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 void updateGroupWatcher(Long userId) throws IOException {
User user = securityManager.getUserById(userId);
if (user != null) {
for (Run r : runs.values()) {
if (user.getGroups().contains(securityManager.getGroupByName("RunWatchers"))) {
addWatcher(r, userId);
} else {
if (r.getSecurityProfile() != null
&& r.getSecurityProfile().getOwner() != null
&& !r.getSecurityProfile().getOwner().equals(user)) {
removeWatcher(r, userId);
}
}
}
}
}
private void update(Run r) throws IOException {
if (enabled) {
Run clone = runs.get(r.getId());
if (clone == null) {
log.debug("Update: no clone - pushing");
// new run - add all RunWatchers!
for (User u : securityManager.listUsersByGroupName("RunWatchers")) {
r.addWatcher(u);
}
push(r);
} else {
log.debug("Update: got clone of " + clone.getId());
if (r.getStatus() != null) {
clone.setStatus(r.getStatus());
}
// run QC added
if (r.getRunQCs().size() > clone.getRunQCs().size()) {
Set<RunQC> clonedQCs = new HashSet<RunQC>(clone.getRunQCs());
for (RunQC qc : r.getRunQCs()) {
if (!clonedQCs.contains(qc)) {
try {
clone.addQc(cloner.deepClone(qc));
} catch (MalformedRunQcException e) {
throw new IOException(e);
}
}
}
}
pop(clone);
push(r);
}
}
}
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());
}
}
@RequestMapping("/tech/groups")
public ModelAndView techListGroups() throws IOException {
try {
return new ModelAndView("/pages/listGroups.jsp", "groups", securityManager.listAllGroups());
} catch (IOException ex) {
if (log.isDebugEnabled()) {
log.debug("Failed to list groups", ex);
}
throw ex;
}
}
public void removeWatcher(Run run, Long userId) throws IOException {
User user = securityManager.getUserById(userId);
if (user != null) {
Run clone = runs.get(run.getId());
if (clone == null) {
run.removeWatcher(user);
push(run);
} else {
clone.removeWatcher(user);
}
}
}
public JSONObject deletePlate(HttpSession session, JSONObject json) {
try {
User user =
securityManager.getUserByLoginName(
SecurityContextHolder.getContext().getAuthentication().getName());
if (user.isAdmin()) {
if (json.has("plateId")) {
Long plateId = json.getLong("plateId");
requestManager.deletePlate(requestManager.getPlateById(plateId));
return JSONUtils.SimpleJSONResponse("Plate deleted");
} else {
return JSONUtils.SimpleJSONError("No plate specified to delete.");
}
} else {
return JSONUtils.SimpleJSONError("Only admins can delete objects.");
}
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Error getting currently logged in user.");
}
}
