Use MCPD#cropName instead of taxonomy to determine crop of accession

doc/ddl/cropname.sql

+
+CREATE TABLE `cropname` (
+  `cropId` bigint(20) NOT NULL,
+  `otherName` varchar(255) NOT NULL,
+  UNIQUE KEY `UK_o6svkv9o98t67jnnxv7i0d4a7` (`otherName`),
+  KEY `FK_tb67bwitjd2dlmmfbxqsfcjmq` (`cropId`),
+  CONSTRAINT `FK_tb67bwitjd2dlmmfbxqsfcjmq` FOREIGN KEY (`cropId`) REFERENCES `crop` (`id`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8;
+
+alter table accession add `cropName` varchar(50) DEFAULT NULL,
+  add `cropId` bigint(20) DEFAULT NULL, 
+  add CONSTRAINT `FK_826wi40aq5ucsmeki61dnr9pt` FOREIGN KEY (`cropId`) REFERENCES `crop` (`id`);
+
+alter table accessionhistoric add `cropName` varchar(50) DEFAULT NULL,
+  add `cropId` bigint(20) DEFAULT NULL, 
+  add CONSTRAINT `FK_tb12h2n6q2ck6wvpp2l73up2a` FOREIGN KEY (`cropId`) REFERENCES `crop` (`id`);
+
+update accession a inner join croptaxonomy ct on ct.taxonomyId=a.taxonomyId2 inner join crop c on c.id=ct.cropId set a.cropName=c.shortName, a.cropId=c.id;
+update accessionhistoric a inner join croptaxonomy ct on ct.taxonomyId=a.taxonomyId2 inner join crop c on c.id=ct.cropId set a.cropName=c.shortName, a.cropId=c.id;

src/main/java/org/genesys2/server/model/elastic/AccessionDetails.java

@@ -153,6 +153,18 @@ public class AccessionDetails {
 		}
 	}
 
+	/**
+	 * Single crop
+	 * 
+	 * @param shortName
+	 */
+	public void crops(String cropName) {
+		if (StringUtils.isBlank(cropName))
+			return;
+		this.crops = new ArrayList<String>();
+		this.crops.add(cropName);
+	}
+
 	public void crops(List<Crop> crops) {
 		if (crops == null || crops.isEmpty())
 			return;
@@ -473,4 +485,5 @@ public class AccessionDetails {
 	public void setLists(Set<String> lists) {
 		this.lists = lists;
 	}
+
 }

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

@@ -26,6 +26,7 @@ import java.util.UUID;
 
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
+import javax.persistence.FetchType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
@@ -39,6 +40,7 @@ import javax.persistence.Version;
 
 import org.genesys2.server.model.IdUUID;
 import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.util.MCPDUtil;
 import org.genesys2.util.NumberUtils;
@@ -92,6 +94,13 @@ public abstract class AccessionData implements IdUUID, Serializable {
 	@Column(name = "seqNo", nullable = false)
 	private float seqNo = 0;
 
+	@Column(name = "cropName", nullable = true, length = 50)
+	private String cropName;
+
+	@ManyToOne(cascade = {}, optional = true, fetch = FetchType.LAZY)
+	@JoinColumn(name = "cropId")
+	private Crop crop;
+
 	// @Cache(usage=CacheConcurrencyStrategy.READ_WRITE)
 	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "taxonomyId2")
@@ -153,7 +162,7 @@ public abstract class AccessionData implements IdUUID, Serializable {
 
 		this.instituteCode = getInstitute().getCode();
 		this.storage = MCPDUtil.toMcpdArray(getStoRage());
-		
+
 		// Update the ACCENUMB number
 		this.seqNo = NumberUtils.numericValue(this.accessionName);
 	}
@@ -388,4 +397,20 @@ public abstract class AccessionData implements IdUUID, Serializable {
 	public void setSeqNo(float acceNumbNumb) {
 		this.seqNo = acceNumbNumb;
 	}
+
+	public String getCropName() {
+		return cropName;
+	}
+
+	public void setCropName(String cropName) {
+		this.cropName = cropName;
+	}
+
+	public Crop getCrop() {
+		return crop;
+	}
+
+	public void setCrop(Crop crop) {
+		this.crop = crop;
+	}
 }

src/main/java/org/genesys2/server/model/impl/Crop.java

@@ -24,12 +24,18 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
+import javax.persistence.CollectionTable;
 import javax.persistence.Column;
+import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.JoinColumn;
 import javax.persistence.Lob;
 import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
 import javax.persistence.Table;
 import javax.persistence.Transient;
+import javax.persistence.UniqueConstraint;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
@@ -56,6 +62,12 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
 	@Column(nullable = false, length = 50, unique = true)
 	private String shortName;
 
+	@Column(name = "otherName", nullable = false)
+	@ElementCollection(fetch = FetchType.LAZY)
+	@CollectionTable(name = "cropname", joinColumns = @JoinColumn(name = "cropId", referencedColumnName = "id"), uniqueConstraints = { @UniqueConstraint(columnNames = "otherName") })
+	@OrderBy("otherName")
+	private List<String> otherNames;
+
 	@Column(nullable = false, length = 200)
 	private String name;
 
@@ -219,4 +231,11 @@ public class Crop extends GlobalVersionedAuditedModel implements AclAwareModel {
 		return buildVernacularMap("description");
 	}
 
+	public List<String> getOtherNames() {
+		return otherNames;
+	}
+
+	public void setOtherNames(List<String> otherNames) {
+		this.otherNames = otherNames;
+	}
 }

src/main/java/org/genesys2/server/model/json/Api1Constants.java

@@ -186,8 +186,13 @@ public interface Api1Constants {
 		 */
 		public static final String ACCEURL = "acceUrl";
 
+		/**
+		 * Gene bank provided MCPD#CROPNAME
+		 */
+		public static final String CROPNAME = "cropName";
+
 	}
-	
+
 	public static interface Institute {
 		/**
 		 * Corresponds to INSTCODE
@@ -197,9 +202,9 @@ public interface Api1Constants {
 		public static final String INSTCODE_COUNTRY = "country.iso3";
 
 	}
-	
+
 	public static interface Taxonomy {
-		
+
 		public static final String SCIENTIFIC_NAME = "sciName";
 
 		/**

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

@@ -19,6 +19,7 @@ package org.genesys2.server.persistence.domain;
 import java.util.List;
 
 import org.genesys2.server.model.impl.Crop;
+import org.springframework.data.elasticsearch.annotations.Query;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface CropRepository extends JpaRepository<Crop, Long> {
@@ -26,4 +27,7 @@ public interface CropRepository extends JpaRepository<Crop, Long> {
 	Crop findByShortName(String shortName);
 
 	List<Crop> findByShortName(List<String> cropNames);
+
+	@Query("select c from Crop c where ?1 member of c.otherNames")
+	Crop findByOtherNames(String cropName);
 }

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

@@ -45,6 +45,7 @@ import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.json.Api1Constants;
 import org.genesys2.server.persistence.domain.AccessionCustomRepository;
 import org.genesys2.server.service.BatchRESTService;
+import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
@@ -78,6 +79,9 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Autowired
 	TaxonomyService taxonomyService;
 
+	@Autowired
+	CropService cropService;
+
 	@Autowired
 	OrganizationService organizationService;
 
@@ -195,10 +199,10 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				throw new RESTApiException("Accession does not belong to instCode=" + institute.getCode() + " acn=" + dataJson);
 			}
 
-			Accession accession = loaded.stream()
-					.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb))
-							: (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus)))
-					.findFirst().orElse(null);
+			Accession accession = loaded
+					.stream()
+					.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(dataJson.acceNumb)) : (a.getAccessionName().equalsIgnoreCase(
+							dataJson.acceNumb) && a.getTaxonomy().getGenus().equalsIgnoreCase(dataJson.genus))).findFirst().orElse(null);
 
 			boolean updated = false;
 
@@ -237,6 +241,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 				updated |= updateTaxonomy(accession, accnJson);
 			}
 
+			updated |= updateCrop(accession, accnJson.get(Api1Constants.Accession.CROPNAME));
 			updated |= updateAcceNumb(accession, accnJson.get(Api1Constants.Accession.ACCENUMB_NEW));
 			updated |= updateOrgCty(accession, accnJson.get(Api1Constants.Accession.ORIGCTY));
 			updated |= updateUuid(accession, accnJson.get(Api1Constants.Accession.UUID));
@@ -520,24 +525,24 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 			List<Accession> savedData = genesysService.saveAccessions(institute, toSave);
 
 			// Iterate savedData to extract UUIDs
-			upsertResponses.stream().forEach(response -> {
-				Accession accession = savedData.stream()
-						.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName()
-								.equalsIgnoreCase(response.getAcceNumb()))
-								: (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb())
-										&& a.getTaxonomy().getGenus().equalsIgnoreCase(response.getGenus())))
-						.findFirst().orElse(null);
-
-				UpsertResult result = response.getResult();
-				if (accession != null) {
-					if (result.getUuid() == null) {
-						result.setAction(UpsertResult.Type.INSERT);
-					} else {
-						result.setAction(UpsertResult.Type.UPDATE);
-					}
-					result.setUUID(accession.getUuid());
-				}
-			});
+			upsertResponses.stream().forEach(
+					response -> {
+						Accession accession = savedData
+								.stream()
+								.filter(a -> useUniqueAcceNumbs ? (a.getAccessionName().equalsIgnoreCase(response.getAcceNumb())) : (a.getAccessionName()
+										.equalsIgnoreCase(response.getAcceNumb()) && a.getTaxonomy().getGenus().equalsIgnoreCase(response.getGenus())))
+								.findFirst().orElse(null);
+
+						UpsertResult result = response.getResult();
+						if (accession != null) {
+							if (result.getUuid() == null) {
+								result.setAction(UpsertResult.Type.INSERT);
+							} else {
+								result.setAction(UpsertResult.Type.UPDATE);
+							}
+							result.setUUID(accession.getUuid());
+						}
+					});
 		}
 
 		if (toSaveColl.size() > 0) {
@@ -584,6 +589,30 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		return upsertResponses;
 	}
 
+	private boolean updateCrop(Accession accession, JsonNode value) throws RESTApiDataTypeException {
+		if (value != null) {
+			if (!value.isTextual()) {
+				throw new RESTApiDataTypeException("cropName must be a String");
+			}
+
+			if (value.isNull()) {
+				if (!StringUtils.equals(null, accession.getCropName())) {
+					accession.setCropName(null);
+					accession.setCrop(null);
+					return true;
+				}
+			}
+
+			final String cropName = value.textValue().trim();
+			if (!StringUtils.equals(cropName, accession.getCropName())) {
+				accession.setCropName(cropName);
+				accession.setCrop(cropService.getCrop(cropName));
+				return true;
+			}
+		}
+		return false;
+	}
+
 	private boolean updateStorage(AccessionData accession, ObjectNode accnJson) throws RESTApiDataTypeException {
 		boolean updated = false;
 
@@ -1043,7 +1072,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'DELETE') or hasPermission(#institute, 'MANAGE')")
-	public List<AccessionOpResponse>  deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> batch) throws RESTApiException {
+	public List<AccessionOpResponse> deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> batch) throws RESTApiException {
 		LOG.info("Batch deleting " + batch.size() + " entries for " + institute);
 
 		final List<AccessionOpResponse> upsertResponses = new ArrayList<AccessionOpResponse>();
@@ -1077,12 +1106,12 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 			if (accession != null) {
 				toDelete.add(accession);
-				upsertResult=new UpsertResult(UpsertResult.Type.DELETE);
+				upsertResult = new UpsertResult(UpsertResult.Type.DELETE);
 				upsertResult.setUUID(accession.getUuid());
 			} else {
-				upsertResult=new UpsertResult(UpsertResult.Type.NOOP);
+				upsertResult = new UpsertResult(UpsertResult.Type.NOOP);
 			}
-			
+
 			upsertResponse.setResult(upsertResult);
 		}
 

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

@@ -72,7 +72,12 @@ public class CropServiceImpl implements CropService {
 
 	@Override
 	public Crop getCrop(String shortName) {
-		return cropRepository.findByShortName(shortName);
+		Crop crop = cropRepository.findByShortName(shortName);
+		if (crop == null) {
+			// Find crop by alias
+			crop = cropRepository.findByOtherNames(shortName);
+		}
+		return crop;
 	}
 
 	@PreAuthorize("hasRole('ADMINISTRATOR')")

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

@@ -110,17 +110,16 @@ public class DirectMysqlQuery {
 			innerJoin("accelist", "al", "al.id=ali.listid");
 		}
 
-		if (filters.hasFilter(FilterConstants.CROPS) || filters.hasFilter(FilterConstants.TAXONOMY_GENUS) || filters.hasFilter(FilterConstants.TAXONOMY_SPECIES)
+		if (filters.hasFilter(FilterConstants.TAXONOMY_GENUS) || filters.hasFilter(FilterConstants.TAXONOMY_SPECIES)
 				|| filters.hasFilter(FilterConstants.TAXONOMY_SUBTAXA) || filters.hasFilter(FilterConstants.TAXONOMY_SCINAME)) {
 
 			innerJoin("taxonomy2", "t", "t.id=a.taxonomyId2");
-
-			if (filters.hasFilter(FilterConstants.CROPS)) {
-				innerJoin("croptaxonomy", "ct", "ct.taxonomyId=t.id");
-				innerJoin("crop", null, "crop.id=ct.cropId");
-			}
 		}
 
+		if (filters.hasFilter(FilterConstants.CROPS)) {
+			innerJoin("crop", null, "crop.id=a.cropId");
+		}
+		
 		// if (filters.hasFilter(FilterConstants.ORGCTY_ISO3)) {
 		// innerJoin("country", "cty", "cty.id=a.orgCtyId");
 		// }

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

@@ -363,6 +363,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			accession.getStoRage().size();
 			if (accession.getCountryOfOrigin() != null)
 				accession.getCountryOfOrigin().getId();
+			if (accession.getCrop() != null)
+				accession.getCrop().getId();
 		}
 		return accession;
 	}
@@ -394,7 +396,11 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		ad.remarks(all.remarks);
 		// ad.traits(listMethods(accession),
 		// getAccessionTraitValues(accession));
-		ad.crops(cropService.getCrops(all.accession.getTaxonomy()));
+		if (all.accession.getCrop() != null) {
+			ad.crops(all.accession.getCrop().getShortName());
+		} else {
+			ad.crops(cropService.getCrops(all.accession.getTaxonomy()));
+		}
 		return ad;
 	}
 
@@ -1105,8 +1111,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		zos.putNextEntry(metaEntry);
 		final BufferedWriter osw = new BufferedWriter(new OutputStreamWriter(zos));
 		osw.write("<?xml version='1.0' encoding='utf-8'?>\n");
-		osw.write(
-				"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
+		osw.write("<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
 		osw.write("<core encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 		osw.write("\t<files><location>core.csv</location></files>\n");
 		osw.write("\t<id index=\"0\" />\n");
@@ -1373,8 +1378,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		zos.putNextEntry(metaEntry);
 		final BufferedWriter osw = new BufferedWriter(new OutputStreamWriter(zos));
 		osw.write("<?xml version='1.0' encoding='utf-8'?>\n");
-		osw.write(
-				"<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
+		osw.write("<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
 		osw.write("<core encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 		osw.write("\t<files><location>core.csv</location></files>\n");
 		osw.write("\t<id index=\"0\" />\n");
@@ -1386,8 +1390,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		for (int i = 0; i < metadataMethods.size(); i++) {
 			final Method method = metadataMethods.get(i);
 
-			osw.write(
-					"<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+			osw.write("<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
 			osw.write("\t<files><location>");
 			osw.write(method.getFieldName().toLowerCase());
 			osw.write(".csv</location></files>\n");

src/main/java/org/genesys2/server/servlet/controller/AccessionController.java

@@ -16,6 +16,7 @@
 
 package org.genesys2.server.servlet.controller;
 
+import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
@@ -24,6 +25,7 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.PDCI;
 import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.DSService;
@@ -95,7 +97,14 @@ public class AccessionController extends BaseController {
 		model.addAttribute("methods", traitService.listMethods(accession.getAccessionId()));
 		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accession.getAccessionId()));
 
-		model.addAttribute("crops", cropService.getCrops(accession.getTaxonomy()));
+		if (accession.getCrop() != null) {
+			List<Crop> crops = new ArrayList<Crop>();
+			crops.add(accession.getCrop());
+			model.addAttribute("crops", crops);
+		} else {
+			// TODO Remove
+			// model.addAttribute("crops", cropService.getCrops(accession.getTaxonomy()));
+		}
 
 		// Worldclim data
 		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
@@ -116,7 +125,7 @@ public class AccessionController extends BaseController {
 				if (existingPdci == null) {
 					existingPdci = genesysService.updatePDCI(accession.getId());
 				}
-				
+
 				if (existingPdci != null && pdci.getTotal() != existingPdci.getTotal()) {
 					_logger.info("Forcing recalculation of PDCI");
 					genesysService.updatePDCI(accession.getId());
@@ -124,7 +133,7 @@ public class AccessionController extends BaseController {
 
 				model.addAttribute("pdci", pdci);
 				model.addAttribute("institutePDCI", statisticsService.statisticsPDCI(accession.getInstitute()));
-				
+
 			} catch (Throwable e) {
 				_logger.warn(e.getMessage(), e);
 			}