Crops, rules and Crop Taxonomies

src/main/java/org/crophub/rest/common/listener/sample/CreateAdminListener.java

@@ -14,7 +14,6 @@
  * limitations under the License.
  **/
 
-
 package org.crophub.rest.common.listener.sample;
 
 import java.util.HashSet;
@@ -30,27 +29,24 @@ import org.springframework.stereotype.Service;
 @Service("createAdminListener")
 public class CreateAdminListener extends RunAsAdminListener {
 
-    @Autowired
-    private UserService userService;
-
-
-    @Override
-    public void init() throws Exception {
-        _logger.info("Start adding sample admin");
-        if(!userService.exists("admin@example.com")){
-            User user = new User();
-            user.setEmail("admin@example.com");
-            user.setPassword("admin");
-            user.setName("Sample Admin");
-            Set<UserRole> userRoles = new HashSet<UserRole>();
-            userRoles.add(UserRole.ADMINISTRATOR);
-            user.setRoles(userRoles);
-//            user.setUserGroups(userGroupService.getUserGroupList());
-
-            userService.addUser(user);
-        }
-
-        _logger.info("Sample admin has been added successfully");
-
-    }
+	@Autowired
+	private UserService userService;
+
+	@Override
+	public void init() throws Exception {
+		_logger.info("Checking for admin account");
+		if (!userService.exists("admin@example.com")) {
+			User user = new User();
+			user.setEmail("admin@example.com");
+			user.setPassword("admin");
+			user.setName("Sample Admin");
+			Set<UserRole> userRoles = new HashSet<UserRole>();
+			userRoles.add(UserRole.ADMINISTRATOR);
+			user.setRoles(userRoles);
+			// user.setUserGroups(userGroupService.getUserGroupList());
+
+			userService.addUser(user);
+			_logger.info("Sample admin has been added successfully");
+		}
+	}
 }

src/main/java/org/crophub/rest/common/model/impl/Crop.java

 package org.crophub.rest.common.model.impl;
 
+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.Table;
 
 import org.crophub.rest.common.model.BusinessModel;
@@ -12,8 +16,8 @@ import org.crophub.rest.common.model.BusinessModel;
 public class Crop extends BusinessModel {
 	private static final long serialVersionUID = -2686341831839109257L;
 
-	@Column(nullable = false, length = 200)
-	private String name;
+	@Column(nullable = false, length = 2)
+	private String language;
 
 	/**
 	 * Crop short name used as short name in URLs
@@ -21,9 +25,18 @@ public class Crop extends BusinessModel {
 	@Column(nullable = false, length = 50, unique = true)
 	private String shortName;
 
+	@Column(nullable = false, length = 200)
+	private String name;
+
 	@Lob
 	private String description;
 
+	/**
+	 * Rules
+	 */
+	@OneToMany(mappedBy = "crop", fetch = FetchType.EAGER, cascade = {}, orphanRemoval = true)
+	private List<CropRule> cropRules;
+
 	public String getName() {
 		return name;
 	}
@@ -48,4 +61,20 @@ public class Crop extends BusinessModel {
 		this.description = description;
 	}
 
+	public String getLanguage() {
+		return language;
+	}
+
+	public void setLanguage(String language) {
+		this.language = language;
+	}
+
+	public List<CropRule> getCropRules() {
+		return cropRules;
+	}
+
+	public void setCropRules(List<CropRule> cropRules) {
+		this.cropRules = cropRules;
+	}
+
 }

src/main/java/org/crophub/rest/common/model/impl/CropRule.java

+package org.crophub.rest.common.model.impl;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.crophub.rest.common.model.BusinessModel;
+
+/**
+ * Crop rules establish which taxonomies are part of a {@link Crop}.
+ * 
+ * @author mobreza
+ */
+@Entity
+@Table(name = "croprule")
+public class CropRule extends BusinessModel {
+	private static final long serialVersionUID = -2336100072991067193L;
+
+	@Column
+	private boolean included;
+
+	@Column(nullable = false, length = 100)
+	private String genus;
+
+	@Column
+	private String species;
+
+	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = false)
+	@JoinColumn(name = "cropId")
+	private Crop crop;
+
+	public boolean isIncluded() {
+		return included;
+	}
+
+	public void setIncluded(boolean included) {
+		this.included = included;
+	}
+
+	public String getGenus() {
+		return genus;
+	}
+
+	public void setGenus(String genus) {
+		this.genus = genus;
+	}
+
+	public String getSpecies() {
+		return species;
+	}
+
+	public void setSpecies(String species) {
+		this.species = species;
+	}
+
+	public Crop getCrop() {
+		return crop;
+	}
+
+	public void setCrop(Crop crop) {
+		this.crop = crop;
+	}
+}

src/main/java/org/crophub/rest/common/model/impl/CropTaxonomy.java

+package org.crophub.rest.common.model.impl;
+
+import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.crophub.rest.common.model.BusinessModel;
+import org.crophub.rest.common.model.genesys.Taxonomy;
+
+@Entity
+@Table(name = "croptaxonomy")
+public class CropTaxonomy extends BusinessModel {
+	private static final long serialVersionUID = 8973799991421179782L;
+
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "cropId")
+	private Crop crop;
+
+	@ManyToOne(cascade = {}, optional = false)
+	@JoinColumn(name = "taxonomyId")
+	private Taxonomy taxonomy;
+
+	public Crop getCrop() {
+		return crop;
+	}
+
+	public void setCrop(Crop crop) {
+		this.crop = crop;
+	}
+
+	public Taxonomy getTaxonomy() {
+		return taxonomy;
+	}
+
+	public void setTaxonomy(Taxonomy taxonomy) {
+		this.taxonomy = taxonomy;
+	}
+
+}

src/main/java/org/crophub/rest/common/persistence/domain/AccessionRepository.java

@@ -77,4 +77,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
 
 	Page<Accession> findByTaxonomy(Taxonomy taxonomy, Pageable pageable);
+
+	@Query("select a from Accession a where a.taxonomy in ( ?1 )")
+	Page<Accession> findByTaxonomy(Collection<Taxonomy> taxonomies, Pageable pageable);
 }

src/main/java/org/crophub/rest/common/persistence/domain/CropRepository.java

@@ -16,10 +16,15 @@
 
 package org.crophub.rest.common.persistence.domain;
 
+import java.util.List;
+
 import org.crophub.rest.common.model.impl.Crop;
+import org.springframework.data.domain.Sort;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface CropRepository extends JpaRepository<Crop, Long> {
 
 	Crop findByShortName(String shortName);
+
+	List<Crop> findByLanguage(String language, Sort sort);
 }

src/main/java/org/crophub/rest/common/persistence/domain/CropRuleRepository.java

+/**
+ * Copyright 2013 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.crophub.rest.common.persistence.domain;
+
+import java.util.List;
+
+import org.crophub.rest.common.model.impl.Crop;
+import org.crophub.rest.common.model.impl.CropRule;
+import org.springframework.data.jpa.repository.JpaRepository;
+ 
+public interface CropRuleRepository extends JpaRepository<CropRule, Long> {
+
+	List<CropRule> findByCrop(Crop crop);
+}

src/main/java/org/crophub/rest/common/persistence/domain/CropTaxonomyRepository.java

+/**
+ * Copyright 2013 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.crophub.rest.common.persistence.domain;
+
+import java.util.List;
+
+import org.crophub.rest.common.model.genesys.Taxonomy;
+import org.crophub.rest.common.model.impl.Crop;
+import org.crophub.rest.common.model.impl.CropTaxonomy;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+ 
+public interface CropTaxonomyRepository extends JpaRepository<CropTaxonomy, Long> {
+
+	List<CropTaxonomy> findByCrop(Crop crop);
+
+	@Query("select distinct t from CropTaxonomy ct inner join ct.taxonomy t where ct.crop = ?1")
+	List<Taxonomy> findTaxonomiesByCrop(Crop crop);
+
+	@Query("select ct from CropTaxonomy ct where ct.taxonomy= ?1 and ct.crop.language = ?2")
+	Crop findByTaxonomyAndLanguage(Taxonomy taxonomy, String language);
+
+	@Modifying
+	@Query("delete from CropTaxonomy ct where ct.crop = ?1")
+	void clearCrop(Crop crop);
+}

src/main/java/org/crophub/rest/common/persistence/domain/TaxonomyRepository.java

@@ -16,9 +16,13 @@
 
 package org.crophub.rest.common.persistence.domain;
 
+import java.util.List;
+
 import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface TaxonomyRepository extends JpaRepository<Taxonomy, Long> {
 	Taxonomy getByGenusAndSpecies(String genus, String species);
+
+	List<Taxonomy> findByGenus(String genus);
 }

src/main/java/org/crophub/rest/common/service/CropService.java

 package org.crophub.rest.common.service;
 
 import java.util.List;
+import java.util.Locale;
 
+import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.Crop;
+import org.crophub.rest.common.model.impl.CropTaxonomy;
 
 public interface CropService {
 
-	List<Crop> list();
-
 	Crop getCrop(String shortName);
 
+	List<Crop> list(Locale locale);
+
+	Crop getCrop(Locale locale, Taxonomy taxonomy);
+
+	void rebuildTaxonomies();
+
+	List<CropTaxonomy> getCropTaxonomies(Crop crop);
 }

src/main/java/org/crophub/rest/common/service/GenesysService.java

@@ -14,6 +14,7 @@ import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.model.genesys.Method;
 import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.Country;
+import org.crophub.rest.common.model.impl.Crop;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
@@ -71,4 +72,6 @@ public interface GenesysService {
 
 	Page<Accession> listAccessions(Pageable pageable);
 
+	Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable);
+
 }

src/main/java/org/crophub/rest/common/service/impl/CropServiceImpl.java

 package org.crophub.rest.common.service.impl;
 
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.Crop;
+import org.crophub.rest.common.model.impl.CropRule;
+import org.crophub.rest.common.model.impl.CropTaxonomy;
 import org.crophub.rest.common.persistence.domain.CropRepository;
+import org.crophub.rest.common.persistence.domain.CropRuleRepository;
+import org.crophub.rest.common.persistence.domain.CropTaxonomyRepository;
+import org.crophub.rest.common.persistence.domain.TaxonomyRepository;
 import org.crophub.rest.common.service.CropService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Sort;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 @Service
@@ -20,14 +30,146 @@ public class CropServiceImpl implements CropService {
 
 	@Autowired
 	CropRepository cropRepository;
-	
+
+	@Autowired
+	CropRuleRepository cropRuleRepository;
+
+	@Autowired
+	CropTaxonomyRepository cropTaxonomyRepository;
+
+	@Autowired
+	TaxonomyRepository taxonomyRepository;
+
 	@Override
 	public Crop getCrop(String shortName) {
 		return cropRepository.findByShortName(shortName);
 	}
-	
+
+	@Override
+	public List<Crop> list(Locale locale) {
+		return cropRepository.findByLanguage(locale.getLanguage(), new Sort("name"));
+	}
+
+	@Override
+	public Crop getCrop(Locale locale, Taxonomy taxonomy) {
+		return cropTaxonomyRepository.findByTaxonomyAndLanguage(taxonomy, locale.getLanguage());
+	}
+
+	@Override
+	@Transactional(readOnly = false, propagation = Propagation.REQUIRES_NEW)
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	public void rebuildTaxonomies() {
+		LOG.warn("REBUILDING ALL CROP TAXONOMIES!");
+
+		// for each crop
+		for (Crop crop : cropRepository.findAll()) {
+			LOG.info("Rebuilding crop taxonomy for: " + crop.getName());
+
+			// for all rules
+			List<CropRule> cropRules = crop.getCropRules();
+			LOG.warn("Using rules: " + cropRules);
+			rebuildCropTaxonomies(crop, cropRules);
+		}
+
+	}
+
+	private void rebuildCropTaxonomies(Crop crop, List<CropRule> cropRules) {
+		List<CropRule> rulesSorted = new ArrayList<CropRule>(cropRules);
+
+		List<CropRule> includedTaxa = new ArrayList<CropRule>();
+		List<CropRule> excludedTaxa = new ArrayList<CropRule>();
+
+		for (CropRule cr : rulesSorted) {
+			if (cr.isIncluded()) {
+				LOG.debug("Included: " + cr);
+				includedTaxa.add(cr);
+			} else {
+				LOG.debug("Excluded: " + cr);
+				excludedTaxa.add(cr);
+			}
+		}
+
+		LOG.info("Included: " + includedTaxa.size());
+		LOG.info("Excluded: " + excludedTaxa.size());
+
+		List<Taxonomy> taxa = new ArrayList<Taxonomy>();
+
+		for (CropRule cr : includedTaxa) {
+			if (cr.getSpecies() == null) {
+				taxa.addAll(taxonomyRepository.findByGenus(cr.getGenus()));
+			} else {
+				taxa.add(taxonomyRepository.getByGenusAndSpecies(cr.getGenus(), cr.getSpecies()));
+			}
+		}
+
+		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);
+						}
+					}
+				}
+			} 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
+		List<CropTaxonomy> existing = cropTaxonomyRepository.findByCrop(crop);
+
+		List<CropTaxonomy> toRemove = new ArrayList<CropTaxonomy>();
+
+		// Remove existing if not in list
+		for (CropTaxonomy ct : existing) {
+			long taxonomyId = ct.getTaxonomy().getId();
+			boolean found = false;
+
+			for (Taxonomy taxonomy : taxa) {
+				if (taxonomyId == taxonomy.getId()) {
+					found = true;
+					break;
+				}
+			}
+			if (!found) {
+				toRemove.add(ct);
+			}
+		}
+		cropTaxonomyRepository.delete(toRemove);
+
+		List<CropTaxonomy> toAdd = new ArrayList<CropTaxonomy>();
+
+		// To add
+		for (Taxonomy taxonomy : taxa) {
+			boolean found = false;
+
+			for (CropTaxonomy ct : existing) {
+				if (ct.getTaxonomy().getId().equals(taxonomy.getId())) {
+					found = true;
+					break;
+				}
+			}
+			if (!found) {
+				CropTaxonomy ct = new CropTaxonomy();
+				ct.setCrop(crop);
+				ct.setTaxonomy(taxonomy);
+				toAdd.add(ct);
+			}
+		}
+
+		cropTaxonomyRepository.save(toAdd);
+	}
+
 	@Override
-	public List<Crop> list() {
-		return cropRepository.findAll(new Sort("name"));
+	public List<CropTaxonomy> getCropTaxonomies(Crop crop) {
+		return cropTaxonomyRepository.findByCrop(crop);
 	}
 }

src/main/java/org/crophub/rest/common/service/impl/GenesysServiceImpl.java

@@ -16,12 +16,14 @@ import org.crophub.rest.common.model.genesys.Metadata;
 import org.crophub.rest.common.model.genesys.Method;
 import org.crophub.rest.common.model.genesys.Taxonomy;
 import org.crophub.rest.common.model.impl.Country;
+import org.crophub.rest.common.model.impl.Crop;
 import org.crophub.rest.common.model.impl.FaoInstitute;
 import org.crophub.rest.common.persistence.domain.AccessionBreedingRepository;
 import org.crophub.rest.common.persistence.domain.AccessionCollectRepository;
 import org.crophub.rest.common.persistence.domain.AccessionNameRepository;
 import org.crophub.rest.common.persistence.domain.AccessionRepository;
 import org.crophub.rest.common.persistence.domain.AccessionTraitRepository;
+import org.crophub.rest.common.persistence.domain.CropTaxonomyRepository;
 import org.crophub.rest.common.persistence.domain.MetadataMethodRepository;
 import org.crophub.rest.common.persistence.domain.MetadataRepository;
 import org.crophub.rest.common.persistence.domain.MethodRepository;
@@ -57,6 +59,9 @@ public class GenesysServiceImpl implements GenesysService {
 	private MetadataMethodRepository metadataMethodRepository;
 	@Autowired
 	private TraitValueRepository traitValueRepository;
+	
+	@Autowired
+	private CropTaxonomyRepository cropTaxonomyRepository;
 
 	@Autowired
 	private MethodRepository methodRepository;
@@ -193,4 +198,9 @@ public class GenesysServiceImpl implements GenesysService {
 	public Page<Accession> listAccessions(Pageable pageable) {
 		return accessionRepository.findAll(pageable);
 	}
+	
+	@Override
+	public Page<Accession> listAccessionsByCrop(Crop crop, Pageable pageable) {