public JSONObject changePlateLocation(HttpSession session, JSONObject json) {
Long plateId = json.getLong("plateId");
String locationBarcode = json.getString("locationBarcode");
try {
String newLocation = LimsUtils.lookupLocation(locationBarcode);
if (newLocation != null) {
User user =
securityManager.getUserByLoginName(
SecurityContextHolder.getContext().getAuthentication().getName());
// Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
// Plateable> getPlateById(plateId);
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
plate.setLocationBarcode(locationBarcode);
/*
Note note = new Note();
note.setInternalOnly(true);
note.setText("Location changed to " + newLocation + " by " + user.getLoginName() + " on " + new Date());
note.setOwner(user);
note.setCreationDate(new Date());
plate.getNotes().add(note);
requestManager.saveSampleNote(sample, note);
*/
requestManager.savePlate(plate);
} else {
return JSONUtils.SimpleJSONError("New location barcode not recognised");
}
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("Plate saved successfully");
}
public JSONObject printPlateBarcodes(HttpSession session, JSONObject json) {
try {
User user =
securityManager.getUserByLoginName(
SecurityContextHolder.getContext().getAuthentication().getName());
String serviceName = null;
if (json.has("serviceName")) {
serviceName = json.getString("serviceName");
}
MisoPrintService<File, PrintContext<File>> mps = null;
if (serviceName == null) {
Collection<MisoPrintService> services =
printManager.listPrintServicesByBarcodeableClass(Plate.class);
if (services.size() == 1) {
mps = services.iterator().next();
} else {
return JSONUtils.SimpleJSONError(
"No serviceName specified, but more than one available service able to print this barcode type.");
}
} else {
mps = printManager.getPrintService(serviceName);
}
Queue<File> thingsToPrint = new LinkedList<File>();
JSONArray ss = JSONArray.fromObject(json.getString("plates"));
for (JSONObject s : (Iterable<JSONObject>) ss) {
try {
Long plateId = s.getLong("plateId");
// Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
// Plateable> getPlateById(plateId);
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
// autosave the barcode if none has been previously generated
if (plate.getIdentificationBarcode() == null
|| "".equals(plate.getIdentificationBarcode())) {
requestManager.savePlate(plate);
}
File f = mps.getLabelFor(plate);
if (f != null) thingsToPrint.add(f);
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error printing barcodes: " + e.getMessage());
}
}
PrintJob pj = printManager.print(thingsToPrint, mps.getName(), user);
return JSONUtils.SimpleJSONResponse("Job " + pj.getJobId() + " : Barcodes printed.");
} catch (MisoPrintException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to print barcodes: " + e.getMessage());
}
}
public JSONObject saveImportedElements(HttpSession session, JSONObject json) {
if (json.has("elements")) {
Plate currentPlate = null;
Pool currentPool = null;
try {
String description = json.getString("description");
String creationDate = json.getString("creationDate");
String plateMaterialType = null;
if (json.has("plateMaterialType") && !json.getString("plateMaterialType").equals("")) {
plateMaterialType = json.getString("plateMaterialType");
}
JSONObject elements = json.getJSONObject("elements");
JSONArray pools = JSONArray.fromObject(elements.get("pools"));
JSONArray savedPlates = new JSONArray();
ObjectMapper mapper = new ObjectMapper();
for (JSONArray innerPoolList : (Iterable<JSONArray>) pools) {
for (JSONObject pool : (Iterable<JSONObject>) innerPoolList) {
log.info(pool.toString());
PlatePool platePool =
mapper.readValue(pool.toString(), new TypeReference<PlatePool>() {});
currentPool = platePool;
for (Plate<LinkedList<Library>, Library> plate : platePool.getPoolableElements()) {
JSONObject j = new JSONObject();
// if (json.has("tagBarcode")) {
// String tagBarcode = json.getString("tagBarcode");
//
// plate.setTagBarcode(requestManager.listAllTagBarcodesByStrategyName());
// }
if (plate.getDescription() == null) {
plate.setDescription(description);
}
if (plate.getCreationDate() == null) {
// plate.setCreationDate(DateFormat.getInstance().parse(creationDate));
}
if (plate.getPlateMaterialType() == null && plateMaterialType != null) {
plate.setPlateMaterialType(PlateMaterialType.valueOf(plateMaterialType));
}
log.info("Saving plate: " + plate.toString());
currentPlate = plate;
long plateId = requestManager.savePlate(plate);
j.put("plateId", plateId);
savedPlates.add(j);
currentPlate = null;
}
log.info("Saving pool: " + pool.toString());
requestManager.savePool(platePool);
currentPool = null;
}
}
JSONObject resp = new JSONObject();
resp.put("plates", savedPlates);
return resp;
} catch (IOException e) {
if (currentPool != null) {
log.error(
"Error saving pool elements on new plate save. Deleting pool "
+ currentPool.toString());
// clear out child elements to make sure plate meets delete requirements
currentPool.getPoolableElements().clear();
try {
requestManager.deletePool(currentPool);
} catch (IOException e1) {
log.error("Cannot delete pool. Nothing left to do.");
e1.printStackTrace();
}
}
if (currentPlate != null) {
log.error(
"Error saving plate elements on new plate save. Deleting plate "
+ currentPlate.toString());
// clear out child elements to make sure plate meets delete requirements
currentPlate.getElements().clear();
try {
requestManager.deletePlate(currentPlate);
} catch (IOException e1) {
log.error("Cannot delete plate. Nothing left to do.");
e1.printStackTrace();
}
}
log.error("Caused by...");
e.printStackTrace();
return JSONUtils.SimpleJSONError("Cannot save imported plate: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("No valid plates available to save");
}
}
