@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);
}
@Test
public void testExperiments() {
try {
// get row count of experiments in the dataset
int expected = getDataSet().getTable("Experiment").getRowCount();
// get number of experiments from the DAO
int actual = getExperimentDAO().count();
// test data contains 2 experiments, check size of returned list
TestCase.assertEquals("Wrong number of experiments", expected, actual);
System.out.println("Expected number of experiments: " + expected + ", actual: " + actual);
for (Experiment d : random(getExperimentDAO(), actual, 5)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
@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");
}
}
@Deprecated
public JSONObject previewExperiment(HttpSession session, JSONObject json) {
String experimentId = (String) json.get("experimentId");
try {
Experiment e = requestManager.getExperimentById(Long.parseLong(experimentId));
Collection<Run> runs = requestManager.listRunsByExperimentId(e.getExperimentId());
session.setAttribute("experiment", e);
StringBuilder rb = new StringBuilder();
for (Run r : runs) {
rb.append("<li><a href='/miso/run/")
.append(r.getRunId())
.append("'>")
.append(r.getName())
.append("</a></li>");
}
StringBuilder sb = new StringBuilder();
if (e.getPool() != null) {
if (e.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
for (Object dil : e.getPool().getDilutions()) {
Sample s = ((LibraryDilution) dil).getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
} else {
for (Object dil : e.getPool().getDilutions()) {
Sample s =
((emPCRDilution) dil).getEmPCR().getLibraryDilution().getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
}
}
StringBuilder b = new StringBuilder();
b.append(
"<div onclick=\"Effect.toggle('preview"
+ experimentId
+ "','blind'); return false;\">"
+ "<img src=\"/styles/images/moreinfo.png\" class=\"previewimage\"/></div>");
b.append("<br/><div id=\"preview" + experimentId + "\" class='exppreview'>");
b.append("Title: <b>").append(e.getTitle()).append("</b><br/>");
b.append("Description: <b>").append(e.getDescription()).append("</b><br/>");
b.append("Samples: <ul class=\"bullets\">").append(sb.toString()).append("</ul>");
b.append("Runs: <ul class=\"bullets\">").append(rb.toString()).append("</ul>");
b.append("</div>");
return JSONUtils.SimpleJSONResponse(b.toString());
} catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed");
}
}