private Element getWellNode(Session sess, char row, int col, int quadrant) {
try {
String plateQuery =
"SELECT p from Plate as p where p.idInstrumentRun="
+ ir.getIdInstrumentRun()
+ " AND p.quadrant="
+ quadrant;
Plate plate = (Plate) sess.createQuery(plateQuery).uniqueResult();
Element wellNode = new Element("PlateWell");
if (plate != null) {
String wellQuery =
"SELECT pw from PlateWell as pw where pw.idPlate="
+ plate.getIdPlate()
+ " AND pw.row='"
+ row
+ "' AND pw.col="
+ col;
PlateWell plateWell = (PlateWell) sess.createQuery(wellQuery).uniqueResult();
if (plateWell != null) {
plateWell.excludeMethodFromXML("getPlate");
plateWell.excludeMethodFromXML("getSample");
plateWell.excludeMethodFromXML("getAssay");
plateWell.excludeMethodFromXML("getPrimer");
wellNode = plateWell.toXMLDocument(null, DetailObject.DATE_OUTPUT_SQL).getRootElement();
if (plateWell.getAssay() != null) {
wellNode.setAttribute("assay", plateWell.getAssay().getDisplay());
} else if (plateWell.getPrimer() != null) {
wellNode.setAttribute("primer", plateWell.getPrimer().getDisplay());
}
} else {
wellNode.setAttribute("idPlateWell", "0");
}
} else {
wellNode.setAttribute("idPlateWell", "0");
}
return wellNode;
} catch (Exception e) {
LOG.error("An exception has occurred in CreateRunFile ", e);
return null;
}
}
private void changeRequestsToProcessing(Session sess, InstrumentRun ir) throws ProductException {
// Get any requests on that run
Map requests = new HashMap();
List wells =
sess.createQuery(
"SELECT pw from PlateWell as pw "
+ " join pw.plate as plate where plate.idInstrumentRun ="
+ ir.getIdInstrumentRun())
.list();
for (Iterator i1 = wells.iterator(); i1.hasNext(); ) {
PlateWell well = (PlateWell) i1.next();
if (well.getIdRequest() == null) {
break;
}
if (!well.getIdRequest().equals("") && !requests.containsKey(well.getIdRequest())) {
Request req = (Request) sess.get(Request.class, well.getIdRequest());
requests.put(req.getIdRequest(), req);
}
}
// Change request Status
for (Iterator i = requests.keySet().iterator(); i.hasNext(); ) {
int idReq = (Integer) i.next();
Request req = (Request) sess.get(Request.class, idReq);
if (req.getCodeRequestStatus() == null) {
ProductUtil.updateLedgerOnRequestStatusChange(
sess, req, req.getCodeRequestStatus(), RequestStatus.PROCESSING);
req.setCodeRequestStatus(RequestStatus.PROCESSING);
} else if (req.getCodeRequestStatus().equals(RequestStatus.NEW)
|| req.getCodeRequestStatus().equals(RequestStatus.SUBMITTED)) {
ProductUtil.updateLedgerOnRequestStatusChange(
sess, req, req.getCodeRequestStatus(), RequestStatus.PROCESSING);
req.setCodeRequestStatus(RequestStatus.PROCESSING);
}
}
sess.flush();
}