BatchRESTService test

src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java

@@ -137,7 +137,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 	}
 
 	public boolean sameAs(Taxonomy2 taxonomy) {
-		return taxonomy == null ? false : taxonomy.getId().equals(id);
+		return taxonomy == null ? false : id.equals(taxonomy.getId());
 	}
 
 	public Long getTaxGenus() {
@@ -166,7 +166,7 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
 
 	@Override
 	public String toString() {
-		return MessageFormat.format("Tax id={0} taxonName={1}", id, getTaxonName());
+		return MessageFormat.format("Tax id={0} taxonName={1} genus={2} sp={3} spauthor={4} subtaxa={5} subtauthor={6}", id, getTaxonName(), genus, species, spAuthor, subtaxa, subtAuthor);
 	}
 
 }

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

@@ -67,8 +67,11 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	@Transactional(readOnly = false)
 	public void updateInstituteAccessionCount(long instituteId) {
 		LOG.info("Updating institute accession count for instituteId=" + instituteId);
+//		int count = jdbcTemplate
+//				.update("UPDATE faoinstitute FI inner join (select instituteId, count(*) X from accession where instituteId= ? group by instituteId) A on A.instituteId=FI.id set FI.accessionCount=A.X where FI.id = ?;",
+//						instituteId, instituteId);
 		int count = jdbcTemplate
-				.update("UPDATE faoinstitute FI inner join (select instituteId, count(*) X from accession where instituteId= ? group by instituteId) A on A.instituteId=FI.id set FI.accessionCount=A.X where FI.id = ?;",
+				.update("UPDATE faoinstitute SET accessionCount = (select count(*) from accession where instituteId=?) where id = ?;",
 						instituteId, instituteId);
 		LOG.info("Institute accession counts updated: " + count);
 	}

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

@@ -123,7 +123,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				accession.setInstitute(institute);
 				accession.setAccessionName(dataJson.acceNumb);
 
-				if (accnJson.get("genus") == null || accnJson.get("newGenus") == null) {
+				if (accnJson.get("genus") == null && accnJson.get("newGenus") == null) {
 					throw new RESTApiException("Cannot create new accession without specifying genus");
 				}
 
@@ -444,12 +444,11 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		boolean updated = false;
 
 		// Do not persist this one, temporary use
-		Taxonomy2 current = accession.getTaxonomy();
-		if (current == null) {
-			current = new Taxonomy2();
-		}
-
+		Taxonomy2 current = new Taxonomy2();
+		Taxonomy2 taxonomy = accession.getTaxonomy();
 		// Load JSON values into "current"
+		if (taxonomy!=null)
+			current.setId(taxonomy.getId());
 		current.setGenus(stringIfProvided(accnJson.get("genus"), current.getGenus()));
 		current.setGenus(stringIfProvided(accnJson.get("newGenus"), current.getGenus()));
 		current.setSpecies(stringIfProvided(accnJson.get("species"), current.getSpecies()));
@@ -457,10 +456,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		current.setSubtaxa(stringIfProvided(accnJson.get("subtaxa"), current.getSubtaxa()));
 		current.setSubtAuthor(stringIfProvided(accnJson.get("subtauthor"), current.getSubtAuthor()));
 
-		Taxonomy2 ensuredTaxonomy = null;
-		if (current.getId() == null
-				|| !((ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(), current.getSubtaxa(),
-						current.getSubtAuthor())).sameAs(current))) {
+		Taxonomy2 ensuredTaxonomy = taxonomyService.ensureTaxonomy2(current.getGenus(), current.getSpecies(), current.getSpAuthor(),
+				current.getSubtaxa(), current.getSubtAuthor());
+		
+		if (!(ensuredTaxonomy.sameAs(current))) {
 
 			accession.setTaxonomy(ensuredTaxonomy);
 			accession.setTaxGenus(ensuredTaxonomy.getTaxGenus());

src/test/java/org/genesys2/server/test/BatchRESTServiceTest.java

+package org.genesys2.server.test;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.velocity.app.VelocityEngine;
+import org.apache.velocity.exception.VelocityException;
+import org.genesys2.server.aspect.AsAdminAspect;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.AclService;
+import org.genesys2.server.service.BatchRESTService;
+import org.genesys2.server.service.ContentService;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.GeoService;
+import org.genesys2.server.service.HtmlSanitizer;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.OrganizationService;
+import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.UserService;
+import org.genesys2.server.service.impl.AclServiceImpl;
+import org.genesys2.server.service.impl.BatchRESTServiceImpl;
+import org.genesys2.server.service.impl.ContentServiceImpl;
+import org.genesys2.server.service.impl.GenesysServiceImpl;
+import org.genesys2.server.service.impl.GeoServiceImpl;
+import org.genesys2.server.service.impl.InstituteServiceImpl;
+import org.genesys2.server.service.impl.OWASPSanitizer;
+import org.genesys2.server.service.impl.OrganizationServiceImpl;
+import org.genesys2.server.service.impl.RESTApiException;
+import org.genesys2.server.service.impl.TaxonomyServiceImpl;
+import org.genesys2.server.service.impl.UserServiceImpl;
+import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.CacheManager;
+import org.springframework.cache.support.NoOpCacheManager;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.ui.velocity.VelocityEngineFactoryBean;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = BatchRESTServiceTest.Config.class, initializers = PropertyPlacholderInitializer.class)
+public class BatchRESTServiceTest {
+	private ObjectMapper mapper = new ObjectMapper();
+
+	@Import(JpaDataConfig.class)
+	@ComponentScan(basePackages = { "org.genesys2.server.persistence.domain" })
+	public static class Config {
+
+		@Bean
+		public AsAdminAspect asAdminAspect() {
+			return new AsAdminAspect();
+		}
+
+		@Bean
+		public UserService userService() {
+			return new UserServiceImpl();
+		}
+
+		@Bean
+		public AclService aclService() {
+			return new AclServiceImpl();
+		}
+
+		@Bean
+		public TaxonomyService taxonomyService() {
+			return new TaxonomyServiceImpl();
+		}
+
+		@Bean
+		public BatchRESTService batchRESTService() {
+			return new BatchRESTServiceImpl();
+		}
+
+		@Bean
+		public GenesysService genesysService() {
+			return new GenesysServiceImpl();
+		}
+
+		@Bean
+		public CacheManager cacheManager() {
+			return new NoOpCacheManager();
+		}
+
+		@Bean
+		public HtmlSanitizer htmlSanitizer() {
+			return new OWASPSanitizer();
+		}
+
+		@Bean
+		public GeoService geoService() {
+			return new GeoServiceImpl();
+		}
+
+		@Bean
+		public ContentService contentService() {
+			return new ContentServiceImpl();
+		}
+
+		@Bean
+		public VelocityEngine velocityEngine() throws VelocityException, IOException {
+			VelocityEngineFactoryBean vf = new VelocityEngineFactoryBean();
+			return vf.createVelocityEngine();
+		}
+
+		@Bean
+		public OrganizationService organizationService() {
+			return new OrganizationServiceImpl();
+		}
+
+		@Bean
+		public InstituteService instituteService() {
+			return new InstituteServiceImpl();
+		}
+	}
+
+	@Autowired
+	private BatchRESTService batchRESTService;
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Autowired
+	private TaxonomyService taxonomyService;
+
+	@Autowired
+	private InstituteService instituteService;
+
+	@Before
+	public void setup() {
+		System.err.println("Setting up");
+		Collection<FaoInstitute> institutes = new ArrayList<FaoInstitute>();
+		for (String instCode : new String[] { "SYR002", "NGA039" }) {
+			FaoInstitute institute = new FaoInstitute();
+			institute.setFullName(instCode + " institute");
+			institute.setCode(instCode);
+			institute.setUniqueAcceNumbs(true);
+			institutes.add(institute);
+		}
+		instituteService.update(institutes);
+	}
+
+	@Test
+	public void testNewAccession() {
+		String instCode = "SYR002";
+		FaoInstitute institute = instituteService.getInstitute(instCode);
+		assertTrue("institute is null", institute != null);
+		System.err.println(institute);
+
+		Map<AccessionJson, ObjectNode> batch = new HashMap<AccessionJson, ObjectNode>();
+
+		AccessionJson dataJson = new AccessionJson();
+		dataJson.acceNumb = "AC 1";
+		dataJson.instCode = instCode;
+
+		ObjectNode json = mapper.createObjectNode();
+		json.put("genus", "Hordeum");
+		batch.put(dataJson, json);
+
+		try {
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (RESTApiException e) {
+			fail(e.getMessage());
+		}
+
+		Accession accession = genesysService.getAccession(instCode, "AC 1");
+		assertTrue(accession.getId() != null);
+		assertTrue(accession.getInstituteCode().equals(instCode));
+		assertTrue(accession.getInstitute().getId().equals(institute.getId()));
+		assertTrue(accession.getTaxonomy() != null);
+		Taxonomy2 tax = accession.getTaxonomy();
+		System.err.println(tax);
+		System.err.println(accession.getTaxGenus());
+		System.err.println(accession.getTaxSpecies());
+
+		// Modify taxonomy
+		json.put("genus", "Hordeum");
+		json.put("species", "vulgare");
+		json.put("spauthor", "L.");
+		json.put("subtaxa", "some subtaxa");
+		json.put("subtauthor", "Subtauthor");
+		try {
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (RESTApiException e) {
+			fail(e.getMessage());
+		}
+		// reload
+		accession = genesysService.getAccession(instCode, "AC 1");
+		Taxonomy2 tax2 = accession.getTaxonomy();
+		System.err.println(tax2);
+		assertFalse(tax2.getId().equals(tax.getId()));
+		System.err.println(accession.getTaxGenus());
+		System.err.println(accession.getTaxSpecies());
+		assertFalse(accession.getTaxGenus() == accession.getTaxSpecies());
+		
+		// test nothing
+		try {
+			System.err.println("NO UPDATE!");
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (RESTApiException e) {
+			fail(e.getMessage());
+		}
+	}
+
+}

src/test/java/org/genesys2/server/test/JpaDataConfig.java

 package org.genesys2.server.test;
 
+import java.util.Properties;
+
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
 import org.junit.Ignore;
 import org.springframework.beans.factory.FactoryBean;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -16,21 +21,21 @@ import org.springframework.orm.hibernate4.HibernateExceptionTranslator;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
+import org.springframework.test.context.transaction.TransactionConfiguration;
 import org.springframework.transaction.PlatformTransactionManager;
-
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-import java.util.Properties;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 @Ignore
 @Configuration
 @PropertySource("classpath:/spring/spring.properties")
 @EnableJpaRepositories(
-        basePackages = "org.genesys2.server.persistence",
-        repositoryImplementationPostfix = "CustomImpl",
+        basePackages = { "org.genesys2.server.persistence.acl", "org.genesys2.server.persistence.domain" },
+        repositoryImplementationPostfix = "Impl",
         entityManagerFactoryRef = "entityManagerFactory",
         transactionManagerRef = "transactionManager"
 )
+@EnableTransactionManagement
+@TransactionConfiguration(transactionManager="transactionManager")
 public class JpaDataConfig {
     @Autowired
     private Environment env;

src/test/java/org/genesys2/server/test/TaxonomyEnsureTest.java

@@ -102,4 +102,28 @@ public class TaxonomyEnsureTest {
 			fail("This should not have any exceptions!");
 		}
 	}
+	
+	@Test
+	public void testFullTaxonomy() {
+		try {
+			Taxonomy2 tax = taxonomyService.ensureTaxonomy2("Aaaaa", "species", "spauthor", "subtaxa", "subtauthor");
+			System.out.println(tax);
+			assertTrue("id missing", tax.getId() != null);
+			assertTrue("species must be sp.", tax.getSpecies().equals("species"));
+			assertTrue("taxGenus should not be null", tax.getTaxGenus() != null);
+			assertTrue("taxSpecies should not be null", tax.getTaxSpecies() != null);
+			assertTrue("taxGenus must not be this", !tax.getTaxGenus().equals(tax.getId()));
+			assertTrue("taxSpecies must not be this", !tax.getTaxSpecies().equals(tax.getId()));
+			assertTrue("taxSpecies should not match taxGenus", !tax.getTaxSpecies().equals(tax.getTaxGenus()));
+
+			Taxonomy2 taxGenus = taxonomyService.get(tax.getTaxGenus());
+			System.out.println(taxGenus);
+			
+			Taxonomy2 taxSpecies = taxonomyService.get(tax.getTaxSpecies());
+			System.out.println(taxSpecies);
+			
+		} catch (Exception e) {
+			fail("This should not have any exceptions!");
+		}
+	}
 }