Fix: Properly handle "newAcceNumb" and "doi" updates.

- Basic unit tests for AccessionUploader
- Report invalid fields in JSON

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

@@ -67,7 +67,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.ObjectReader;
 import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.google.common.base.Stopwatch;
 import com.google.common.collect.Iterators;
 
 import javassist.util.proxy.Proxy;
@@ -150,17 +149,6 @@ public class AccessionUploader implements InitializingBean {
 			}
 		}
 
-		// 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());
-			}
-		}
-
 		LOG.debug("Processsed incoming JSON for {} accessions in {}ms", updates.size(), stopWatch.getTime());
 
 		List<Accession> existingAccessions = accessionRepository.find(accessions);
@@ -200,6 +188,16 @@ public class AccessionUploader implements InitializingBean {
 			}
 
 			try {
+
+				// Accessions with registered DOI require the DOI to be provided
+				if (accession.getDoi() != null && updateA.getDoi() == null) {
+					throw new InvalidApiUsageException("DOI not included for accession with registered DOI=" + accession.getDoi());
+				}
+				
+				if (! accession.getInstitute().getId().equals(institute.getId())) {
+					throw new InvalidApiUsageException("Accession does not belong to institute " + institute.getCode());
+				}
+
 				accession = applyChanges(update, updateA, accession);
 				LOG.trace("Applied changes to 1 accession after {}ms", stopWatch.getTime());
 
@@ -218,7 +216,11 @@ public class AccessionUploader implements InitializingBean {
 			} catch (PleaseRetryException e) {
 				throw e;
 			} catch (InvalidApiUsageException e) {
-				LOG.error(e.getMessage(), e);
+				if (LOG.isDebugEnabled()) {
+					LOG.error(e.getMessage(), e);
+				} else {
+					LOG.error(e.getMessage());
+				}
 				response.setError(e.getMessage());
 			}
 		}
@@ -235,9 +237,9 @@ public class AccessionUploader implements InitializingBean {
 	/**
 	 * Check incoming JSON and update values accordingly
 	 * 
-	 * @param update
-	 * @param updateA
-	 * @param accession
+	 * @param update JSON node
+	 * @param updateA Received accession data
+	 * @param accession Genesys accession data
 	 * @return
 	 */
 	private Accession applyChanges(JsonNode update, Accession updateA, Accession accession) {
@@ -245,7 +247,13 @@ public class AccessionUploader implements InitializingBean {
 		update.fieldNames().forEachRemaining(fieldName -> {
 			LOG.trace("Updating {}", fieldName);
 
-			if ("taxonomy".equals(fieldName)) {
+			if ("doi".equals(fieldName)) {
+				updateDoi(updateA.getDoi(), accession);
+			
+			} else if ("accessionNumber".equals(fieldName) || "newAcceNumb".equals(fieldName)) {
+				updateAccessionNumber(update.get("accessionNumber"), update.get("newAcceNumb"), accession);
+
+			} else if ("taxonomy".equals(fieldName)) {
 				stopWatch.split();
 				updateTaxonomy(update.get("taxonomy"), updateA.getTaxonomy(), accession);
 				LOG.debug("Updated taxonomy for 1 accession in {}ms", stopWatch.getSplitTime());
@@ -302,6 +310,41 @@ public class AccessionUploader implements InitializingBean {
 		return accession;
 	}
 
+	private void updateDoi(String doi, Accession accession) {
+		if (StringUtils.isNotBlank(doi)) {
+			if (accession.getDoi() != null && ! StringUtils.equals(doi, accession.getDoi())) {
+				throw new InvalidApiUsageException("Cannot update DOI from " + accession.getDoi() + " to " + doi);
+			}
+			accession.setDoi(doi);
+		} else if (accession.getDoi() != null) {
+			// Only reaches here if DOI is provided and blank
+			throw new InvalidApiUsageException("Missing DOI for accession " + accession.getAccessionNumber() + " with doi=" + accession.getDoi());
+		}
+	}
+
+	private void updateAccessionNumber(JsonNode nodeAcceNumb, JsonNode nodeNewNumb, Accession accession) {
+		String accessionNumber = nodeAcceNumb.textValue();
+		String newAcceNumb = nodeNewNumb == null ? null : nodeNewNumb.textValue();
+
+		if (! accession.isPersisted()) {
+			if (newAcceNumb != null) {
+				throw new InvalidApiUsageException("Refusing insert when NEWACCENUMB (newAcceNumb) is provided");
+			}
+			// Set provided accessionNumber and ignore newAcceNumb
+			accession.setAccessionNumber(accessionNumber);
+
+		} else if (accession.getDoi() != null) {
+			// When accession has a DOI, override accession number
+			accession.setAccessionNumber(accessionNumber);
+			
+		} else if (newAcceNumb != null) {
+			if (! StringUtils.equals(newAcceNumb, accession.getAccessionNumber())) {
+				LOG.warn("Renaming accession {}: {} to {}", accession.getInstitute().getCode(), accession.getAccessionNumber(), newAcceNumb);
+				accession.setAccessionNumber(newAcceNumb);
+			}
+		}
+	}
+
 	private void updateCrop(JsonNode jsonNode, Accession accession) {
 		if (jsonNode.isNull()) {
 			accession.setCropName(null);
@@ -460,6 +503,10 @@ public class AccessionUploader implements InitializingBean {
 		while (fieldNames.hasNext() && (fieldName = fieldNames.next()) != null) {
 			LOG.trace("Copying {}.{}", clazz.getName(), fieldName);
 			Field field = ReflectionUtils.findField(clazz, fieldName);
+			if (field == null) {
+				LOG.warn("Client provided field {} that does not exist on {}", fieldName, clazz);
+				throw new InvalidApiUsageException("Field " + fieldName + " not valid for " + clazz.getName());
+			}
 			ReflectionUtils.makeAccessible(field);
 
 			// Find getter for lazy-loading