@Override
public Map<Integer, Set<TagBarcode>> getApplicableBarcodes() {
if (tagBarcodeMap.isEmpty()) {
if (requestManager != null) {
tagBarcodeMap.put(1, new TreeSet<TagBarcode>());
try {
List<TagBarcode> barcodes =
new ArrayList<TagBarcode>(
requestManager.listAllTagBarcodesByPlatform(PlatformType.ILLUMINA.getKey()));
for (TagBarcode t : barcodes) {
if (getName().equals(t.getStrategyName())
&& t.getName() != null
&& t.getName().startsWith("Index ")) {
log.debug("Registering tag barcode: " + t.getName());
tagBarcodeMap.get(1).add(t);
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
}
return tagBarcodeMap;
}
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");
}
}
