@Override
protected Void doInBackground() throws Exception {
// protein identification id
Collection<Comparable> protIdentIds = controller.getIdentificationIds();
// protein identification id and accession buffer
Map<Comparable, String> accBuffer = new LinkedHashMap<Comparable, String>();
// protein map
Map<String, Protein> proteins = new HashMap<String, Protein>();
try {
// iterate over each protein
for (Comparable protIdentId : protIdentIds) {
// get mapped protein accession
String protAcc = controller.getProteinAccession(protIdentId);
String protAccVersion = controller.getProteinAccessionVersion(protIdentId);
String database = controller.getSearchDatabase(protIdentId);
AccessionResolver resolver = new AccessionResolver(protAcc, protAccVersion, database, true);
String mappedProtAcc = resolver.isValidAccession() ? resolver.getAccession() : null;
if (mappedProtAcc != null) {
// get existing protein details
Protein protDetails =
PrideInspectorCacheManager.getInstance().getProteinDetails(mappedProtAcc);
if (protDetails != null) {
proteins.put(mappedProtAcc, protDetails);
}
accBuffer.put(protIdentId, mappedProtAcc);
if (accBuffer.size() == MAX_BATCH_DOWNLOAD_SIZE) {
// fetch and publish protein details
fetchAndPublish(accBuffer, proteins);
// clear accession buffer
accBuffer.clear();
// clear protein map
proteins = new HashMap<String, Protein>();
}
}
}
// this is important for cancelling
if (Thread.interrupted()) {
throw new InterruptedException();
}
if (!accBuffer.isEmpty() || !proteins.isEmpty()) {
fetchAndPublish(accBuffer, proteins);
}
} catch (InterruptedException e) {
logger.warn("Protein name download has been cancelled");
}
return null;
}
