Question

我正在尝试解组我从NCBI获取的BLAST输出的XML。不幸的是，它似乎失败了。我得到的堆栈跟踪是：

org.xml.sax.SAXParseException; systemId: file:/C:/blast_output.xml; lineNumber: 578; columnNumber: 17; XML document structures must start and end within the same entity.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:441)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:368)
    at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1436)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.endEntity(XMLDocumentFragmentScannerImpl.java:911)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.endEntity(XMLDocumentScannerImpl.java:563)
    at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.endEntity(XMLEntityManager.java:1384)
    at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1774)
    at com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.skipSpaces(XMLEntityScanner.java:1502)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.seekCloseOfStartTag(XMLDocumentFragmentScannerImpl.java:1386)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:246)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2778)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:117)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649)
    at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:203)
    ... 37 more

stacktrace中引用的XML行：

<Hsp_identity>8</Hsp_identity>

解组编码：

JAXBContext jc = JAXBContext.newInstance(BlastOutput.class);
Unmarshaller u = jc.createUnmarshaller();
return (BlastOutput) u.unmarshal(outputFile);

也许有人可以解释这里失败的原因。

Answer 1

您的XML可能存在问题，或者您的配置中JAXB正在使用解析器中的错误。您可以尝试解组XMLStreamReader的实例以强制使用不同的解析器。

import java.io.File;
import javax.xml.bind.*;
import javax.xml.stream.*;
import javax.xml.transform.stream.StreamSource;

public class Demo {

    public static void main(String[] args) throws Exception {
        Demo demo = new Demo();

        XMLInputFactory xif = XMLInputFactory.newFactory();
        File outputFile = new File("input.xml");
        XMLStreamReader xsr = xif.createXMLStreamReader(new StreamSource(outputFile));
        BlastOutput blastOutput = demo.unmarshalBlastOutput(xsr);
    }

    private BlastOutput unmarshalBlastOutput(XMLStreamReader xsr) throws Exception {
        JAXBContext jc = JAXBContext.newInstance(BlastOutput.class);
        Unmarshaller u = jc.createUnmarshaller();
        return (BlastOutput) u.unmarshal(xsr);
    }

}

javax.xml.bind.UnmarshalException：XML文档结构必须在同一实体中开始和结束

1 个答案: