@Cacheable must not have unless = "#result == null"

Ensuring taxonomies exist before upserting accession data

src/main/java/org/genesys2/server/service/BatchRESTService.java

@@ -35,4 +35,6 @@ public interface BatchRESTService {
 	int deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> batch) throws RESTApiException;
 
 	int deleteAccessionsById(FaoInstitute institute, List<Long> batch);
+
+	void ensureTaxonomies(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException;
 }

src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java

@@ -61,7 +61,6 @@ import com.fasterxml.jackson.databind.node.ArrayNode;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @Service
-@Transactional(readOnly = true)
 public class BatchRESTServiceImpl implements BatchRESTService {
 
 	private final Log LOG = LogFactory.getLog(getClass());
@@ -87,6 +86,47 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Autowired
 	private TaxonomyManager taxonomyManager;
 
+	@Override
+	// Read-only, everything happens in manager
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
+	public void ensureTaxonomies(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException {
+		for (final AccessionHeaderJson dataJson : batch.keySet()) {
+			final ObjectNode accnJson = batch.get(dataJson);
+
+			final Taxonomy2 current = new Taxonomy2();
+			// Load JSON values into "current"
+			current.setGenus(stringIfProvided(accnJson.get("genus"), current.getGenus()));
+			current.setGenus(stringIfProvided(accnJson.get("newGenus"), current.getGenus()));
+			current.setSpecies(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("species"), current.getSpecies()), "sp."));
+			current.setSpAuthor(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("spauthor"), current.getSpAuthor()), ""));
+			current.setSubtaxa(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("subtaxa"), current.getSubtaxa()), ""));
+			current.setSubtAuthor(StringUtils.defaultIfBlank(stringIfProvided(accnJson.get("subtauthor"), current.getSubtAuthor()), ""));
+
+			Taxonomy2 ensuredTaxonomy = null;
+			try {
+				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
+						current.getSubtAuthor());
+			} catch (Throwable e) {
+				LOG.warn("*** lower(t.genus)=lower(" + current.getGenus() + ") and lower(t.species)=lower(" + current.getSpecies()
+						+ ") and lower(t.spauthor)=lower(" + current.getSpAuthor() + ") and lower(t.subtaxa)=lower(" + current.getSubtaxa()
+						+ ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
+			}
+			if (ensuredTaxonomy == null) {
+				LOG.warn("Adding new taxonomy: " + current);
+				ensuredTaxonomy = taxonomyManager.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
+						current.getSubtAuthor());
+				LOG.info("Registered: " + ensuredTaxonomy);
+
+				ensuredTaxonomy = taxonomyService.find(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
+						current.getSubtAuthor());
+
+				if (ensuredTaxonomy == null) {
+					throw new RuntimeException("Something is seriously wrong with taxonomyManager!");
+				}
+			}
+		}
+	}
+
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
@@ -498,7 +538,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return updated;
 	}
 
-	public static boolean updateAccessionStorage(Accession accession, ArrayNode arr) {
+	private static boolean updateAccessionStorage(Accession accession, ArrayNode arr) {
 		boolean updated = false;
 
 		List<Integer> as = accession.getStoRage();
@@ -698,9 +738,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 					+ ") and lower(t.spauthor)=lower(" + current.getSpAuthor() + ") and lower(t.subtaxa)=lower(" + current.getSubtaxa()
 					+ ") and lower(subtauthor)=lower(" + current.getSubtAuthor() + ")");
 		}
+
 		if (ensuredTaxonomy == null) {
-			ensuredTaxonomy = taxonomyManager.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-					current.getSubtAuthor());
+			LOG.warn("Could not find taxonomy for upsert " + current);
+			throw new RESTApiException("Could not find taxonomy " + current.getTaxonName());
 		}
 
 		if (!ensuredTaxonomy.sameAs(taxonomy)) {
@@ -733,25 +774,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return currentValue;
 	}
 
-	public static <T> String listToString(List<T> list) {
-		if (list == null || list.isEmpty()) {
-			return null;
-		}
-
-		final StringBuffer mcpdArr = new StringBuffer(20);
-
-		for (final T st : list) {
-			if (st != null && !StringUtils.isBlank(st.toString())) {
-				if (mcpdArr.length() > 0) {
-					mcpdArr.append(";");
-				}
-				mcpdArr.append(st.toString());
-			}
-		}
-
-		return StringUtils.defaultIfBlank(mcpdArr.toString(), null);
-	}
-
 	private String arrayToString(ArrayNode arr) {
 		if (arr == null || arr.isNull()) {
 			return null;

src/main/java/org/genesys2/server/service/impl/TaxonomyServiceImpl.java

@@ -83,7 +83,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	}
 
 	@Override
-	@Cacheable(value = "hibernate.org.genesys2.server.model.impl.Taxonomy2.fullname", key = "#genus + '-' + #species + '-' + #spAuthor + '-' + #subtaxa + '-' + #subtAuthor")
+	@Cacheable(value = "hibernate.org.genesys2.server.model.impl.Taxonomy2.fullname", key = "#genus + '-' + #species + '-' + #spAuthor + '-' + #subtaxa + '-' + #subtAuthor", unless = "#result == null")
 	public Taxonomy2 find(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) {
 		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
 	}

src/main/java/org/genesys2/server/servlet/controller/rest/AccessionController.java

@@ -223,6 +223,10 @@ public class AccessionController extends RestController {
 			}
 			batch.put(dataJson, (ObjectNode) json);
 		}
+		
+		// Step 1: Ensure all taxonomic data provided by client is persisted
+		batchRESTService.ensureTaxonomies(institute, batch);
+		
 
 		for (int i = 0; i < 10; i++) {
 			try {

src/test/java/org/genesys2/server/service/impl/ListToStringTest.java

-package org.genesys2.server.service.impl;
-
-import static org.junit.Assert.assertTrue;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.Test;
-
-public class ListToStringTest {
-
-	@Test
-	public void testLongListToString() {
-		List<Long> list = null;
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list = new ArrayList<Long>();
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list.add(1l);
-		assertTrue("1".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add(2l);
-		list.add(3l);
-		assertTrue("1;2;3".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add(3l);
-		assertTrue("1;2;3;3".equals(BatchRESTServiceImpl.listToString(list)));
-	}
-	
-	@Test
-	public void testIntListToString() {
-		List<Integer> list = null;
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list = new ArrayList<Integer>();
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list.add(1);
-		assertTrue("1".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add(2);
-		list.add(3);
-		assertTrue("1;2;3".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add(3);
-		assertTrue("1;2;3;3".equals(BatchRESTServiceImpl.listToString(list)));
-	}
-
-	@Test
-	public void testStringListToString() {
-		List<String> list = null;
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list = new ArrayList<String>();
-		assertTrue(null == BatchRESTServiceImpl.listToString(list));
-		list.add("1");
-		assertTrue("1".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add("2");
-		list.add("3");
-		assertTrue("1;2;3".equals(BatchRESTServiceImpl.listToString(list)));
-		list.add("3");
-		assertTrue("1;2;3;3".equals(BatchRESTServiceImpl.listToString(list)));
-	}
-}