@Override
public Set<File> generateFilePaths(SequencerPoolPartition partition) throws SubmissionException {
Set<File> filePaths = new HashSet<File>();
if ((partition.getSequencerPartitionContainer().getRun().getFilePath()) == null) {
throw new SubmissionException("No valid run filepath!");
}
Pool<? extends Poolable> pool = partition.getPool();
if (pool == null) {
throw new SubmissionException("partition.getPool=null!");
} else {
Collection<Experiment> experiments = pool.getExperiments();
if (experiments.isEmpty()) {
throw new SubmissionException("Collection or experiments is empty");
} else {
Collection<? extends Dilution> libraryDilutions = pool.getDilutions();
if (libraryDilutions.isEmpty()) {
throw new SubmissionException("Collection of libraryDilutions is empty");
} else {
for (Dilution l : libraryDilutions) {
Set<File> files = generateFilePath(partition, l);
filePaths.addAll(files);
}
}
}
}
return filePaths;
}
@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");
}
}
@Test
public void testPools() {
try {
int expected = getDataSet().getTable("Pool").getRowCount();
int actual = getPoolDAO().count();
TestCase.assertEquals("Wrong number of Pools", expected, actual);
System.out.println("Expected number of Pools: " + expected + ", actual: " + actual);
for (Pool d : random(getPoolDAO(), actual, 1)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
@Override
public Set<File> generateFilePaths(SequencerPoolPartition partition) throws SubmissionException {
log.debug("Generating filepaths for partition " + partition.getId());
Set<File> filePaths = new HashSet<File>();
Pool pool = partition.getPool();
if (pool == null) {
throw new SubmissionException("partition.getPool=null!");
} else {
Collection<Experiment> experiments = pool.getExperiments();
if (experiments.isEmpty()) {
throw new SubmissionException("Collection or experiments is empty");
} else {
Collection<LibraryDilution> libraryDilutions = pool.getDilutions();
if (libraryDilutions.isEmpty()) {
throw new SubmissionException("Collection or libraryDilutions is empty");
} else {
for (Experiment e : experiments) {
StringBuilder filePath = new StringBuilder();
filePath.append(partition.getSequencerPartitionContainer().getRun().getFilePath());
filePath.append("/Data/Intensities/BaseCalls/PAP/Project_");
filePath.append(e.getStudy().getProject().getAlias());
filePath.append("/Sample_");
for (LibraryDilution l : libraryDilutions) {
// filePath.append(l.getLibrary().getName()+"/");
/*
+l.getLibrary().getName()+"_"+l.getLibrary().getTagBarcode().getSequence());
filePath.append("L00"+lane.getPartitionNumber())
*/
String folder = filePath.toString() + l.getLibrary().getName() + "/*.fastq.gz";
// System.out.println(folder);
File file = new File(folder);
filePaths.add(file);
}
}
}
}
}
return (filePaths);
}
@Override
public File generateFilePath(SequencerPoolPartition partition, LibraryDilution l)
throws SubmissionException {
log.debug("Generating filepaths for partition " + partition.getId());
Pool pool = partition.getPool();
if (pool != null) {
if (pool.getExperiments() != null) {
Collection<Experiment> experiments = pool.getExperiments();
Experiment experiment = experiments.iterator().next();
// String filePath =
// lane.getFlowcell().getRun().getFilePath()+"/Data/Intensities/BaseCalls/PAP/Project_"+
String filePath =
partition.getSequencerPartitionContainer().getRun().getFilePath()
+ "/Data/Intensities/BaseCalls/PAP/Project_"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName()
+ "_"
+ l.getLibrary().getTagBarcode().getSequence()
+ "_L00"
+ partition.getPartitionNumber()
+ "*.fastq.gz";
// System.out.println(filePath);
File file = new File(filePath);
return (file);
} else {
throw new SubmissionException("partition.getPool=null!");
}
} else {
throw new SubmissionException("Collection of experiments is empty");
}
}
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");
}
}