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Commit 85e789a5 authored by Matija Obreza's avatar Matija Obreza
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CropTaxonomy linked to Taxonomy2

parent b52fcf56
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src/main/java/org/genesys2/server/model/genesys/Taxonomy.java
View file @ 85e789a5
......@@ -17,17 +17,13 @@
package org.genesys2.server.model.genesys;
import java.text.MessageFormat;
import java.util.List;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.OneToMany;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
import org.genesys2.server.model.BusinessModel;
import org.genesys2.server.model.impl.CropTaxonomy;
import org.hibernate.search.annotations.Field;
import org.hibernate.search.annotations.Indexed;
import org.hibernate.search.annotations.Store;
......@@ -50,9 +46,6 @@ public class Taxonomy extends BusinessModel {
@Field(name = "title", store = Store.NO)
private String taxonName;
@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
private List<CropTaxonomy> cropTaxonomies;
public String getGenus() {
return this.genus;
}
......@@ -77,14 +70,6 @@ public class Taxonomy extends BusinessModel {
this.taxonName = taxonName;
}
public List<CropTaxonomy> getCropTaxonomies() {
return cropTaxonomies;
}
public void setCropTaxonomies(List<CropTaxonomy> cropTaxonomies) {
this.cropTaxonomies = cropTaxonomies;
}
@Override
public String toString() {
return MessageFormat.format("Tax id={0} genus={1} sp={2}, full={3}", id, genus, species, taxonName);
......
src/main/java/org/genesys2/server/model/genesys/Taxonomy2.java
View file @ 85e789a5
......@@ -17,15 +17,19 @@
package org.genesys2.server.model.genesys;
import java.text.MessageFormat;
import java.util.List;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.Lob;
import javax.persistence.OneToMany;
import javax.persistence.PrePersist;
import javax.persistence.Table;
import javax.persistence.UniqueConstraint;
import org.genesys2.server.model.GlobalVersionedAuditedModel;
import org.genesys2.server.model.impl.CropTaxonomy;
import org.hibernate.search.annotations.Indexed;
@Entity
......@@ -59,8 +63,8 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
private Long taxSpecies;
// @OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
// private List<CropTaxonomy> cropTaxonomies;
@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "taxonomy")
private List<CropTaxonomy> cropTaxonomies;
@PrePersist
private void prePersist() {
......@@ -152,6 +156,14 @@ public class Taxonomy2 extends GlobalVersionedAuditedModel {
this.taxSpecies = taxSpecies;
}
public List<CropTaxonomy> getCropTaxonomies() {
return cropTaxonomies;
}
public void setCropTaxonomies(List<CropTaxonomy> cropTaxonomies) {
this.cropTaxonomies = cropTaxonomies;
}
@Override
public String toString() {
return MessageFormat.format("Tax id={0} taxonName={1}", id, getTaxonName());
......
src/main/java/org/genesys2/server/model/impl/CropTaxonomy.java
View file @ 85e789a5
......@@ -22,9 +22,8 @@ import javax.persistence.ManyToOne;
import javax.persistence.Table;
import org.genesys2.server.model.BusinessModel;
import org.genesys2.server.model.genesys.Taxonomy;
import org.genesys2.server.model.genesys.Taxonomy2;
// TODO FIXME Need to link to {@link Taxonomy2}
@Entity
@Table(name = "croptaxonomy")
public class CropTaxonomy extends BusinessModel {
......@@ -36,7 +35,7 @@ public class CropTaxonomy extends BusinessModel {
@ManyToOne(cascade = {}, optional = false)
@JoinColumn(name = "taxonomyId")
private Taxonomy taxonomy;
private Taxonomy2 taxonomy;
public Crop getCrop() {
return crop;
......@@ -46,11 +45,11 @@ public class CropTaxonomy extends BusinessModel {
this.crop = crop;
}
public Taxonomy getTaxonomy() {
public Taxonomy2 getTaxonomy() {
return taxonomy;
}
public void setTaxonomy(Taxonomy taxonomy) {
public void setTaxonomy(Taxonomy2 taxonomy) {
this.taxonomy = taxonomy;
}
......
src/main/java/org/genesys2/server/persistence/domain/CropTaxonomyRepository.java
View file @ 85e789a5
......@@ -18,7 +18,7 @@ package org.genesys2.server.persistence.domain;
import java.util.List;
import org.genesys2.server.model.genesys.Taxonomy;
import org.genesys2.server.model.genesys.Taxonomy2;
import org.genesys2.server.model.impl.Crop;
import org.genesys2.server.model.impl.CropTaxonomy;
import org.springframework.data.domain.Page;
......@@ -39,12 +39,11 @@ public interface CropTaxonomyRepository extends JpaRepository<CropTaxonomy, Long
Page<CropTaxonomy> findByCrop(Crop crop, Pageable pageable);
// TODO FIXME todo
@Query("select distinct t from CropTaxonomy ct inner join ct.taxonomy t where ct.crop = ?1")
List<Taxonomy> findTaxonomiesByCrop(Crop crop);
List<Taxonomy2> findTaxonomiesByCrop(Crop crop);
@Query("select distinct ct.crop from CropTaxonomy ct where ct.taxonomy= ?1")
List<Crop> findByTaxonomy(Taxonomy taxonomy);
List<Crop> findByTaxonomy(Taxonomy2 taxonomy);
@Modifying
@Query("delete from CropTaxonomy ct where ct.crop = ?1")
......
src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java
View file @ 85e789a5
......@@ -32,4 +32,10 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
List<String> autocompleteTaxonomy(String term, Pageable page);
Taxonomy2 findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(String genus, String species, String spAuthor, String subtaxa, String subtAuthor);
List<Taxonomy2> findByGenus(String genus);
List<Taxonomy2> findByGenusAndSpecies(String genus, String species);
List<Taxonomy2> findByGenusAndSpeciesAndSubtaxa(String genus, String species, String subtaxa);
}
src/main/java/org/genesys2/server/service/CropService.java
View file @ 85e789a5
......@@ -19,7 +19,6 @@ package org.genesys2.server.service;
import java.util.List;
import java.util.Locale;
import org.genesys2.server.model.genesys.Taxonomy;
import org.genesys2.server.model.genesys.Taxonomy2;
import org.genesys2.server.model.impl.Crop;
import org.genesys2.server.model.impl.CropRule;
......@@ -35,8 +34,6 @@ public interface CropService {
List<Crop> list(Locale locale);
List<Crop> getCrops(Taxonomy taxonomy);
List<Crop> getCrops(Taxonomy2 taxonomy2);
void rebuildTaxonomies();
......
src/main/java/org/genesys2/server/service/impl/CropServiceImpl.java
View file @ 85e789a5
......@@ -22,10 +22,11 @@ import java.util.Comparator;
import java.util.List;
import java.util.Locale;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.Predicate;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.genesys2.server.model.genesys.Taxonomy;
import org.genesys2.server.model.genesys.Taxonomy2;
import org.genesys2.server.model.impl.Crop;
import org.genesys2.server.model.impl.CropRule;
......@@ -33,7 +34,7 @@ import org.genesys2.server.model.impl.CropTaxonomy;
import org.genesys2.server.persistence.domain.CropRepository;
import org.genesys2.server.persistence.domain.CropRuleRepository;
import org.genesys2.server.persistence.domain.CropTaxonomyRepository;
import org.genesys2.server.persistence.domain.TaxonomyRepository;
import org.genesys2.server.persistence.domain.Taxonomy2Repository;
import org.genesys2.server.service.CropService;
import org.genesys2.server.service.HtmlSanitizer;
import org.springframework.beans.factory.annotation.Autowired;
......@@ -60,10 +61,10 @@ public class CropServiceImpl implements CropService {
CropTaxonomyRepository cropTaxonomyRepository;
@Autowired
TaxonomyRepository taxonomyRepository;
private HtmlSanitizer htmlSanitizer;
@Autowired
private HtmlSanitizer htmlSanitizer;
private Taxonomy2Repository taxonomy2Repository;
@Override
public Crop getCrop(String shortName) {
......@@ -87,15 +88,9 @@ public class CropServiceImpl implements CropService {
return crops;
}
@Override
public List<Crop> getCrops(Taxonomy taxonomy) {
return cropTaxonomyRepository.findByTaxonomy(taxonomy);
}
@Override
public List<Crop> getCrops(Taxonomy2 taxonomy2) {
// TODO FIXME get the crops!
return null;
return cropTaxonomyRepository.findByTaxonomy(taxonomy2);
}
@Override
......@@ -135,35 +130,35 @@ public class CropServiceImpl implements CropService {
LOG.info("Included: " + includedTaxa.size());
LOG.info("Excluded: " + excludedTaxa.size());
List<Taxonomy> taxa = new ArrayList<Taxonomy>();
List<Taxonomy2> taxa = new ArrayList<Taxonomy2>();
for (CropRule cr : includedTaxa) {
if (cr.getSpecies() == null) {
taxa.addAll(taxonomyRepository.findByGenus(cr.getGenus()));
if (cr.getSpecies() == null && cr.getSubtaxa() == null) {
taxa.addAll(taxonomy2Repository.findByGenus(cr.getGenus()));
} else if (cr.getSubtaxa() == null) {
taxa.addAll(taxonomy2Repository.findByGenusAndSpecies(cr.getGenus(), cr.getSpecies()));
} else {
taxa.add(taxonomyRepository.getByGenusAndSpecies(cr.getGenus(), cr.getSpecies()));
taxa.addAll(taxonomy2Repository.findByGenusAndSpeciesAndSubtaxa(cr.getGenus(), cr.getSpecies(), cr.getSubtaxa()));
}
}
for (CropRule cr : excludedTaxa) {
if (cr.getSpecies() == null) {
for (Taxonomy notincluded : taxonomyRepository.findByGenus(cr.getGenus())) {
for (int i = taxa.size() - 1; i >= 0; i--) {
if (taxa.get(i).getId().equals(notincluded.getId())) {
taxa.remove(i);
}
for (final CropRule cr : excludedTaxa) {
CollectionUtils.filterInverse(taxa, new Predicate<Taxonomy2>() {
@Override
public boolean evaluate(Taxonomy2 taxonomy) {
if (cr.getSpecies() == null && cr.getSubtaxa() == null) {
return StringUtils.equalsIgnoreCase(taxonomy.getSubtaxa(), cr.getSubtaxa())
&& StringUtils.equalsIgnoreCase(taxonomy.getSpecies(), cr.getSpecies());
} else if (cr.getSubtaxa() == null) {
return StringUtils.equalsIgnoreCase(taxonomy.getSpecies(), cr.getSpecies());
} else {
return StringUtils.equalsIgnoreCase(taxonomy.getGenus(), cr.getGenus());
}
}
} else {
Taxonomy notincluded = taxonomyRepository.getByGenusAndSpecies(cr.getGenus(), cr.getSpecies());
for (int i = taxa.size() - 1; i >= 0; i--) {
if (taxa.get(i).getId().equals(notincluded.getId())) {
taxa.remove(i);
}
}
}
});
}
LOG.warn("Clearing crop taxonomy for " + crop.getName());
// To check
......@@ -176,7 +171,7 @@ public class CropServiceImpl implements CropService {
long taxonomyId = ct.getTaxonomy().getId();
boolean found = false;
for (Taxonomy taxonomy : taxa) {
for (Taxonomy2 taxonomy : taxa) {
if (taxonomyId == taxonomy.getId()) {
found = true;
break;
......@@ -191,7 +186,7 @@ public class CropServiceImpl implements CropService {
List<CropTaxonomy> toAdd = new ArrayList<CropTaxonomy>();
// To add
for (Taxonomy taxonomy : taxa) {
for (Taxonomy2 taxonomy : taxa) {
boolean found = false;
for (CropTaxonomy ct : existing) {
......
src/main/java/org/genesys2/server/service/impl/GenesysFilterServiceImpl.java
View file @ 85e789a5
......@@ -70,7 +70,6 @@ import com.fasterxml.jackson.databind.node.ObjectNode;
@Service
@Transactional(readOnly = true)
// FIXME TODO Change taxonomy to taxonomy2
public class GenesysFilterServiceImpl implements GenesysFilterService {
private static final Log LOG = LogFactory.getLog(GenesysFilterServiceImpl.class);
......@@ -215,7 +214,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
StringBuffer sb = new StringBuffer();
sb.append(" from accession a ");
if (jsonTree.has("crop") || jsonTree.has("genus") || jsonTree.has("taxon")) {
sb.append(" inner join taxonomy t on t.id=a.taxonomyId ");
sb.append(" inner join taxonomy2 t on t.id=a.taxonomyId2 ");
if (jsonTree.has("crop")) {
sb.append(" inner join croptaxonomy ct on ct.taxonomyId=t.id inner join crop on crop.id=ct.cropId ");
}
......@@ -682,7 +681,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
final StringBuffer sb = new StringBuffer();
sb.append(" from accessiongeo geo inner join accession a on a.id=geo.accessionId ");
if (jsonTree.has("crop") || jsonTree.has("genus") || jsonTree.has("taxon")) {
sb.append(" inner join taxonomy t on t.id=a.taxonomyId ");
sb.append(" inner join taxonomy2 t on t.id=a.taxonomyId2 ");
if (jsonTree.has("crop")) {
sb.append(" inner join croptaxonomy ct on ct.taxonomyId=t.id inner join crop on crop.id=ct.cropId ");
}
......
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @ 85e789a5
......@@ -389,7 +389,7 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
@Override
public Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable) {
List<Taxonomy2> taxonomies = null;// FIXME TODO cropTaxonomyRepository.findTaxonomiesByCrop(crop);
List<Taxonomy2> taxonomies = cropTaxonomyRepository.findTaxonomiesByCrop(crop);
if (taxonomies == null || taxonomies.size() == 0) {
return null;
}
......
src/main/java/org/genesys2/server/service/impl/TaxonomyServiceImpl.java
View file @ 85e789a5
......@@ -86,12 +86,12 @@ public class TaxonomyServiceImpl implements TaxonomyService {
@Override
public List<String> autocompleteGenus(String term) {
return taxonomyRepository.autocompleteGenus(term + "%", new PageRequest(0, 10));
return taxonomy2Repository.autocompleteGenus(term + "%", new PageRequest(0, 10));
}
@Override
public List<String> autocompleteTaxonomy(String term) {
return taxonomyRepository.autocompleteTaxonomy("%" + term + "%", new PageRequest(0, 10));
return taxonomy2Repository.autocompleteTaxonomy("%" + term + "%", new PageRequest(0, 10));
}
@Override
......@@ -207,11 +207,19 @@ public class TaxonomyServiceImpl implements TaxonomyService {
return taxonomy2Repository.count();
}
/**
* @deprecated Will be removed when {@link Taxonomy} is removed.
*/
// TODO FIXME Remove
@Override
public List<Taxonomy> findAll() {
return taxonomyRepository.findAll();
}
/**
* @deprecated Will be removed when {@link Taxonomy} is removed.
*/
// TODO FIXME Remove
@Override
@Transactional
public long upgradeTaxonomy(Taxonomy t1, Taxonomy2 t2) {
......
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