Fixed NPE when JSON cannot be parsed to Accession

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -132,31 +132,31 @@ public class AccessionUploader implements InitializingBean {
 				responses.add(new AccessionOpResponse(accession.getInstituteCode(), accession.getAccessionNumber(), accession.getTaxonomy().getGenus()));
 			} catch (IOException e) {
 				LOG.error("Could not parse input: {}", e.getMessage(), e);
-				accessions.add(null);
+				accessions.add(null); // need to match get(index) with responses and updates
 				responses.add(new AccessionOpResponse(accn.get("instituteCode").asText(), accn.get("accessionNumber").asText(), accn.get("taxonomy").get("genus").asText())
 					.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(e.getMessage()));
 			}
 		}
 
-		List<Accession> forUpdate = new ArrayList<>(accessions.size());
-		forUpdate.addAll(accessions);
-
 		// Security check
 		for (int i = 0; i < accessions.size(); i++) {
 			Accession accession = accessions.get(i);
+			if (accession == null) {
+				continue;
+			}
 			if (!institute.getCode().equals(accession.getInstituteCode())) {
 				throw new InvalidApiUsageException("Accession does not belong to institute " + institute.getCode());
 			}
 		}
 
-		List<Accession> existingAccessions = accessionRepository.find(forUpdate);
-		LOG.debug("Have {} accessions for update and {} exist", forUpdate.size(), existingAccessions.size());
+		List<Accession> existingAccessions = accessionRepository.find(accessions);
+		LOG.debug("Have {} accessions for update and {} exist", accessions.size(), existingAccessions.size());
 
-		for (int i = 0; i < forUpdate.size(); i++) {
+		for (int i = 0; i < accessions.size(); i++) {
 			final JsonNode update = updates.get(i);
 
 			// Should we?
-			final Accession forU = forUpdate.get(i);
+			final Accession forU = accessions.get(i);
 			if (forU == null) {
 				LOG.debug("Skipping update of {}", update);
 				continue;