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");
}
}
@Override
public Set<File> generateFilePath(SequencerPoolPartition partition, Dilution l)
throws SubmissionException {
Pool<? extends Poolable> pool = partition.getPool();
if (pool != null) {
if (pool.getExperiments() != null) {
Collection<Experiment> experiments = pool.getExperiments();
Experiment experiment = experiments.iterator().next();
StringBuilder filePath = new StringBuilder();
if (!"".equals(basePath)) {
filePath.append(
partition.getSequencerPartitionContainer().getRun().getFilePath()
+ "/Data/Intensities/BaseCalls/PAP/Project_"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
} else {
filePath.append(
basePath
+ "/"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
}
if (l.getLibrary().getTagBarcodes() != null && !l.getLibrary().getTagBarcodes().isEmpty()) {
filePath.append("_");
for (TagBarcode tb : l.getLibrary().getTagBarcodes().values()) {
filePath.append(tb.getSequence());
}
}
filePath.append("_L00" + partition.getPartitionNumber() + "*.fastq.gz");
Set<File> files = new HashSet<File>();
files.add(new File(filePath.toString()));
return files;
} else {
throw new SubmissionException("partition.getPool=null!");
}
} else {
throw new SubmissionException("Collection of experiments is empty");
}
}