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[Bug #202] Add test reproducing the issue.

jopa-integration-tests/src/main/java/cz/cvut/kbss/jopa/test/runner/UpdateOperationsRunner.java

Martin Ledvinka at 3:42 PM 9/14/23

[Bug #202] Modify RDF4J driver to remove all property assertions on its update to prevent transaction concurrency issues.

ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/loader/GraphDBStatementLoaderTest.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/EpistemicAxiomRemoverTest.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/Rdf4jAdapterTest.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/StorageConnector.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModel.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/SubjectPredicateContext.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/ListHandlerTestBase.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/loader/DefaultContextInferenceStatementLoaderTest.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/GraphDBStorageConnector.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/EpistemicAxiomRemover.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModelTest.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/SimpleListHandlerTest.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/Connector.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/PoolingStorageConnector.java

Martin Ledvinka at 6:32 PM 9/14/23

[Bug #202] Modify Jena driver to remove all property assertions on its update to prevent transaction concurrency issues.

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemover.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemoverTest.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/ChangeTrackingStorageConnector.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SnapshotStorageConnector.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/JenaAdapterTest.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/ChangeTrackingStorageConnectorTest.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SharedStorageConnector.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModel.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SubjectPredicateContext.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/StorageConnector.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModelTest.java

Martin Ledvinka at 5:05 PM 9/19/23

[Bug #202] Ensure removeStatementsBySubjectAndPredicate removes also statements added with transaction to LocalModel.

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModel.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModelTest.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModelTest.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModel.java

Martin Ledvinka at 1:06 PM 9/20/23

[Bug #202] Modify OWLAPI driver to remove all property assertions on its update to prevent transaction concurrency issues.

jopa-integration-tests-owlapi/src/test/java/cz/cvut/kbss/jopa/test/environment/OwlapiDataAccessor.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectClassAssertionRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/EpistemicAxiomRemover.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/MutableRemoveAxiom.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/util/MutableAddAxiom.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/OwlapiListIterator.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/connector/OntologySnapshot.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/list/OwlapiListIteratorBase.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/ListHandler.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/util/MutableAxiomChange.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/TypesHandlerTest.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/InferredSimpleListIterator.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/ReferencedListHandler.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/MutableAddAxiom.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/AxiomSaverTest.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectAnnotationPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/SimpleListIterator.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/ReferencedListIterator.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/AxiomSaver.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/TypesHandler.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/util/MutableRemoveAxiom.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/OwlapiAdapterTest.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/TransactionalChange.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/OwlapiAdapter.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/connector/Connector.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/SimpleListHandler.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/list/InferredReferencedListIterator.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/connector/BasicStorageConnectorTest.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectObjectPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectDataPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/MutableAxiomChange.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/EpistemicAxiomRemoverTest.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/connector/BasicStorageConnector.java

Martin Ledvinka at 12:43 PM 9/22/23

[Ref] Minor refactoring of transactional changes in the OWL API driver.

ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/connector/OntologySnapshot.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/connector/BasicStorageConnector.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectAnnotationPropertyRemove.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/list/OwlapiListIteratorBase.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectDataPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/MutableRemoveAxiom.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectClassAssertionRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/TransactionalChange.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectObjectPropertyRemove.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/MutableAddAxiom.java

Martin Ledvinka at 1:02 PM 9/22/23

Minor refactoring and documentation for the epistemic axiom removal mechanism.

ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/EpistemicAxiomRemoverTest.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemover.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/StorageConnector.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SubjectPredicateContext.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/StorageConnector.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModel.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SnapshotStorageConnector.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/ChangeTrackingStorageConnector.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemoverTest.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/SubjectPredicateContext.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/Rdf4jAdapterTest.java ontodriver-rdf4j/src/test/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModelTest.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModelTest.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/JenaAdapterTest.java ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/ChangeTrackingStorageConnectorTest.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SharedStorageConnector.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/EpistemicAxiomRemover.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/Connector.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/LocalModel.java ontodriver-rdf4j/src/main/java/cz/cvut/kbss/ontodriver/rdf4j/connector/PoolingStorageConnector.java

Martin Ledvinka at 1:14 PM 9/22/23

Extend RDF vocabulary with RDF lists.

jopa-api/src/main/java/cz/cvut/kbss/jopa/vocabulary/RDF.java

Martin Ledvinka at 1:55 PM 9/22/23

[Bug #204] Use namespace resolver when processing @Sequence values.

jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/ClassFieldMetamodelProcessor.java jopa-impl/src/test/java/cz/cvut/kbss/jopa/model/metamodel/ClassFieldMetamodelProcessorTest.java

Martin Ledvinka at 2:09 PM 9/22/23

[SCA] SCA-based code improvements.

jopa-impl/src/main/java/cz/cvut/kbss/jopa/query/mapper/ResultSetMappingProcessor.java ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/query/JenaStatement.java jopa-owl2java/src/main/java/cz/cvut/kbss/jopa/owl2java/JavaTransformer.java ontodriver-owlapi/src/main/java/cz/cvut/kbss/ontodriver/owlapi/change/SubjectPropertyRemove.java jopa-impl/src/main/java/cz/cvut/kbss/jopa/model/metamodel/ClassFieldMetamodelProcessor.java modelgen/src/main/java/cz/cvut/kbss/jopa/modelgen/ModelGenProcessor.java ontodriver-owlapi/src/test/java/cz/cvut/kbss/ontodriver/owlapi/OwlapiAdapterTest.java jopa-impl/src/main/java/cz/cvut/kbss/jopa/query/sparql/SparqlQueryHolder.java

Martin Ledvinka at 4:35 PM 9/22/23

[1.1.3] Bump version, update changelog.

jopa-maven-plugin/pom.xml jopa-integration-tests-jena/pom.xml ontodriver-jena/pom.xml CHANGELOG.md pom.xml jopa-distribution/pom.xml jopa-owlapi-utils/pom.xml jopa-integration-tests/pom.xml ontodriver-rdf4j/pom.xml jopa-api/pom.xml ontodriver-owlapi/pom.xml jopa-impl/pom.xml modelgen/pom.xml datatype/pom.xml jopa-integration-tests-owlapi/pom.xml jopa-owl2java/pom.xml jopa-integration-tests-rdf4j/pom.xml ontodriver-api/pom.xml

Martin Ledvinka at 4:38 PM 9/22/23