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 downloadPlateInputForm(HttpSession session, JSONObject json) {
if (json.has("documentFormat")) {
String documentFormat = json.getString("documentFormat");
try {
File f =
misoFileManager.getNewFile(
Plate.class,
"forms",
"PlateInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
FormUtils.createPlateInputSpreadsheet(f);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
} catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to get plate input form: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
}
}
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.");
}
}
@Deprecated
public JSONObject previewExperiment(HttpSession session, JSONObject json) {
String experimentId = (String) json.get("experimentId");
try {
Experiment e = requestManager.getExperimentById(Long.parseLong(experimentId));
Collection<Run> runs = requestManager.listRunsByExperimentId(e.getExperimentId());
session.setAttribute("experiment", e);
StringBuilder rb = new StringBuilder();
for (Run r : runs) {
rb.append("<li><a href='/miso/run/")
.append(r.getRunId())
.append("'>")
.append(r.getName())
.append("</a></li>");
}
StringBuilder sb = new StringBuilder();
if (e.getPool() != null) {
if (e.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
for (Object dil : e.getPool().getDilutions()) {
Sample s = ((LibraryDilution) dil).getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
} else {
for (Object dil : e.getPool().getDilutions()) {
Sample s =
((emPCRDilution) dil).getEmPCR().getLibraryDilution().getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
}
}
StringBuilder b = new StringBuilder();
b.append(
"<div onclick=\"Effect.toggle('preview"
+ experimentId
+ "','blind'); return false;\">"
+ "<img src=\"/styles/images/moreinfo.png\" class=\"previewimage\"/></div>");
b.append("<br/><div id=\"preview" + experimentId + "\" class='exppreview'>");
b.append("Title: <b>").append(e.getTitle()).append("</b><br/>");
b.append("Description: <b>").append(e.getDescription()).append("</b><br/>");
b.append("Samples: <ul class=\"bullets\">").append(sb.toString()).append("</ul>");
b.append("Runs: <ul class=\"bullets\">").append(rb.toString()).append("</ul>");
b.append("</div>");
return JSONUtils.SimpleJSONResponse(b.toString());
} catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed");
}
}
