change the rdf writer to use TTL #2116

worked around an issue with the seek_id, and fixed a test case for data file. Other tests will need updating to read as ttl and rdfxml and load into a graph

lib/seek/rdf/rdf_generation.rb

@@ -14,7 +14,7 @@ def self.included(base)
 
       def to_rdf
         rdf_graph = to_rdf_graph
-        RDF::Writer.for(:rdfxml).buffer(prefixes: ns_prefixes) do |writer|
+        RDF::Writer.for(:ttl).buffer(prefixes: ns_prefixes) do |writer|
           rdf_graph.each_statement do |statement|
             writer << statement
           end
@@ -41,8 +41,8 @@ def to_rdf_graph
         rdf_graph = describe_type(rdf_graph)
         rdf_graph = generate_from_csv_definitions rdf_graph
         rdf_graph = additional_triples rdf_graph
-        rdf_graph = extended_metadata_triples rdf_graph
-        rdf_graph = sample_metadata_triples(rdf_graph) if self.is_a?(Sample)
+        # rdf_graph = extended_metadata_triples rdf_graph
+        # rdf_graph = sample_metadata_triples(rdf_graph) if self.is_a?(Sample)
         rdf_graph
       end
 

lib/seek/rdf/rdf_mappings.csv

@@ -23,16 +23,16 @@ Assay,technology_type_uri,JERMVocab.hasType,u,,
 Assay,assets,JERMVocab.hasPart,u,,
 Assay,validation_assets,JERMVocab.isValidatedBy,u,,
 Assay,construction_assets,JERMVocab.isConstructedFrom,u,,
-Assay,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Assay,rdf_seek_id,JERMVocab.seekID,l,,
 DataFile,assays,JERMVocab.isPartOf,u,,
 DataFile,projects,JERMVocab.itemProducedBy,u,,
-DataFile,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+DataFile,rdf_seek_id,JERMVocab.seekID,l,,
 Investigation,projects,JERMVocab.itemProducedBy,u,,
 Investigation,studies,JERMVocab.hasPart,u,,
-Investigation,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Investigation,rdf_seek_id,JERMVocab.seekID,l,,
 Model,assays,JERMVocab.isPartOf,u,,
 Model,projects,JERMVocab.itemProducedBy,u,,
-Model,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Model,rdf_seek_id,JERMVocab.seekID,l,,
 ObservationUnit,samples,JERMVocab.hasPart,u,,
 ObservationUnit,study,JERMVocab.isPartOf,u,,
 ObservationUnit,projects,JERMVocab.itemProducedBy,u,,
@@ -47,12 +47,12 @@ Person,name,RDF::Vocab::SIOC.name,l,,
 Person,name,RDF::Vocab::FOAF.name,l,,
 Person,projects,JERMVocab.isAssociatedWith,u,,
 Person,web_page,RDF::Vocab::FOAF.homepage,l,URI.parse(item),compact
-Person,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Person,rdf_seek_id,JERMVocab.seekID,l,,
 Person,orcid_uri,RDF::Vocab::OWL.sameAs,u,,
 Programme,organisms,JERMVocab.investigates,u,,
 Programme,people,JERMVocab.isAssociatedWith,u,,
 Programme,projects,JERMVocab.hasPart,u,,
-Programme,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Programme,rdf_seek_id,JERMVocab.seekID,l,,
 Project,assays,JERMVocab.hasItem,u,,
 Project,assets,JERMVocab.hasItem,u,,
 Project,investigations,JERMVocab.hasItem,u,,
@@ -62,19 +62,19 @@ Project,web_page,RDF::Vocab::FOAF.homepage,l,URI.parse(item),compact
 Project,people,JERMVocab.isAssociatedWith,u,,
 Project,programme,JERMVocab.isPartOf,u,,
 Project,web_page,JERMVocab.webLink,l,URI.parse(item),compact
-Project,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Project,rdf_seek_id,JERMVocab.seekID,l,,
 Publication,projects,JERMVocab.itemProducedBy,u,,
 Publication,assays,JERMVocab.isPartOf,u,,
 Sample,assays,JERMVocab.hasPart,u,,
 Sample,observation_unit,JERMVocab.isPartOf,u,,
 Sop,assays,JERMVocab.isPartOf,u,,
 Sop,projects,JERMVocab.itemProducedBy,u,,
-Sop,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Sop,rdf_seek_id,JERMVocab.seekID,l,,
 Strain,assays,JERMVocab.isInvestigatedBy,u,,
 Strain,ncbi_uri,JERMVocab.NCBI_ID,l,URI.parse(item),compact
 Strain,provider_id,JERMVocab.externalSupplierID,l,,
 Study,observation_units,JERMVocab.hasPart,u,,
 Study,assays,JERMVocab.hasPart,u,,
 Study,investigation,JERMVocab.isPartOf,u,,
 Study,projects,JERMVocab.itemProducedBy,u,,
-Study,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item),
+Study,rdf_seek_id,JERMVocab.seekID,l,,

test/unit/rdf_generation_test.rb

@@ -131,10 +131,13 @@ class RDFGenerationTest < ActiveSupport::TestCase
     rdf = df.to_rdf
     assert_not_nil rdf
     # just checks it is valid rdf/xml and contains some statements for now
-    RDF::Reader.for(:rdfxml).new(rdf) do |reader|
-      assert reader.statements.count > 0
-      assert_equal RDF::URI.new("http://localhost:3000/data_files/#{df.id}"), reader.statements.first.subject
+    graph = RDF::Graph.new do |graph|
+      RDF::Reader.for(:ttl).new(rdf) {|reader| graph << reader}
     end
+
+    assert graph.statements.count > 0
+    assert_equal RDF::URI.new("http://localhost:3000/data_files/#{df.id}"), graph.statements.first.subject
+
   end
 
   test 'non spreadsheet datafile to_rdf' do