@Override
public List<GeneRank> listByGeneId(Integer geneId) {
SmartDBObject query = new SmartDBObject("geneId", geneId);
query.put("mixturePerc", new BasicDBObject("$lte", 0.01));
query.addReturnFields("sampleId", "tss5kRank", "source", "etype");
return super.find(query);
}
@Override
public List<Double> percentile(GeneRankCriteria criteria) {
SmartDBObject query = buildQueryByCriteria(criteria);
SortType sortType = SortType.ASC;
query.addReturnFields("mixturePerc");
query.addSort("mixturePerc", sortType);
return super.find(query, Double.class);
}
@Override
public List<Integer> listRankByCriteria(GeneRankCriteria criteria, String field) {
SmartDBObject query = buildQueryByCriteria(criteria);
field = null == field ? "TSS5K" : field.toUpperCase();
SortType sortType = SortType.ASC;
String _field =
"TSSTES".equals(field) ? "tssTesRank" : "TSS5K".equals(field) ? "tss5kRank" : "tssT5Rank";
query.addReturnFields(_field);
query.addSort(_field, sortType);
return super.find(query, Integer.class);
}
/*
* (non-Javadoc)
*
* @see
* com.omicseq.store.dao.IGeneRankDAO#findByCriteria(com.omicseq.store.dao
* .IGeneRankDAO.GeneRankCriteria, java.lang.Integer, java.lang.Integer)
*/
@Override
public List<GeneRank> findByCriteria(GeneRankCriteria criteria, Integer start, Integer limit) {
SmartDBObject query = buildQueryByCriteria(criteria);
SortType sortType = criteria.getSortType();
if (sortType == null) {
sortType = SortType.ASC;
}
query.addSort("mixturePerc", sortType);
// query.addSort("etype", SortType.ASC);
// query.addSort("tssTesCount", SortType.DESC);
// List<BasicDBObject> sortList = new ArrayList<BasicDBObject>();
// BasicDBObject sortObject = new SmartDBObject("mixturePerc", 1);
// sortObject.append("tssTesCount", -1);
// sortObject.append("etype", 1);
// sortList.add(sortObject);
// query.setSortList(sortList);
return super.find(query, start, limit);
}
private SmartDBObject buildQueryByCriteria(GeneRankCriteria criteria) {
Integer geneId = criteria.getGeneId();
SmartDBObject query = new SmartDBObject();
if (null != criteria.getSampleId()) {
query.put("sampleId", criteria.getSampleId());
}
if (null != geneId) {
query.put("geneId", geneId);
}
if (CollectionUtils.isNotEmpty(criteria.getSourceList())) {
query =
MongodbHelper.and(query, MongodbHelper.in("source", criteria.getSourceList().toArray()));
}
if (CollectionUtils.isNotEmpty(criteria.getEtypeList())) {
query =
MongodbHelper.and(query, MongodbHelper.in("etype", criteria.getEtypeList().toArray()));
}
if (null != criteria.getMixturePerc()) {
query.put("mixturePerc", new BasicDBObject("$lte", 0.01));
}
return query;
}
