/**
* Given a <code>List<BibliosDAO></code>, this method returns a new list, which is a copy of
* the original list, with updates applied from the biblios web service for valid pubmed_id
* values.
*
* @param oldBiblioList the original list of biblios
* @return a new list, which is a copy of the original list, with updates applied from the biblios
* web service for valid pubmed_id values
*/
private List<BibliosDAO> createNewBiblioListFromWebService(List<BibliosDAO> oldBiblioList) {
String volume;
List<BibliosDAO> newBiblioList = new ArrayList<>();
DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
String last_change = dateFormat.format(new Date());
for (BibliosDAO oldBiblio : oldBiblioList) {
BibliosDAO newBiblio = new BibliosDAO(); // Clone the original BibliosDAO.
newBiblio.setAuthor1(oldBiblio.getAuthor1());
newBiblio.setAuthor2(oldBiblio.getAuthor2());
newBiblio.setId_biblio(oldBiblio.getId_biblio());
newBiblio.setJournal(oldBiblio.getJournal());
newBiblio.setLast_change(last_change);
newBiblio.setNotes(oldBiblio.getNotes());
newBiblio.setPages(oldBiblio.getPages());
newBiblio.setPubmed_id(oldBiblio.getPubmed_id());
newBiblio.setTitle(oldBiblio.getTitle());
newBiblio.setUpdated(oldBiblio.getUpdated());
newBiblio.setUsername(oldBiblio.getUsername());
newBiblio.setVolume(oldBiblio.getVolume());
newBiblio.setYear(oldBiblio.getYear());
Integer pubmed_id =
Utils.tryParseInt(
oldBiblio
.getPubmed_id()); // If we have a valid pubmed_id, load the new BibliosDAO with
// the paper data.
if (pubmed_id != null) {
FetchBiblio paperFromWs = fetchPaper(pubmed_id);
if (paperFromWs != null) {
if (!paperFromWs.issue.isEmpty()) {
volume = paperFromWs.volume + "(" + paperFromWs.issue + ")";
} else {
volume = paperFromWs.volume;
}
newBiblio.setTitle(paperFromWs.title);
newBiblio.setAuthor1(paperFromWs.author1);
newBiblio.setAuthor2(paperFromWs.author2);
newBiblio.setYear("" + paperFromWs.year);
newBiblio.setJournal(paperFromWs.journal);
newBiblio.setVolume(volume);
newBiblio.setPages(paperFromWs.pages);
newBiblio.setUsername("EMMA");
newBiblio.setUpdated("Y");
newBiblioList.add(newBiblio);
}
}
}
return newBiblioList;
}
/** Test validation: invalid year. */
@Test
public void testPubmed_idWithWhitespace() {
System.out.println("testPubmed_idWithWhitespace");
EmmaBiblioValidator instance = new EmmaBiblioValidator();
List<BibliosDAO> inputList = new ArrayList<>();
BibliosDAO dao = new BibliosDAO();
inputList.add(dao); // Add an empty dao to the list just to make the list longer than 1 element.
dao = new BibliosDAO();
dao.setId_biblio(777);
dao.setPubmed_id(
" 12345 "); // NOTE: Leading or trailing whitespace fails the int conversion.
inputList.add(dao);
Map<Integer, BibliosDAO> actuals;
actuals = instance.validate(inputList);
assert (actuals.isEmpty());
}
/** Test validation: invalid year. */
@Test
public void testInvalidPubmed_id() {
System.out.println("testInvalidPubmed_id");
EmmaBiblioValidator instance = new EmmaBiblioValidator();
List<BibliosDAO> inputList = new ArrayList<>();
BibliosDAO dao = new BibliosDAO();
inputList.add(dao); // Add an empty dao to the list just to make the list longer than 1 element.
dao = new BibliosDAO();
dao.setId_biblio(888);
dao.setPubmed_id("invalid number");
inputList.add(dao);
Map<Integer, BibliosDAO> actuals;
actuals = instance.validate(inputList);
assert (actuals.size() == 1);
BibliosDAO resultDAO = actuals.get(888);
assertEquals(dao, resultDAO);
}
/**
* This method replaces any null <code>BibliosDAO</code> fields with the string '<null>' so
* that proper length computations and display can be performed against null fields. A throw-away
* copy of the biblio is returned and may be used for field length computations and display
* without fear of null pointer exceptions.
*
* @param biblio the biblio record to be patched
* @return a new <code>BibliosDAO</code> instance with any null fields replaced by the string
* '<null>'
*/
private BibliosDAO patchNullFields(BibliosDAO biblio) {
BibliosDAO newBiblio = new BibliosDAO();
newBiblio.setId_biblio(biblio.getId_biblio());
newBiblio.setPubmed_id(biblio.getPubmed_id() == null ? "<null>" : biblio.getPubmed_id());
newBiblio.setYear(biblio.getYear() == null ? "<null>" : biblio.getYear());
newBiblio.setJournal(biblio.getJournal() == null ? "<null>" : biblio.getJournal());
newBiblio.setVolume(biblio.getVolume() == null ? "<null>" : biblio.getVolume());
newBiblio.setPages(biblio.getPages() == null ? "<null>" : biblio.getPages());
newBiblio.setUsername(biblio.getUsername() == null ? "<null>" : biblio.getUsername());
newBiblio.setUpdated(biblio.getUpdated() == null ? "<null>" : biblio.getUpdated());
newBiblio.setLast_change(biblio.getLast_change() == null ? "<null>" : biblio.getLast_change());
newBiblio.setTitle(biblio.getTitle() == null ? "<null>" : biblio.getTitle());
newBiblio.setAuthor1(biblio.getAuthor1() == null ? "<null>" : biblio.getAuthor1());
newBiblio.setAuthor2(biblio.getAuthor2() == null ? "<null>" : biblio.getAuthor2());
return newBiblio;
}