PDCI calculation and display

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

@@ -85,6 +85,9 @@ public class AccessionDetails {
 
 	private boolean historic;
 
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private String bredCode;
+
 	public static AccessionDetails from(AccessionData accession) {
 		AccessionDetails ad = new AccessionDetails();
 		ad.version = accession.getVersion();
@@ -159,6 +162,7 @@ public class AccessionDetails {
 		if (breeding == null)
 			return;
 		this.pedigree = StringUtils.defaultIfBlank(breeding.getPedigree(), null);
+		this.bredCode = StringUtils.defaultIfBlank(breeding.getBreederCode(), null);
 	}
 
 	public void exch(AccessionExchange exch) {
@@ -188,7 +192,7 @@ public class AccessionDetails {
 	public UUID getUuid() {
 		return uuid;
 	}
-	
+
 	public void setUuid(UUID uuid) {
 		this.uuid = uuid;
 	}
@@ -337,6 +341,14 @@ public class AccessionDetails {
 		this.coll = coll;
 	}
 
+	public String getBredCode() {
+		return bredCode;
+	}
+	
+	public void setBredCode(String bredCode) {
+		this.bredCode = bredCode;
+	}
+	
 	public String getPedigree() {
 		return pedigree;
 	}
@@ -404,11 +416,11 @@ public class AccessionDetails {
 	public boolean getHistoric() {
 		return historic;
 	}
-	
+
 	public void setHistoric(boolean historic) {
 		this.historic = historic;
 	}
-	
+
 	public void networks(List<Organization> organizations) {
 		if (organizations == null || organizations.isEmpty())
 			return;

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

+/**
+ * Copyright 2015 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.genesys2.server.model.genesys;
+
+import java.io.Serializable;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.persistence.PrePersist;
+import javax.persistence.Transient;
+
+public class PDCI implements Serializable {
+	public static final String[] independentItems = { "genus", "species", "spAuthor", "subTaxa", "subtAuthor", "cropName", "acqDate", "sampStat", "donorCode",
+			"donorNumb", "otherNumb", "duplSite", "storage", "donorName", "duplInstName", "acceUrl", "mlsStat" };
+	public static final String[] dependentItems = { "origCty", "collSite", "latitude", "longitude", "elevation", "collDate", "bredCode", "ancest", "collSrc",
+			"acceName", "collNumb", "collCode", "collName" };
+	
+	private Float score = null;
+
+	private int acqDate = 0;
+	private int sampStat = 0;
+	private int donorCode = 0;
+	private int genus = 0;
+	private int species = 0;
+	private int spAuthor = 0;
+	private int subTaxa = 0;
+	private int subtAuthor = 0;
+	private int donorNumb = 0;
+	private int otherNumb = 0;
+	private int duplSite = 0;
+	private int storage = 0;
+	private int donorName = 0;
+	private int duplInstName = 0;
+	private int acceUrl = 0;
+	private int mlsStat = 0;
+	private int origCty = 0;
+	private int latitude = 0;
+	private int longitude = 0;
+	private int collSite = 0;
+	private int elevation = 0;
+	private int collDate = 0;
+	private int collSrc = 0;
+	private int collNumb = 0;
+	private int collCode = 0;
+	private int collName = 0;
+	private int ancest = 0;
+	private int acceName = 0;
+
+	private int bredCode = 0;
+	private int cropName = 0;
+
+	@PrePersist
+	protected void prePersist() {
+		this.score = calculateScore();
+	}
+
+	public int getAcqDate() {
+		return acqDate;
+	}
+
+	public int getSampStat() {
+		return sampStat;
+	}
+
+	public int getDonorCode() {
+		return donorCode;
+	}
+
+	public int getGenus() {
+		return genus;
+	}
+
+	public int getSpecies() {
+		return species;
+	}
+
+	public int getSpAuthor() {
+		return spAuthor;
+	}
+
+	public int getSubTaxa() {
+		return subTaxa;
+	}
+
+	public int getSubtAuthor() {
+		return subtAuthor;
+	}
+
+	public int getDonorNumb() {
+		return donorNumb;
+	}
+
+	public int getOtherNumb() {
+		return otherNumb;
+	}
+
+	public int getDuplSite() {
+		return duplSite;
+	}
+
+	public int getStorage() {
+		return storage;
+	}
+
+	public int getDonorName() {
+		return donorName;
+	}
+
+	public int getDuplInstName() {
+		return duplInstName;
+	}
+
+	public int getAcceUrl() {
+		return acceUrl;
+	}
+
+	public int getMlsStat() {
+		return mlsStat;
+	}
+
+	public int getOrigCty() {
+		return origCty;
+	}
+
+	public int getLatitude() {
+		return latitude;
+	}
+
+	public int getLongitude() {
+		return longitude;
+	}
+
+	public int getCollSite() {
+		return collSite;
+	}
+
+	public int getElevation() {
+		return elevation;
+	}
+
+	public int getCollDate() {
+		return collDate;
+	}
+
+	public int getCollSrc() {
+		return collSrc;
+	}
+
+	public int getCollNumb() {
+		return collNumb;
+	}
+
+	public int getCollCode() {
+		return collCode;
+	}
+
+	public int getCollName() {
+		return collName;
+	}
+
+	public int getAncest() {
+		return ancest;
+	}
+
+	public int getAcceName() {
+		return acceName;
+	}
+
+	public int getBredCode() {
+		return bredCode;
+	}
+
+	public void setAcqDate(int score) {
+		this.acqDate = score;
+	}
+
+	public void setSampStat(int score) {
+		this.sampStat = score;
+	}
+
+	public void setDonorCode(int score) {
+		this.donorCode = score;
+	}
+
+	public void setGenus(int score) {
+		this.genus = score;
+	}
+
+	public void setSpecies(int score) {
+		this.species = score;
+	}
+
+	public void setSpAuthor(int score) {
+		this.spAuthor = score;
+	}
+
+	public void setSubTaxa(int score) {
+		this.subTaxa = score;
+	}
+
+	public void setSubtAuthor(int score) {
+		this.subtAuthor = score;
+	}
+
+	public void setDonorNumb(int score) {
+		this.donorNumb = score;
+	}
+
+	public void setOtherNumb(int score) {
+		this.otherNumb = score;
+	}
+
+	public void setDuplSite(int score) {
+		this.duplSite = score;
+	}
+
+	public void setStorage(int score) {
+		this.storage = score;
+	}
+
+	public void setDonorName(int score) {
+		this.donorName = score;
+	}
+
+	public void setDuplInstName(int score) {
+		this.duplInstName = score;
+	}
+
+	public void setAcceUrl(int score) {
+		this.acceUrl = score;
+	}
+
+	public void setMlsStat(int score) {
+		this.mlsStat = score;
+	}
+
+	public void setOrigCty(int score) {
+		this.origCty = score;
+	}
+
+	public void setLatitude(int score) {
+		this.latitude = score;
+	}
+
+	public void setLongitude(int score) {
+		this.longitude = score;
+	}
+
+	public void setCollSite(int score) {
+		this.collSite = score;
+	}
+
+	public void setElevation(int score) {
+		this.elevation = score;
+	}
+
+	public void setCollDate(int score) {
+		this.collDate = score;
+	}
+
+	public void setCollSrc(int score) {
+		this.collSrc = score;
+	}
+
+	public void setCollNumb(int score) {
+		this.collNumb = score;
+	}
+
+	public void setCollCode(int score) {
+		this.collCode = score;
+	}
+
+	public void setCollName(int score) {
+		this.collName = score;
+	}
+
+	public void setAncest(int score) {
+		this.ancest = score;
+	}
+
+	public void setAcceName(int score) {
+		this.acceName = score;
+	}
+
+	public void setBredCode(int score) {
+		this.bredCode = score;
+	}
+
+	public Float getScore() {
+		if (score == null) {
+			score = calculateScore();
+		}
+		return score;
+	}
+
+	public void setScore(Float score) {
+		this.score = score;
+	}
+
+	private Float calculateScore() {
+		float total = getTotal();
+		return total / 100f;
+	}
+
+	@Transient
+	public float getTotal() {
+		float score = 0;
+
+		score += acqDate;
+		score += sampStat;
+		score += donorCode;
+		score += genus;
+		score += species;
+		score += spAuthor;
+		score += subTaxa;
+		score += subtAuthor;
+		score += donorNumb;
+		score += otherNumb;
+		score += duplSite;
+		score += storage;
+		score += donorName;
+		score += duplInstName;
+		score += acceUrl;
+		score += mlsStat;
+		score += origCty;
+		score += latitude;
+		score += longitude;
+		score += collSite;
+		score += elevation;
+		score += collDate;
+		score += collSrc;
+		score += collNumb;
+		score += collCode;
+		score += collName;
+		score += ancest;
+		score += acceName;
+
+		score += bredCode;
+		score += cropName;
+		return score;
+	}
+
+	public void setCropName(int score) {
+		this.cropName = score;
+	}
+
+	public int getCropName() {
+		return cropName;
+	}
+
+	public String[] getIndependentItems() {
+		return independentItems;
+	}
+	
+	public String[] getDependentItems() {
+		return dependentItems;
+	}
+
+	public static Set<String> getPdciItems() {
+		Set<String> descriptors = new HashSet<String>();
+		for (java.lang.reflect.Method method : PDCI.class.getMethods()) {
+			if (method.getName().startsWith("get") && method.getReturnType() == int.class) {
+				String str = method.getName().substring(3);
+				descriptors.add(str.substring(0, 1).toLowerCase() + str.substring(1));
+			}
+		}
+		return descriptors;
+	}
+}

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

@@ -199,10 +199,15 @@ public interface GenesysService {
 	List<Long> listAccessionsIds(Taxonomy2 taxonomy);
 
 	public static class AllStuff {
-		public AllStuff(Long id) {
+		public AllStuff(long id) {
 			this.id = id;
 		}
 
+		public AllStuff(AccessionData accession) {
+			this.accession = accession;
+			this.id = accession.getId();
+		}
+
 		public Long id;
 		public AccessionData accession = null;
 		public AccessionGeo geo = null;

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

@@ -319,14 +319,17 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 
 	@Override
 	public AccessionDetails getAccessionDetails(long accessionId) {
-		AccessionData accession = getAccession(accessionId);
-		if (accession == null)
+		AccessionData accession = getAccessionData(accessionId);
+		if (accession == null) {
+			LOG.warn("No such accession with id=" + accessionId);
 			return null;
+		}
 
 		return toAccessionDetails(loadAllStuff(accession));
 	}
 
 	private AccessionDetails toAccessionDetails(AllStuff all) {
+		// LOG.info("Converting to AccessionDetails " + all);
 		if (all == null || all.accession == null)
 			return null;
 
@@ -432,7 +435,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public AllStuff loadAllStuff(AccessionData accession) {
 		if (accession == null)
 			return null;
-		AllStuff all = new AllStuff(accession.getAccessionId().getId());
+		AllStuff all = new AllStuff(accession);
 		all.bred = listAccessionBreeding(accession.getAccessionId());
 		all.collect = listAccessionCollect(accession.getAccessionId());
 		all.exch = listAccessionExchange(accession.getAccessionId());
@@ -582,11 +585,17 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	private AccessionData getAccessionData(AccessionId accessionId) {
 		if (accessionId == null)
 			return null;
-		Accession a = accessionRepository.findOne(accessionId.getId());
-		if (a != null)
+		return getAccessionData(accessionId.getId());
+	}
+
+	private AccessionData getAccessionData(Long id) {
+		Accession a = accessionRepository.findOne(id);
+		if (a != null) {
 			return a;
-		AccessionHistoric ah = accessionHistoricRepository.findOne(accessionId.getId());
-		return ah;
+		} else {
+			AccessionHistoric ah = accessionHistoricRepository.findOne(id);
+			return ah;
+		}
 	}
 
 	@Override

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

+/**
+ * Copyright 2015 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.genesys2.server.service.impl;
+
+import java.util.ArrayList;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.genesys2.server.model.elastic.AccessionDetails;
+import org.genesys2.server.model.elastic.Alias;
+import org.genesys2.server.model.elastic.Collect;
+import org.genesys2.server.model.elastic.Geo;
+import org.genesys2.server.model.elastic.Taxonomy;
+import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
+import org.genesys2.server.model.genesys.PDCI;
+import org.genesys2.server.service.GenesysService;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+/**
+ * Calculates PDCI value for an accession.
+ * 
+ * <p>
+ * Theo van Hintum, Frank Menting and Elisabeth van Strien (2011). <b>Quality
+ * indicators for passport data in ex situ genebanks.</b> Plant Genetic Resources,
+ * 9, pp 478-485.
+ * 
+ * doi:10.1017/S1479262111000682
+ * </p>
+ */
+@Component
+public class PDCICalculator implements InitializingBean {
+	public static final Log LOG = LogFactory.getLog(PDCICalculator.class);
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+	}
+
+	public PDCI getPdci(long accessionId) {
+		return calculatePDCI(accessionId);
+	}
+
+	private PDCI calculatePDCI(long accessionId) {
+		AccessionDetails accessionDetails = genesysService.getAccessionDetails(accessionId);
+		if (accessionDetails == null) {
+			LOG.warn("No such accession " + accessionId);
+			return null;
+		}
+
+		PDCI pdci = new PDCI();
+
+		independentDescriptors(pdci, accessionDetails);
+
+		switch (accessionDetails.getSampStat() == null ? -1 : accessionDetails.getSampStat() / 100) {
+		case 1:
+		case 2:
+			wildOrWeedy(pdci, accessionDetails);
+			break;
+
+		case 3:
+			landrace(pdci, accessionDetails);
+			break;
+		case 4:
+			breedingMaterial(pdci, accessionDetails);
+			break;
+		case 5:
+			cultivar(pdci, accessionDetails);
+		default:
+			otherTypes(pdci, accessionDetails);
+		}
+
+		return pdci;
+	}
+
+	private void independentDescriptors(PDCI pdci, AccessionDetails accessionDetails) {