One big JSON for accession

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

@@ -27,6 +27,7 @@ import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.json.AccessionJson;
 import org.genesys2.server.service.BatchRESTService;
+import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysFilterService;
 import org.genesys2.server.service.GenesysRESTService;
 import org.genesys2.server.service.GenesysService;
@@ -70,7 +71,10 @@ public class AccessionController extends RestController {
 
 	@Autowired
 	private GenesysFilterService filterService;
-	
+
+	@Autowired
+	private CropService cropService;
+
 	@Autowired
 	BatchRESTService batchRESTService;
 
@@ -88,7 +92,7 @@ public class AccessionController extends RestController {
 
 	/**
 	 * Check if accessions exists in the system
-	 *
+	 * 
 	 * @return
 	 */
 	@RequestMapping(value = "/exists/{instCode}/{genus:.+}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
@@ -109,7 +113,7 @@ public class AccessionController extends RestController {
 
 	/**
 	 * Check if accessions exists in the system
-	 *
+	 * 
 	 * @return
 	 * @throws IOException
 	 * @throws JsonProcessingException
@@ -170,7 +174,7 @@ public class AccessionController extends RestController {
 
 	/**
 	 * Update accessions in the system
-	 *
+	 * 
 	 * @return
 	 * @throws IOException
 	 * @throws JsonProcessingException
@@ -212,7 +216,7 @@ public class AccessionController extends RestController {
 
 	/**
 	 * Update accessions in the system
-	 *
+	 * 
 	 * @return
 	 * @throws IOException
 	 * @throws JsonProcessingException
@@ -239,7 +243,7 @@ public class AccessionController extends RestController {
 
 	/**
 	 * Update accessions in the system
-	 *
+	 * 
 	 * @return
 	 * @throws IOException
 	 * @throws JsonProcessingException
@@ -265,35 +269,61 @@ public class AccessionController extends RestController {
 		return restService.getAccessionJSON(instCode, accessionId);
 	}
 
+	@RequestMapping(value = "/{id}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody
+	AccessionDetails getDetails(@PathVariable("id") long accessionId) {
+		
+		final Accession accession = genesysService.getAccession(accessionId);
+		if (accession == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		AccessionDetails ad = AccessionDetails.from(accession);
+		// ad.names(genesysService.listAccessionNames(accession));
+		ad.aliases(genesysService.listAccessionAliases(accession));
+		ad.exch(genesysService.listAccessionExchange(accession));
+		ad.collect(genesysService.listAccessionCollect(accession));
+		ad.breeding(genesysService.listAccessionBreeding(accession));
+		ad.geo(genesysService.listAccessionGeo(accession));
+		ad.svalbard(genesysService.getSvalbardData(accession));
+		ad.remarks(genesysService.listAccessionRemarks(accession));
+
+		// model.addAttribute("metadatas",
+		// genesysService.listMetadata(accession));
+		ad.traits(genesysService.listMethods(accession), genesysService.getAccessionTraitValues(accession));
+
+		ad.crops(cropService.getCrops(accession.getTaxonomy()));
+
+		return ad;
+	}
+
 	@RequestMapping(value = "/list", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public @ResponseBody
 	List<AccessionJson> get(@RequestBody Set<Long> accessionIds) {
 		return restService.getAccessionJSON(accessionIds);
 	}
-	
-
-    @RequestMapping(value = "/filter", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE)
-    @ResponseBody
-    public Object getAcc(@RequestBody JsonData jsonData) throws IOException {
 
-        String filter = "{\"crop\":[\"" + jsonData.crop + "\"]}";
-        ObjectNode jsonTree = null;
+	@RequestMapping(value = "/filter", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE)
+	@ResponseBody
+	public Object getAcc(@RequestBody JsonData jsonData) throws IOException {
 
+		String filter = "{\"crop\":[\"" + jsonData.crop + "\"]}";
+		ObjectNode jsonTree = null;
 
-        jsonTree = (ObjectNode) mapper.readTree(filter);
+		jsonTree = (ObjectNode) mapper.readTree(filter);
 
-        LOG.debug(jsonTree.toString());
+		LOG.debug(jsonTree.toString());
 
-        Page<Accession> accessions = filterService.listAccessions(jsonTree, new PageRequest(jsonData.startAt - 1, jsonData.maxRecords, new Sort("acceNumb")));
-        return accessions;
-    }
+		Page<Accession> accessions = filterService.listAccessions(jsonTree, new PageRequest(jsonData.startAt - 1, jsonData.maxRecords, new Sort("acceNumb")));
+		return accessions;
+	}
 
-    public static class JsonData {
-     public String crop;
-     public Integer startAt;
-     public Integer maxRecords;
-     public String otherOptions;
-    }
+	public static class JsonData {
+		public String crop;
+		public Integer startAt;
+		public Integer maxRecords;
+		public String otherOptions;
+	}
 
 	private AccessionHeaderJson readAid3(JsonNode json) {
 		final AccessionHeaderJson dataJson = new AccessionHeaderJson();

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

+package org.genesys2.server.servlet.controller.rest;
+
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionAlias;
+import org.genesys2.server.model.genesys.AccessionBreeding;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.AccessionExchange;
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionRemark;
+import org.genesys2.server.model.genesys.ExperimentTrait;
+import org.genesys2.server.model.genesys.Method;
+import org.genesys2.server.model.genesys.SvalbardData;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.model.impl.FaoInstitute;
+
+public class AccessionDetails {
+
+	public long version;
+	public Long id;
+	public String uuid;
+	public String acceNumb;
+	public String acqDate;
+	public String acqSrc;
+	public Boolean availability;
+	public Date createdDate;
+	public String duplSite;
+	public Boolean mlsStatus;
+	public Integer sampStat;
+	public List<Integer> storage;
+
+	public Institute institute;
+	public Country orgCty;
+	public Taxonomy taxonomy;
+	public ArrayList<Alias> aliases;
+	public Svalbard sgsv;
+	public ArrayList<Remark> remarks;
+	public ArrayList<String> crops;
+	public Geo geo;
+	public Collect coll;
+	public String pedigree;
+	public String donorCode;
+	public String donorName;
+	public String donorNumb;
+	public HashMap<String, List<Object>> traits;
+
+	public static AccessionDetails from(Accession accession) {
+		AccessionDetails ad = new AccessionDetails();
+		ad.version = accession.getVersion();
+		ad.id = accession.getId();
+		ad.uuid = accession.getUuid();
+		ad.acceNumb = accession.getAccessionName();
+		ad.acqDate = accession.getAcquisitionDate();
+		ad.acqSrc = accession.getAcquisitionSource();
+		ad.availability = accession.getAvailability();
+		ad.orgCty = Country.from(accession.getCountryOfOrigin());
+		ad.createdDate = accession.getCreatedDate();
+		ad.duplSite = accession.getDuplSite();
+		ad.institute = AccessionDetails.Institute.from(accession.getInstitute());
+		ad.mlsStatus = accession.getMlsStatus();
+		ad.sampStat = accession.getSampleStatus();
+		ad.storage = accession.getStoRage();
+		ad.taxonomy = Taxonomy.from(accession.getTaxonomy());
+		return ad;
+	}
+
+	public static class Institute {
+
+		public Long id;
+		public String acronym;
+		public String code;
+		public Country country;
+		public String fullName;
+
+		public static Institute from(FaoInstitute institute) {
+			Institute i = new Institute();
+			i.id = institute.getId();
+			i.acronym = institute.getAcronym();
+			i.code = institute.getCode();
+			i.country = Country.from(institute.getCountry());
+			i.fullName = institute.getFullName();
+			return i;
+		}
+	}
+
+	public static class Country {
+
+		public String iso3;
+		public String iso2;
+		public String name;
+
+		public static Country from(org.genesys2.server.model.impl.Country country) {
+			Country c = new Country();
+			c.iso3 = country.getCode3();
+			c.iso2 = country.getCode2();
+			c.name = country.getName();
+			return c;
+		}
+	}
+
+	public static class Taxonomy {
+
+		public String sciName;
+		public String genus;
+		public String species;
+		public String spAuthor;
+		public String subtax;
+		public String subtAuthor;
+
+		public static Taxonomy from(Taxonomy2 taxonomy) {
+			Taxonomy t = new Taxonomy();
+			t.sciName = taxonomy.getTaxonName();
+			t.genus = taxonomy.getGenus();
+			t.species = taxonomy.getSpecies();
+			t.spAuthor = StringUtils.defaultIfBlank(taxonomy.getSpAuthor(), null);
+			t.subtax = StringUtils.defaultIfBlank(taxonomy.getSubtaxa(), null);
+			t.subtAuthor = StringUtils.defaultIfBlank(taxonomy.getSubtAuthor(), null);
+			return t;
+		}
+
+	}
+
+	public void aliases(List<AccessionAlias> listAccessionAliases) {
+		if (listAccessionAliases == null || listAccessionAliases.isEmpty())
+			return;
+		this.aliases = new ArrayList<Alias>();
+		for (AccessionAlias aa : listAccessionAliases) {
+			this.aliases.add(Alias.from(aa));
+		}
+	}
+
+	public static class Alias {
+
+		public String name;
+		public String lang;
+		public String usedBy;
+
+		public static Alias from(AccessionAlias aa) {
+			Alias a = new Alias();
+			a.name = aa.getName();
+			a.lang = StringUtils.defaultIfBlank(aa.getLang(), null);
+			a.usedBy = StringUtils.defaultIfBlank(aa.getUsedBy(), null);
+			return a;
+		}
+
+	}
+
+	public void svalbard(SvalbardData svalbardData) {
+		this.sgsv = Svalbard.from(svalbardData);
+	}
+
+	public static class Svalbard {
+
+		public Float qty;
+		public String boxNo;
+		public String depositDate;
+
+		public static Svalbard from(SvalbardData svalbardData) {
+			if (svalbardData == null)
+				return null;
+			Svalbard s = new Svalbard();
+			s.boxNo = svalbardData.getBoxNumber();
+			s.qty = svalbardData.getQuantity();
+			s.depositDate = svalbardData.getDepositDate();
+			return s;
+		}
+
+	}
+
+	public void remarks(List<AccessionRemark> listAccessionRemarks) {
+		if (listAccessionRemarks == null || listAccessionRemarks.isEmpty())
+			return;
+		this.remarks = new ArrayList<Remark>();
+		for (AccessionRemark ar : listAccessionRemarks) {
+			this.remarks.add(Remark.from(ar));
+		}
+	}
+
+	public static class Remark {
+
+		public String field;
+		public String remark;
+
+		public static Remark from(AccessionRemark ar) {
+			Remark r = new Remark();
+			r.field = StringUtils.defaultIfBlank(ar.getFieldName(), null);
+			r.remark = StringUtils.defaultIfBlank(ar.getRemark(), null);
+			return r;
+		}
+
+	}
+
+	public void crops(List<Crop> crops) {
+		if (crops == null || crops.isEmpty())
+			return;
+		this.crops = new ArrayList<String>();
+		for (Crop c : crops) {
+			this.crops.add(c.getShortName());
+		}
+	}
+
+	public void geo(AccessionGeo ag) {
+		if (ag == null)
+			return;
+		this.geo = Geo.from(ag);
+	}
+
+	public static class Geo {
+
+		public String method;
+		public Double uncertainty;
+		public Double latitude;
+		public Double longitude;
+		public Double[] coordinates;
+		public Double elevation;
+		public String datum;
+
+		public static Geo from(AccessionGeo ag) {
+			if (ag == null)
+				return null;
+			Geo g = new Geo();
+			g.datum = StringUtils.defaultIfBlank(ag.getDatum(), null);
+			g.elevation = ag.getElevation();
+			g.coordinates = new Double[] { ag.getLongitude(), ag.getLatitude() };
+			g.longitude = ag.getLongitude();
+			g.latitude = ag.getLatitude();
+			g.uncertainty = ag.getUncertainty();
+			g.method = StringUtils.defaultIfBlank(ag.getMethod(), null);
+			return g;
+		}
+
+	}
+
+	public void collect(AccessionCollect collect) {
+		this.coll = Collect.from(collect);
+	}
+
+	public static class Collect {
+
+		public String collCode;
+		public String collDate;
+		public String collInstAddr;
+		public String collMissId;
+		public String collName;
+		public String collNumb;
+		public String collSite;
+		public Integer collSrc;
+
+		public static Collect from(AccessionCollect collect) {
+			if (collect == null)
+				return null;
+
+			Collect c = new Collect();
+			c.collCode = StringUtils.defaultIfBlank(collect.getCollCode(), null);
+			c.collDate = StringUtils.defaultIfBlank(collect.getCollDate(), null);
+			c.collInstAddr = StringUtils.defaultIfBlank(collect.getCollInstAddress(), null);
+			c.collMissId = StringUtils.defaultIfBlank(collect.getCollMissId(), null);
+			c.collName = StringUtils.defaultIfBlank(collect.getCollName(), null);
+			c.collNumb = StringUtils.defaultIfBlank(collect.getCollNumb(), null);
+			c.collSite = StringUtils.defaultIfBlank(collect.getCollSite(), null);
+			c.collSrc = collect.getCollSrc();
+			return c;
+		}
+
+	}
+
+	public void breeding(AccessionBreeding breeding) {
+		if (breeding == null)
+			return;
+		this.pedigree = StringUtils.defaultIfBlank(breeding.getPedigree(), null);
+	}
+
+	public void exch(AccessionExchange exch) {
+		if (exch == null)
+			return;
+		this.donorCode = StringUtils.defaultIfBlank(exch.getDonorInstitute(), null);
+		this.donorName = StringUtils.defaultIfBlank(exch.getDonorName(), null);
+		this.donorNumb = StringUtils.defaultIfBlank(exch.getAccNumbDonor(), null);
+	}
+
+	public void traits(List<Method> listMethods, Map<Long, List<ExperimentTrait>> accessionTraitValues) {
+		this.traits = new HashMap<String, List<Object>>();
+		for (Method m : listMethods) {
+			List<ExperimentTrait> vals = accessionTraitValues.get(m.getId());
+			ArrayList<Object> values = new ArrayList<Object>();
+			for (ExperimentTrait et : vals) {
+				if (et == null)
+					continue;
+				values.add(et.getValue());
+			}
+			this.traits.put("gm:"+m.getId(), values);
+		}
+	}
+
+	// public static class Trait {
+	//
+	// public String category;
+	// public String parameter;
+	// public String method;
+	// public ArrayList<Object> values;
+	//
+	// public static Trait from(Method m, List<ExperimentTrait> vals) {
+	// if (vals == null || vals.isEmpty())
+	// return null;
+	//
+	// Trait t = new Trait();
+	// t.category = m.getParameter().getCategory().getName();
+	// t.parameter = m.getParameter().getTitle();
+	// t.method = m.getMethod();
+	//
+	// t.values = new ArrayList<Object>();
+	// for (ExperimentTrait et : vals) {
+	// if (et == null)
+	// continue;
+	// t.values.add(et.getValue());
+	// }
+	//
+	// return t;
+	// }
+	//
+	// }
+}