test_class.file: phenol-io/src/test/java/org/monarchinitiative/phenol/io/OntologyLoaderTest.java
test_class.identifier: OntologyLoaderTest
test_case.body: @Test
    void loadOwl() {
      Path ontologyPath = Paths.get("src/test/resources/ncit_module.owl");
      Ontology ontology = OntologyLoader.loadOntology(ontologyPath.toFile());
      // the ncit_module.owl has 6 classes
      assertEquals(6, ontology.countAllTerms());
    }
test_case.class_method_signature: OntologyLoaderTest.loadOwl()
test_case.full_signature: @Test void loadOwl()
test_case.identifier: loadOwl
test_case.invocations: get loadOntology toFile assertEquals countAllTerms
test_case.modifiers: @Test
test_case.parameters: ()
test_case.return: void
test_case.signature: void loadOwl()
focal_class.declarator: logger = LoggerFactory.getLogger(OntologyLoader.class)
focal_class.modifier: private static final
focal_class.original_string: private static final Logger logger = LoggerFactory.getLogger(OntologyLoader.class);
focal_class.type: Logger
focal_class.var_name: logger
focal_class.file: phenol-io/src/main/java/org/monarchinitiative/phenol/io/OntologyLoader.java
focal_class.identifier: OntologyLoader
focal_class.class_method_signature: OntologyLoader.OntologyLoader()
focal_class.full_signature: private  OntologyLoader()
focal_class.identifier: OntologyLoader
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.signature:  OntologyLoader()
focal_class.class_method_signature: OntologyLoader.loadOntology(File file)
focal_class.full_signature: public static Ontology loadOntology(File file)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (File file)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(File file)
focal_class.class_method_signature: OntologyLoader.loadOntology(File file, String... termIdPrefixes)
focal_class.full_signature: public static Ontology loadOntology(File file, String... termIdPrefixes)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (File file, String... termIdPrefixes)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(File file, String... termIdPrefixes)
focal_class.class_method_signature: OntologyLoader.loadOntology(File file, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.full_signature: public static Ontology loadOntology(File file, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (File file, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(File file, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.class_method_signature: OntologyLoader.loadOntology(InputStream inputStream)
focal_class.full_signature: public static Ontology loadOntology(InputStream inputStream)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (InputStream inputStream)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(InputStream inputStream)
focal_class.class_method_signature: OntologyLoader.loadOntology(InputStream inputStream, String... termIdPrefixes)
focal_class.full_signature: public static Ontology loadOntology(InputStream inputStream, String... termIdPrefixes)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (InputStream inputStream, String... termIdPrefixes)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(InputStream inputStream, String... termIdPrefixes)
focal_class.class_method_signature: OntologyLoader.loadOntology(InputStream inputStream, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.full_signature: public static Ontology loadOntology(InputStream inputStream, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (InputStream inputStream, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(InputStream inputStream, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.class_method_signature: OntologyLoader.loadOntology(GraphDocument graphDocument, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.full_signature: public static Ontology loadOntology(GraphDocument graphDocument, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.identifier: loadOntology
focal_class.modifiers: public static
focal_class.parameters: (GraphDocument graphDocument, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.return: Ontology
focal_class.signature: Ontology loadOntology(GraphDocument graphDocument, CurieUtil curieUtil, String... termIdPrefixes)
focal_class.class_method_signature: OntologyLoader.loadGraphDocument(File file)
focal_class.full_signature: private static GraphDocument loadGraphDocument(File file)
focal_class.identifier: loadGraphDocument
focal_class.modifiers: private static
focal_class.parameters: (File file)
focal_class.return: GraphDocument
focal_class.signature: GraphDocument loadGraphDocument(File file)
focal_class.class_method_signature: OntologyLoader.loadGraphDocument(InputStream inputStream)
focal_class.full_signature: private static GraphDocument loadGraphDocument(InputStream inputStream)
focal_class.identifier: loadGraphDocument
focal_class.modifiers: private static
focal_class.parameters: (InputStream inputStream)
focal_class.return: GraphDocument
focal_class.signature: GraphDocument loadGraphDocument(InputStream inputStream)
focal_class.class_method_signature: OntologyLoader.readBytes(InputStream bufferedStream, int readlimit)
focal_class.full_signature: private static String readBytes(InputStream bufferedStream, int readlimit)
focal_class.identifier: readBytes
focal_class.modifiers: private static
focal_class.parameters: (InputStream bufferedStream, int readlimit)
focal_class.return: String
focal_class.signature: String readBytes(InputStream bufferedStream, int readlimit)
focal_class.class_method_signature: OntologyLoader.isJsonGraphDoc(String firstBytes)
focal_class.full_signature: private static boolean isJsonGraphDoc(String firstBytes)
focal_class.identifier: isJsonGraphDoc
focal_class.modifiers: private static
focal_class.parameters: (String firstBytes)
focal_class.return: boolean
focal_class.signature: boolean isJsonGraphDoc(String firstBytes)
focal_method.body: public static Ontology loadOntology(File file) {
      return loadOntology(file, CurieUtilBuilder.defaultCurieUtil());
    }
focal_method.class_method_signature: OntologyLoader.loadOntology(File file)
focal_method.full_signature: public static Ontology loadOntology(File file)
focal_method.identifier: loadOntology
focal_method.invocations: loadOntology defaultCurieUtil
focal_method.modifiers: public static
focal_method.parameters: (File file)
focal_method.return: Ontology
focal_method.signature: Ontology loadOntology(File file)