diff --git a/bin/owlapi-wrapper-1.6.0.jar b/bin/owlapi-wrapper-1.7.0.jar similarity index 95% rename from bin/owlapi-wrapper-1.6.0.jar rename to bin/owlapi-wrapper-1.7.0.jar index 38603a96..1a252f92 100755 Binary files a/bin/owlapi-wrapper-1.6.0.jar and b/bin/owlapi-wrapper-1.7.0.jar differ diff --git a/lib/ontologies_linked_data/parser/owlapi.rb b/lib/ontologies_linked_data/parser/owlapi.rb index 88e45b7f..74a095bd 100644 --- a/lib/ontologies_linked_data/parser/owlapi.rb +++ b/lib/ontologies_linked_data/parser/owlapi.rb @@ -13,7 +13,7 @@ class RDFFileNotGeneratedException < Parser::ParserException class OWLAPICommand def initialize(input_file, output_repo, opts = {}) - @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.6.0.jar" + @owlapi_wrapper_jar_path = LinkedData.bindir + "/owlapi-wrapper-1.7.0.jar" @input_file = input_file @output_repo = output_repo @master_file = opts[:master_file] diff --git a/test/models/test_ontology_submission.rb b/test/models/test_ontology_submission.rb index 3749b14b..a78a8793 100644 --- a/test/models/test_ontology_submission.rb +++ b/test/models/test_ontology_submission.rb @@ -192,7 +192,7 @@ def test_obo_part_of Goo.sparql_query_client.query(qthing).each_solution do |sol| count += 1 end - assert count == 0 + assert_equal 0, count qthing = <<-eos PREFIX rdfs: @@ -204,20 +204,35 @@ def test_obo_part_of count += 1 assert sol[:x].to_s["TAO_0000732"] end - assert count == 1 + assert_equal 1, count qcount = <<-eos PREFIX rdfs: SELECT DISTINCT * WHERE { - ?x . } + ?x . } eos count = 0 Goo.sparql_query_client.query(qcount).each_solution do |sol| count += 1 assert sol[:x].to_s["TAO_0000732"] end - assert count == 1 + assert_equal 1, count + + # The owlapi-wrapper used to emit each OBO relationship twice: once under + # http://data.bioontology.org/metadata/obo/ and again under the + # property's own IRI. Only the latter is emitted now, so guard against the + # duplicate annotation coming back. + qlegacy = <<-eos +SELECT DISTINCT * WHERE { + + ?x . } + eos + count = 0 + Goo.sparql_query_client.query(qlegacy).each_solution do |sol| + count += 1 + end + assert_equal 0, count sub = LinkedData::Models::OntologySubmission.where(ontology: [acronym: "TAO-TEST"]).first assert_equal(3, sub.roots.length, "Incorrect number of root classes")