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 final org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Constructor	Description
PubMedXMLParser()

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Details

log

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

Constructor Details

PubMedXMLParser

public PubMedXMLParser()

Method Details

parse

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

Throws:

IOException

processContributionDate

public static void processContributionDate(Node item,
 BibliographicReference bibRef)

extractPublisher

public static void extractPublisher(BibliographicReference bibRef,
 Node item)