Program: 33922
Project: 33922
Buggy source:
public static MedlineDocument handleRecord(final MedlineCitation medlineCitation) throws Exception {
  MedlineDocument document=new MedlineDocument();
  Article article=medlineCitation.getArticle();
  AuthorList authorList=article.getAuthorList();
  if (authorList != null) {
    for (    Author author : authorList.getAuthor()) {
      String valid=author.getValidYN();
      if (valid != null && valid.equals("String_Node_Str")) {
        List<Object> names=author.getLastNameOrForeNameOrInitialsOrSuffixOrCollectiveName();
        String firstName=null;
        @SuppressWarnings("String_Node_Str") String initials=null;
        String lastName=null;
        String suffix=null;
        String collectiveName=null;
        for (        Object name : names) {
          if (name instanceof LastName) {
            LastName ln=(LastName)name;
            lastName=ln.getvalue();
          }
 else           if (name instanceof ForeName) {
            ForeName fn=(ForeName)name;
            firstName=fn.getvalue();
          }
 else           if (name instanceof Initials) {
            Initials it=(Initials)name;
            initials=it.getvalue();
          }
 else           if (name instanceof Suffix) {
            Suffix sf=(Suffix)name;
            suffix=sf.getvalue();
          }
 else           if (name instanceof CollectiveName) {
            CollectiveName cn=(CollectiveName)name;
            collectiveName=cn.getvalue();
          }
        }
        if (collectiveName != null) {
          document.addAuthor(collectiveName);
        }
        if (firstName != null && lastName != null && suffix != null) {
          String authorName=firstName + "String_Node_Str" + lastName+ "String_Node_Str"+ suffix;
          document.addAuthor(authorName);
        }
        if (firstName != null && lastName != null) {
          String authorName=firstName + "String_Node_Str" + lastName;
          document.addAuthor(authorName);
        }
      }
    }
  }
  List<Object> paginationOrELocationID=medlineCitation.getArticle().getPaginationOrELocationID();
  StringBuilder fullPagination=new StringBuilder();
  for (  Object obj : paginationOrELocationID) {
    if (obj instanceof Pagination) {
      Pagination page=(Pagination)obj;
      List<Object> startPageOrEndPageOrMedlinePgn=page.getStartPageOrEndPageOrMedlinePgn();
      String start=null;
      String end=null;
      for (      Object o : startPageOrEndPageOrMedlinePgn) {
        if (o instanceof StartPage) {
          StartPage startPage=(StartPage)o;
          start=startPage.getvalue();
        }
        if (o instanceof EndPage) {
          EndPage endPage=(EndPage)o;
          end=endPage.getvalue();
        }
        if (o instanceof MedlinePgn) {
          MedlinePgn medlinePgn=(MedlinePgn)o;
          fullPagination.append(medlinePgn.getvalue());
        }
      }
      if (start != null && !start.isEmpty()) {
        fullPagination.append(start);
      }
      if (!Strings.isNullOrEmpty(end)) {
        fullPagination.append("String_Node_Str").append(end);
      }
    }
  }
  document.setPagination(fullPagination.toString());
  String pmid=medlineCitation.getPMID().getvalue();
  document.setPmid(pmid);
  Journal journal=article.getJournal();
  document.setJournalTitle(journal.getTitle());
  document.setJournalIso(journal.getISOAbbreviation());
  JournalIssue journalIssue=journal.getJournalIssue();
  ArticleTitle title=medlineCitation.getArticle().getArticleTitle();
  if (title != null) {
    document.setTitle(title.getvalue());
  }
  Abstract articleAbstract=article.getAbstract();
  if (articleAbstract != null) {
    StringBuilder text=new StringBuilder();
    for (    AbstractText abstractText : articleAbstract.getAbstractText()) {
      text.append(abstractText.getvalue());
      text.append("String_Node_Str");
    }
    document.setAbstractText(text.toString().trim());
  }
  MedlineJournalInfo medlineJournalInfo=medlineCitation.getMedlineJournalInfo();
  if (medlineJournalInfo != null) {
    String issn=medlineJournalInfo.getISSNLinking();
    if (issn != null) {
      document.setIssn(issn);
    }
    String country=medlineJournalInfo.getCountry();
    if (country != null && !country.isEmpty()) {
      document.setJournalCountry(country);
    }
  }
  if (journalIssue != null) {
    String issue=journalIssue.getIssue();
    if (issue != null) {
      document.setJournalIssue(issue);
    }
    String volume=journalIssue.getVolume();
    if (volume != null) {
      document.setJournalVolume(volume);
    }
    PubDate pubDate=journalIssue.getPubDate();
    if (pubDate != null) {
      String year=null;
      String month=null;
      String day=null;
      for (      Object o : pubDate.getYearOrMonthOrDayOrSeasonOrMedlineDate()) {
        if (o instanceof Year) {
          Year y=(Year)o;
          year=y.getvalue();
        }
 else         if (o instanceof Month) {
          Month m=(Month)o;
          month=m.getvalue();
        }
 else         if (o instanceof Day) {
          Day d=(Day)o;
          day=d.getvalue();
        }
      }
      Date d=null;
      if (year != null) {
        document.setPubYear(year);
        int yearInt=Integer.parseInt(year);
        DateTime dateTime=new DateTime().withYear(yearInt);
        if (month != null) {
          dateTime=dateTime.withMonthOfYear(shortMonths.indexOf(month) + 1);
        }
 else {
          dateTime=dateTime.withMonthOfYear(1);
        }
        if (day != null) {
          dateTime=dateTime.withDayOfMonth(Integer.parseInt(day));
        }
 else {
          dateTime=dateTime.withDayOfMonth(1);
        }
        d=dateTime.withTimeAtStartOfDay().toDate();
      }
      if (d != null) {
        document.setPublicationDate(d);
      }
    }
  }
  String citation="String_Node_Str";
  if (document.getAuthors() != null) {
    citation=joiner.join(document.getAuthors()) + "String_Node_Str";
  }
  if (document.getTitle() != null) {
    citation=citation + title + "String_Node_Str";
  }
  if (document.getJournalIso() != null) {
    citation=citation + document.getJournalIso() + "String_Node_Str";
  }
  if (document.getPubYear() != null) {
    citation=citation + document.getPubYear() + "String_Node_Str";
  }
  if (document.getJournalVolume() != null) {
    citation=citation + document.getJournalVolume() + "String_Node_Str";
  }
  if (document.getJournalIssue() != null) {
    citation=citation + "String_Node_Str" + document.getJournalVolume()+ "String_Node_Str";
  }
  if (document.getPagination() != null) {
    citation=citation + "String_Node_Str" + document.getPagination()+ "String_Node_Str";
  }
  citation=citation.trim();
  document.setCitation(citation);
  return document;
}

Fixed version (ground truth):
public static MedlineDocument handleRecord(final MedlineCitation medlineCitation) throws Exception {
  MedlineDocument document=new MedlineDocument();
  Article article=medlineCitation.getArticle();
  AuthorList authorList=article.getAuthorList();
  if (authorList != null) {
    for (    Author author : authorList.getAuthor()) {
      String valid=author.getValidYN();
      if (valid != null && valid.equals("String_Node_Str")) {
        List<Object> names=author.getLastNameOrForeNameOrInitialsOrSuffixOrCollectiveName();
        String firstName=null;
        @SuppressWarnings("String_Node_Str") String initials=null;
        String lastName=null;
        String suffix=null;
        String collectiveName=null;
        for (        Object name : names) {
          if (name instanceof LastName) {
            LastName ln=(LastName)name;
            lastName=ln.getvalue();
          }
 else           if (name instanceof ForeName) {
            ForeName fn=(ForeName)name;
            firstName=fn.getvalue();
          }
 else           if (name instanceof Initials) {
            Initials it=(Initials)name;
            initials=it.getvalue();
          }
 else           if (name instanceof Suffix) {
            Suffix sf=(Suffix)name;
            suffix=sf.getvalue();
          }
 else           if (name instanceof CollectiveName) {
            CollectiveName cn=(CollectiveName)name;
            collectiveName=cn.getvalue();
          }
        }
        if (collectiveName != null) {
          document.addAuthor(collectiveName);
        }
        if (firstName != null && lastName != null && suffix != null) {
          String authorName=firstName + "String_Node_Str" + lastName+ "String_Node_Str"+ suffix;
          document.addAuthor(authorName);
        }
        if (firstName != null && lastName != null) {
          String authorName=firstName + "String_Node_Str" + lastName;
          document.addAuthor(authorName);
        }
      }
    }
  }
  List<Object> paginationOrELocationID=medlineCitation.getArticle().getPaginationOrELocationID();
  StringBuilder fullPagination=new StringBuilder();
  for (  Object obj : paginationOrELocationID) {
    if (obj instanceof Pagination) {
      Pagination page=(Pagination)obj;
      List<Object> startPageOrEndPageOrMedlinePgn=page.getStartPageOrEndPageOrMedlinePgn();
      String start=null;
      String end=null;
      for (      Object o : startPageOrEndPageOrMedlinePgn) {
        if (o instanceof StartPage) {
          StartPage startPage=(StartPage)o;
          start=startPage.getvalue();
        }
        if (o instanceof EndPage) {
          EndPage endPage=(EndPage)o;
          end=endPage.getvalue();
        }
        if (o instanceof MedlinePgn) {
          MedlinePgn medlinePgn=(MedlinePgn)o;
          fullPagination.append(medlinePgn.getvalue());
        }
      }
      if (start != null && !start.isEmpty()) {
        fullPagination.append(start);
      }
      if (!Strings.isNullOrEmpty(end)) {
        fullPagination.append("String_Node_Str").append(end);
      }
    }
  }
  document.setPagination(fullPagination.toString());
  String pmid=medlineCitation.getPMID().getvalue();
  document.setPmid(pmid);
  Journal journal=article.getJournal();
  document.setJournalTitle(journal.getTitle());
  document.setJournalIso(journal.getISOAbbreviation());
  JournalIssue journalIssue=journal.getJournalIssue();
  ArticleTitle title=medlineCitation.getArticle().getArticleTitle();
  if (title != null) {
    document.setTitle(title.getvalue());
  }
  Abstract articleAbstract=article.getAbstract();
  if (articleAbstract != null) {
    StringBuilder text=new StringBuilder();
    for (    AbstractText abstractText : articleAbstract.getAbstractText()) {
      text.append(abstractText.getvalue());
      text.append("String_Node_Str");
    }
    document.setAbstractText(text.toString().trim());
  }
  MedlineJournalInfo medlineJournalInfo=medlineCitation.getMedlineJournalInfo();
  if (medlineJournalInfo != null) {
    String issn=medlineJournalInfo.getISSNLinking();
    if (issn != null) {
      document.setIssn(issn);
    }
    String country=medlineJournalInfo.getCountry();
    if (country != null && !country.isEmpty()) {
      document.setJournalCountry(country);
    }
  }
  if (journalIssue != null) {
    String issue=journalIssue.getIssue();
    if (issue != null) {
      document.setJournalIssue(issue);
    }
    String volume=journalIssue.getVolume();
    if (volume != null) {
      document.setJournalVolume(volume);
    }
    PubDate pubDate=journalIssue.getPubDate();
    if (pubDate != null) {
      String year=null;
      String month=null;
      String day=null;
      for (      Object o : pubDate.getYearOrMonthOrDayOrSeasonOrMedlineDate()) {
        if (o instanceof Year) {
          Year y=(Year)o;
          year=y.getvalue();
        }
 else         if (o instanceof Month) {
          Month m=(Month)o;
          month=m.getvalue();
        }
 else         if (o instanceof Day) {
          Day d=(Day)o;
          day=d.getvalue();
        }
      }
      Date d=null;
      if (year != null) {
        document.setPubYear(year);
        int yearInt=Integer.parseInt(year);
        DateTime dateTime=new DateTime().withYear(yearInt);
        if (month != null) {
          dateTime=dateTime.withMonthOfYear(shortMonths.indexOf(month) + 1);
        }
 else {
          dateTime=dateTime.withMonthOfYear(1);
        }
        if (day != null) {
          dateTime=dateTime.withDayOfMonth(Integer.parseInt(day));
        }
 else {
          dateTime=dateTime.withDayOfMonth(1);
        }
        d=dateTime.withTimeAtStartOfDay().toDate();
      }
      if (d != null) {
        document.setPublicationDate(d);
      }
    }
  }
  String citation="String_Node_Str";
  if (document.getAuthors() != null) {
    citation=joiner.join(document.getAuthors()) + "String_Node_Str";
  }
  if (document.getTitle() != null) {
    citation=citation + document.getTitle() + "String_Node_Str";
  }
  if (document.getJournalIso() != null) {
    citation=citation + document.getJournalIso() + "String_Node_Str";
  }
  if (document.getPubYear() != null) {
    citation=citation + document.getPubYear() + "String_Node_Str";
  }
  if (document.getJournalVolume() != null) {
    citation=citation + document.getJournalVolume() + "String_Node_Str";
  }
  if (document.getJournalIssue() != null) {
    citation=citation + "String_Node_Str" + document.getJournalVolume()+ "String_Node_Str";
  }
  if (document.getPagination() != null) {
    citation=citation + "String_Node_Str" + document.getPagination()+ "String_Node_Str";
  }
  citation=citation.trim();
  document.setCitation(citation);
  return document;
}