better method names and rubocop #2134

app/controllers/sample_types_controller.rb

@@ -212,7 +212,7 @@ def build_sample_type_from_fair_ds_ttl
         fds_sample = inv&.studies.first&.observation_units.first&.samples.first
       end
     end
-    if fds_sample && fds_sample.all_additional_metadata_annotations_for_type_details.any?
+    if fds_sample && fds_sample.all_additional_potential_annotation_details.any?
       string_attribute_type = SampleAttributeType.where(title: 'String').first
       @sample_type.sample_attributes.build({
                                              title: 'Title',
@@ -228,7 +228,7 @@ def build_sample_type_from_fair_ds_ttl
                                              pid: RDF::Vocab::SCHEMA.description,
                                              sample_attribute_type: string_attribute_type
                                            })
-      fds_sample.all_additional_metadata_annotations_for_type_details.each do |details|
+      fds_sample.all_additional_potential_annotation_details.each do |details|
         @sample_type.sample_attributes.build({
                                                title: details.label,
                                                description: details.description,

lib/seek/fair_data_station/base.rb

@@ -89,18 +89,18 @@ def additional_metadata_annotation_details
         end
       end
 
-      def all_annotations_for_type
-        @all_annotations_for_type ||= query_all_annotations
+      def all_potential_annotation_predicates
+        @all_potential_annotation_predicates ||= query_all_annotations
       end
 
-      def all_additional_metadata_annotations_for_type
-        all_annotations_for_type.reject do |annotation|
+      def all_additional_potential_annotation_predicates
+        all_potential_annotation_predicates.reject do |annotation|
           core_annotations.include?(annotation)
         end
       end
 
-      def all_additional_metadata_annotations_for_type_details
-        all_additional_metadata_annotations_for_type.collect do |annotation|
+      def all_additional_potential_annotation_details
+        all_additional_potential_annotation_predicates.collect do |annotation|
           annotation_details(annotation)
         end
       end
@@ -110,7 +110,7 @@ def to_extended_metadata_type_json
         json['title'] = "FDS #{type_name.underscore.humanize} - #{package_name || UUID.generate}"
         json['supported_type'] = type_name
         json['enabled'] = true
-        seek_attributes = all_additional_metadata_annotations_for_type_details.collect(&:to_extended_metadata_attribute_json)
+        seek_attributes = all_additional_potential_annotation_details.collect(&:to_extended_metadata_attribute_json)
         json['attributes'] = seek_attributes
         json
       end

lib/seek/fair_data_station/reader.rb

@@ -26,7 +26,7 @@ def to_extended_metadata_type_json(path)
         obs_unit = study&.observation_units&.first
         assay = study&.assays&.first
         necessary = [inv, study, obs_unit, assay].compact.select do |type|
-          type.all_additional_metadata_annotations_for_type.any?
+          type.all_additional_potential_annotation_predicates.any?
         end
         necessary.collect(&:to_extended_metadata_type_json)
       end

test/unit/fair_data_station/fair_data_station_reader_test.rb

@@ -90,7 +90,8 @@ class FairDataStationReaderTest < ActiveSupport::TestCase
     # packageName not included
     assay = study.assays.first
     assert_equal 12, assay.additional_metadata_annotations.count
-    refute_includes assay.additional_metadata_annotations, ['http://fairbydesign.nl/ontology/packageName', 'Amplicon demultiplexed']
+    refute_includes assay.additional_metadata_annotations,
+                    ['http://fairbydesign.nl/ontology/packageName', 'Amplicon demultiplexed']
     assert_equal 'Amplicon demultiplexed', assay.package_name
     assert_nil study.package_name
 
@@ -222,48 +223,53 @@ class FairDataStationReaderTest < ActiveSupport::TestCase
     study = inv.studies.first
     details = study.additional_metadata_annotation_details
     assert_equal 3, details.count
-    assert_equal ["end date of study", "experimental site name", "start date of study"], details.collect(&:label).sort
+    assert_equal ['end date of study', 'experimental site name', 'start date of study'], details.collect(&:label).sort
 
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/indpensim.ttl"
     inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
     obs_unit = inv.studies.first.observation_units.first
     details = obs_unit.additional_metadata_annotation_details
     assert_equal 5, details.count
-    assert_equal ["brand", "fermentation", "ncbi taxonomy id", "scientific name", "volume"], details.collect(&:label).sort
+    assert_equal ['brand', 'fermentation', 'ncbi taxonomy id', 'scientific name', 'volume'],
+                 details.collect(&:label).sort
   end
 
-  test 'all_additional_metadata_annotations_for_type_details' do
+  test 'all_additional_potential_annotations_details' do
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/seek-fair-data-station-test-case-irregular.ttl"
     inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
     study = inv.studies.first
-    details = study.all_additional_metadata_annotations_for_type_details
+    details = study.all_additional_potential_annotation_details
     assert_equal 3, details.count
-    assert_equal ["end date of study", "experimental site name", "start date of study"], details.collect(&:label).sort
+    assert_equal ['end date of study', 'experimental site name', 'start date of study'], details.collect(&:label).sort
 
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/indpensim.ttl"
     inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
     obs_unit = inv.studies.first.observation_units.first
-    details = obs_unit.all_additional_metadata_annotations_for_type_details
+    details = obs_unit.all_additional_potential_annotation_details
     assert_equal 6, details.count
-    assert_equal ["brand", "data stream", "fermentation", "ncbi taxonomy id", "scientific name", "volume"], details.collect(&:label).sort
+    assert_equal ['brand', 'data stream', 'fermentation', 'ncbi taxonomy id', 'scientific name', 'volume'],
+                 details.collect(&:label).sort
   end
 
-  test 'get all additional annotations for type' do
+  test 'get all_additional_potential_annotation_predicates' do
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/seek-fair-data-station-test-case-irregular.ttl"
     inv = Seek::FairDataStation::Reader.new.parse_graph(path).first
     study = inv.studies.first
-    assert_equal ["http://fairbydesign.nl/ontology/end_date_of_study", "http://fairbydesign.nl/ontology/experimental_site_name", "http://fairbydesign.nl/ontology/start_date_of_study"], study.all_additional_metadata_annotations_for_type.sort
+    assert_equal ['http://fairbydesign.nl/ontology/end_date_of_study', 'http://fairbydesign.nl/ontology/experimental_site_name', 'http://fairbydesign.nl/ontology/start_date_of_study'],
+                 study.all_additional_potential_annotation_predicates.sort
     obs_unit = study.observation_units.first
-    assert_equal ["http://fairbydesign.nl/ontology/birth_weight", "http://fairbydesign.nl/ontology/date_of_birth", "https://w3id.org/mixs/0000811"], obs_unit.all_additional_metadata_annotations_for_type.sort
+    assert_equal ['http://fairbydesign.nl/ontology/birth_weight', 'http://fairbydesign.nl/ontology/date_of_birth', 'https://w3id.org/mixs/0000811'],
+                 obs_unit.all_additional_potential_annotation_predicates.sort
     sample = obs_unit.samples.first
-    assert_equal ["http://fairbydesign.nl/ontology/biosafety_level", "http://gbol.life/0.1/scientificName", "http://purl.uniprot.org/core/organism", "https://w3id.org/mixs/0000011"], sample.all_additional_metadata_annotations_for_type.sort
+    assert_equal ['http://fairbydesign.nl/ontology/biosafety_level', 'http://gbol.life/0.1/scientificName', 'http://purl.uniprot.org/core/organism', 'https://w3id.org/mixs/0000011'],
+                 sample.all_additional_potential_annotation_predicates.sort
   end
 
   test 'to extended metadata types json' do
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/seek-fair-data-station-test-case.ttl"
     jsons = Seek::FairDataStation::Reader.new.to_extended_metadata_type_json(path)
     assert_equal 4, jsons.count
-    assert_equal ['Investigation', 'Study', 'ObservationUnit', 'Assay'], jsons.collect{|j| j['supported_type']}
+    assert_equal(%w[Investigation Study ObservationUnit Assay], jsons.collect { |j| j['supported_type'] })
     jsons.each do |json|
       assert_nothing_raised do
         Seek::ExtendedMetadataType::ExtendedMetadataTypeExtractor.valid_emt_json?(json)
@@ -273,7 +279,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase
     path = "#{Rails.root}/test/fixtures/files/fair_data_station/demo.ttl"
     jsons = Seek::FairDataStation::Reader.new.to_extended_metadata_type_json(path)
     assert_equal 2, jsons.count
-    assert_equal ['Study', 'Assay'], jsons.collect{|j| j['supported_type']}
+    assert_equal(%w[Study Assay], jsons.collect { |j| j['supported_type'] })
     jsons.each do |json|
       assert_nothing_raised do
         Seek::ExtendedMetadataType::ExtendedMetadataTypeExtractor.valid_emt_json?(json)