CropTaxonomy linked to Taxonomy2

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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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) {