Merge pull request #1665 from ELIXIR-Belgium/replace_fixtures_by_fact…

…ories Replace fixtures by factories
seek4science · Nov 20, 2023 · df3195f · df3195f
2 parents 9b55b7a + 265b4fc
commit df3195f
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Showing 16 changed files with 225 additions and 202 deletions.
diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
@@ -258,7 +258,7 @@ async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
         obj[attr] = val;
       }
     }
-    if (!hasHiddenInputs) data.push(obj);
+    if (!hasHiddenInputs && obj["selected"]) data.push(obj);
   }
 
   // Use ajax for POST request with table data in the body

diff --git a/app/models/template.rb b/app/models/template.rb
@@ -57,12 +57,12 @@ def resolve_controlled_vocabs_inconsistencies
   end
 
   def none_empty_isa_tag
-    template_attributes.reject { |ta| ta&.title == 'Input' }.map(&:isa_tag_id).none? nil
+    template_attributes.select { |ta| !ta.title.include?('Input') && ta.isa_tag_id.nil? }.none?
   end
 
   def test_tag_occurences
     %w[source protocol sample data_file other_material].map do |tag|
-      tag if template_attributes.reject { |ta| ta&.title == 'Input' }.map(&:isa_tag).compact.map(&:title).count(tag) > 1
+      tag if template_attributes.reject { |ta| ta.title.include?('Input') }.map(&:isa_tag).compact.map(&:title).count(tag) > 1
     end.compact
   end
 

diff --git a/lib/isa_exporter.rb b/lib/isa_exporter.rb
@@ -549,7 +549,7 @@ def next_process(samples_hash)
 
     def previous_process(samples_hash)
       sample = Sample.find(samples_hash.first[:id])
-      # hvfjkbdfk
+
       sample_type = sample.linked_samples.first&.sample_type
       if (sample_type)
         protocol = detect_protocol(sample_type)

diff --git a/test/factories/isa_tags.rb b/test/factories/isa_tags.rb
@@ -0,0 +1,57 @@
+FactoryBot.define do
+  # source ISA tag
+  factory(:source_isa_tag, class: IsaTag) do
+    title { "source" }
+  end
+
+  # sample ISA tag
+  factory(:sample_isa_tag, class: IsaTag) do
+    title { "sample" }
+  end
+
+  # protocol ISA tag
+  factory(:protocol_isa_tag, class: IsaTag) do
+    title { "protocol" }
+  end
+
+  # source characteristic ISA tag
+  factory(:source_characteristic_isa_tag, class: IsaTag) do
+    title { "source_characteristic" }
+  end
+
+  # sample characteristic ISA tag
+  factory(:sample_characteristic_isa_tag, class: IsaTag) do
+    title { "sample_characteristic" }
+  end
+
+  # other material ISA tag
+  factory(:other_material_isa_tag, class: IsaTag) do
+    title { "other_material" }
+  end
+
+  # other material characteristic ISA tag
+  factory(:other_material_characteristic_isa_tag, class: IsaTag) do
+    title { "other_material_characteristic" }
+  end
+
+  # data file ISA tag
+  factory(:data_file_isa_tag, class: IsaTag) do
+    title { "data_file" }
+  end
+
+  # data file comment ISA tag
+  factory(:data_file_comment_isa_tag, class: IsaTag) do
+    title { "data_file_comment" }
+  end
+
+  # parameter value ISA tag
+  factory(:parameter_value_isa_tag, class: IsaTag) do
+    title { "parameter_value" }
+  end
+
+  # default ISA tag
+  factory(:default_isa_tag, class: IsaTag) do
+    title { "default isa-tag" }
+  end
+
+end
diff --git a/test/factories/sample_types.rb b/test/factories/sample_types.rb
diff --git a/test/factories/template_attributes.rb b/test/factories/template_attributes.rb
@@ -3,7 +3,7 @@
   factory(:template_attribute) do
     sequence(:title) { |n| "Template attribute #{n}" }
     association :template, factory: :template
-    isa_tag_id { IsaTag.find_by_title('default isa-tag')&.id }
+    isa_tag_id { FactoryBot.create(:default_isa_tag).id }
   end
 
   factory(:apples_controlled_vocab_template_attribute, parent: :template_attribute) do

diff --git a/test/factories/templates.rb b/test/factories/templates.rb
diff --git a/test/fixtures/isa_tags.yml b/test/fixtures/isa_tags.yml
diff --git a/test/fixtures/templates.yml b/test/fixtures/templates.yml
diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb
@@ -1928,7 +1928,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
     sample_collection_st = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project],
     linked_sample_type: source_st)
 
-    assay_sample_type = FactoryBot.create :isa_assay_sample_type, linked_sample_type: sample_collection_st, contributor: person, isa_template: Template.find_by_title('ISA Assay 1')
+    assay_sample_type = FactoryBot.create :isa_assay_material_sample_type, linked_sample_type: sample_collection_st, contributor: person, isa_template: FactoryBot.build(:isa_assay_material_template)
     assay = FactoryBot.create(:assay,
                               policy:FactoryBot.create(:private_policy, permissions:[FactoryBot.create(:permission,contributor: person, access_type:Policy::EDITING)]),
                               sample_type: assay_sample_type,
@@ -1953,14 +1953,16 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links
     sample_collection_st = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project],
                                                                                  linked_sample_type: source_st)
 
-    assay_st1 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
-                                                          linked_sample_type: sample_collection_st, isa_template: Template.find_by_title('ISA Assay 1'))
 
-    assay_st2 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
-                                                          linked_sample_type: assay_st1, isa_template: Template.find_by_title('ISA Assay 1'))
+    assay_template_1 = FactoryBot.create(:isa_assay_material_template)
+    assay_st1 = FactoryBot.create(:isa_assay_material_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: sample_collection_st, isa_template: assay_template_1)
 
-    assay_st3 = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
-                                                          linked_sample_type: assay_st2, isa_template: Template.find_by_title('ISA Assay 1'))
+    assay_st2 = FactoryBot.create(:isa_assay_material_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: assay_st1, isa_template: assay_template_1)
+
+    assay_st3 = FactoryBot.create(:isa_assay_material_sample_type, contributor: person, projects: [project],
+                                                          linked_sample_type: assay_st2, isa_template: assay_template_1)
 
     study = FactoryBot.create(:study, investigation:, contributor: person,
                                       policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]),

diff --git a/test/functional/isa_assays_controller_test.rb b/test/functional/isa_assays_controller_test.rb
@@ -52,23 +52,23 @@ def setup
                                                               '0' => {
                                                                 pos: '1', title: 'a string', required: '1', is_title: '1',
                                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id, _destroy: '0',
-                                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::OTHER_MATERIAL).id
+                                                                isa_tag_id: FactoryBot.create(:other_material_isa_tag).id
                                                               },
                                                               '1' => {
                                                                 pos: '2', title: 'protocol', required: '1', is_title: '0',
                                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id,
-                                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::PROTOCOL).id, _destroy: '0'
+                                                                isa_tag_id: FactoryBot.create(:protocol_isa_tag).id, _destroy: '0'
                                                               },
                                                               '2' => {
                                                                 pos: '3', title: 'Input', required: '1',
                                                                 sample_attribute_type_id: FactoryBot.create(:sample_multi_sample_attribute_type).id,
                                                                 linked_sample_type_id: 'self', _destroy: '0'
                                                               },
                                                               '3' => {
-                                                                pos: '4', title: 'Som material characteristic', required: '1',
+                                                                pos: '4', title: 'Some material characteristic', required: '1',
                                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id,
                                                                 _destroy: '0',
-                                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::OTHER_MATERIAL_CHARACTERISTIC).id
+                                                                isa_tag_id: FactoryBot.create(:other_material_characteristic_isa_tag).id
                                                               }
                                                             } } } }
       end
@@ -128,7 +128,7 @@ def setup
     source_type = FactoryBot.create(:isa_source_sample_type, contributor: person, projects: [project])
     sample_collection_type = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project],
                                                                                    linked_sample_type: source_type)
-    assay_type = FactoryBot.create(:isa_assay_sample_type, contributor: person, projects: [project],
+    assay_type = FactoryBot.create(:isa_assay_material_sample_type, contributor: person, projects: [project],
                                                            linked_sample_type: sample_collection_type)
 
     study = FactoryBot.create(:study, investigation:, contributor: person,
@@ -197,23 +197,23 @@ def setup
                                               '0' => {
                                                 pos: '1', title: 'a string', required: '1', is_title: '1',
                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id, _destroy: '0',
-                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::OTHER_MATERIAL).id
+                                                isa_tag_id: FactoryBot.create(:other_material_isa_tag).id
                                               },
                                               '1' => {
                                                 pos: '2', title: 'protocol', required: '1', is_title: '0',
                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id,
-                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::PROTOCOL).id, _destroy: '0'
+                                                isa_tag_id: FactoryBot.create(:protocol_isa_tag).id, _destroy: '0'
                                               },
                                               '2' => {
                                                 pos: '3', title: 'Input', required: '1',
                                                 sample_attribute_type_id: FactoryBot.create(:sample_multi_sample_attribute_type).id,
                                                 linked_sample_type_id: 'self', _destroy: '0'
                                               },
                                               '3' => {
-                                                pos: '4', title: 'Som material characteristic', required: '1',
+                                                pos: '4', title: 'Some material characteristic', required: '1',
                                                 sample_attribute_type_id: FactoryBot.create(:string_sample_attribute_type).id,
                                                 _destroy: '0',
-                                                isa_tag_id: IsaTag.find_by_title(Seek::ISA::TagType::OTHER_MATERIAL_CHARACTERISTIC).id
+                                                isa_tag_id: FactoryBot.create(:other_material_characteristic_isa_tag).id
                                               }
                                             } } }