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 plateElementsDataTable(HttpSession session, JSONObject json) {
if (json.has("plateId")) {
try {
JSONObject j = new JSONObject();
JSONArray jsonArray = new JSONArray();
long plateId = json.getLong("plateId");
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
if (plate != null) {
for (Plateable p : plate.getElements()) {
if (p instanceof Library) {
Library l = (Library) p;
String strategyName = "No barcode";
StringBuilder seqbuilder = new StringBuilder();
if (!l.getTagBarcodes().isEmpty()) {
int count = 1;
Collection<TagBarcode> barcodes = l.getTagBarcodes().values();
for (TagBarcode tb : barcodes) {
strategyName = tb.getStrategyName();
seqbuilder.append(tb.getSequence());
if (l.getTagBarcodes().values().size() > 1
&& count < l.getTagBarcodes().values().size()) {
seqbuilder.append("-");
}
count++;
}
} else {
log.info("No tag barcodes!");
}
jsonArray.add(
"['"
+ l.getName()
+ "','"
+ l.getAlias()
+ "','"
+ strategyName
+ "','"
+ seqbuilder.toString()
+ "','"
+ "<a href=\"/miso/library/"
+ l.getId()
+ "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>"
+ "']");
}
}
}
j.put("elementsArray", jsonArray);
return j;
} catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("No plates to show");
}
}
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 getPlateBarcode(HttpSession session, JSONObject json) {
Long plateId = json.getLong("plateId");
File temploc = new File(session.getServletContext().getRealPath("/") + "temp/");
try {
// Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
// Plateable> getPlateById(plateId);
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
barcodeFactory.setPointPixels(1.5f);
barcodeFactory.setBitmapResolution(600);
RenderedImage bi = null;
if (json.has("barcodeGenerator")) {
BarcodeDimension dim = new BarcodeDimension(100, 100);
if (json.has("dimensionWidth") && json.has("dimensionHeight")) {
dim =
new BarcodeDimension(
json.getDouble("dimensionWidth"), json.getDouble("dimensionHeight"));
}
BarcodeGenerator bg = BarcodeFactory.lookupGenerator(json.getString("barcodeGenerator"));
if (bg != null) {
bi = barcodeFactory.generateBarcode(plate, bg, dim);
} else {
return JSONUtils.SimpleJSONError(
"'" + json.getString("barcodeGenerator") + "' is not a valid barcode generator type");
}
} else {
bi = barcodeFactory.generateSquareDataMatrix(plate, 400);
}
if (bi != null) {
File tempimage = misoFileManager.generateTemporaryFile("barcode-", ".png", temploc);
if (ImageIO.write(bi, "png", tempimage)) {
return JSONUtils.JSONObjectResponse("img", tempimage.getName());
}
return JSONUtils.SimpleJSONError("Writing temp image file failed.");
} else {
return JSONUtils.SimpleJSONError("Plate has no parseable barcode");
}
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(
e.getMessage() + ": Cannot seem to access " + temploc.getAbsolutePath());
}
}
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 getTagBarcodesForMaterialType(HttpSession session, JSONObject json) {
Map<String, Object> responseMap = new HashMap<String, Object>();
if (json.has("materialType") && !"".equals(json.getString("materialType"))) {
String materialType = json.getString("materialType");
StringBuilder srb = new StringBuilder();
srb.append("<select name='tagBarcode' id='tagBarcodes'>");
srb.append("<option value='0' selected='selected'>No barcode</option>");
// for (TagBarcode tb :
// requestManager.listPlateBarcodesByMaterialType(PlateMaterialType.get(materialType))) {
// srb.append("<option value='" + tb.getTagBarcodeId() + "'>" + tb.getName() + " ("+
// tb.getSequence()+")</option>");
// }
srb.append("</select>");
responseMap.put("plateBarcodes", srb.toString());
} else {
return JSONUtils.SimpleJSONError("Unrecognised MaterialType");
}
return JSONUtils.JSONObjectResponse(responseMap);
}
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.");
}
}
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");
}
}
@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");
}
}
