GraphQL: Add filtering on metadata to Samples and Attachments (#768)

* feat: add in jcont and jcont_key ransackers for jsonb columns, update sample and attachments graphql filters to include metadata_jcont and metadat_jcont_key filter * chore: introduce BaseRansackFilterInputObject which all FilterInputs are based off of * chore: add in tests for new metadata filters * chore: exclude jcont_all, jcont_any, jcont_key_all, jcont_key_any
phac-nml · Sep 19, 2024 · c02efb0 · c02efb0
1 parent b92a2b4
commit c02efb0
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Showing 11 changed files with 184 additions and 14 deletions.
diff --git a/app/graphql/schema.graphql b/app/graphql/schema.graphql
@@ -425,6 +425,16 @@ input AttachmentFilter {
   filename_start_all: [String!]
   filename_start_any: [String!]
   filename_true: String
+
+  """
+  Filter attachments by metadata which contains the supplied key value pairs
+  """
+  metadata_jcont: JSON
+
+  """
+  Filter attachments by metadata which contains the key
+  """
+  metadata_jcont_key: String
   puid_blank: String
   puid_cont: String
   puid_cont_all: [String!]
@@ -2275,6 +2285,16 @@ input SampleFilter {
   created_at_start_all: [String!]
   created_at_start_any: [String!]
   created_at_true: String
+
+  """
+  Filter samples by metadata which contains the supplied key value pairs
+  """
+  metadata_jcont: JSON
+
+  """
+  Filter samples by metadata which contains the key
+  """
+  metadata_jcont_key: String
   name_blank: String
   name_cont: String
   name_cont_all: [String!]

diff --git a/app/graphql/types/attachment_filter_input_type.rb b/app/graphql/types/attachment_filter_input_type.rb
@@ -2,16 +2,26 @@
 
 module Types
   # Attachment Filter Input Type
-  class AttachmentFilterInputType < BaseInputObject # rubocop:disable GraphQL/ObjectDescription
+  class AttachmentFilterInputType < BaseRansackFilterInputObject # rubocop:disable GraphQL/ObjectDescription
     graphql_name 'AttachmentFilter'
-    Attachment.ransackable_attributes.each do |attr|
-      Ransack.predicates.keys.map do |key|
+    Attachment.ransackable_attributes.excluding(DEFAULT_EXCLUDED_ATTRIBUTES).each do |attr|
+      default_predicate_keys.map do |key|
         value_type = Ransack.predicates[key].wants_array ? [String] : String
         argument :"#{attr}_#{key}".to_sym,
                  value_type,
                  required: false,
                  camelize: false
       end
     end
+
+    argument :metadata_jcont, GraphQL::Types::JSON,
+             required: false, camelize: false,
+             prepare: lambda { |json, _ctx|
+               JSON.generate(json)
+             },
+             description: 'Filter attachments by metadata which contains the supplied key value pairs'
+    argument :metadata_jcont_key, String,
+             required: false, camelize: false,
+             description: 'Filter attachments by metadata which contains the key'
   end
 end
diff --git a/app/graphql/types/base_ransack_filter_input_object.rb b/app/graphql/types/base_ransack_filter_input_object.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Types
+  # Bsse Ransack Filter Input Object
+  class BaseRansackFilterInputObject < BaseInputObject
+    DEFAULT_EXCLUDED_ATTRIBUTES = %w[id metadata deleted_at].freeze
+    JSONB_PREDICATE_KEYS = %w[jcont jcont_all jcont_any jcont_key jcont_key_all jcont_key_any].freeze
+
+    def self.default_predicate_keys
+      Ransack.predicates.keys.excluding(JSONB_PREDICATE_KEYS)
+    end
+  end
+end
diff --git a/app/graphql/types/group_filter_type.rb b/app/graphql/types/group_filter_type.rb
@@ -2,9 +2,9 @@
 
 module Types
   # Group Filter Type
-  class GroupFilterType < BaseInputObject # rubocop:disable GraphQL/ObjectDescription
-    Group.ransackable_attributes.excluding(%w[id deleted_at]).each do |attr|
-      Ransack.predicates.keys.map do |key|
+  class GroupFilterType < BaseRansackFilterInputObject # rubocop:disable GraphQL/ObjectDescription
+    Group.ransackable_attributes.excluding(DEFAULT_EXCLUDED_ATTRIBUTES).each do |attr|
+      default_predicate_keys.map do |key|
         value_type = Ransack.predicates[key].wants_array ? [String] : String
         argument :"#{attr}_#{key}".to_sym,
                  value_type,

diff --git a/app/graphql/types/project_filter_type.rb b/app/graphql/types/project_filter_type.rb
@@ -2,9 +2,9 @@
 
 module Types
   # Project Filter Type
-  class ProjectFilterType < BaseInputObject # rubocop:disable GraphQL/ObjectDescription
-    Project.ransackable_attributes.excluding('id').each do |attr|
-      Ransack.predicates.keys.map do |key|
+  class ProjectFilterType < BaseRansackFilterInputObject # rubocop:disable GraphQL/ObjectDescription
+    Project.ransackable_attributes.excluding(DEFAULT_EXCLUDED_ATTRIBUTES).each do |attr|
+      default_predicate_keys.map do |key|
         value_type = Ransack.predicates[key].wants_array ? [String] : String
         argument :"#{attr}_#{key}".to_sym,
                  value_type,

diff --git a/app/graphql/types/sample_filter_type.rb b/app/graphql/types/sample_filter_type.rb
@@ -2,15 +2,25 @@
 
 module Types
   # Sample Filter Type
-  class SampleFilterType < BaseInputObject # rubocop:disable GraphQL/ObjectDescription
-    Sample.ransackable_attributes.excluding('id').each do |attr|
-      Ransack.predicates.keys.map do |key|
+  class SampleFilterType < BaseRansackFilterInputObject # rubocop:disable GraphQL/ObjectDescription
+    Sample.ransackable_attributes.excluding(DEFAULT_EXCLUDED_ATTRIBUTES).each do |attr|
+      default_predicate_keys.map do |key|
         value_type = Ransack.predicates[key].wants_array ? [String] : String
         argument :"#{attr}_#{key}".to_sym,
                  value_type,
                  required: false,
                  camelize: false
       end
     end
+
+    argument :metadata_jcont, GraphQL::Types::JSON,
+             required: false, camelize: false,
+             prepare: lambda { |json, _ctx|
+               JSON.generate(json)
+             },
+             description: 'Filter samples by metadata which contains the supplied key value pairs'
+    argument :metadata_jcont_key, String,
+             required: false, camelize: false,
+             description: 'Filter samples by metadata which contains the key'
   end
 end
diff --git a/app/models/attachment.rb b/app/models/attachment.rb
@@ -43,7 +43,7 @@ def self.model_prefix
   end
 
   def self.ransackable_attributes(_auth_object = nil)
-    %w[puid created_at updated_at] + _ransack_aliases.keys
+    %w[puid metadata created_at updated_at] + _ransack_aliases.keys
   end
 
   def self.ransackable_associations(_auth_object = nil)

diff --git a/app/models/sample.rb b/app/models/sample.rb
@@ -32,7 +32,7 @@ def self.model_prefix
   end
 
   def self.ransackable_attributes(_auth_object = nil)
-    %w[id puid name created_at updated_at attachments_updated_at]
+    %w[id puid name metadata created_at updated_at attachments_updated_at]
   end
 
   def self.ransackable_associations(_auth_object = nil)

diff --git a/config/initializers/ransack.rb b/config/initializers/ransack.rb
@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Arel
+  module Predications # rubocop:disable Style/Documentation
+    def contains_key(other)
+      Arel::Nodes::InfixOperation.new(:'?', self, Arel::Nodes::Quoted.new(other))
+    end
+  end
+end
+
+Ransack.configure do |config|
+  config.add_predicate 'jcont', arel_predicate: 'contains', formatter: proc { |v| JSON.parse(v.to_s) }
+  config.add_predicate 'jcont_key', arel_predicate: 'contains_key'
+end
diff --git a/test/graphql/attachments_query_test.rb b/test/graphql/attachments_query_test.rb
@@ -357,4 +357,71 @@ def setup
     assert_equal attachment1['id'], "gid://irida/Attachment/#{metadata2['associated_attachment_id']}"
     assert_equal attachment2['id'], "gid://irida/Attachment/#{metadata1['associated_attachment_id']}"
   end
+
+  test 'attachment query should work with metadata_jcont filter' do
+    result = IridaSchema.execute(
+      ATTACHMENTS_QUERY,
+      context: { current_user: @user_paired },
+      variables: { attachmentFilter: { metadata_jcont: { type: 'pe' } }, puid: @sample_paired.puid }
+    )
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['sample']['attachments']['nodes']
+
+    assert_equal 6, data.count
+
+    attachment1 = data[0]
+    attachment2 = data[1]
+    metadata1 = attachment1['metadata']
+    metadata2 = attachment2['metadata']
+
+    assert_equal 'forward', metadata1['direction']
+    assert_equal 'reverse', metadata2['direction']
+
+    assert_equal 'pe', metadata1['type']
+    assert_equal 'pe', metadata2['type']
+
+    # check they reference each other
+    assert_equal attachment1['id'], "gid://irida/Attachment/#{metadata2['associated_attachment_id']}"
+    assert_equal attachment2['id'], "gid://irida/Attachment/#{metadata1['associated_attachment_id']}"
+  end
+
+  test 'attachment query should work with metadata_jcont filter to select only forward files' do
+    result = IridaSchema.execute(
+      ATTACHMENTS_QUERY,
+      context: { current_user: @user_paired },
+      variables: { attachmentFilter: { metadata_jcont: { type: 'pe', direction: 'forward' } },
+                   puid: @sample_paired.puid }
+    )
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['sample']['attachments']['nodes']
+    assert_equal 3, data.count
+
+    attachment1 = data[0]
+    metadata1 = attachment1['metadata']
+
+    assert_equal 'forward', metadata1['direction']
+
+    assert_equal 'pe', metadata1['type']
+  end
+
+  test 'attachment query should work with metadata_jcont_key filter' do
+    result = IridaSchema.execute(
+      ATTACHMENTS_QUERY,
+      context: { current_user: @user_paired },
+      variables: { attachmentFilter: { metadata_jcont_key: 'thisone' },
+                   puid: @sample_paired.puid }
+    )
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    attachments = result['data']['sample']['attachments']['nodes']
+
+    puts attachments
+
+    assert_equal 0, attachments.count
+  end
 end
diff --git a/test/graphql/samples_query_ransack_test.rb b/test/graphql/samples_query_ransack_test.rb
@@ -179,4 +179,40 @@ def setup
       assert_nil data
     end
   end
+
+  test 'ransack samples query with metadata_jcont_key filter should work' do
+    result = IridaSchema.execute(SAMPLES_RANSACK_QUERY,
+                                 context: { current_user: @user },
+                                 variables: { filter: { metadata_jcont_key: 'metadatafield1' } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['samples']['nodes']
+
+    assert_equal 4, data.count
+  end
+
+  test 'ransack samples query with metadata_jcont filter should work' do
+    result = IridaSchema.execute(SAMPLES_RANSACK_QUERY,
+                                 context: { current_user: @user },
+                                 variables: { filter: { metadata_jcont: { metadatafield1: 'value1' } } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['samples']['nodes']
+
+    assert_equal 4, data.count
+  end
+
+  test 'ransack samples query with metadata_jcont_key filter should work with non_existent key' do
+    result = IridaSchema.execute(SAMPLES_RANSACK_QUERY,
+                                 context: { current_user: @user },
+                                 variables: { filter: { metadata_jcont_key: 'non_existent' } })
+
+    assert_nil result['errors'], 'should work and have no errors.'
+
+    data = result['data']['samples']['nodes']
+
+    assert_equal 0, data.count
+  end
 end