Merge branch '270-debug-upsert' into 'master'

Resolve "Debug upsert"

Closes #270

See merge request genesys-pgr/genesys-server!155

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

@@ -165,6 +165,10 @@ public class AccessionAlias extends BasicModel implements AccessionRelated, Self
 	public void setUsedBy(final String usedBy) {
 		this.usedBy = usedBy;
 	}
+	
+	public boolean isEmpty() {
+		return StringUtils.isBlank(name);
+	}
 
 	@Override
 	public String toString() {

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

@@ -19,6 +19,7 @@ package org.genesys2.server.model.genesys;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 import javax.persistence.CascadeType;
 import javax.persistence.CollectionTable;
@@ -37,6 +38,7 @@ import javax.persistence.OrderBy;
 import javax.persistence.PrePersist;
 import javax.persistence.Table;
 
+import org.elasticsearch.common.lang3.StringUtils;
 import org.genesys.blocks.auditlog.annotations.Audited;
 import org.genesys.blocks.model.AuditedVersionedModel;
 import org.genesys.blocks.model.IdUUID;
@@ -136,6 +138,29 @@ public class AccessionId extends AuditedVersionedModel implements IdUUID {
 		if (this.coll != null && this.coll.isEmpty()) {
 			this.coll = null;
 		}
+		
+		// Remove empty AccessionAlias
+		if (this.aliases != null && !this.aliases.isEmpty()) {
+			List<AccessionAlias> empties = this.aliases.stream().filter(alias -> alias.isEmpty()).collect(Collectors.toList());
+			this.aliases.removeAll(empties);
+		}
+
+		// Remove empty AccessionRemark
+		if (this.remarks != null && !this.remarks.isEmpty()) {
+			List<AccessionRemark> empties = this.remarks.stream().filter(remark -> !remark.isEmpty()).collect(Collectors.toList());
+			this.remarks.removeAll(empties);
+		}
+
+		this.breederCode = removeEmptyStrings(this.breederCode);
+		this.breederName = removeEmptyStrings(this.breederName);
+		this.duplSite = removeEmptyStrings(this.duplSite);
+	}
+
+	private static Set<String> removeEmptyStrings(Set<String> set) {
+		if (set == null || set.isEmpty()) {
+			return set;
+		}
+		return set.stream().filter(s -> StringUtils.isNotBlank(s)).collect(Collectors.toSet());
 	}
 
 	@Override

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

@@ -138,4 +138,8 @@ public class AccessionRemark extends BasicModel implements AccessionRelated, Sel
 	public String toString() {
 		return "" + this.fieldName + ":" + this.remark;
 	}
+
+	public boolean isEmpty() {
+		return StringUtils.isBlank(this.remark);
+	}
 }

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -267,19 +267,21 @@ public class AccessionUploader implements InitializingBean {
 		final List<AccessionAlias> existing = accession.getAliases() != null ? accession.getAliases() : new ArrayList<>();
 
 		AliasType aliasType = AccessionAlias.AliasType.valueOf(fieldName.toUpperCase());
-		List<AccessionAlias> names = new ArrayList<>();
+		final List<AccessionAlias> newaliases = new ArrayList<>();
 
 		if (jsonNode.isArray()) {
 			ArrayNode ns = (ArrayNode) jsonNode;
-			ns.forEach(n -> names.add(new AccessionAlias(aliasType, n.textValue())));
+			ns.forEach(n -> newaliases.add(new AccessionAlias(aliasType, n.textValue())));
 
 		} else if (jsonNode.isTextual()) {
-			names.add(new AccessionAlias(aliasType, jsonNode.textValue()));
+			newaliases.add(new AccessionAlias(aliasType, jsonNode.textValue()));
 		} else if (jsonNode.isNull()) {
 			// NOOP
 		} else {
 			throw new InvalidApiUsageException("Don't know what to do with " + fieldName + "=" + jsonNode);
 		}
+		
+		List<AccessionAlias> names = newaliases.stream().filter(alias -> ! alias.isEmpty()).collect(Collectors.toList());
 
 		List<AccessionAlias> toAdd = names.stream().filter(name -> existing.stream().filter(ex -> ex.equalTo(name)).count() == 0).collect(Collectors.toList());
 		List<AccessionAlias> toRemove = existing.stream().filter(alias -> alias.getAliasType() == aliasType).filter(alias -> names.stream().filter(name -> alias.equalTo(name))

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

@@ -173,7 +173,7 @@ public class WiewsController extends BaseController {
 
 		model.addAttribute("blurp", contentService.getArticle(faoInstitute, "blurp", getLocale()));
 
-		model.addAttribute("countByInstitute", genesysService.countByInstitute(faoInstitute));
+		model.addAttribute("countByInstitute", faoInstitute.getAccessionCount());
 		long datasetCount = genesysService.countDatasets(faoInstitute);
 		model.addAttribute("datasetCount", datasetCount);