@Test public void testParseRetracted() { try { testStream = PubMedXMLParserTest.class.getResourceAsStream( "/data/pubmed-retracted.xml" ); Collection<BibliographicReference> brl = testParser.parse( testStream ); BibliographicReference br = brl.iterator().next(); assertNotNull( br.getAbstractText() ); assertEquals( "Retracted [In: Garey CE, Schwarzman AL, Rise ML, Seyfried TN. Nat Genet. 1995 Sep;11(1):104 PMID=7550304]", br.getDescription() ); assertTrue( br.getRetracted() ); } catch ( RuntimeException e ) { this.logOrThrowException( e ); } }
public Collection<BibliographicReference> parse( InputStream is ) { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setIgnoringComments( true ); factory.setValidating( false ); builder = factory.newDocumentBuilder(); Document document = builder.parse( is ); PubMedXMLParser.log.debug( "done parsing" ); return this.extractBibRefs( document ); } catch ( IOException | SAXException | ParserConfigurationException e ) { throw new RuntimeException( e ); } }
PubMedXMLParser { public Collection<BibliographicReference> parse( InputStream is ) { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setIgnoringComments( true ); factory.setValidating( false ); builder = factory.newDocumentBuilder(); Document document = builder.parse( is ); PubMedXMLParser.log.debug( "done parsing" ); return this.extractBibRefs( document ); } catch ( IOException | SAXException | ParserConfigurationException e ) { throw new RuntimeException( e ); } } }
PubMedXMLParser { public Collection<BibliographicReference> parse( InputStream is ) { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setIgnoringComments( true ); factory.setValidating( false ); builder = factory.newDocumentBuilder(); Document document = builder.parse( is ); PubMedXMLParser.log.debug( "done parsing" ); return this.extractBibRefs( document ); } catch ( IOException | SAXException | ParserConfigurationException e ) { throw new RuntimeException( e ); } }  }
PubMedXMLParser { public Collection<BibliographicReference> parse( InputStream is ) { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setIgnoringComments( true ); factory.setValidating( false ); builder = factory.newDocumentBuilder(); Document document = builder.parse( is ); PubMedXMLParser.log.debug( "done parsing" ); return this.extractBibRefs( document ); } catch ( IOException | SAXException | ParserConfigurationException e ) { throw new RuntimeException( e ); } }  void extractBookPublicationYear( BibliographicReference bibRef, Node item ); void extractPublisher( BibliographicReference bibRef, Node item ); Collection<BibliographicReference> parse( InputStream is ); }
PubMedXMLParser { public Collection<BibliographicReference> parse( InputStream is ) { try { DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); factory.setIgnoringComments( true ); factory.setValidating( false ); builder = factory.newDocumentBuilder(); Document document = builder.parse( is ); PubMedXMLParser.log.debug( "done parsing" ); return this.extractBibRefs( document ); } catch ( IOException | SAXException | ParserConfigurationException e ) { throw new RuntimeException( e ); } }  void extractBookPublicationYear( BibliographicReference bibRef, Node item ); void extractPublisher( BibliographicReference bibRef, Node item ); Collection<BibliographicReference> parse( InputStream is );  }