private List<Sample> getFileSamples(
Study study,
File file,
ObjectMap indexFileModifyParams,
boolean simulate,
QueryOptions options,
String sessionId)
throws CatalogException {
List<Sample> sampleList;
QueryOptions queryOptions =
new QueryOptions(
"include",
Arrays.asList("projects.studies.samples.id", "projects.studies.samples.name"));
if (file.getSampleIds() == null || file.getSampleIds().isEmpty()) {
// Read samples from file
List<String> sampleNames = null;
switch (file.getBioformat()) {
case VARIANT:
{
if (file.getAttributes().containsKey("variantSource")) {
Object variantSource = file.getAttributes().get("variantSource");
if (variantSource instanceof VariantSource) {
sampleNames = ((VariantSource) variantSource).getSamples();
} else if (variantSource instanceof Map) {
sampleNames = new ObjectMap((Map) variantSource).getAsStringList("samples");
} else {
logger.warn(
"Unexpected object type of variantSource ({}) in file attributes. Expected {} or {}",
variantSource.getClass(),
VariantSource.class,
Map.class);
}
}
if (sampleNames == null) {
VariantSource variantSource = readVariantSource(catalogManager, study, file);
indexFileModifyParams
.get("attributes", ObjectMap.class)
.put("variantSource", variantSource);
sampleNames = variantSource.getSamples();
}
}
break;
default:
return new LinkedList<>();
// throw new CatalogException("Unknown to get samples names from
// bioformat " + file.getBioformat());
}
// Find matching samples in catalog with the sampleName from the VariantSource.
queryOptions.add("name", sampleNames);
sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();
// check if all file samples exists on Catalog
if (sampleList.size()
!= sampleNames.size()) { // Size does not match. Find the missing samples.
Set<String> set = new HashSet<>(sampleNames);
for (Sample sample : sampleList) {
set.remove(sample.getName());
}
logger.warn("Missing samples: m{}", set);
if (options.getBoolean(CREATE_MISSING_SAMPLES, true)) {
for (String sampleName : set) {
if (simulate) {
sampleList.add(new Sample(-1, sampleName, file.getName(), null, null));
} else {
sampleList.add(
catalogManager
.createSample(
study.getId(), sampleName, file.getName(), null, null, null, sessionId)
.first());
}
}
} else {
throw new CatalogException(
"Can not find samples " + set + " in catalog"); // FIXME: Create missing samples??
}
}
} else {
// Get samples from file.sampleIds
queryOptions.add("id", file.getSampleIds());
sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();
}
List<Integer> sampleIdsList = new ArrayList<>(sampleList.size());
for (Sample sample : sampleList) {
sampleIdsList.add(sample.getId());
//
// sampleIdsString.append(sample.getName()).append(":").append(sample.getId()).append(",");
}
indexFileModifyParams.put("sampleIds", sampleIdsList);
return sampleList;
}
