Spring configuration, hibernate.properties

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

@@ -23,8 +23,6 @@ import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.List;
 
-import javax.sql.DataSource;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Method;
@@ -47,16 +45,12 @@ import org.springframework.transaction.annotation.Transactional;
 public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository {
 	public static final Log LOG = LogFactory.getLog(GenesysLowlevelRepositoryImpl.class);
 
+	@Autowired
 	private JdbcTemplate jdbcTemplate;
 
 	@Autowired
 	private MethodRepository methodRepository;
 
-	@Autowired
-	public void setDataSource(final DataSource dataSource) {
-		this.jdbcTemplate = new JdbcTemplate(dataSource);
-	}
-
 	@Override
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	@Transactional(readOnly = false)

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

@@ -132,7 +132,8 @@ public interface GenesysService {
 
 	Set<Long> filterAvailableForDistribution(Set<Long> accessionIds);
 
-	List<Accession> saveAccession(Accession... accession);
+	Accession saveAccession(Accession accession);
+	List<Accession> saveAccessions(Iterable<Accession> accession);
 
 	void updateAccessionCount(FaoInstitute institute);
 

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

@@ -441,7 +441,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		for (Accession a : accessionRepository.findAll(accessionIds)) {
 			AllStuff all = map.get(a.getId());
 			all.accession = a;
-			a.getStoRage().size();
+			// Can use a#getStorage() instead
+			// a.getStoRage().size();
 			all.names = new ArrayList<AccessionAlias>();
 			all.remarks = new ArrayList<AccessionRemark>();
 		}
@@ -630,6 +631,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Transactional(readOnly = false)
 	@CacheEvict(value = "statistics", allEntries = true)
 	public void updateAccessionCount(FaoInstitute institute) {
+		if (institute == null)
+			return;
 		long accessionCount = accessionRepository.countByInstitute(institute);
 		institute.setAccessionCount(accessionCount);
 		instituteRepository.save(institute);
@@ -670,15 +673,29 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Override
 	@Transactional(readOnly = false)
 	@CacheEvict(value = "statistics", allEntries = true)
-	public List<Accession> saveAccession(Accession... accession) {
-		List<Accession> list = new ArrayList<Accession>();
-		for (final Accession a : accession) {
+	public Accession saveAccession(Accession accession) {
 			if (LOG.isDebugEnabled())
-				LOG.debug("Updating " + a);
-			accessionRepository.save(a);
-			list.add(a);
+			LOG.debug("Updating " + accession);
+
+		System.err.println("Saving " + accession + " ST=" + accession.getStorage());
+		Accession res = accessionRepository.save(accession);
+		updateAccessionCount(accession.getInstitute());
+		return res;
+		}
+
+	@Override
+	@Transactional(readOnly = false)
+	@CacheEvict(value = "statistics", allEntries = true)
+	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=" + accession.getStorage());
+			institutes.add(accession.getInstitute());
 		}
-		return list;
+		List<Accession> res = accessionRepository.save(accessions);
+		for (FaoInstitute institute : institutes)
+			updateAccessionCount(institute);
+		return res;
 	}
 
 	@Override

src/main/java/org/genesys2/spring/config/SpringDataBaseConfig.java

@@ -18,12 +18,18 @@ package org.genesys2.spring.config;
 
 import java.util.Properties;
 
+import javax.persistence.EntityManagerFactory;
+
 import org.apache.tomcat.jdbc.pool.DataSource;
+import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.beans.factory.config.PropertiesFactoryBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.ImportResource;
+import org.springframework.core.io.ClassPathResource;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
@@ -51,11 +57,8 @@ public class SpringDataBaseConfig {
 	@Value("${db.showSql}")
 	private boolean dbShowSql;
 
-	@Value("${db.dialect}")
-	private String dbDialect;
-
 	@Value("${db.hbm2ddl}")
-	private String dbHbm2ddl;
+	private boolean dbGenerateDdl;
 
 	@Bean
 	public DataSource dataSource() {
@@ -70,14 +73,24 @@ public class SpringDataBaseConfig {
 
 		return dataSource;
 	}
+	
+	@Bean
+	public JdbcTemplate jdbcTemplate(DataSource dataSource) {
+		return new JdbcTemplate(dataSource);
+	}
 
 	@Bean(name = "entityManagerFactory")
-	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory() throws Exception {
 		final LocalContainerEntityManagerFactoryBean entityManager = new LocalContainerEntityManagerFactoryBean();
 		entityManager.setDataSource(dataSource());
 		entityManager.setPersistenceUnitName("spring-jpa");
 		entityManager.setJpaVendorAdapter(hibernateJpaVendorAdapter());
-		entityManager.setJpaProperties(jpaProperties());
+		entityManager.setPersistenceProvider(new HibernatePersistenceProvider());
+		Properties jpaProperties = jpaProperties();
+		for (Object key : jpaProperties.keySet()) {
+			System.err.println("JPA: " + key + " = " + jpaProperties.get(key));
+		}
+		entityManager.setJpaProperties(jpaProperties);
 		entityManager.setPackagesToScan("org.genesys2.server.model.acl", "org.genesys2.server.model.impl", "org.genesys2.server.model.genesys",
 				"org.genesys2.server.model.oauth", "org.genesys2.server.model.kpi");
 
@@ -85,25 +98,23 @@ public class SpringDataBaseConfig {
 	}
 
 	@Bean
-	public JpaTransactionManager transactionManager() {
+	public JpaTransactionManager transactionManager(DataSource dataSource, EntityManagerFactory emf) {
 		final JpaTransactionManager transactionManager = new JpaTransactionManager();
-		transactionManager.setDataSource(dataSource());
-		transactionManager.setEntityManagerFactory(entityManagerFactory().getObject());
+		transactionManager.setDataSource(dataSource);
+		transactionManager.setEntityManagerFactory(emf);
 		return transactionManager;
 	}
 
-	private Properties jpaProperties() {
-		final Properties properties = new Properties();
-		properties.setProperty("hibernate.dialect", dbDialect);
-		properties.setProperty("hibernate.connection.charSet", "utf8");
-		properties.setProperty("hibernate.connection.autocommit", "false");
-		properties.setProperty("hibernate.hbm2ddl.auto", dbHbm2ddl);
-		return properties;
+	private Properties jpaProperties() throws Exception {
+		Properties jpaProp = new Properties();
+		jpaProp.load(getClass().getResourceAsStream("/spring/hibernate.properties"));
+		return jpaProp;
 	}
 
 	private HibernateJpaVendorAdapter hibernateJpaVendorAdapter() {
 		final HibernateJpaVendorAdapter jpaVendorAdapter = new HibernateJpaVendorAdapter();
 		jpaVendorAdapter.setShowSql(dbShowSql);
+		jpaVendorAdapter.setGenerateDdl(dbGenerateDdl);
 		return jpaVendorAdapter;
 	}
 

src/main/resources/spring/hibernate.properties

+#Hibernate specific properties
+hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
+hibernate.connection.charSet=utf8
+hibernate.connection.autocommit=false
+hibernate.jdbc.batch_size=50
+hibernate.order_updates=true
+hibernate.order_inserts=true

src/main/resources/spring/spring.properties

@@ -23,11 +23,10 @@ base.cookie-http-only=false
 
 db.url=jdbc:mysql://localhost/genesyslive?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
 db.driverClassName=com.mysql.jdbc.Driver
-db.dialect=org.hibernate.dialect.MySQL5Dialect
 db.username=root
 db.password=
 db.showSql=false
-db.hbm2ddl=do-nothing
+db.hbm2ddl=false
 
 c3p0.acquireIncrement=1
 c3p0.minPoolSize=1

src/test/java/org/genesys2/server/service/worker/ElasticUpdaterTest.java

@@ -17,6 +17,8 @@
 package org.genesys2.server.service.worker;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -211,13 +213,14 @@ public class ElasticUpdaterTest {
 
 	@Test
 	public void testAspect2() throws InterruptedException {
-		Accession[] a = new Accession[100];
+		List<Accession> a = new ArrayList<Accession>();
 		for (int i = 0; i < 100; i++) {
-			a[i] = new Accession();
-			a[i].setAccessionName("A-" + i);
-			a[i].setInstituteCode("INS000");
+			Accession accn;
+			a.add(accn = new Accession());
+			accn.setAccessionName("A-" + i);
+			accn.setInstituteCode("INS000");
 		}
-		genesysService.saveAccession(a);
+		genesysService.saveAccessions(a);
 		LOG.info("Accessions saved");
 		Thread.sleep(5000);
 	}

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

@@ -21,15 +21,13 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.junit.Ignore;
-import org.springframework.beans.factory.FactoryBean;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.config.PropertiesFactoryBean;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.core.env.Environment;
-import org.springframework.core.io.ClassPathResource;
 import org.springframework.dao.support.PersistenceExceptionTranslator;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.jdbc.datasource.DriverManagerDataSource;
@@ -51,15 +49,6 @@ public class JpaDataConfig {
 	@Autowired
 	private Environment env;
 
-	@Bean(name = "hibernateProperties")
-	public PropertiesFactoryBean hibernateProperties() throws Exception {
-		final PropertiesFactoryBean bean = new PropertiesFactoryBean();
-
-		bean.setLocation(new ClassPathResource("/spring/hibernate.properties"));
-
-		return bean;
-	}
-
 	@Bean(name = "dataSource")
 	public DataSource dataSource() throws Exception {
 		final DriverManagerDataSource dataSource = new DriverManagerDataSource();
@@ -73,18 +62,19 @@ public class JpaDataConfig {
 	}
 
 	@Bean(name = "entityManagerFactory")
-	public FactoryBean<EntityManagerFactory> entityManagerFactory(Properties hibernateProperties) throws Exception {
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory() throws Exception {
 		final LocalContainerEntityManagerFactoryBean bean = new LocalContainerEntityManagerFactoryBean();
 
 		bean.setDataSource(dataSource());
 		bean.setPersistenceUnitName("spring-jpa");
 		bean.setPackagesToScan("org.genesys2.server.model");
+		bean.setPersistenceProvider(new HibernatePersistenceProvider());
 
 		final HibernateJpaVendorAdapter jpaVendorAdapter = new HibernateJpaVendorAdapter();
 		jpaVendorAdapter.setShowSql(env.getProperty("db.show.sql", Boolean.TYPE, true));
 		jpaVendorAdapter.setGenerateDdl(env.getProperty("db.generate.ddl", Boolean.TYPE, true));
 
-		bean.setJpaProperties(hibernateProperties);
+		bean.setJpaProperties(jpaProperties());
 
 		bean.setJpaVendorAdapter(jpaVendorAdapter);
 
@@ -103,5 +93,10 @@ public class JpaDataConfig {
 	public PersistenceExceptionTranslator hibernateExceptionTranslator() {
 		return new HibernateExceptionTranslator();
 	}
-
+	
+	private Properties jpaProperties() throws Exception {
+		Properties jpaProp = new Properties();
+		jpaProp.load(getClass().getResourceAsStream("/spring/hibernate.properties"));
+		return jpaProp;
+	}
 }

src/test/resources/spring/hibernate.properties

 #Hibernate specific properties
 hibernate.dialect=org.hibernate.dialect.HSQLDialect
-hibernate.connection.autocommit=true
-hibernate.hbm2ddl.auto=update
-hibernate.search.default.indexBase=./lucene/
-hibernate.search.default.exclusive_index_use=false
-hibernate.search.default.worker.execution=async
+hibernate.connection.charSet=utf8
+hibernate.connection.autocommit=false
+hibernate.jdbc.batch_size=50
+hibernate.order_updates=true
+hibernate.order_inserts=true