@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"); } }
@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); }