Entity cleanup

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

@@ -39,7 +39,7 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.util.MCPDUtil;
 
 @Entity
-@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(name="UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }) })
+@Table(name = "accession", uniqueConstraints = { @UniqueConstraint(name = "UQ_accession_genus_inst", columnNames = { "instituteId", "taxGenus", "acceNumb" }) })
 public class Accession extends VersionedAuditedModel {
 	private static final long serialVersionUID = -7630113633534038876L;
 
@@ -49,22 +49,22 @@ public class Accession extends VersionedAuditedModel {
 	@Column(name = "instCode", length = 10, nullable = false)
 	private String instituteCode;
 
-	@ManyToOne(cascade = {}, optional = true)
+	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "instituteId")
 	private FaoInstitute institute;
 
 	@Column(name = "acceNumb", nullable = false, length = 128)
 	private String accessionName;
 
-//	@Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
-	@ManyToOne(cascade = {}, optional = true)
+	// @Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
+	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "taxonomyId2")
 	private Taxonomy2 taxonomy;
 
 	@Column(name = "acqSrc", length = 3)
 	private String acquisitionSource;
 
-	@Column(name = "acqDate", length = 8)
+	@Column(name = "acqDate", length = 12)
 	private String acquisitionDate;
 
 	@Column(name = "orgCty", length = 3)
@@ -74,7 +74,7 @@ public class Accession extends VersionedAuditedModel {
 	@JoinColumn(name = "orgCtyId", nullable = true)
 	private Country countryOfOrigin;
 
-	@Column(name = "duplSite", length = 32)
+	@Column(name = "duplSite", length = 64)
 	private String duplSite;
 
 	@Column(name = "sampStat", length = 3)
@@ -101,7 +101,7 @@ public class Accession extends VersionedAuditedModel {
 	@OrderBy("storage")
 	private List<Integer> stoRage = new ArrayList<Integer>();
 
-	@Column(name = "storage", length = 50, nullable = true)
+	@Column(name = "storage", length = 64, nullable = true)
 	private String storage;
 
 	public Accession() {
@@ -113,6 +113,9 @@ public class Accession extends VersionedAuditedModel {
 	@PrePersist
 	@PreUpdate
 	private void prePersist() {
+		this.origin = getCountryOfOrigin().getCode3();
+		this.taxGenus = getTaxonomy().getTaxGenus();
+		this.instituteCode = getInstitute().getCode();
 		this.storage = MCPDUtil.toMcpdArray(this.stoRage);
 	}
 
@@ -136,7 +139,7 @@ public class Accession extends VersionedAuditedModel {
 		return instituteCode;
 	}
 
-	public void setInstituteCode(final String instituteCode) {
+	protected void setInstituteCode(final String instituteCode) {
 		this.instituteCode = instituteCode;
 	}
 
@@ -172,7 +175,7 @@ public class Accession extends VersionedAuditedModel {
 		return this.origin;
 	}
 
-	public void setOrigin(final String origin) {
+	protected void setOrigin(final String origin) {
 		this.origin = origin;
 	}
 
@@ -236,7 +239,7 @@ public class Accession extends VersionedAuditedModel {
 		return taxGenus;
 	}
 
-	public void setTaxGenus(long taxGenus) {
+	protected void setTaxGenus(long taxGenus) {
 		this.taxGenus = taxGenus;
 	}
 

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

@@ -22,6 +22,7 @@ import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -50,40 +51,15 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query(value = "select t.taxSpecies, count(a) from Accession a inner join a.taxonomy t where a.institute = ?1 group by t.taxSpecies order by count(a) desc", countQuery = "select count(distinct a.taxonomy.taxSpecies) from Accession a where a.institute = ?1")
 	Page<Object[]> statisticsSpeciesInInstitute(FaoInstitute institute, Pageable pageable);
 
-	// FIXME Slow query
-	// FIXME TOOD taxonomy1!
-	// @Query(value =
-	// "select ct.crop, count(a) from Accession a inner join a.taxonomy1 t join t.cropTaxonomies ct where a.institute = ?1 group by ct.crop order by count(a) desc",
-	// countQuery =
-	// "select count(distinct ct.crop) from Accession a inner join a.taxonomy t join t.cropTaxonomies ct where a.institute = ?1")
-	// Page<Object[]> statisticsCropInInstitute(FaoInstitute institute, Pageable
-	// pageable);
+	@Query("select count(a) from Accession a where a.countryOfOrigin = ?1")
+	long countByOrigin(Country country);
 
-	@Query("select count(a) from Accession a where a.origin = ?1")
-	long countByOrigin(String isoCode3);
-
-	@Query("select count(a) from Accession a inner join a.institute i inner join i.country c where c.code3 = ?1")
-	long countByLocation(String isoCode3);
+	@Query("select count(a) from Accession a where a.institute.country = ?1")
+	long countByLocation(Country country);
 
 	@Query("select a from Accession a where a.institute in ( ?1 )")
 	Page<Accession> findByInstitute(List<FaoInstitute> institutes, Pageable pageable);
 
-	// @Query("select a from Accession a where a.genus in ( ?1 )")
-	// Page<Accession> findByGenus(List<String> genus, Pageable pageable);
-
-	// @Query("select a.institute, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.institute order by total desc")
-	// List<Object[]> statisticsInstitute(List<String> genus);
-
-	// @Query("select a.origin, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.origin order by total desc")
-	// List<Object[]> statisticsOrigin(List<String> genus);
-
-	// @Query("select a.taxonomy, count(a.id) as total from Accession a where a.genus in ( ?1 ) group by a.taxonomy order by total desc")
-	// List<Object[]> statisticsTaxonomy(List<String> genus);
-
-	// List<Accession> findByOrigin(String origin);
-
-	Page<Accession> findByOrigin(String isoCode3, Pageable pageable);
-
 	List<Accession> findByInstituteAndAccessionName(FaoInstitute faoInstitute, String accessionName);
 
 	@Query("from Accession a where a.id in ( ?1 )")

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

@@ -51,13 +51,9 @@ public interface GenesysService {
 
 	long countByInstitute(FaoInstitute institute);
 
-	long countByOrigin(String isoCode3);
+	long countByOrigin(Country country);
 
-	long countByLocation(String isoCode3);
-
-	Page<Accession> listAccessionsByOrigin(Country country, Pageable pageable);
-
-	Page<Accession> listAccessionsByInstitute(FaoInstitute faoInstitute, Pageable pageable);
+	long countByLocation(Country country);
 
 	Accession getAccession(long accessionId);
 

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

@@ -134,7 +134,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				LOG.warn("New accession " + dataJson);
 
 				accession = new Accession();
-				accession.setInstituteCode(dataJson.instCode);
 				accession.setInstitute(institute);
 				accession.setAccessionName(dataJson.acceNumb);
 
@@ -602,7 +601,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 						throw new RESTApiValueException("No country with ISO3 code: " + orgCty);
 					}
 				}
-				accession.setOrigin(orgCty);
 				accession.setCountryOfOrigin(country);
 				return true;
 			}
@@ -659,7 +657,6 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		if (!ensuredTaxonomy.sameAs(taxonomy)) {
 
 			accession.setTaxonomy(ensuredTaxonomy);
-			accession.setTaxGenus(ensuredTaxonomy.getTaxGenus());
 
 			updated = true;
 		}

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

@@ -99,16 +99,32 @@ public class DirectMysqlQuery {
 	protected DirectMysqlQuery join(AppliedFilters filters) {
 		if (hasFilter(filters, FilterConstants.CROPS) || hasFilter(filters, FilterConstants.TAXONOMY_GENUS)
 				|| hasFilter(filters, FilterConstants.TAXONOMY_SPECIES) || hasFilter(filters, FilterConstants.TAXONOMY_SCINAME)) {
+			
 			innerJoin("taxonomy2", "t", "t.id=a.taxonomyId2");
+			
 			if (hasFilter(filters, FilterConstants.CROPS)) {
 				innerJoin("croptaxonomy", "ct", "ct.taxonomyId=t.id");
 				innerJoin("crop", null, "crop.id=ct.cropId");
 			}
 		}
-		if (hasFilter(filters, FilterConstants.INSTITUTE_NETWORK)) {
+		
+//		if (hasFilter(filters, FilterConstants.ORGCTY_ISO3)) {
+//			innerJoin("country", "cty", "cty.id=a.orgCtyId");
+//		}
+		
+		if (hasFilter(filters, FilterConstants.INSTCODE) || hasFilter(filters, FilterConstants.INSTITUTE_COUNTRY_ISO3)
+				|| hasFilter(filters, FilterConstants.INSTITUTE_NETWORK)) {
+			
 			innerJoin("faoinstitute", "fao", "fao.id=a.instituteId");
-			innerJoin("organizationinstitute", "oi", "oi.instituteId=fao.id");
-			innerJoin("organization", "org", "org.id=oi.organizationId");
+			
+			if (hasFilter(filters, FilterConstants.INSTITUTE_COUNTRY_ISO3)) {
+				innerJoin("country", "faocty", "faocty.id=fao.countryId");
+			}
+			
+			if (hasFilter(filters, FilterConstants.INSTITUTE_NETWORK)) {
+				innerJoin("organizationinstitute", "oi", "oi.instituteId=fao.id");
+				innerJoin("organization", "org", "org.id=oi.organizationId");
+			}
 		}
 
 		if (hasFilter(filters, FilterConstants.GEO_LATITUDE) || hasFilter(filters, FilterConstants.GEO_LONGITUDE)
@@ -146,6 +162,7 @@ public class DirectMysqlQuery {
 		createQuery(whereBuffer, "a.acceNumb", filters.get(FilterConstants.ACCENUMB), params);
 		createQuery(whereBuffer, "a.orgCty", filters.get(FilterConstants.ORGCTY_ISO3), params);
 		createQuery(whereBuffer, "a.instCode", filters.get(FilterConstants.INSTCODE), params);
+		createQuery(whereBuffer, "faocty.code3", filters.get(FilterConstants.INSTITUTE_COUNTRY_ISO3), params);
 		createQuery(whereBuffer, "a.inSGSV", filters.get(FilterConstants.SGSV), params);
 		createQuery(whereBuffer, "a.mlsStat", filters.get(FilterConstants.MLSSTATUS), params);
 		createQuery(whereBuffer, "a.inTrust", filters.get(FilterConstants.ART15), params);

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

@@ -178,23 +178,13 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	@Override
-	public long countByOrigin(String isoCode3) {
-		return accessionRepository.countByOrigin(isoCode3);
+	public long countByOrigin(Country country) {
+		return accessionRepository.countByOrigin(country);
 	}
 
 	@Override
-	public long countByLocation(String isoCode3) {
-		return accessionRepository.countByLocation(isoCode3);
-	}
-
-	@Override
-	public Page<Accession> listAccessionsByOrigin(Country country, Pageable pageable) {
-		return accessionRepository.findByOrigin(country.getCode3(), pageable);
-	}
-
-	@Override
-	public Page<Accession> listAccessionsByInstitute(FaoInstitute faoInstitute, Pageable pageable) {
-		return accessionRepository.findByInstitute(faoInstitute, pageable);
+	public long countByLocation(Country country) {
+		return accessionRepository.countByLocation(country);
 	}
 
 	@Override

src/main/java/org/genesys2/server/servlet/controller/CountryController.java

@@ -85,8 +85,8 @@ public class CountryController extends BaseController {
 		// Active ones
 		model.addAttribute("genesysInstitutes", instituteService.listByCountryActive(country));
 
-		model.addAttribute("countByOrigin", genesysService.countByOrigin(country.getCode3()));
-		model.addAttribute("countByLocation", genesysService.countByLocation(country.getCode3()));
+		model.addAttribute("countByOrigin", genesysService.countByOrigin(country));
+		model.addAttribute("countByLocation", genesysService.countByLocation(country));
 
 		return "/country/details";
 	}

src/main/resources/spring/spring.properties

@@ -25,7 +25,7 @@ db.url=jdbc:mysql://localhost/genesys20141230?useUnicode=true&characterEncoding=
 db.driverClassName=com.mysql.jdbc.Driver
 db.username=root
 db.password=
-db.showSql=true
+db.showSql=false
 db.hbm2ddl=false
 
 c3p0.acquireIncrement=1

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

@@ -48,7 +48,6 @@ public class AccessionStorageTest {
 	@Test
 	public void nullStorage() {
 		Accession a = new Accession();
-		a.setInstituteCode("INS000");
 		a.setAccessionName("A-1");
 		genesysService.saveAccession(a);
 	}
@@ -56,7 +55,6 @@ public class AccessionStorageTest {
 	@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);
@@ -72,7 +70,6 @@ public class AccessionStorageTest {
 	@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);
@@ -89,7 +86,6 @@ public class AccessionStorageTest {
 	@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);
@@ -107,7 +103,6 @@ public class AccessionStorageTest {
 	@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);
@@ -134,7 +129,6 @@ public class AccessionStorageTest {
 	@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);

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

@@ -205,7 +205,6 @@ public class ElasticUpdaterTest {
 	public void testAspect() throws InterruptedException {
 		Accession a = new Accession();
 		a.setAccessionName("A-1");
-		a.setInstituteCode("INS000");
 		genesysService.saveAccession(a);
 		LOG.info("Accession saved");
 		Thread.sleep(1000);
@@ -218,7 +217,6 @@ public class ElasticUpdaterTest {
 			Accession accn;
 			a.add(accn = new Accession());
 			accn.setAccessionName("A-" + i);
-			accn.setInstituteCode("INS000");
 		}
 		genesysService.saveAccessions(a);
 		LOG.info("Accessions saved");

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

@@ -210,7 +210,6 @@ public class SGSVUpdateTest {
 
 		final Accession a = new Accession();
 		a.setInstitute(institute);
-		a.setInstituteCode(institute.getCode());
 		a.setAccessionName(acceNumb);
 		a.setTaxonomy(taxonomyService.ensureTaxonomy2(genus, species, null, null, null));
 

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

@@ -16,8 +16,13 @@
 
 package org.genesys2.server.test;
 
-import static org.junit.Assert.*;
-import static org.hamcrest.Matchers.*;
+import static org.hamcrest.Matchers.is;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -69,7 +74,6 @@ 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.data.domain.PageRequest;
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
@@ -201,9 +205,6 @@ public class BatchRESTServiceTest {
 		System.err.println("Tearing down");
 		for (final String instCode : new String[] { "INS002", "INS001" }) {
 			final FaoInstitute institute = instituteService.getInstitute(instCode);
-			System.err.println("Deleting accessions for " + institute);
-			genesysService.removeAccessions(institute, genesysService.listAccessionsByInstitute(institute, new PageRequest(0, Integer.MAX_VALUE)).getContent());
-			System.err.println("Deleting " + institute);
 			instituteService.delete(institute.getCode());
 		}