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Commit b26d0a06 authored by Matija Obreza's avatar Matija Obreza
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Entity cleanup

parent 068020fe
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Showing with 54 additions and 83 deletions
src/main/java/org/genesys2/server/model/genesys/Accession.java
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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
View file @ b26d0a06
......@@ -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());
}
......
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