Feature #32756 - Taxonomy2: Cleanup.

Created service method which removes all obsolete Taxonomy2 records.

src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java

@@ -16,12 +16,15 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.math.BigInteger;
 import java.util.List;
+import java.util.Set;
 
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Crop;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 
 public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
@@ -68,4 +71,19 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 
 	List<Taxonomy2> findByGenusAndSpeciesAndSubtaxa(String genus, String species, String subtaxa);
 
+	@Query(nativeQuery = true, value = "SELECT ct.taxonomyId FROM croptaxonomy ct " +
+			"UNION ALL SELECT t2.taxGenus FROM taxonomy2 t2 " +
+			"UNION ALL SELECT t3.taxSpecies FROM taxonomy2 t3 " +
+			"UNION ALL SELECT a.taxonomyId2 FROM accession a " +
+			"UNION ALL SELECT a2.taxGenus FROM accession a2 " +
+			"UNION ALL SELECT ah.taxGenus FROM accessionhistoric ah " +
+			"UNION ALL SELECT ah2.taxonomyId2 FROM accessionhistoric ah2;")
+	Set<BigInteger> findTaxonomyReferencedIds();
+
+	@Query("select t.id from Taxonomy2 t")
+	Set<Long> findTaxonomyIds();
+
+	@Query("delete from Taxonomy2 t where t.id in (?1)")
+	@Modifying
+	void removeUnusedIds(Set<Long> ids);
 }

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

@@ -47,4 +47,5 @@ public interface TaxonomyService {
 
 	List<String> autocompleteSubtaxa(String ac, Crop crop, List<String> genus, List<String> species);
 
+	void cleanupTaxonomies();
 }

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

@@ -16,7 +16,9 @@
 
 package org.genesys2.server.service.impl;
 
+import java.math.BigInteger;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
@@ -199,4 +201,18 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 	public Taxonomy2 get(String genus) {
 		return find(genus, "sp.", "", "", "");
 	}
+
+	@Override
+	@Transactional
+	public void cleanupTaxonomies() {
+		Set<BigInteger> referencedIds = taxonomy2Repository.findTaxonomyReferencedIds();
+		Set<Long> allIds = taxonomy2Repository.findTaxonomyIds();
+		for (BigInteger integer: referencedIds) {
+			allIds.remove(integer.longValue());
+		}
+
+		if (allIds.size() > 0) {
+			taxonomy2Repository.removeUnusedIds(allIds);
+		}
+	}
 }

src/main/java/org/genesys2/server/servlet/controller/admin/AdminController.java

@@ -31,12 +31,7 @@ import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.persistence.domain.GenesysLowlevelRepository;
-import org.genesys2.server.service.CountryNamesUpdater;
-import org.genesys2.server.service.ElasticService;
-import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.GeoRegionService;
-import org.genesys2.server.service.GeoService;
-import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.*;
 import org.genesys2.server.service.impl.ContentSanitizer;
 import org.genesys2.server.service.worker.ElasticUpdater;
 import org.genesys2.server.service.worker.ITPGRFAStatusUpdater;
@@ -98,6 +93,9 @@ public class AdminController {
 	@Autowired
 	private GeoRegionService geoRegionService;
 
+	@Autowired
+	private TaxonomyService taxonomyService;
+
 	ObjectMapper mapper = new ObjectMapper();
 
 	@RequestMapping("/")
@@ -355,4 +353,11 @@ public class AdminController {
 		elasticService.regenerateAccessionSequentialNumber();
 		return "redirect:/admin/";
 	}
+
+	@RequestMapping(value = "/cleanup-taxonomies", method = RequestMethod.POST)
+	public String cleanupTaxonomies() {
+		taxonomyService.cleanupTaxonomies();
+
+		return "redirect:/admin/";
+	}
 }

src/main/webapp/WEB-INF/jsp/admin/index.jsp

@@ -116,5 +116,12 @@
     <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
   </form>
 
+  <h3>Taxonomy</h3>
+  <form method="post" action="<c:url value="/admin/cleanup-taxonomies" />">
+    <input type="submit" class="btn btn-default" value="Cleanup taxonomies" />
+    <!-- CSRF protection -->
+    <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
+  </form>
+
 </body>
 </html>
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