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Loading GEO on Ontobee #41

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mcourtot opened this issue May 13, 2015 · 2 comments
Closed

Loading GEO on Ontobee #41

mcourtot opened this issue May 13, 2015 · 2 comments

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@mcourtot
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From http://purl.obolibrary.org/obo/geo.owl

Thanks,
Melanie
@ontoden
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ontoden commented May 15, 2015

Loading GEO failed.

The error messages:

Loading RDF store:
geo: loading data from http://purl.obolibrary.org/obo/geo.owl
geo: getting final url http://purl.obolibrary.org/obo/geo.owl
Coult not load ontology:
org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: http://www.ifomis.org/bfo/1.1 Cause: Problem parsing http://www.ifomis.org/bfo/1.1
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:

  1. RDFXMLParser
  2. OWLXMLParser
  3. OWLFunctionalSyntaxOWLParser
  4. TurtleOntologyParser
  5. OWLOBOParser
  6. KRSS2OWLParser
  7. ManchesterOWLSyntaxOntologyParser

Detailed logs:

Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""

Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)

    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1077)
    at org.coode.owlapi.owlxmlparser.OWLImportsHandler.endElement(OWLImportsHandler.java:28)
    at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:895)
    at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
    at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
    at org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:47)
    at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:602)
    at org.hegroup.rdfstore.OWLMerge.main(OWLMerge.java:65)

Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.ifomis.org/bfo/1.1
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:

  1. RDFXMLParser
  2. OWLXMLParser
  3. OWLFunctionalSyntaxOWLParser
  4. TurtleOntologyParser
  5. OWLOBOParser
  6. KRSS2OWLParser
  7. ManchesterOWLSyntaxOntologyParser

Detailed logs:

Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""

Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)

    at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:197)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1045)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1070)
    ... 21 more

geo: loading data from http://purl.obolibrary.org/obo/geo.owl
geo: getting final url http://purl.obolibrary.org/obo/geo.owl
Coult not load ontology:
org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: http://www.ifomis.org/bfo/1.1 Cause: Problem parsing http://www.ifomis.org/bfo/1.1
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:

  1. RDFXMLParser
  2. OWLXMLParser
  3. OWLFunctionalSyntaxOWLParser
  4. TurtleOntologyParser
  5. OWLOBOParser
  6. KRSS2OWLParser
  7. ManchesterOWLSyntaxOntologyParser

Detailed logs:

Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""

Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)

    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1077)
    at org.coode.owlapi.owlxmlparser.OWLImportsHandler.endElement(OWLImportsHandler.java:28)
    at org.coode.owlapi.owlxmlparser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:895)
    at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
    at org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
    at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
    at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
    at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
    at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
    at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
    at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
    at org.coode.owlapi.owlxmlparser.OWLXMLParser.parse(OWLXMLParser.java:47)
    at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:165)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:602)
    at org.hegroup.rdfstore.OWLMerge.main(OWLMerge.java:65)

Caused by: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://www.ifomis.org/bfo/1.1
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:

  1. RDFXMLParser
  2. OWLXMLParser
  3. OWLFunctionalSyntaxOWLParser
  4. TurtleOntologyParser
  5. OWLOBOParser
  6. KRSS2OWLParser
  7. ManchesterOWLSyntaxOntologyParser

Detailed logs:

Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLXMLParser
org.xml.sax.SAXParseException; systemId: http://www.ifomis.org/bfo/1.1; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.

Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""

Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)

    at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:197)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:687)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:628)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1045)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1070)
    ... 21 more

Failed to download owl file!

Done!

Oliver

From: Melanie Courtot [mailto:notifications@github.com]
Sent: Wednesday, May 13, 2015 6:32 PM
To: ontoden/ontobee
Subject: [ontobee] Loading GEO on Ontobee (#41)

From http://purl.obolibrary.org/obo/geo.owl

Thanks,
Melanie

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/41.

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

@e4ong1031
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GEO is already loaded into Ontobee.

I am closing this issue. Thanks.

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@mcourtot @e4ong1031 @ontoden