AccessionJson model

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

+package org.genesys2.server.model.json;
+
+public class AccessionJson {
+	private long version = 0;
+	private Long genesysId;
+
+	private String instCode;
+	private String acceNumb;
+	private String genus;
+	private String species;
+	private String spauthor;
+	private String subtaxa;
+	private String subtauthor;
+	private String uuid;
+	private String orgCty;
+	private String acqDate;
+	private Boolean mlsStat;
+	private Boolean inTrust;
+	private Boolean available;
+	private int[] storage;
+	private Integer sampStat;
+	private String[] duplSite;
+	private String bredCode;
+	private String ancest;
+	private String donorCode;
+	private String donorNumb;
+	private String donorName;
+	private CollectingJson coll;
+	private GeoJson geo;
+
+	public long getVersion() {
+		return version;
+	}
+
+	public void setVersion(long l) {
+		this.version = l;
+	}
+
+	public Long getGenesysId() {
+		return genesysId;
+	}
+
+	public void setGenesysId(Long genesysId) {
+		this.genesysId = genesysId;
+	}
+
+	public String getInstCode() {
+		return instCode;
+	}
+
+	public void setInstCode(String instCode) {
+		this.instCode = instCode;
+	}
+
+	public String getAcceNumb() {
+		return acceNumb;
+	}
+
+	public void setAcceNumb(String acceNumb) {
+		this.acceNumb = acceNumb;
+	}
+
+	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 String getSpauthor() {
+		return spauthor;
+	}
+
+	public void setSpauthor(String spauthor) {
+		this.spauthor = spauthor;
+	}
+
+	public String getSubtaxa() {
+		return subtaxa;
+	}
+
+	public void setSubtaxa(String subtaxa) {
+		this.subtaxa = subtaxa;
+	}
+
+	public String getSubtauthor() {
+		return subtauthor;
+	}
+
+	public void setSubtauthor(String subtauthor) {
+		this.subtauthor = subtauthor;
+	}
+
+	public String getUuid() {
+		return uuid;
+	}
+
+	public void setUuid(String uuid) {
+		this.uuid = uuid;
+	}
+
+	public String getOrgCty() {
+		return orgCty;
+	}
+
+	public void setOrgCty(String orgCty) {
+		this.orgCty = orgCty;
+	}
+
+	public String getAcqDate() {
+		return acqDate;
+	}
+
+	public void setAcqDate(String acqDate) {
+		this.acqDate = acqDate;
+	}
+
+	public Boolean getMlsStat() {
+		return mlsStat;
+	}
+
+	public void setMlsStat(Boolean mlsStat) {
+		this.mlsStat = mlsStat;
+	}
+
+	public Boolean getInTrust() {
+		return inTrust;
+	}
+
+	public void setInTrust(Boolean inTrust) {
+		this.inTrust = inTrust;
+	}
+
+	public Boolean getAvailable() {
+		return available;
+	}
+
+	public void setAvailable(Boolean available) {
+		this.available = available;
+	}
+
+	public int[] getStorage() {
+		return storage;
+	}
+
+	public void setStorage(int[] storage) {
+		this.storage = storage;
+	}
+
+	public Integer getSampStat() {
+		return sampStat;
+	}
+
+	public void setSampStat(Integer sampStat) {
+		this.sampStat = sampStat;
+	}
+
+	public String[] getDuplSite() {
+		return duplSite;
+	}
+
+	public void setDuplSite(String[] duplSite) {
+		this.duplSite = duplSite;
+	}
+
+	public String getBredCode() {
+		return bredCode;
+	}
+
+	public void setBredCode(String bredCode) {
+		this.bredCode = bredCode;
+	}
+
+	public String getAncest() {
+		return ancest;
+	}
+
+	public void setAncest(String ancest) {
+		this.ancest = ancest;
+	}
+
+	public String getDonorCode() {
+		return donorCode;
+	}
+
+	public void setDonorCode(String donorCode) {
+		this.donorCode = donorCode;
+	}
+
+	public String getDonorNumb() {
+		return donorNumb;
+	}
+
+	public void setDonorNumb(String donorNumb) {
+		this.donorNumb = donorNumb;
+	}
+
+	public String getDonorName() {
+		return donorName;
+	}
+
+	public void setDonorName(String donorName) {
+		this.donorName = donorName;
+	}
+
+	public CollectingJson getColl() {
+		return coll;
+	}
+
+	public void setColl(CollectingJson coll) {
+		this.coll = coll;
+	}
+
+	public GeoJson getGeo() {
+		return geo;
+	}
+
+	public void setGeo(GeoJson geo) {
+		this.geo = geo;
+	}
+
+}

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

+package org.genesys2.server.model.json;
+
+public class CollectingJson {
+	private String collDate;
+	private String collSite;
+	private String collNumb;
+	private Integer collSrc;
+	private String collCode;
+	private String collName;
+	private String collInstAddress;
+	private String collMissId;
+
+	public String getCollDate() {
+		return collDate;
+	}
+
+	public void setCollDate(String collDate) {
+		this.collDate = collDate;
+	}
+
+	public String getCollSite() {
+		return collSite;
+	}
+
+	public void setCollSite(String collSite) {
+		this.collSite = collSite;
+	}
+
+	public String getCollNumb() {
+		return collNumb;
+	}
+
+	public void setCollNumb(String collNumb) {
+		this.collNumb = collNumb;
+	}
+
+	public Integer getCollSrc() {
+		return collSrc;
+	}
+
+	public void setCollSrc(Integer integer) {
+		this.collSrc = integer;
+	}
+
+	public String getCollCode() {
+		return collCode;
+	}
+
+	public void setCollCode(String collCode) {
+		this.collCode = collCode;
+	}
+
+	public String getCollName() {
+		return collName;
+	}
+
+	public void setCollName(String collName) {
+		this.collName = collName;
+	}
+
+	public String getCollInstAddress() {
+		return collInstAddress;
+	}
+
+	public void setCollInstAddress(String collInstAddress) {
+		this.collInstAddress = collInstAddress;
+	}
+
+	public String getCollMissId() {
+		return collMissId;
+	}
+
+	public void setCollMissId(String collMissId) {
+		this.collMissId = collMissId;
+	}
+
+}

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

+package org.genesys2.server.model.json;
+
+import org.apache.commons.lang3.StringUtils;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.Taxonomy2;
+
+public class GenesysJsonFactory {
+
+	public static AccessionJson from(Accession accession) {
+		if (accession == null)
+			return null;
+
+		AccessionJson aj = new AccessionJson();
+		aj.setVersion(accession.getVersion());
+		aj.setGenesysId(accession.getId());
+
+		aj.setInstCode(accession.getInstitute().getCode());
+		aj.setAcceNumb(accession.getAccessionName());
+		aj.setUuid(accession.getUuid());
+
+		Taxonomy2 tax = accession.getTaxonomy();
+		aj.setGenus(tax.getGenus());
+		aj.setSpecies(tax.getSpecies());
+		aj.setSpauthor(tax.getSpAuthor());
+		aj.setSubtaxa(tax.getSubtaxa());
+		aj.setSubtauthor(tax.getSubtAuthor());
+		aj.setOrgCty(accession.getCountryOfOrigin().getCode3());
+		aj.setAcqDate(accession.getAcquisitionDate());
+		aj.setMlsStat(accession.getMlsStatus());
+		aj.setInTrust(accession.getInTrust());
+		aj.setAvailable(accession.getAvailability());
+		// private int[] storage;
+		aj.setStorage(toIntArray(accession.getStorage()));
+		// private Integer sampStat;
+		aj.setSampStat(accession.getSampleStatus());
+		// private String[] duplSite;
+		aj.setDuplSite(toStrArr(accession.getDuplSite()));
+
+		// private String bredCode;
+		// private String ancest;
+		// private String donorCode;
+		// private String donorNumb;
+		// private String donorName;
+		// private CollectingJson coll;
+		// private GeoJson geo;
+
+		return aj;
+	}
+
+	private static String[] toStrArr(String arrString) {
+		if (StringUtils.isBlank(arrString))
+			return null;
+		return arrString.split("\\s*;\\s*");
+	}
+
+	private static int[] toIntArray(String arrString) {
+		if (StringUtils.isBlank(arrString))
+			return null;
+		String[] split = arrString.trim().split(";");
+		int[] intArr = new int[split.length];
+		for (int i = 0; i < split.length; i++) {
+			// TODO Could throw NFE
+			intArr[i] = Integer.parseInt(split[i]);
+		}
+		return intArr;
+	}
+
+	public static GeoJson from(AccessionGeo geo) {
+		if (geo == null)
+			return null;
+
+		GeoJson gj = new GeoJson();
+		gj.setCoordDatum(geo.getDatum());
+		gj.setCoordUncert(geo.getUncertainty());
+		gj.setElevation(geo.getElevation());
+		gj.setGeorefMeth(geo.getMethod());
+		gj.setLatitude(geo.getLatitude());
+		gj.setLongitude(geo.getLongitude());
+		return gj;
+	}
+
+	public static CollectingJson from(AccessionCollect collect) {
+		if (collect == null)
+			return null;
+
+		CollectingJson col = new CollectingJson();
+		col.setCollCode(collect.getCollCode());
+		col.setCollDate(collect.getCollDate());
+		col.setCollInstAddress(collect.getCollInstAddress());
+		col.setCollMissId(collect.getCollMissId());
+		col.setCollName(collect.getCollName());
+		col.setCollNumb(collect.getCollNumb());
+		col.setCollSite(collect.getCollSite());
+		col.setCollSrc(collect.getCollSrc());
+		return col;
+	}
+
+}

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

+package org.genesys2.server.model.json;
+
+public class GeoJson {
+	private Double latitude;
+	private Double longitude;
+	private Double elevation;
+	private Double coordUncert;
+	private String coordDatum;
+	private String georefMeth;
+
+	public Double getLatitude() {
+		return latitude;
+	}
+
+	public void setLatitude(Double latitude) {
+		this.latitude = latitude;
+	}
+
+	public Double getLongitude() {
+		return longitude;
+	}
+
+	public void setLongitude(Double longitude) {
+		this.longitude = longitude;
+	}
+
+	public Double getElevation() {
+		return elevation;
+	}
+
+	public void setElevation(Double elevation) {
+		this.elevation = elevation;
+	}
+
+	public Double getCoordUncert() {
+		return coordUncert;
+	}
+
+	public void setCoordUncert(Double coordUncert) {
+		this.coordUncert = coordUncert;
+	}
+
+	public String getCoordDatum() {
+		return coordDatum;
+	}
+
+	public void setCoordDatum(String coordDatum) {
+		this.coordDatum = coordDatum;
+	}
+
+	public String getGeorefMeth() {
+		return georefMeth;
+	}
+
+	public void setGeorefMeth(String georefMeth) {
+		this.georefMeth = georefMeth;
+	}
+
+}

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

@@ -21,16 +21,16 @@ import java.util.Map;
 
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.impl.RESTApiException;
-import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
 
 import com.fasterxml.jackson.databind.node.ObjectNode;
 
 public interface BatchRESTService {
 
-	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) throws RESTApiException;
+	boolean upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException;
 
 	void upsertAccessionNames(FaoInstitute institute, List<AccessionNamesJson> batch);
 
-	int deleteAccessions(FaoInstitute institute, List<AccessionJson> batch);
+	int deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> batch);
 }

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

+package org.genesys2.server.service;
+
+import org.genesys2.server.model.json.AccessionJson;
+
+public interface GenesysRESTService {
+
+	AccessionJson getAccessionJSON(String instCode, long accessionId);
+
+}

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

@@ -46,7 +46,7 @@ import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.OrganizationService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.servlet.controller.rest.model.AccessionAliasJson;
-import org.genesys2.server.servlet.controller.rest.model.AccessionJson;
+import org.genesys2.server.servlet.controller.rest.model.AccessionHeaderJson;
 import org.genesys2.server.servlet.controller.rest.model.AccessionNamesJson;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -81,7 +81,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE') or hasPermission(#institute, 'CREATE')")
-	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionJson, ObjectNode> batch) throws RESTApiException {
+	public boolean upsertAccessionData(FaoInstitute institute, Map<AccessionHeaderJson, ObjectNode> batch) throws RESTApiException {
 		LOG.info("Batch processing " + batch.size() + " entries for " + institute);
 
 		boolean useUniqueAcceNumbs = institute.hasUniqueAcceNumbs();
@@ -97,7 +97,7 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 		Map<Accession, ArrayNode> donorNumbs = new HashMap<Accession, ArrayNode>();
 		Map<Accession, ArrayNode> collNumbs = new HashMap<Accession, ArrayNode>();
 
-		for (AccessionJson dataJson : batch.keySet()) {
+		for (AccessionHeaderJson dataJson : batch.keySet()) {
 			if (LOG.isDebugEnabled())
 				LOG.debug("Loading accession " + dataJson);
 
@@ -666,12 +666,12 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 	@Override
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'DELETE') or hasPermission(#institute, 'MANAGE')")
-	public int deleteAccessions(FaoInstitute institute, List<AccessionJson> batch) {
+	public int deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> batch) {
 		LOG.info("Batch deleting " + batch.size() + " entries for " + institute);
 		List<Accession> toDelete = new ArrayList<Accession>(batch.size());
 		boolean useUniqueAcceNumbs = institute.hasUniqueAcceNumbs();
 
-		for (AccessionJson dataJson : batch) {
+		for (AccessionHeaderJson dataJson : batch) {
 			if (LOG.isDebugEnabled())
 				LOG.debug("Loading accession " + dataJson);
 

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

+package org.genesys2.server.service.impl;
+
+import org.apache.commons.lang3.StringUtils;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionBreeding;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.json.AccessionJson;
+import org.genesys2.server.model.json.GenesysJsonFactory;
+import org.genesys2.server.service.GenesysRESTService;
+import org.genesys2.server.service.GenesysService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+@Service
+@Transactional(readOnly = true)
+public class GenesysRESTServiceImpl implements GenesysRESTService {
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Override
+	public AccessionJson getAccessionJSON(String instCode, long accessionId) {
+		Accession accession = genesysService.getAccession(accessionId);
+		if (accession == null) {
+			return null;
+		}
+		if (!StringUtils.equalsIgnoreCase(accession.getInstituteCode(), instCode)) {
+			throw new RuntimeException("Accession " + accessionId + " does not belong to " + instCode);
+		}
+
+		AccessionJson aj = GenesysJsonFactory.from(accession);
+
+		AccessionBreeding breeding = genesysService.listAccessionBreeding(accession);
+		if (breeding != null) {
+			aj.setBredCode(breeding.getBreederCode());
+			aj.setAncest(breeding.getPedigree());
+		}
+		AccessionCollect collect = genesysService.listAccessionCollect(accession);
+		aj.setColl(GenesysJsonFactory.from(collect));
+
+		AccessionGeo geo = genesysService.listAccessionGeo(accession);
+		aj.setGeo(GenesysJsonFactory.from(geo));
+		return aj;
+	}
+}

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

@@ -24,14 +24,16 @@ imp