Fix: Update accession count on startup

src/main/java/org/genesys2/server/listener/sample/FirstRunListener.java

@@ -34,6 +34,7 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.persistence.domain.AccessionRepository;
 import org.genesys2.server.service.BatchRESTService;
 import org.genesys2.server.service.CropService;
+import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoRegionService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
@@ -83,6 +84,9 @@ public class FirstRunListener extends RunAsAdminListener {
 	@Autowired
 	BatchRESTService batchService;
 
+	@Autowired
+	private GenesysService genesysService;
+
 	@Override
 	protected void init() throws Exception {
 		if (!createContent) {
@@ -167,6 +171,7 @@ public class FirstRunListener extends RunAsAdminListener {
 					LOG.warn("Upserting " + batch.size() + " accession records for " + instCode);
 					batchService.ensureTaxonomies(institute, batch);
 					batchService.upsertAccessionData(institute, batch);
+					genesysService.updateAccessionCount(institute);
 				}
 
 			} catch (JsonParseException e) {

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

@@ -151,7 +151,7 @@ public interface GenesysService {
 
 	List<Accession> saveAccessions(Iterable<Accession> accession);
 
-	void updateAccessionCount(FaoInstitute institute);
+	FaoInstitute updateAccessionCount(FaoInstitute institute);
 
 	List<SvalbardDeposit> getSvalbardData(AccessionId accession);
 

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

-/**
- * Copyright 2014 Global Crop Diversity Trust
+/*
+ * Copyright 2017 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,7 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- **/
+ */
 
 package org.genesys2.server.service.impl;
 
@@ -248,12 +248,12 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		return accessionRepository.countByHistoric(true);
 	}
 
-    @Override
-    public long countByCrop(final Crop crop) {
-        return accessionRepository.countByCrop(crop);
-    }
+	@Override
+	public long countByCrop(final Crop crop) {
+		return accessionRepository.countByCrop(crop);
+	}
 
-    @Override
+	@Override
 	public long countByInstitute(FaoInstitute institute) {
 		return accessionRepository.countByInstitute(institute);
 	}
@@ -401,7 +401,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		if (all.accession.getCrop() != null) {
 			ad.crops(all.accession.getCrop().getShortName());
 		} else {
-			// Ignore taxonomy crops: ad.crops(cropService.getCrops(all.accession.getTaxonomy()));
+			// Ignore taxonomy crops:
+			// ad.crops(cropService.getCrops(all.accession.getTaxonomy()));
 		}
 		return ad;
 	}
@@ -755,14 +756,15 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	@Override
-	@Transactional(readOnly = false)
+	@Transactional
 	// @CacheEvict(value = "statistics", allEntries = true)
-	public void updateAccessionCount(FaoInstitute institute) {
+	public FaoInstitute updateAccessionCount(FaoInstitute institute) {
 		if (institute == null)
-			return;
+			return institute;
 		long accessionCount = accessionRepository.countByInstitute(institute);
+		institute = instituteRepository.getOne(institute.getId());
 		institute.setAccessionCount(accessionCount);
-		instituteRepository.save(institute);
+		return instituteRepository.save(institute);
 	}
 
 	/**
@@ -811,7 +813,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public List<Accession> saveAccessions(Iterable<Accession> accessions) {
 		Set<FaoInstitute> institutes = new HashSet<FaoInstitute>();
 		for (Accession accession : accessions) {
-			// System.out.println("Saving " + accession + " STO=" + accession.getStoRage() + " ST=" +
+			// System.out.println("Saving " + accession + " STO=" + accession.getStoRage() +
+			// " ST=" +
 			// accession.getStorage());
 			institutes.add(accession.getInstitute());
 		}
@@ -863,10 +866,12 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	/**
-	 * Update {@link SvalbardDeposit} data and link with Genesys accessions. The primary key for {@link SvalbardDeposit} is the <code>sgsv_id</code> as provided by
-	 * NordGen.
+	 * Update {@link SvalbardDeposit} data and link with Genesys accessions. The
+	 * primary key for {@link SvalbardDeposit} is the <code>sgsv_id</code> as
+	 * provided by NordGen.
 	 * 
-	 * Any existing SGSV records are first deleted. Inserted and linked with accessions in this method.
+	 * Any existing SGSV records are first deleted. Inserted and linked with
+	 * accessions in this method.
 	 * 
 	 * @param svalbardDeposits
 	 * @return
@@ -897,7 +902,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			LOG.debug("Linked " + updatedCount + " accessions by alias in set " + sgsvIds);
 		}
 
-		// link indirectly where INSTCODE matches alternative sgsvCode, GENUS and ACCENUMB match
+		// link indirectly where INSTCODE matches alternative sgsvCode, GENUS and
+		// ACCENUMB match
 		updatedCount = svalbardRepository.linkInDirectly(sgsvIds);
 		if (updatedCount > 0 && LOG.isDebugEnabled()) {
 			LOG.debug("Linked " + updatedCount + " accessions using alternate code in set " + sgsvIds);

src/main/resources/dummy-data/PER001.json

 [{
   "instCode": "PER001",
+  "doi": "10.0155/43X~",
   "acceNumb": "CIP 102081.28",
   "genus": "Solanum",
   "cropName": "Sweetpotato",