TaxonomyService#find(genus, sp, ...) is cached

src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java

@@ -44,6 +44,7 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 	@Query("select distinct t.taxonName from Taxonomy2 t where t.taxonName like ?1")
 	List<String> autocompleteTaxonomy(String term, Pageable page);
 
+	@Query("select t from Taxonomy2 t where lower(t.genus) = lower(?1) and lower(t.species) = lower(?2) and lower(t.spAuthor) = lower(?3) and lower(t.subtaxa) = lower(?4) and lower(t.subtAuthor) = lower(?5)")
 	Taxonomy2 findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
 
 	List<Taxonomy2> findByGenus(String genus);

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

@@ -43,4 +43,6 @@ public interface TaxonomyService {
 
 	Taxonomy2 get(String genus, String species);
 
+	Taxonomy2 find(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
+
 }

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

@@ -41,6 +41,7 @@ import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.persistence.domain.AccessionCustomRepository;
 import org.genesys2.server.service.BatchRESTService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
@@ -80,6 +81,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Autowired
 	InstituteService instituteService;
 
+	@Autowired
+	AccessionCustomRepository accessionCustomRepository;
+
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
@@ -105,6 +109,22 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		final Map<Accession, ArrayNode> donorNumbs = new HashMap<Accession, ArrayNode>();
 		final Map<Accession, ArrayNode> collNumbs = new HashMap<Accession, ArrayNode>();
 
+		List<String> acceNumbs = new ArrayList<String>();
+		List<String> genera = new ArrayList<String>();
+		for (AccessionHeaderJson dataJson : batch.keySet()) {
+			acceNumbs.add(dataJson.acceNumb);
+			genera.add(dataJson.genus);
+		}
+
+		List<Accession> loaded = null;
+
+		try {
+			loaded = accessionCustomRepository.find(institute, acceNumbs, genera);
+		} catch (NonUniqueAccessionException e) {
+			LOG.warn(e.getMessage());
+			throw new RESTApiException(e.getMessage());
+		}
+
 		for (final AccessionHeaderJson dataJson : batch.keySet()) {
 			if (LOG.isDebugEnabled()) {
 				LOG.debug("Loading accession " + dataJson);
@@ -114,24 +134,24 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				throw new RuntimeException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = null;
-			try {
-				if (useUniqueAcceNumbs) {
-					accession = genesysService.getAccession(dataJson.instCode, dataJson.acceNumb);
-				} else {
-					accession = genesysService.getAccession(dataJson.instCode, dataJson.acceNumb, dataJson.genus);
+			Accession accession = CollectionUtils.find(loaded, new Predicate<Accession>() {
+				@Override
+				public boolean evaluate(Accession a) {
+					if (useUniqueAcceNumbs) {
+						return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb);
+					} else {
+						return a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus);
+					}
 				}
-			} catch (NonUniqueAccessionException e) {
-				LOG.warn(e.getMessage());
-				throw new RESTApiException(e.getMessage());
-			}
+			});
 
 			boolean updated = false;
 
 			final ObjectNode accnJson = batch.get(dataJson);
 
 			if (accession == null) {
-				LOG.warn("New accession " + dataJson);
+				if (LOG.isDebugEnabled())
+					LOG.debug("New accession " + dataJson);
 
 				accession = new Accession();
 				accession.setInstitute(institute);
@@ -142,6 +162,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				}
 
 				updated = true;
+			} else {
+				if (LOG.isTraceEnabled())
+					LOG.trace("*** Updating accession " + dataJson);
 			}
 
 			if (accession.getId() == null || useUniqueAcceNumbs && accnJson.get("genus") != null || accnJson.get("newGenus") != null
@@ -646,18 +669,27 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		// Load JSON values into "current"
 		current.setGenus(stringIfProvided(accnJson.get("genus"), current.getGenus()));
 		current.setGenus(stringIfProvided(accnJson.get("newGenus"), current.getGenus()));
-		current.setSpecies(stringIfProvided(accnJson.get("species"), current.getSpecies()));
-		current.setSpAuthor(stringIfProvided(accnJson.get("spauthor"), current.getSpAuthor()));
-		current.setSubtaxa(stringIfProvided(accnJson.get("subtaxa"), current.getSubtaxa()));
-		current.setSubtAuthor(stringIfProvided(accnJson.get("subtauthor"), current.getSubtAuthor()));
+		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()), ""));
 
-		final Taxonomy2 ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(),
-				current.getSubtaxa(), 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) {
+			ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
+					current.getSubtAuthor());
+		}
 
 		if (!ensuredTaxonomy.sameAs(taxonomy)) {
-
 			accession.setTaxonomy(ensuredTaxonomy);
-
 			updated = true;
 		}
 

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

@@ -31,6 +31,7 @@ import org.genesys2.server.persistence.domain.Taxonomy2Repository;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.TaxonomyService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Propagation;
@@ -45,7 +46,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 	@Autowired
 	private Taxonomy2Repository taxonomy2Repository;
-	
+
 	@Autowired
 	private CropService cropService;
 
@@ -121,7 +122,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 			species = "sp.";
 		}
 
-		final Taxonomy2 existing = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
+		final Taxonomy2 existing = find(genus, species, spAuthor, subtaxa, subtAuthor);
 		if (existing == null) {
 			try {
 				Taxonomy2 taxonomy = internalEnsure(genus, species, spAuthor, subtaxa, subtAuthor);
@@ -134,6 +135,12 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 		return existing;
 	}
 
+	@Override
+	@Cacheable(value = "hibernate.org.genesys2.server.model.impl.Taxonomy2.fullname", key = "#genus + '-' + #species + '-' + #spAuthor + '-' + #subtaxa + '-' + #subtAuthor")
+	public Taxonomy2 find(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) {
+		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, spAuthor, subtaxa, subtAuthor);
+	}
+
 	private synchronized Taxonomy2 internalEnsure(String genus, String species, String spAuthor, String subtaxa, String subtAuthor) throws InterruptedException {
 		Long taxSpeciesId = null, taxGenusId = null;
 
@@ -185,7 +192,7 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 						// Update crop taxonomy lists
 						cropService.updateCropTaxonomyLists(taxonomy);
-						
+
 						return taxonomy;
 
 					} catch (final Throwable e) {
@@ -204,18 +211,18 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 	@Override
 	public long getTaxonomy2Id(String genus) {
-		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, "sp.", "", "", "").getId();
+		return find(genus, "sp.", "", "", "").getId();
 	}
 
 	@Override
 	public long getTaxonomy2Id(String genus, String species) {
-		final Taxonomy2 tax = taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, "", "", "");
+		final Taxonomy2 tax = find(genus, species, "", "", "");
 		return tax.getId();
 	}
 
 	@Override
 	public Taxonomy2 get(String genus, String species) {
-		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, "", "", "");
+		return find(genus, species, "", "", "");
 	}
 
 	@Override
@@ -225,6 +232,6 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 
 	@Override
 	public Taxonomy2 get(String genus) {
-		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, "sp.", "", "", "");
+		return find(genus, "sp.", "", "", "");
 	}
 }