Accession#storage (MCPD)

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

@@ -28,11 +28,14 @@ import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.OrderBy;
+import javax.persistence.PrePersist;
+import javax.persistence.PreUpdate;
 import javax.persistence.Table;
 
 import org.genesys2.server.model.VersionedAuditedModel;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.util.MCPDUtil;
 
 @Entity
 @Table(name = "accession")
@@ -106,9 +109,21 @@ public class Accession extends VersionedAuditedModel {
 	@OrderBy("storage")
 	private List<Integer> stoRage = new ArrayList<Integer>();
 
+	@Column(name = "storage", length = 50, nullable = true)
+	private String storage;
+
 	public Accession() {
 	}
 
+	/**
+	 * Update MCPD {@link #storage}
+	 */
+	@PrePersist
+	@PreUpdate
+	private void prePersist() {
+		this.storage = MCPDUtil.toMcpdArray(this.stoRage);
+	}
+
 	public String getUuid() {
 		return uuid;
 	}
@@ -262,6 +277,22 @@ public class Accession extends VersionedAuditedModel {
 		this.stoRage = stoRage;
 	}
 
+	/**
+	 * Returns {@link #getStoRage()} as MCPD string
+	 * 
+	 * @return MCPD array string
+	 */
+	public String getStorage() {
+		return storage;
+	}
+
+	/**
+	 * Use {@link #setStoRage(List)} instead.
+	 */
+	protected void setStorage(String storage) {
+		this.storage = storage;
+	}
+
 	@Override
 	public String toString() {
 		return MessageFormat.format("Accession id={0,number,#} A={3} inst={1} genus={2}", id, instituteCode, taxGenus, accessionName);

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

@@ -230,7 +230,7 @@ public class DownloadServiceImpl implements DownloadService {
 		}
 
 		createCell(row, 33, accession.getDuplSite());
-		createCell(row, 35, toMcpdArray(accession.getStoRage()));
+		createCell(row, 35, accession.getStorage());
 		createCell(row, 36, accession.getMlsStatus());
 
 		if (names != null && names.size() > 0) {
@@ -321,18 +321,4 @@ public class DownloadServiceImpl implements DownloadService {
 			return name;
 		return otherNames + ";" + name;
 	}
-
-	public static String toMcpdArray(List<Integer> integers) {
-		if (integers == null || integers.size() == 0)
-			return null;
-		String s = "";
-		for (Integer i : integers) {
-			if (i == null)
-				continue;
-			if (s.length() > 0)
-				s += ";";
-			s += i;
-		}
-		return s;
-	}
 }

src/main/java/org/genesys2/util/MCPDUtil.java

+/**
+ * Copyright 2014 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.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * 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.util;
+
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+public class MCPDUtil {
+
+	public static String toMcpdArray(List<Integer> integers) {
+		if (integers == null || integers.size() == 0)
+			return null;
+		String s = "";
+		for (Integer i : integers) {
+			if (i == null)
+				continue;
+			if (s.length() > 0)
+				s += ";";
+			s += i;
+		}
+		return StringUtils.defaultIfBlank(s, null);
+	}
+
+}

src/test/java/org/genesys2/server/model/impl/AccessionStorageTest.java

+/**
+ * Copyright 2014 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.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * 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.model.impl;
+
+import static org.hamcrest.Matchers.is;
+import static org.hamcrest.Matchers.nullValue;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.test.BatchRESTServiceTest;
+import org.genesys2.server.test.PropertyPlacholderInitializer;
+import org.genesys2.util.MCPDUtil;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = BatchRESTServiceTest.Config.class, initializers = PropertyPlacholderInitializer.class)
+@ActiveProfiles("dev")
+public class AccessionStorageTest {
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Test
+	public void nullStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-1");
+		genesysService.saveAccession(a);
+	}
+
+	@Test
+	public void blankStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-" + System.currentTimeMillis());
+		List<Integer> stoRage = new ArrayList<Integer>();
+		a.setStoRage(stoRage);
+		genesysService.saveAccession(a);
+
+		Long accessionId = a.getId();
+		Accession b = genesysService.getAccession(accessionId);
+		assertTrue(b.getStorage() == null);
+		assertTrue(b.getStoRage() != null);
+		assertThat("Accession#stoRage size is not 0", b.getStoRage().size(), is(0));
+	}
+
+	@Test
+	public void oneStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-" + System.currentTimeMillis());
+		List<Integer> stoRage = new ArrayList<Integer>();
+		stoRage.add(1);
+		a.setStoRage(stoRage);
+		genesysService.saveAccession(a);
+
+		Long accessionId = a.getId();
+		Accession b = genesysService.getAccession(accessionId);
+		assertTrue(b.getStorage() != null);
+		assertThat("Storage value should be '1'", a.getStorage(), is("1"));
+		assertTrue(b.getStoRage() != null);
+	}
+
+	@Test
+	public void twoStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-" + System.currentTimeMillis());
+		List<Integer> stoRage = new ArrayList<Integer>();
+		stoRage.add(1);
+		stoRage.add(2);
+		a.setStoRage(stoRage);
+		genesysService.saveAccession(a);
+
+		Long accessionId = a.getId();
+		Accession b = genesysService.getAccession(accessionId);
+		assertTrue(b.getStorage() != null);
+		assertThat("Storage value should be '1'", a.getStorage(), is("1;2"));
+		assertTrue(b.getStoRage() != null);
+	}
+
+	@Test
+	public void clearStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-" + System.currentTimeMillis());
+		List<Integer> stoRage = new ArrayList<Integer>();
+		stoRage.add(1);
+		stoRage.add(2);
+		a.setStoRage(stoRage);
+		genesysService.saveAccession(a);
+
+		Long accessionId = a.getId();
+		assertNotNull("Accession#id must not be null", a.getId());
+		Accession b = genesysService.getAccession(accessionId);
+		assertTrue(b.getStorage() != null);
+		assertThat("Storage value should be '1'", a.getStorage(), is("1;2"));
+		assertTrue(b.getStoRage() != null);
+
+		b.getStoRage().clear();
+		genesysService.saveAccession(b);
+
+		Accession c = genesysService.getAccession(accessionId);
+		assertNotNull("Accession#stoRage must not be null", c.getStoRage());
+		assertThat("Accession#stoRage size is not 0", c.getStoRage().size(), is(0));
+		assertThat("Accession#storage is not null", c.getStorage(), is(nullValue()));
+	}
+
+	@Test
+	public void updateStorage() {
+		Accession a = new Accession();
+		a.setInstituteCode("INS000");
+		a.setAccessionName("A-" + System.currentTimeMillis());
+		List<Integer> stoRage = new ArrayList<Integer>();
+		stoRage.add(1);
+		stoRage.add(2);
+		stoRage.add(3);
+		a.setStoRage(stoRage);
+		System.out.println("Saving 1");
+		genesysService.saveAccession(a);
+		System.out.println("Saving 2");
+		genesysService.saveAccession(a);
+
+		Long accessionId = a.getId();
+		assertNotNull("Accession#id must not be null", a.getId());
+		Accession b = genesysService.getAccession(accessionId);
+		assertNotNull(b.getStorage());
+		assertNotNull(b.getStoRage());
+		assertThat("StoRage length is not 3", a.getStoRage().size(), is(3));
+		assertThat("Storage value should be '1;2;3'", a.getStorage(), is("1;2;3"));
+
+		b.getStoRage().remove(0);
+		genesysService.saveAccession(b);
+
+		Accession c = genesysService.getAccession(accessionId);
+		assertNotNull("Accession#stoRage must not be null", c.getStoRage());
+		assertThat("Accession#stoRage size is not 2", c.getStoRage().size(), is(2));
+		assertThat("Accession#storage is not '2;3'", c.getStorage(), is("2;3"));
+		assertThat("Accession#stoRage does not generate MCPD style string'", c.getStorage(), is(MCPDUtil.toMcpdArray(c.getStoRage())));
+		System.out.println("Saving 3");
+		genesysService.saveAccession(c);
+	}
+
+}

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

@@ -16,9 +16,8 @@
 
 package org.genesys2.server.test;
 
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.*;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -37,6 +36,7 @@ import org.genesys2.server.persistence.domain.CountryRepository;
 import org.genesys2.server.service.AclService;
 import org.genesys2.server.service.BatchRESTService;
 import org.genesys2.server.service.ContentService;
+import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.HtmlSanitizer;
@@ -47,6 +47,7 @@ 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.CropServiceImpl;
 import org.genesys2.server.service.impl.GenesysServiceImpl;
 import org.genesys2.server.service.impl.GeoServiceImpl;
 import org.genesys2.server.service.impl.InstituteServiceImpl;
@@ -57,6 +58,7 @@ 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.AccessionHeaderJson;
+import org.genesys2.spring.config.HazelcastConfig;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -68,6 +70,7 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Import;
 import org.springframework.data.domain.PageRequest;
+import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.ui.velocity.VelocityEngineFactoryBean;
@@ -76,11 +79,12 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @RunWith(SpringJUnit4ClassRunner.class)
+@ActiveProfiles("dev")
 @ContextConfiguration(classes = BatchRESTServiceTest.Config.class, initializers = PropertyPlacholderInitializer.class)
 public class BatchRESTServiceTest {
 	private final ObjectMapper mapper = new ObjectMapper();
 
-	@Import(JpaDataConfig.class)
+	@Import({ JpaDataConfig.class, HazelcastConfig.class })
 	@ComponentScan(basePackages = { "org.genesys2.server.persistence.domain" })
 	public static class Config {
 
@@ -109,6 +113,11 @@ public class BatchRESTServiceTest {
 			return new BatchRESTServiceImpl();
 		}
 
+		@Bean
+		public CropService cropService() {
+			return new CropServiceImpl();
+		}
+
 		@Bean
 		public GenesysService genesysService() {
 			return new GenesysServiceImpl();
@@ -311,4 +320,72 @@ public class BatchRESTServiceTest {
 		assertTrue(accession.getCountryOfOrigin() == null);
 	}
 
+	@Test
+	public void testUpdateStorage() throws NonUniqueAccessionException {
+		final String instCode = "INS002";
+		final FaoInstitute institute = instituteService.getInstitute(instCode);
+		assertTrue("institute is null", institute != null);
+		System.err.println(institute);
+
+		final Map<AccessionHeaderJson, ObjectNode> batch = new HashMap<AccessionHeaderJson, ObjectNode>();
+
+		final AccessionHeaderJson dataJson = new AccessionHeaderJson();
+		dataJson.acceNumb = "AC 100";
+		dataJson.instCode = instCode;
+
+		final ObjectNode json = mapper.createObjectNode();
+		json.put("genus", "Hordeum");
+		json.put("orgCty", "CTY");
+		json.put("storage", "10;30");
+		batch.put(dataJson, json);
+		System.err.println(json);
+
+		try {
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (final RESTApiException e) {
+			fail(e.getMessage());
+		}
+
+		Accession accession = genesysService.getAccession(instCode, "AC 100");
+		assertTrue(accession.getId() != null);
+		assertTrue(accession.getInstituteCode().equals(instCode));
+		assertTrue(accession.getInstitute().getId().equals(institute.getId()));
+		assertTrue(accession.getOrigin() != null);
+		assertTrue("CTY".equals(accession.getOrigin()));
+		assertTrue(accession.getCountryOfOrigin() != null);
+		assertTrue("Country".equals(accession.getCountryOfOrigin().getName()));
+
+		assertNotNull("StoRage must be", accession.getStoRage());
+		assertNotNull("Storage must be", accession.getStorage());
+		assertThat("Storage must be 10;30", accession.getStorage(), is("10;30"));
+
+		// Modify STORAGE
+		json.put("storage", "40");
+		System.err.println(json);
+		try {
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (final RESTApiException e) {
+			fail(e.getMessage());
+		}
+		// reload
+		accession = genesysService.getAccession(instCode, "AC 100");
+		assertNotNull("storage should not be null", accession.getStorage());
+		assertThat("stoRage should 40", accession.getStorage(), is("40"));
+		assertThat("stoRage should be 0-size", accession.getStoRage().size(), is(1));
+
+		// Clear STORAGE
+		json.putNull("storage");
+		System.err.println(json);
+		try {
+			batchRESTService.upsertAccessionData(institute, batch);
+		} catch (final RESTApiException e) {
+			fail(e.getMessage());
+		}
+		// reload
+		accession = genesysService.getAccession(instCode, "AC 100");
+		assertNull("storage should be null", accession.getStorage());
+		assertNotNull("stoRage should be null", accession.getStoRage());
+		assertThat("stoRage should be 0-size", accession.getStoRage().size(), is(0));
+	}
+
 }

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

@@ -30,6 +30,7 @@ import org.springframework.context.annotation.PropertySource;
 import org.springframework.core.env.Environment;
 import org.springframework.dao.support.PersistenceExceptionTranslator;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.jdbc.datasource.DriverManagerDataSource;
 import org.springframework.orm.hibernate4.HibernateExceptionTranslator;
 import org.springframework.orm.jpa.JpaTransactionManager;
@@ -44,7 +45,7 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
 @PropertySource("classpath:/spring/spring.properties")
 @EnableJpaRepositories(basePackages = { "org.genesys2.server.persistence.acl", "org.genesys2.server.persistence.domain" }, repositoryImplementationPostfix = "CustomImpl", entityManagerFactoryRef = "entityManagerFactory", transactionManagerRef = "transactionManager")
 @EnableTransactionManagement
-@TransactionConfiguration(transactionManager = "transactionManager")
+@TransactionConfiguration(defaultRollback = false, transactionManager = "transactionManager")
 public class JpaDataConfig {
 	@Autowired
 	private Environment env;
@@ -61,6 +62,11 @@ public class JpaDataConfig {
 		return dataSource;
 	}
 
+	@Bean
+	public JdbcTemplate jdbcTemplate(DataSource dataSource) {
+		return new JdbcTemplate(dataSource);
+	}
+
 	@Bean(name = "entityManagerFactory")
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() throws Exception {
 		final LocalContainerEntityManagerFactoryBean bean = new LocalContainerEntityManagerFactoryBean();
@@ -93,7 +99,7 @@ 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"));