@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> 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);
}