Package ubic.gemma.core.loader.entrez.pubmed

Class PubMedXMLParser

java.lang.Object

ubic.gemma.core.loader.entrez.pubmed.PubMedXMLParser

public class PubMedXMLParser
extends Object

Simple class to parse XML in the format defined by ncbi. The resulting BibliographicReference object is associated with (transient) DatabaseEntry, in turn to a (transient) ExternalDatabase and MeSH.

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
protected static org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor	Description
PubMedXMLParser()

Method Summary

Modifier and Type	Method	Description
void	extractBookPublicationYear(BibliographicReference bibRef, Node item)
void	extractPublisher(BibliographicReference bibRef, Node item)
Collection<BibliographicReference>	parse(InputStream is)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

protected static final org.apache.commons.logging.Log log

Constructor Detail

PubMedXMLParser

public PubMedXMLParser()

Method Detail

extractBookPublicationYear

public void extractBookPublicationYear(BibliographicReference bibRef,
                                       Node item)

extractPublisher

public void extractPublisher(BibliographicReference bibRef,
                             Node item)

parse

public Collection<BibliographicReference> parse(InputStream is)
                                         throws IOException

Throws:

IOException