Accession API v1: Geo info

src/main/java/org/genesys2/server/api/v1/AccessionController.java

@@ -87,7 +87,7 @@ import io.swagger.annotations.Api;
 @Api(tags = { "accession" })
 public class AccessionController {
 
-    private static final Logger LOG = LoggerFactory.getLogger(AccessionController.class);
+	private static final Logger LOG = LoggerFactory.getLogger(AccessionController.class);
 
 	/** The Constant API_BASE. */
 	public static final String API_BASE = ApiBaseController.APIv1_BASE + "/acn";
@@ -115,13 +115,15 @@ public class AccessionController {
 
 	@Value("${base.url}")
 	private String baseUrl;
-	
+
+	@Value("${cdn.servers}")
+	private String[] cdnServers;
+
 	private final Set<String> terms = Sets.newHashSet("institute.code", "institute.country.code3", "cropName", "crop.shortName", "taxonomy.genus", "taxonomy.species",
 		"taxonomy.genusSpecies", "countryOfOrigin.code3", "sampStat", "available", "mlsStatus", "donorCode", "sgsv", "storage", "duplSite", "breederCode");
 
 	private ObjectMapper objectMapper = new ObjectMapper();
 
-
 	/**
 	 * Gets the accession
 	 *
@@ -238,6 +240,21 @@ public class AccessionController {
 		return accessionDetails;
 	}
 
+	@PostMapping(value = "/geo", produces = MediaType.APPLICATION_JSON_VALUE)
+	@JsonView({ JsonViews.Public.class })
+	public GeoInfoJson getGeoInfo(@PathVariable(value = "f", required = false) String filterCode, @RequestBody(required = false) AccessionFilter filter) throws IOException {
+		if (filterCode != null) {
+			filter = shortFilterService.filterByCode(filterCode, AccessionFilter.class);
+		}
+
+		GeoInfoJson geoInfo = new GeoInfoJson();
+		geoInfo.bounds = accessionService.getBounds(filter);
+		geoInfo.accessionCount = accessionService.countAccessions(filter);
+		geoInfo.tileServers = cdnServers;
+
+		return geoInfo;
+	}
+
 	/**
 	 * Get term overview for filters
 	 *
@@ -321,9 +338,9 @@ public class AccessionController {
 		response.setContentType("application/vnd.google-earth.kml+xml");
 		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-kml-" + filterCode + ".kml\""));
 
-		DecimalFormatSymbols dfs=new DecimalFormatSymbols();
+		DecimalFormatSymbols dfs = new DecimalFormatSymbols();
 		dfs.setDecimalSeparator('.');
-		DecimalFormat decimalFormat=new DecimalFormat("0.#", dfs);
+		DecimalFormat decimalFormat = new DecimalFormat("0.#", dfs);
 		decimalFormat.setMinimumIntegerDigits(1);
 		decimalFormat.setMinimumFractionDigits(6);
 		decimalFormat.setGroupingUsed(false);
@@ -339,13 +356,13 @@ public class AccessionController {
 				if (geo != null && geo.getLongitude() != null && geo.getLatitude() != null) {
 					writer.append("<Placemark>");
 					writer.append("<name>").append(accession.getAccessionNumber()).append("</name>");
-					
+
 					writer.append("<description><![CDATA[\n");
 					writer.append("<p>").append(accession.getTaxonomy().getTaxonNameHtml()).append("</p>");
 					writer.append("<p>").append(accession.getInstitute().getCode()).append(" ").append(accession.getInstitute().getFullName()).append("</p>");
 					writer.append("<p><a href=\"").append(baseUrl).append("/acn/").append(accession.getUuid().toString()).append("\">Passport data</a></p>");
 					writer.append("\n]]></description>");
-					
+
 					writer.append("<Point><coordinates>");
 					writer.append(decimalFormat.format(geo.getLongitude())).append(",").append(decimalFormat.format(geo.getLatitude()));
 					writer.append("</coordinates></Point>");
@@ -357,13 +374,13 @@ public class AccessionController {
 			writer.write("</Document>\n</kml>\n");
 
 		} catch (EOFException e) {
-			 LOG.warn("Download was aborted: {}", e.getMessage());
+			LOG.warn("Download was aborted: {}", e.getMessage());
 		} catch (Exception e) {
-			 LOG.warn("Error generating KML: {}", e.getMessage());
+			LOG.warn("Error generating KML: {}", e.getMessage());
 		} finally {
 			writer.flush();
 			writer.close();
-			response.flushBuffer();			
+			response.flushBuffer();
 		}
 	}
 
@@ -374,4 +391,10 @@ public class AccessionController {
 		public List<Subset> subsets;
 	}
 
+	public static class GeoInfoJson {
+		public List<Object[]> bounds;
+		public long accessionCount;
+		public String[] tileServers;
+	}
+
 }

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

@@ -28,10 +28,11 @@ import org.springframework.data.domain.Pageable;
 public interface AccessionService {
 
 	/**
-	 * Count accessions. Uses Elasticsearch, but counts from database when number is small enough.
+	 * Count accessions. Uses Elasticsearch, but counts from database when number is
+	 * small enough.
 	 *
 	 * @param filter the filter
-	 * @return the count 
+	 * @return the count
 	 */
 	long countAccessions(AccessionFilter filter);
 
@@ -44,6 +45,14 @@ public interface AccessionService {
 	 */
 	Page<Accession> list(AccessionFilter filter, Pageable page);
 
+	/**
+	 * Gets the bounds.
+	 *
+	 * @param filter the filter
+	 * @return the bounds
+	 */
+	List<Object[]> getBounds(AccessionFilter filter);
+
 	/**
 	 * Gets accession by uuid
 	 *
@@ -62,6 +71,7 @@ public interface AccessionService {
 
 	/**
 	 * Converts AccessionIdentifiers to UUID
+	 * 
 	 * @param identifiers accession identifiers to lookup in DB
 	 * @return map with UUIDs and related AccessionIdentifiers
 	 */
@@ -70,7 +80,7 @@ public interface AccessionService {
 	/**
 	 * Loads {@link Accession} by IDs and executes the action on each accession in a
 	 * Spring transaction. Spring security context not supported.
-	 * 
+	 *
 	 * @param accessionIds List of accession IDs
 	 * @param action the action to execute on each accession
 	 * @return the list of processed accessions
@@ -80,7 +90,7 @@ public interface AccessionService {
 	public static interface IAccessionAction {
 		/**
 		 * Run action on Accession
-		 * 
+		 *
 		 * @param a the accession
 		 * @return must return the resulting {@link Accession}
 		 */

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

@@ -15,15 +15,19 @@
  */
 package org.genesys2.server.service.impl;
 
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 import java.util.UUID;
 
+import javax.persistence.EntityManager;
+
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionData;
 import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.QAccession;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.service.AccessionService;
@@ -37,10 +41,16 @@ import org.springframework.cache.annotation.Cacheable;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.repository.support.Querydsl;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
+import com.querydsl.core.Tuple;
+import com.querydsl.core.types.dsl.PathBuilder;
+import com.querydsl.core.types.dsl.PathBuilderFactory;
+import com.querydsl.jpa.JPQLQuery;
+
 /**
  * Accession services.
  */
@@ -56,10 +66,14 @@ public class AccessionServiceImpl implements AccessionService {
 
 	@Autowired
 	private ElasticsearchService elasticsearchService;
-	
+
 	@Autowired
 	private AccessionCounter accessionCounter;
 
+	@Autowired
+	private EntityManager entityManager;
+
+	private PathBuilder<Accession> accessionPathBuilder = new PathBuilderFactory().create(Accession.class);
 
 	private <T extends AccessionData> T lazyLoad(T accession) {
 		if (accession != null) {
@@ -116,12 +130,9 @@ public class AccessionServiceImpl implements AccessionService {
 		Map<UUID, AccessionIdentifier3> res = new HashMap<>();
 		List<Accession> foundAccessions = accessionRepository.findById(identifiers);
 
-		for(Accession accession: foundAccessions) {
-			Optional<? extends AccessionIdentifier3> toPut = identifiers.stream()
-					.filter(id -> id.getAccessionNumber().equals(accession.getAccessionNumber())
-							&& id.getGenus().equals(accession.getGenus())
-							&& id.getHoldingInstitute().equals(accession.getInstCode())
-					).findFirst();
+		for (Accession accession : foundAccessions) {
+			Optional<? extends AccessionIdentifier3> toPut = identifiers.stream().filter(id -> id.getAccessionNumber().equals(accession.getAccessionNumber()) && id.getGenus()
+				.equals(accession.getGenus()) && id.getHoldingInstitute().equals(accession.getInstCode())).findFirst();
 
 			toPut.ifPresent(accessionIdentifier3 -> res.put(accession.getUuid(), accessionIdentifier3));
 		}
@@ -137,7 +148,7 @@ public class AccessionServiceImpl implements AccessionService {
 			// If total is below 10K, use actual count
 			total = accessionRepository.count(filter.buildQuery());
 		}
-		
+
 		return total;
 	}
 
@@ -151,15 +162,32 @@ public class AccessionServiceImpl implements AccessionService {
 	@Cacheable(value = "apiResponses.accessionApi1.list", unless = "#result == null", keyGenerator = "shortFilterKeyGenerator")
 	public Page<Accession> list(AccessionFilter filter, Pageable page) {
 		List<Accession> content = accessionRepository.findAll(filter, page);
-		long total = elasticsearchService.count(Accession.class, filter);
 
-		if (total < 10000) {
-			// If total is below 10K, use actual count
-			total = accessionRepository.count(filter.buildQuery());
-		}
+		long total = countAccessions(filter);
+
 		return new PageImpl<>(content, page, total);
 	}
 
+	@Override
+	public List<Object[]> getBounds(AccessionFilter filter) {
+		QAccession accession = QAccession.accession;
+
+		Querydsl querydsl = new Querydsl(entityManager, accessionPathBuilder);
+
+		JPQLQuery<Tuple> query = querydsl.createQuery(accession).select(accession.accessionId.geo.latitude.min(), accession.accessionId.geo.longitude.max(),
+			accession.accessionId.geo.latitude.max(), accession.accessionId.geo.longitude.min()).from(accession).where(filter.buildQuery());
+
+		Object[] results = query.fetchOne().toArray();
+
+		List<Object[]> latLngBounds = new ArrayList<>();
+		// corner1
+		latLngBounds.add(new Object[] { results[0], results[1] });
+		// corner2
+		latLngBounds.add(new Object[] { results[2], results[3] });
+
+		return latLngBounds;
+	}
+
 	@Override
 	@Transactional(readOnly = false, propagation = Propagation.REQUIRES_NEW)
 	public List<Accession> processAccessions(List<Long> accessionIds, IAccessionAction action) {