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Upgrade the owlapi-wrapper JAR to 1.7.0 #317

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Merged
jvendetti merged 4 commits into from
Aug 18, 2026
Merged

Upgrade the owlapi-wrapper JAR to 1.7.0 #317

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daf6abf
Bump owlapi-wrapper to 1.7.0
jvendetti Aug 17, 2026
2f5b682
Restore executable bit on owlapi-wrapper-1.7.0.jar
jvendetti Aug 18, 2026
c68ed68
Use clearer assertions
jvendetti Aug 18, 2026
b5839b5
Update test_obo_part_of for owlapi-wrapper 1.7.0
jvendetti Aug 18, 2026
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Binary file renamed bin/owlapi-wrapper-1.6.0.jar → bin/owlapi-wrapper-1.7.0.jar
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2 changes: 1 addition & 1 deletion lib/ontologies_linked_data/parser/owlapi.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
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23 changes: 19 additions & 4 deletions test/models/test_ontology_submission.rb
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Expand Up @@ -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: <http://www.w3.org/2000/01/rdf-schema#>
Expand All @@ -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: <http://www.w3.org/2000/01/rdf-schema#>
SELECT DISTINCT * WHERE {
<http://purl.obolibrary.org/obo/TAO_0001044>
<http://data.bioontology.org/metadata/obo/part_of> ?x . }
<http://purl.obolibrary.org/obo/OBO_REL#_part_of> ?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/<rel> 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 {
<http://purl.obolibrary.org/obo/TAO_0001044>
<http://data.bioontology.org/metadata/obo/part_of> ?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")
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