,8 @@
   # Raise exceptions for disallowed deprecations.
   config.active_support.disallowed_deprecation = :raise
 
+  config.active_job.queue_adapter = :test
+
   # Tell Active Support which deprecation messages to disallow.
   config.active_support.disallowed_deprecation_warnings = []
 

server/test/controllers/links_controller_test.rb

@@ -0,0 +1,48 @@
+require "test_helper"
+
+class LinksControllerTest < ActionDispatch::IntegrationTest
+  test "it should 404 rather than redirect when the entity isn't found" do
+    get "/links/features/999999"
+    assert_response :not_found
+  end
+
+  test 'it should 400 bad request when its an invalid link type' do
+    get '/links/footures/9999'
+    assert_response :bad_request
+  end
+
+  test 'gene, feature, factor permalinks work' do
+    feature = features.first
+    feature_path = "/features/#{feature.id}"
+    check_redirect "/links/features/#{feature.id}", feature_path
+    check_redirect "/links/id/FID#{feature.id}", feature_path
+
+    gene = feature_genes.first
+    gene_path = "/features/#{gene.feature.id}"
+    check_redirect "/links/genes/#{gene.id}", gene_path
+    check_redirect "/links/id/GID#{gene.id}", gene_path
+    check_redirect "/links/entrez_id/#{gene.entrez_id}", gene_path
+    check_redirect "/links/entrez_name/#{gene.name}", gene_path
+  end
+
+  test 'variant links work' do
+    variant = variants(:v600e)
+    variant_path = "/variants/#{variant.id}"
+
+    check_redirect "/links/id/VID#{variant.id}", variant_path
+    check_redirect "/links/allele_registry/#{variant.allele_registry_id}", variant_path
+    check_redirect "/links/variants/#{variant.id}", variant_path
+  end
+
+  test 'redirect legacy frontend gene route to corresponding feature' do
+    gene = feature_genes.first
+    check_redirect "/genes/#{gene.id}", "/features/#{gene.feature.id}"
+  end
+
+  def check_redirect(input_path, output_path)
+    get input_path
+    assert_response :redirect
+    redirect_url = URI.parse(@response['Location']).path
+    assert_equal output_path, redirect_url
+  end
+end

server/test/fixtures/feature_factors.yml

@@ -0,0 +1,3 @@
+msi:
+  ncit_id: NCIT123
+

server/test/fixtures/features.yml

@@ -1,8 +1,15 @@
 braf:
   name: BRAF
+  full_name: B-Raf proto-oncogene, serine/threonine kinase
   feature_instance: braf (Features::Gene)
 
 vhl:
   name: VHL
+  full_name: von Hippel-Lindau tumor suppressor
   feature_instance: vhl (Features::Gene)
 
+msi:
+  name: MSI
+  full_name: Microsatellite Instability
+  description: The description for the MSI factor
+  feature_instance: msi (Features::Factor)

server/test/fixtures/variants.yml

@@ -4,6 +4,7 @@ v600e:
   gene_id: 1
   type: 'Variants::GeneVariant'
   single_variant_molecular_profile: mp1
+  allele_registry_id: CAFOO
 
 v600k:
   name: V600K

server/test/graphql/mutations/create_molecular_profile_test.rb

@@ -106,6 +106,6 @@ def setup
     mp_id = response["data"]["createMolecularProfile"]["molecularProfile"]['id']
     mp = MolecularProfile.find(mp_id)
     assert_equal(mp.display_name, "NOT BRAF V600K AND BRAF V600E AND ( VHL W88* OR VHL V87E (c.260T>A) )")
-    assert_equal(mp.variants, [@variant, v2, v3, v4])
+    assert_equal(mp.variants.to_a, [@variant, v2, v3, v4])
   end
 end

server/test/test_helper.rb

@@ -7,6 +7,7 @@ class ActiveSupport::TestCase
   fixtures :all
 
   set_fixture_class feature_genes: Features::Gene
+  set_fixture_class feature_factors: Features::Factor
 
   # Add more helper methods to be used by all tests here...
 end