GraphQL: Samples filtering and ordering (#743)

* feat: add in filtering and ordering to project samples resolver and add ordering to samples resolver

* chore: add in tests for filtering and ordering project samples, and fixed scope_items to preserve ordering

* chore: add tests for samples ordering

* chore: fix rubocop violations

* chore: fix rubocop warnings

* chore: fix rubocop warnings

* chore: fixed last remaining rubocop warning

app/graphql/resolvers/project_samples_resolver.rb

@@ -5,9 +5,21 @@ module Resolvers
   class ProjectSamplesResolver < BaseResolver
     alias project object
 
-    def resolve
-      scope = project
-      scope.samples
+    argument :filter, Types::SampleFilterType,
+             required: false,
+             description: 'Ransack filter',
+             default_value: nil
+
+    argument :order_by, Types::SampleOrderInputType,
+             required: false,
+             description: 'Order by',
+             default_value: nil
+
+    def resolve(filter:, order_by:)
+      ransack_obj = project.samples.ransack(filter&.to_h)
+      ransack_obj.sorts = ["#{order_by.field} #{order_by.direction}"] if order_by.present?
+
+      ransack_obj.result
     end
   end
 end

app/graphql/resolvers/samples_resolver.rb

@@ -15,9 +15,17 @@ class SamplesResolver < BaseResolver
              description: 'Ransack filter',
              default_value: nil
 
-    def resolve(group_id:, filter:)
+    argument :order_by, Types::SampleOrderInputType,
+             required: false,
+             description: 'Order by',
+             default_value: nil
+
+    def resolve(group_id:, filter:, order_by:)
       samples = group_id ? samples_by_group_scope(group_id:) : samples_by_project_scope
-      filter ? samples.ransack(filter.to_h).result : samples
+      ransack_obj = samples.ransack(filter&.to_h)
+      ransack_obj.sorts = ["#{order_by.field} #{order_by.direction}"] if order_by.present?
+
+      ransack_obj.result
     end
 
     def ready?(**_args)

app/graphql/schema.graphql

@@ -923,6 +923,11 @@ type Project implements Node {
     """
     before: String
 
+    """
+    Ransack filter
+    """
+    filter: SampleFilter = null
+
     """
     Returns the first _n_ elements from the list.
     """
@@ -932,6 +937,11 @@ type Project implements Node {
     Returns the last _n_ elements from the list.
     """
     last: Int
+
+    """
+    Order by
+    """
+    orderBy: SampleOrder = null
   ): SampleConnection
 
   """
@@ -1183,6 +1193,11 @@ type Query {
     Returns the last _n_ elements from the list.
     """
     last: Int
+
+    """
+    Order by
+    """
+    orderBy: SampleOrder = null
   ): SampleConnection
 }
 
@@ -1629,6 +1644,22 @@ input SampleFilter {
   updated_at_true: String
 }
 
+"""
+Specify a sort for the samples
+"""
+input SampleOrder {
+  direction: OrderDirection
+  field: SampleOrderField!
+}
+
+"""
+Field to sort the samples by
+"""
+enum SampleOrderField {
+  created_at
+  updated_at
+}
+
 """
 Autogenerated input type of UpdateSampleMetadata
 """

app/graphql/types/project_type.rb

@@ -34,7 +34,8 @@ def self.authorized?(object, context)
     def self.scope_items(items, context)
       scope = authorized_scope Project, type: :relation,
                                         context: { user: context[:current_user], token: context[:token] }
-      scope.where(id: items.select(:id))
+      project_ids = items.pluck(:id)
+      scope.where(id: project_ids).in_order_of(:id, project_ids)
     end
 
     reauthorize_scoped_objects(false)

app/graphql/types/sample_order_input_type.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+module Types
+  class SampleOrderFieldInputType < BaseEnum # rubocop:disable Style/Documentation
+    graphql_name 'SampleOrderField'
+    description 'Field to sort the samples by'
+    value 'created_at'
+    value 'updated_at'
+  end
+
+  class SampleOrderInputType < BaseInputObject # rubocop:disable Style/Documentation
+    graphql_name 'SampleOrder'
+    description 'Specify a sort for the samples'
+
+    argument :direction, OrderDirectionType, required: false # rubocop:disable GraphQL/ArgumentDescription
+    argument :field, SampleOrderFieldInputType, required: true # rubocop:disable GraphQL/ArgumentDescription
+  end
+end

app/graphql/types/sample_type.rb

@@ -40,7 +40,8 @@ def self.authorized?(object, context)
     def self.scope_items(items, context)
       scope = authorized_scope Project, type: :relation,
                                         context: { user: context[:current_user], token: context[:token] }
-      Sample.where(id: items.select(:id), project_id: scope.select(:id))
+      sample_ids = items.pluck(:id)
+      Sample.where(id: sample_ids, project_id: scope.select(:id)).in_order_of(:id, sample_ids)
     end
 
     reauthorize_scoped_objects(false)

test/graphql/project_samples_query_test.rb

@@ -4,12 +4,12 @@
 
 class ProjectSamplesQueryTest < ActiveSupport::TestCase
   PROJECT_QUERY = <<~GRAPHQL
-    query($projectPath: ID!) {
+    query($projectPath: ID!, $sampleFilter: SampleFilter, $sampleOrderBy: SampleOrder) {
       project(fullPath: $projectPath) {
         name
         path
         id
-        samples(first:10) {
+        samples(first:10, filter: $sampleFilter, orderBy: $sampleOrderBy) {
           nodes {
             id
             name
@@ -44,9 +44,9 @@ def setup
 
     # verify fetched sample data matches data on project
     project.samples.each_with_index do |sample, index|
-      assert_equal data['samples']['nodes'][index]['id'], sample.to_global_id.to_s
-      assert_equal data['samples']['nodes'][index]['name'], sample.name
-      assert_equal data['samples']['nodes'][index]['project']['id'], project.to_global_id.to_s
+      assert_equal sample.name, data['samples']['nodes'][index]['name']
+      assert_equal sample.to_global_id.to_s, data['samples']['nodes'][index]['id']
+      assert_equal project.to_global_id.to_s, data['samples']['nodes'][index]['project']['id']
     end
   end
 
@@ -70,9 +70,9 @@ def setup
 
     # verify fetched sample data matches data on project
     project.samples.each_with_index do |sample, index|
-      assert_equal data['samples']['nodes'][index]['id'], sample.to_global_id.to_s
-      assert_equal data['samples']['nodes'][index]['name'], sample.name
-      assert_equal data['samples']['nodes'][index]['project']['id'], project.to_global_id.to_s
+      assert_equal sample.name, data['samples']['nodes'][index]['name']
+      assert_equal sample.to_global_id.to_s, data['samples']['nodes'][index]['id']
+      assert_equal project.to_global_id.to_s, data['samples']['nodes'][index]['project']['id']
     end
   end
 
@@ -92,4 +92,54 @@ def setup
 
     assert_equal I18n.t('action_policy.policy.project.read?', name: project.name), error_message
   end
+
+  test 'project with sample query should work with filter' do
+    project = projects(:project1)
+
+    result = IridaSchema.execute(PROJECT_QUERY, context: { current_user: @user },
+                                                variables: { projectPath: project.full_path,
+                                                             sampleFilter: { name_cont: 'Sample 2' } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['project']
+
+    assert_not_empty data, 'project type should work'
+    assert_equal project.name, data['name']
+
+    assert_equal project.to_global_id.to_s, data['id'], 'id should be GlobalID'
+    assert_equal 2, data['samples']['nodes'].count
+
+    # verify fetched sample data only includes ones with `Sample 2` in the name
+    project.samples.where('name ILIKE \'%Sample 2%\'').each_with_index do |sample, index|
+      assert_equal sample.name, data['samples']['nodes'][index]['name']
+      assert_equal sample.to_global_id.to_s, data['samples']['nodes'][index]['id']
+      assert_equal project.to_global_id.to_s, data['samples']['nodes'][index]['project']['id']
+    end
+  end
+
+  test 'project with sample query should work with order by' do
+    project = projects(:project1)
+
+    result = IridaSchema.execute(PROJECT_QUERY, context: { current_user: @user },
+                                                variables: { projectPath: project.full_path,
+                                                             sampleOrderBy: { field: 'created_at', direction: 'asc' } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['project']
+
+    assert_not_empty data, 'project type should work'
+    assert_equal project.name, data['name']
+
+    assert_equal project.to_global_id.to_s, data['id'], 'id should be GlobalID'
+    assert_equal project.samples.count, data['samples']['nodes'].count
+
+    # verify fetched sample data matches data on project
+    project.samples.order(created_at: :asc).each_with_index do |sample, index|
+      assert_equal sample.name, data['samples']['nodes'][index]['name']
+      assert_equal sample.to_global_id.to_s, data['samples']['nodes'][index]['id']
+      assert_equal project.to_global_id.to_s, data['samples']['nodes'][index]['project']['id']
+    end
+  end
 end

test/graphql/samples_query_ransack_test.rb

@@ -4,8 +4,8 @@
 
 class SamplesQueryRansackTest < ActiveSupport::TestCase
   SAMPLES_RANSACK_QUERY = <<~GRAPHQL
-    query($filter: SampleFilter) {
-      samples(filter: $filter) {
+    query($filter: SampleFilter, $orderBy: SampleOrder) {
+      samples(filter: $filter, orderBy: $orderBy) {
         nodes {
           name
           description
@@ -22,8 +22,8 @@ class SamplesQueryRansackTest < ActiveSupport::TestCase
   GRAPHQL
 
   SAMPLES_RANSACK_WITH_GROUP_QUERY = <<~GRAPHQL
-    query($filter: SampleFilter, $group_id: ID!) {
-      samples(filter: $filter, groupId: $group_id) {
+    query($filter: SampleFilter, $group_id: ID!, $orderBy: SampleOrder) {
+      samples(filter: $filter, groupId: $group_id, orderBy: $orderBy) {
         nodes {
           name
           description
@@ -64,6 +64,20 @@ def setup
     end
   end
 
+  test 'samples query should work with order by' do
+    result = IridaSchema.execute(SAMPLES_RANSACK_QUERY,
+                                 context: { current_user: @user },
+                                 variables: { filter: { name_start: 'Project 1' },
+                                              orderBy: { field: 'created_at', direction: 'asc' } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['samples']['nodes']
+
+    assert_equal samples(:sample2).name, data[0]['name']
+    assert_equal samples(:sample2).puid, data[0]['puid']
+  end
+
   test 'ransack samples query with group id should work' do
     original_date = Time.zone.today
 
@@ -86,6 +100,25 @@ def setup
     end
   end
 
+  test 'ransack samples query with group id should work with order by' do
+    Timecop.travel(5.days.from_now) do
+      @sample.created_at = Time.zone.now
+      @sample.save!
+
+      result = IridaSchema.execute(SAMPLES_RANSACK_WITH_GROUP_QUERY,
+                                   context: { current_user: @user },
+                                   variables:
+                                   { group_id: groups(:group_one).to_global_id.to_s,
+                                     orderBy: { field: 'created_at', direction: 'desc' } })
+
+      assert_nil result['errors'], 'should work and have no errors.'
+
+      data = result['data']['samples']['nodes']
+
+      assert_equal @sample.puid, data[0]['puid']
+    end
+  end
+
   test 'ransack group samples query should throw authorization error' do
     original_date = Time.zone.today