@SuppressWarnings("unchecked")
private AnnotationView buildAnnotationView(Annotation annotation, boolean loadAllReplies) {
Object values[];
try {
values =
(Object[])
hibernateTemplate
.findByCriteria(
DetachedCriteria.forClass(Article.class)
.add(Restrictions.eq("ID", annotation.getArticleID()))
.setProjection(
Projections.projectionList()
.add(Projections.property("doi"))
.add(Projections.property("title"))),
0,
1)
.get(0);
} catch (IndexOutOfBoundsException e) {
// this should never happen
throw new IllegalStateException(
"Annotation "
+ annotation.getID()
+ " pointed to an article that didn't exist;"
+ " articleID: "
+ annotation.getArticleID());
}
String articleDoi = (String) values[0];
String articleTitle = (String) values[1];
return buildAnnotationView(annotation, articleDoi, articleTitle, loadAllReplies);
}
/**
* Build up a map of id, and replies to that id so we can initialize the reply tree
*
* @param articleId
* @return
*/
@SuppressWarnings("unchecked")
private Map<Long, List<Annotation>> buildReplyMap(Long articleId) {
Map<Long, List<Annotation>> fullReplyMap = new HashMap<Long, List<Annotation>>();
List<Annotation> allReplies =
hibernateTemplate.findByCriteria(
DetachedCriteria.forClass(Annotation.class)
.add(Restrictions.eq("articleID", articleId))
.add(Restrictions.eq("type", AnnotationType.REPLY)));
for (Annotation reply : allReplies) {
// parent id should never be null on a reply
if (reply.getParentID() == null) {
log.warn("Found a reply with null parent id. Reply id: " + reply.getID());
} else {
if (!fullReplyMap.containsKey(reply.getParentID())) {
fullReplyMap.put(reply.getParentID(), new ArrayList<Annotation>());
}
fullReplyMap.get(reply.getParentID()).add(reply);
}
}
return Collections.unmodifiableMap(fullReplyMap);
}
/**
* Get a list of all annotations satisfying the given criteria.
*
* @param startDate search for annotation after start date.
* @param endDate is the date to search until. If null, search until present date
* @param annotTypes List of annotation types
* @param maxResults the maximum number of results to return, or 0 for no limit
* @param journal journalName
* @return the (possibly empty) list of article annotations.
* @throws ParseException if any of the dates or query could not be parsed
* @throws URISyntaxException if an element of annotType cannot be parsed as a URI
*/
@Override
@Transactional(readOnly = true)
@SuppressWarnings("unchecked")
public List<AnnotationView> getAnnotations(
final Date startDate,
final Date endDate,
final Set<String> annotTypes,
final int maxResults,
final String journal)
throws ParseException, URISyntaxException {
/**
* * There may be a more efficient way to do this other than querying the database twice, at
* some point in time we might improve how hibernate does the object mappings
*
* <p>This execute returns annotationIDs, article DOIs and titles, which are needed to
* construction the annotionView object
*/
Map<Long, String[]> results =
(Map<Long, String[]>)
hibernateTemplate.execute(
new HibernateCallback() {
@Override
public Object doInHibernate(Session session)
throws HibernateException, SQLException {
/**
* URIGen We have to do this with SQL because of how the mappings are currently
* defined And hence, there is no way to unit test this
*/
StringBuilder sqlQuery = new StringBuilder();
Map<String, Object> params = new HashMap<String, Object>(3);
sqlQuery.append("select ann.annotationID, art.doi, art.title ");
sqlQuery.append("from annotation ann ");
sqlQuery.append("join article art on art.articleID = ann.articleID ");
sqlQuery.append("join journal j on art.eIssn = j.eIssn ");
sqlQuery.append("where j.journalKey = :journal ");
params.put("journal", journal);
if (startDate != null) {
sqlQuery.append(" and ann.created > :startDate");
params.put("startDate", startDate);
}
if (endDate != null) {
sqlQuery.append(" and ann.created < :endDate");
params.put("endDate", endDate);
}
if (annotTypes != null) {
sqlQuery.append(" and ann.type in (:annotTypes)");
params.put("annotTypes", annotTypes);
}
sqlQuery.append(" order by ann.created desc");
SQLQuery query = session.createSQLQuery(sqlQuery.toString());
query.setProperties(params);
if (maxResults > 0) {
query.setMaxResults(maxResults);
}
List<Object[]> tempResults = query.list();
Map<Long, String[]> results = new HashMap<Long, String[]>(tempResults.size());
for (Object[] obj : tempResults) {
// This forces this method to return Long values and not BigInteger
results.put(
(((Number) obj[0]).longValue()),
new String[] {(String) obj[1], (String) obj[2]});
}
return results;
}
});
// The previous query puts annotationID and doi into the map. annotationID is key
// I do this to avoid extra doi lookups later in the code.
if (results.size() > 0) {
DetachedCriteria criteria =
DetachedCriteria.forClass(Annotation.class)
.add(Restrictions.in("ID", results.keySet()))
.addOrder(Order.desc("created"))
.setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY);
List<Annotation> annotations = hibernateTemplate.findByCriteria(criteria);
List<AnnotationView> views = new ArrayList<AnnotationView>(annotations.size());
for (Annotation ann : annotations) {
String articleDoi = results.get(ann.getID())[0];
String articleTitle = results.get(ann.getID())[1];
views.add(buildAnnotationView(ann, articleDoi, articleTitle, false));
}
return views;
} else {
return new ArrayList<AnnotationView>();
}
}