Merge branch 'seek-1.17' into extended-publication-type

whomingbird · whomingbird · commit 38eb87556e2d · 2025-11-19T07:37:50.000+01:00
diff --git a/app/assets/javascripts/single_page/index.js.erb b/app/assets/javascripts/single_page/index.js.erb
@@ -223,7 +223,7 @@ function rowHasHiddenFields(row) {
 // This function is called when 'excel-export' btn is clicked.
 // Posts the content of the dynamic table to the single_pages_controller,
 // which generates an excel workbook based on a template.
-async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
+async function exportToExcel(tableName, studyId, assayId, sampleTypeId, projectId) {
   const table = $j(`table[id=${tableName}]`);
 
   // Checks whether the dynamic table has errors
@@ -296,7 +296,16 @@ async function exportToExcel(tableName, studyId, assayId, sampleTypeId) {
     alert(`Failed to export through excel!\nStatus: ${response.status} - ${JSON.stringify(response.error().statusText)}\nError: ${response.responseText}`);
   })
   .always( function(response){
-    setTimeout(() => {location.reload()}, 2000);
+    setTimeout(() => {
+      const itemType = assayId == null ? 'study' : 'assay';
+      const itemId = assayId == null ? studyId : assayId;
+      if (projectId != null && itemType && itemId != null) {
+        window.location.href = `/single_pages/${projectId}?item_type=${itemType}&item_id=${itemId}`;
+      } else {
+        // If one of the variables is missing, just reload the current page.
+        location.reload();
+      }
+    }, 2000);
   });
 }
 
diff --git a/app/models/sop.rb b/app/models/sop.rb
@@ -1,6 +1,7 @@
 class Sop < ApplicationRecord
 
   include Seek::Rdf::RdfGeneration
+  include Seek::BioSchema::Support
 
   has_and_belongs_to_many :direct_studies, class_name: 'Study'
 
diff --git a/app/views/isa_assays/_assay_samples.html.erb b/app/views/isa_assays/_assay_samples.html.erb
@@ -73,7 +73,7 @@
         }
 
         function sampleExportExcel() {
-            exportToExcel("assay-samples-table", '<%=assay.study_id%>', '<%=assay.id%>', '<%=sample_type.id%>');
+            exportToExcel("assay-samples-table", <%= assay&.study_id %>, <%= assay&.id %>, <%= sample_type.id %>, <%= project&.id %>);
         }
 
         function assaySampleUploadExcel(){
diff --git a/app/views/isa_studies/_source_material.html.erb b/app/views/isa_studies/_source_material.html.erb
@@ -60,10 +60,6 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>
             $j(".dataTables_scrollBody").css("min-height", "300px");
         });
 
-        function SourcePasteFromClipboard(){
-            window.sourceDynamicTable.pasteFromClipboard()
-        }
-
         function SourceSave(){
             window.sourceDynamicTable.save()
         }
@@ -77,7 +73,7 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>
         }
 
         function sourceExportExcel() {
-            exportToExcel("source-material-table", '<%=study.id%>', null, '<%=sample_type.id%>');
+            exportToExcel("source-material-table", <%=study.id%>, null, <%=sample_type.id%>, <%= project.id %>);
         }
 
         function sourceUploadExcel(){
diff --git a/app/views/isa_studies/_study_design.html.erb b/app/views/isa_studies/_study_design.html.erb
@@ -1,10 +1,10 @@
-<% study ||= nil %>
-<% valid_study = study&.sample_types.present? %>
 <%
-	source_table_action = displaying_single_page? ? "highlightTreeviewItem('source_table')" : "loadDynamicTableFromDefaultView('source_table')"
-	study_protocol_action = displaying_single_page? ? "highlightTreeviewItem('study_protocol')" : "loadDynamicTableFromDefaultView('study_protocol')"
-	study_samples_table_action = displaying_single_page? ? "highlightTreeviewItem('study_samples_table')" : "loadDynamicTableFromDefaultView('study_samples_table')"
-	study_experiment_overview_action = displaying_single_page? ? "highlightTreeviewItem('study_experiment_overview')" : "loadDynamicTableFromDefaultView('study_experiment_overview')"
+  study ||= nil
+  valid_study = study&.sample_types.present?
+  source_table_action = displaying_single_page? ? "highlightTreeviewItem('source_table')" : "loadDynamicTableFromDefaultView('source_table')"
+  study_protocol_action = displaying_single_page? ? "highlightTreeviewItem('study_protocol')" : "loadDynamicTableFromDefaultView('study_protocol')"
+  study_samples_table_action = displaying_single_page? ? "highlightTreeviewItem('study_samples_table')" : "loadDynamicTableFromDefaultView('study_samples_table')"
+  study_experiment_overview_action = displaying_single_page? ? "highlightTreeviewItem('study_experiment_overview')" : "loadDynamicTableFromDefaultView('study_experiment_overview')"
 %>
 
 <% if valid_study %>
diff --git a/app/views/isa_studies/_study_samples.html.erb b/app/views/isa_studies/_study_samples.html.erb
@@ -70,7 +70,7 @@
         }
 
         function sampleExportExcel() {
-            exportToExcel("study-samples-table", '<%=study.id%>', null, '<%=sample_type.id%>');
+            exportToExcel("study-samples-table", <%= study&.id %>, null, <%= sample_type.id %>, <%= project&.id %>);
         }
 
         function studySampleUploadExcel(){
diff --git a/lib/seek/bio_schema/resource_decorators/assets_creator.rb b/lib/seek/bio_schema/resource_decorators/assets_creator.rb
@@ -3,7 +3,7 @@ module BioSchema
     module ResourceDecorators
       # Decorator that provides extensions for a creator
       class AssetsCreator < Thing
-        PERSON_PROFILE = 'https://bioschemas.org/profiles/Person/0.2-DRAFT-2019_07_19/'.freeze
+        PERSON_PROFILE = 'https://bioschemas.org/profiles/Person/0.3-DRAFT'.freeze
 
         schema_mappings given_name: :givenName,
                         family_name: :familyName,
diff --git a/lib/seek/bio_schema/resource_decorators/collection.rb b/lib/seek/bio_schema/resource_decorators/collection.rb
@@ -9,10 +9,6 @@ def schema_type
           'Collection'
         end
 
-        def conformance
-          'https://schema.org/Collection'
-        end
-
         def schema_enabled_assets
           assets.reject(&:blank?).select(&:schema_org_supported?)
         end
diff --git a/lib/seek/bio_schema/resource_decorators/creative_work.rb b/lib/seek/bio_schema/resource_decorators/creative_work.rb
@@ -17,7 +17,7 @@ class CreativeWork < Thing
                         subject_of: :subjectOf,
                         part_of: :isPartOf,
                         doi: :identifier,
-			 previous_version_url: :isBasedOn
+                        previous_version_url: :isBasedOn
 
         def doi
           "https://doi.org/#{resource.doi}" if resource.try(:doi).present?
diff --git a/lib/seek/bio_schema/resource_decorators/data_file.rb b/lib/seek/bio_schema/resource_decorators/data_file.rb
@@ -8,7 +8,7 @@ class DataFile < CreativeWork
         
         schema_mappings distribution: :distribution
 
-        DATASET_PROFILE = 'https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14/'.freeze
+        DATASET_PROFILE = 'https://bioschemas.org/profiles/Dataset/1.0-RELEASE'.freeze
 
         def description
           description = resource.description&.truncate(4999)
@@ -19,6 +19,7 @@ def description
         def distribution
           return unless resource.content_blob
           return if resource.content_blob.show_as_external_link?
+
           blob = resource.content_blob
           data = {
             '@type': 'DataDownload',
diff --git a/lib/seek/bio_schema/resource_decorators/dataset.rb b/lib/seek/bio_schema/resource_decorators/dataset.rb
@@ -7,7 +7,7 @@ class Dataset < CreativeWork
         schema_mappings distribution: :distribution,
                         data_catalog: :includedInDataCatalog
 
-        DATASET_PROFILE = 'https://bioschemas.org/profiles/Dataset/0.3-RELEASE-2019_06_14/'.freeze
+        DATASET_PROFILE = 'https://bioschemas.org/profiles/Dataset/1.0-RELEASE'.freeze
 
         def resource_url(r, opts = {})
           super(r.model, opts) # For some reason delegation doesn't work here, so have to call `model` explicitly.
diff --git a/lib/seek/bio_schema/resource_decorators/document.rb b/lib/seek/bio_schema/resource_decorators/document.rb
@@ -9,9 +9,6 @@ def schema_type
           'DigitalDocument'
         end
 
-        def conformance
-          'https://schema.org/DigitalDocument'
-        end
       end
     end
   end
diff --git a/lib/seek/bio_schema/resource_decorators/event.rb b/lib/seek/bio_schema/resource_decorators/event.rb
@@ -3,7 +3,7 @@ module BioSchema
     module ResourceDecorators
       # Decorator that provides extensions for a Event
       class Event < Thing
-        EVENT_PROFILE = 'https://bioschemas.org/profiles/Event/0.2-DRAFT-2019_06_14/'.freeze
+        EVENT_PROFILE = 'https://bioschemas.org/profiles/Event/0.3-DRAFT'.freeze
 
         associated_items contact: :contributors,
                          host_institution: :projects,
diff --git a/lib/seek/bio_schema/resource_decorators/human_disease.rb b/lib/seek/bio_schema/resource_decorators/human_disease.rb
@@ -6,7 +6,7 @@ class HumanDisease < Thing
         schema_mappings synonyms: :alternateName,
                         ncbi_uri: :sameAs
 
-        TAXON_PROFILE = 'https://bioschemas.org/profiles/Taxon/0.6-RELEASE/'.freeze
+        TAXON_PROFILE = 'https://bioschemas.org/profiles/Taxon/1.0-RELEASE'.freeze
 
         def synonyms
           if concept && concept[:synonyms]
diff --git a/lib/seek/bio_schema/resource_decorators/institution.rb b/lib/seek/bio_schema/resource_decorators/institution.rb
@@ -25,10 +25,6 @@ def url
           web_page.blank? ? identifier : web_page
         end
 
-        def conformance
-          'https://schema.org/ResearchOrganization'
-        end
-
         def full_address
           full = {}
           full[:@type]='PostalAddress'
diff --git a/lib/seek/bio_schema/resource_decorators/organism.rb b/lib/seek/bio_schema/resource_decorators/organism.rb
@@ -6,7 +6,7 @@ class Organism < Thing
         schema_mappings synonyms: :alternateName,
                         ncbi_uri: :sameAs
 
-        TAXON_PROFILE = 'https://bioschemas.org/profiles/Taxon/0.6-RELEASE/'.freeze
+        TAXON_PROFILE = 'https://bioschemas.org/profiles/Taxon/1.0-RELEASE'.freeze
 
         def synonyms
           if concept && concept[:synonyms]
diff --git a/lib/seek/bio_schema/resource_decorators/person.rb b/lib/seek/bio_schema/resource_decorators/person.rb
@@ -3,7 +3,7 @@ module BioSchema
     module ResourceDecorators
       # Decorator that provides extensions for a Person
       class Person < Thing
-        PERSON_PROFILE = 'https://bioschemas.org/profiles/Person/0.2-DRAFT-2019_07_19/'.freeze
+        PERSON_PROFILE = 'https://bioschemas.org/profiles/Person/0.3-DRAFT'.freeze
 
         associated_items member_of: :projects,
                          works_for: :institutions
diff --git a/lib/seek/bio_schema/resource_decorators/presentation.rb b/lib/seek/bio_schema/resource_decorators/presentation.rb
@@ -7,9 +7,6 @@ def schema_type
           'PresentationDigitalDocument'
         end
 
-        def conformance
-          'https://schema.org/PresentationDigitalDocument'
-        end
       end
     end
   end
diff --git a/lib/seek/bio_schema/resource_decorators/programme.rb b/lib/seek/bio_schema/resource_decorators/programme.rb
@@ -9,10 +9,6 @@ def schema_type
           'FundingScheme'
         end
 
-        def conformance
-          'https://schema.org/FundingScheme'
-        end
-
         def url
           web_page.blank? ? identifier : web_page
         end
diff --git a/lib/seek/bio_schema/resource_decorators/project.rb b/lib/seek/bio_schema/resource_decorators/project.rb
@@ -12,10 +12,6 @@ class Project < Thing
                         funder: :funder,
                         event: :event
 
-        def conformance
-          'https://schema.org/Project'
-        end
-
         def programme_set
           [programme].reject(&:blank?)
         end
diff --git a/lib/seek/bio_schema/resource_decorators/sample.rb b/lib/seek/bio_schema/resource_decorators/sample.rb
@@ -8,7 +8,7 @@ class Sample < Thing
         SAMPLE_PROFILE = 'https://bioschemas.org/profiles/Sample/0.2-RELEASE-2018_11_10/'.freeze
 
         def schema_type
-          %w[Thing Sample]
+          'Sample'
         end
 
         def conformance
@@ -30,6 +30,9 @@ def describe_attribute(attribute)
             'name' => attribute.title,
             'value' => value.to_s
           }
+          if attribute.pid
+            data['propertyId'] = attribute.pid
+          end
           resolved = attribute.resolve(value)
           data['identifier'] = resolved if resolved
           if attribute.unit
diff --git a/lib/seek/bio_schema/resource_decorators/sop.rb b/lib/seek/bio_schema/resource_decorators/sop.rb
@@ -0,0 +1,17 @@
+module Seek
+  module BioSchema
+    module ResourceDecorators
+      # Decorator that provides extensions for a Sop
+      class Sop < CreativeWork
+
+        associated_items computational_tool: :workflows
+        schema_mappings computational_tool: :computationalTool
+
+        def schema_type
+          'LabProtocol'
+        end
+
+      end
+    end
+  end
+end
diff --git a/lib/seek/bio_schema/resource_decorators/workflow.rb b/lib/seek/bio_schema/resource_decorators/workflow.rb
@@ -63,7 +63,7 @@ def formal_parameters(properties, group_name)
               "@type": 'FormalParameter',
               "@id": ROCrate::ContextualEntity.format_local_id("#{wf_name}-#{group_name}-#{property.id}"),
               name: property.name || property.id,
-              "dct:conformsTo": FORMALPARAMETER_PROFILE
+              "dct:conformsTo": { '@id' => FORMALPARAMETER_PROFILE }
             }
           end
         end
diff --git a/lib/seek/bio_schema/serializer.rb b/lib/seek/bio_schema/serializer.rb
@@ -15,13 +15,15 @@ def initialize(resource)
       end
 
       def json_representation
-        repr = {
+        representation = {
           '@context' => resource_decorator.context,
           '@type' => resource_decorator.schema_type
         }
-        repr['dct:conformsTo'] = resource_decorator.conformance if resource_decorator.respond_to? 'conformance'
-        repr = repr.merge(attributes_json)
-        repr.deep_stringify_keys
+        if resource_decorator.respond_to? 'conformance'
+          representation['dct:conformsTo'] = { '@id' => resource_decorator.conformance }
+        end
+        representation = representation.merge(attributes_json)
+        representation.deep_stringify_keys
       end
 
       # returns the JSON-LD as a String, for the resource
@@ -58,7 +60,7 @@ def self.supported_types
       private
 
       SUPPORTED_TYPES = [Person, Project, Event, DataFile, Organism, HumanDisease,
-                         Seek::BioSchema::DataCatalogMockModel,
+                         Seek::BioSchema::DataCatalogMockModel, Sop,
                          Document, Presentation, Workflow, Collection,
                          Institution, Programme, Sample, AssetsCreator].freeze
 
diff --git a/lib/seek/workflow_extractors/rocrate.rb b/lib/seek/workflow_extractors/rocrate.rb
@@ -86,7 +86,7 @@ def metadata_from_crate(crate, m)
               author_meta = author_meta.dereference if author_meta.respond_to?(:dereference)
               if author_meta.is_a?(::ROCrate::ContextualEntity) && !author_meta.is_a?(::ROCrate::Person)
                 other_creators << author_meta['name'] if author_meta['name'].present?
-              else
+              elsif author_meta.present?
                 author = extract_author(author_meta)
                 authors << author unless author.blank?
               end
diff --git a/test/factories/sample_types.rb b/test/factories/sample_types.rb
@@ -110,6 +110,16 @@
     end
   end
 
+  factory(:schema_org_sample_type, parent: :sample_type) do
+    title { 'SampleType to test schema.org' }
+    after(:build) do |type|
+      type.sample_attributes << FactoryBot.build(:sample_attribute, title: 'title', pid: 'dc:title', sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), required: true, is_title: true, sample_type: type)
+      type.sample_attributes << FactoryBot.build(:sample_attribute, title: 'description', pid: 'dc:description', sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), required: false, is_title: false, sample_type: type)
+      type.sample_attributes << FactoryBot.build(:sample_attribute, title: 'enzyme', pid: 'http://purl.uniprot.org/core/enzyme', sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), required: false, is_title: false, sample_type: type)
+      type.sample_attributes << FactoryBot.build(:sample_attribute, title: 'weight', sample_attribute_type: FactoryBot.create(:weight_sample_attribute_type), unit: Unit.find_or_create_by(symbol: 'g', comment: 'gram'), required: false, is_title: false, sample_type: type)
+    end
+  end
+
   factory(:min_sample_type, parent: :sample_type) do
     title { 'A Minimal SampleType' }
     after(:build) do |type|
diff --git a/test/integration/fair_signposting_test.rb b/test/integration/fair_signposting_test.rb
@@ -86,9 +86,11 @@ class FairSignpostingTest < ActionDispatch::IntegrationTest
 
     assert_response :success
     links = parse_link_header
-    assert_equal 3, links.size
+
+    assert_equal 4, links.size
     assert_link(links, sop_url(sop, version: 1), rel: 'describedby', type: :datacite_xml)
     assert_link(links, sop_url(sop, version: 1), rel: 'describedby', type: :rdf)
+    assert_link(links, sop_url(sop, version: 1), rel: 'describedby', type: :jsonld)
     assert_link(links, download_sop_url(sop, version: 1), rel: 'item', type: :pdf)
   end
 
diff --git a/test/unit/bio_schema/data_catalog_mock_model_test.rb b/test/unit/bio_schema/data_catalog_mock_model_test.rb
@@ -78,7 +78,7 @@ def setup
                 assert_equal 'Organization', provider['@type']
                 assert_equal 'WIBBLE', provider['name']
                 assert_equal 'http://wibble.eu', provider['url']
-                assert_equal 13, json['dataset'].count
+                assert_equal 14, json['dataset'].count
               end
             end
           end
diff --git a/test/unit/bio_schema/schema_ld_generation_test.rb b/test/unit/bio_schema/schema_ld_generation_test.rb
diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb
diff --git a/test/unit/workflow_extraction/ro_crate_extraction_test.rb b/test/unit/workflow_extraction/ro_crate_extraction_test.rb
diff --git a/test/vcr_cassettes/doi/cross_ref1.yml b/test/vcr_cassettes/doi/cross_ref1.yml
diff --git a/test/vcr_cassettes/doi/cross_ref2.yml b/test/vcr_cassettes/doi/cross_ref2.yml
diff --git a/test/vcr_cassettes/doi/cross_ref3.yml b/test/vcr_cassettes/doi/cross_ref3.yml
diff --git a/test/vcr_cassettes/doi/cross_ref4.yml b/test/vcr_cassettes/doi/cross_ref4.yml
diff --git a/test/vcr_cassettes/doi/cross_ref5.yml b/test/vcr_cassettes/doi/cross_ref5.yml
diff --git a/test/vcr_cassettes/doi/cross_ref6.yml b/test/vcr_cassettes/doi/cross_ref6.yml
diff --git a/test/vcr_cassettes/doi/cross_ref7.yml b/test/vcr_cassettes/doi/cross_ref7.yml
diff --git a/test/vcr_cassettes/doi/cross_ref8.yml b/test/vcr_cassettes/doi/cross_ref8.yml

Original file line number	Diff line number	Diff line change
`@@ -73,7 +73,7 @@`
`73`	`73`	`}`
`74`	`74`
`75`	`75`	`function sampleExportExcel() {`
`76`		`- exportToExcel("assay-samples-table", '<%=assay.study_id%>', '<%=assay.id%>', '<%=sample_type.id%>');`
	`76`	`+ exportToExcel("assay-samples-table", <%= assay&.study_id %>, <%= assay&.id %>, <%= sample_type.id %>, <%= project&.id %>);`
`77`	`77`	`}`
`78`	`78`
`79`	`79`	`function assaySampleUploadExcel(){`
Original file line number	Diff line number	Diff line change
`@@ -60,10 +60,6 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>`
`60`	`60`	`$j(".dataTables_scrollBody").css("min-height", "300px");`
`61`	`61`	`});`
`62`	`62`
`63`		`- function SourcePasteFromClipboard(){`
`64`		`- window.sourceDynamicTable.pasteFromClipboard()`
`65`		`- }`
`66`		`-`
`67`	`63`	`function SourceSave(){`
`68`	`64`	`window.sourceDynamicTable.save()`
`69`	`65`	`}`
`@@ -77,7 +73,7 @@ uploadExcel: 'sourceUploadExcel()', sample_type_id: sample_type&.id} %>`
`77`	`73`	`}`
`78`	`74`
`79`	`75`	`function sourceExportExcel() {`
`80`		`- exportToExcel("source-material-table", '<%=study.id%>', null, '<%=sample_type.id%>');`
	`76`	`+ exportToExcel("source-material-table", <%=study.id%>, null, <%=sample_type.id%>, <%= project.id %>);`
`81`	`77`	`}`
`82`	`78`
`83`	`79`	`function sourceUploadExcel(){`
Original file line number	Diff line number	Diff line change
`@@ -70,7 +70,7 @@`
`70`	`70`	`}`
`71`	`71`
`72`	`72`	`function sampleExportExcel() {`
`73`		`- exportToExcel("study-samples-table", '<%=study.id%>', null, '<%=sample_type.id%>');`
	`73`	`+ exportToExcel("study-samples-table", <%= study&.id %>, null, <%= sample_type.id %>, <%= project&.id %>);`
`74`	`74`	`}`
`75`	`75`
`76`	`76`	`function studySampleUploadExcel(){`