Silencing import errors does not seem to work for OBO files
Opened this issue · 6 comments
reckart commented
When loading an OBO file that contains an import (such as the example1.obo file from this project's test data), it fails with an exception if network access is not available.
Using a AutoIRIMapper and/or MissingImportHandlingStrategy.SILENT (as suggested here) does not seem to work.
var manager = OWLManager.createOWLOntologyManager();
// Does not seem to work for imports in OBO files....
var iriMappers = manager.getIRIMappers();
iriMappers.add(
new AutoIRIMapper(new File(kbRepositoriesRoot, "materializedOntologies"), true));
manager.getOntologyLoaderConfiguration()
.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
manager.getOntologyConfigurator()
.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
var ontology = manager.loadOntologyFromOntologyDocument(... input stream for OBO file ...);
ignazio1977 commented
OWLOntologyLoaderConfiguration is an immutable object. When you set a property on it, you need to tell the manager to use the new object:
manager.setOntologyLoaderConfiguration(
manager.getOntologyConfigurator()
.setMissingImportHandlingStrategy(
MissingImportHandlingStrategy.SILENT));
reckart commented
Thanks - doesn't help though unfortunately:
var iriMappers = manager.getIRIMappers();
iriMappers.add(
new AutoIRIMapper(new File(kbRepositoriesRoot, "materializedOntologies"), true));
manager.setOntologyLoaderConfiguration(manager.getOntologyLoaderConfiguration()
.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT));
manager.setOntologyConfigurator(manager.getOntologyConfigurator()
.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT));
Stack trace:
Caused by: org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://purl.obolibrary.org/obo/po/imports/ncbitaxon_import.owl> Cause: OWLOntologyCreationIOException: java.net.SocketException: Bad file descriptor
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1710)
at org.obolibrary.obo2owl.OWLAPIObo2Owl.tr(OWLAPIObo2Owl.java:505)
at org.obolibrary.obo2owl.OWLAPIObo2Owl.convert(OWLAPIObo2Owl.java:445)
at org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:47)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1025)
at de.tudarmstadt.ukp.inception.kb.KnowledgeBaseServiceImpl.transduceOboToOwlFunctionalSyntax(KnowledgeBaseServiceImpl.java:690)
at de.tudarmstadt.ukp.inception.kb.KnowledgeBaseServiceImpl.importData(KnowledgeBaseServiceImpl.java:650)
... 5 more
Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: OWLOntologyCreationIOException: java.net.SocketException: Bad file descriptor
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:216)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:955)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1663)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1703)
... 15 more
Caused by: org.semanticweb.owlapi.io.OWLOntologyInputSourceException: java.net.SocketException: Bad file descriptor
at org.semanticweb.owlapi.io.DocumentSources.getInputStream(DocumentSources.java:218)
at org.semanticweb.owlapi.io.DocumentSources.wrapInput(DocumentSources.java:143)
at org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:88)
at org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:105)
at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:38)
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:49)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
... 20 more
Caused by: java.net.SocketException: Bad file descriptor
at java.base/sun.nio.ch.NioSocketImpl.implRead(NioSocketImpl.java:325)
at java.base/sun.nio.ch.NioSocketImpl.read(NioSocketImpl.java:350)
at java.base/sun.nio.ch.NioSocketImpl$1.read(NioSocketImpl.java:803)
at java.base/java.net.Socket$SocketInputStream.read(Socket.java:976)
at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:244)
at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:284)
at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:343)
at java.base/sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:824)
at java.base/sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:759)
at java.base/sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:783)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1691)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1592)
at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:529)
at org.semanticweb.owlapi.io.DocumentSources.connect(DocumentSources.java:229)
at org.semanticweb.owlapi.io.DocumentSources.getInputStream(DocumentSources.java:209)
... 26 more
reckart commented
I believe the OBO code is neither considering the IRI mapper nor the silence mode.
ignazio1977 commented
which OWLAPI version are you using?
reckart commented
5.5.0
reckart commented
When I walked through the stack trace in the code, I had the impression that the OBO import code should catch Exception, wrap it in an UnloadableImportException and throw that. But I'm not sure even that would be enough. Probably the OBO code would actually need to consider the silencing flag itself.