/**
* This method gets the list of update candidates, validates it, removes any failed candidates
* from the update list, then updates the database with the [validated] update candidate list.
*
* @return The number of records updated
*/
public int validateAndUpdateCandidates() {
int updateCount = 0;
List<BibliosDAO> bibliosList =
bibliosManager.getUpdateCandidateBiblios(); // Get update candidates.
Map<Integer, BibliosDAO> errorMap = validator.validate(bibliosList); // Validate the list.
if (!bibliosList.isEmpty()) { // If there are update candidates ...
if (!errorMap.isEmpty()) { // If there were validation errors ...
Iterator<BibliosDAO> iterator = bibliosList.iterator();
while (iterator.hasNext()) { // ... remove the failed candidates from the update list.
BibliosDAO biblio = iterator.next();
int pk = biblio.getId_biblio();
if (errorMap.containsKey(pk)) {
Object[] parms = new Object[] {biblio.getId_biblio()};
String logMsg = messages.getMessage("Biblios.RemoveFailedCandidate", parms, Locale.UK);
logger.warn(logMsg);
iterator.remove();
}
}
}
bibliosList =
updateBibliosFromWebService(
bibliosList); // Update any biblios with valid pubmed_ids from web service.
updateCount = save(bibliosList); // Save the changes.
}
return updateCount;
}
/** 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);
}
/**
* Save the given biblio record in the database. Transaction management is the caller's
* responsibility.
*
* @param bibliosDAO the data to be saved
*/
@Override
public void save(BibliosDAO bibliosDAO) {
java.sql.Date sqlDate = Utils.tryParseToDbDate(bibliosDAO.getLast_change());
final String statement =
"UPDATE biblios SET title = ?, author1 = ?, author2 = ?, year = ?, journal = ?, username = ?, "
+ "volume = ?, pages = ?, pubmed_id = ?, updated = ?, last_change = ?, notes = ?"
+ "WHERE id_biblio = ?";
jdbcTemplate.update(
statement,
new Object[] {
bibliosDAO.getTitle(),
bibliosDAO.getAuthor1(),
bibliosDAO.getAuthor2(),
bibliosDAO.getYear(),
bibliosDAO.getJournal(),
bibliosDAO.getUsername(),
bibliosDAO.getVolume(),
bibliosDAO.getPages(),
bibliosDAO.getPubmed_id(),
bibliosDAO.getUpdated(),
sqlDate,
bibliosDAO.getNotes(),
bibliosDAO.getId_biblio()
});
}
/**
* 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;
}
/**
* 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;
}
/**
* This method computes the maximum field widths for all logged fields. It is needed for proper
* logfile formatting output for correctly aligning the old and new <code>BibliosDAO</code>
* records.
*
* @param oldBiblio the old [existing] biblio record
* @param newBiblio the new biblio record
* @param allowForQuotes If true, two extra bytes are added to each required field length to
* account for leading and trailing quotation marks.
*/
private void accumulateMaxWidths(BibliosDAO oldBiblio, BibliosDAO newBiblio) {
String sId_biblio = Integer.toString(oldBiblio.getId_biblio());
// Add two bytes to each biblio field (old and new) to account for leading and trailing quotes.
maxWidths[0] = Math.max(Math.max(sId_biblio.length(), heading1[0].length()), maxWidths[0]);
maxWidths[1] =
Math.max(
Math.max(
Math.max(
oldBiblio.getPubmed_id().length() + 2, newBiblio.getPubmed_id().length() + 2),
heading1[1].length()),
maxWidths[1]);
maxWidths[2] =
Math.max(
Math.max(
Math.max(oldBiblio.getYear().length() + 2, newBiblio.getYear().length() + 2),
heading1[2].length()),
maxWidths[2]);
maxWidths[3] =
Math.max(
Math.max(
Math.max(oldBiblio.getJournal().length() + 2, newBiblio.getJournal().length() + 2),
heading1[3].length()),
maxWidths[3]);
maxWidths[4] =
Math.max(
Math.max(
Math.max(oldBiblio.getVolume().length() + 2, newBiblio.getVolume().length() + 2),
heading1[4].length()),
maxWidths[4]);
maxWidths[5] =
Math.max(
Math.max(
Math.max(oldBiblio.getPages().length() + 2, newBiblio.getPages().length() + 2),
heading1[5].length()),
maxWidths[5]);
maxWidths[6] =
Math.max(
Math.max(
Math.max(
oldBiblio.getUsername().length() + 2, newBiblio.getUsername().length() + 2),
heading1[6].length()),
maxWidths[6]);
maxWidths[7] =
Math.max(
Math.max(
Math.max(oldBiblio.getUpdated().length() + 2, newBiblio.getUpdated().length() + 2),
heading1[7].length()),
maxWidths[7]);
maxWidths[8] =
Math.max(
Math.max(
Math.max(
oldBiblio.getLast_change().length() + 2,
newBiblio.getLast_change().length() + 2),
heading1[8].length()),
maxWidths[8]);
maxWidths[9] =
Math.max(
Math.max(
Math.max(oldBiblio.getTitle().length() + 2, newBiblio.getTitle().length()),
heading1[9].length() + 2),
maxWidths[9]);
maxWidths[10] =
Math.max(
Math.max(
Math.max(oldBiblio.getAuthor1().length() + 2, newBiblio.getAuthor1().length()),
heading1[10].length() + 2),
maxWidths[10]);
maxWidths[11] =
Math.max(
Math.max(
Math.max(oldBiblio.getAuthor2().length() + 2, newBiblio.getAuthor2().length()),
heading1[11].length() + 2),
maxWidths[11]);
}