Merge branch '295-accession-overview-api'

* 295-accession-overview-api:
  Accession Overview and filter suggestions API

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

@@ -17,6 +17,8 @@
 package org.genesys2.server.api.v1;
 
 import java.io.IOException;
+import java.util.Map;
+import java.util.Set;
 import java.util.UUID;
 
 import javax.servlet.http.HttpServletRequest;
@@ -27,7 +29,10 @@ import org.genesys.catalog.service.ShortFilterService;
 import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.service.AccessionService;
+import org.genesys2.server.service.ElasticsearchService;
+import org.genesys2.server.service.ElasticsearchService.TermResult;
 import org.genesys2.server.service.filter.AccessionFilter;
+import org.genesys2.server.service.impl.SearchException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Sort;
@@ -44,6 +49,12 @@ import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.HandlerMapping;
 
 import com.fasterxml.jackson.annotation.JsonView;
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Sets;
+import com.hazelcast.util.CollectionUtil;
 
 import io.swagger.annotations.Api;
 
@@ -57,7 +68,7 @@ import io.swagger.annotations.Api;
 public class AccessionController {
 
 	/** The Constant API_BASE. */
-	public static final String API_BASE =  ApiBaseController.APIv1_BASE + "/acn";
+	public static final String API_BASE = ApiBaseController.APIv1_BASE + "/acn";
 
 	@Autowired
 	private AccessionService accessionService;
@@ -66,6 +77,13 @@ public class AccessionController {
 	@Autowired
 	protected ShortFilterService shortFilterService;
 
+	@Autowired
+	private ElasticsearchService elasticsearchService;
+
+	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
@@ -79,23 +97,21 @@ public class AccessionController {
 		return accessionService.getByUuid(uuid);
 	}
 
-
 	/**
 	 * Gets the accession
 	 *
 	 * @param uuid the uuid
 	 * @return the subset
 	 */
-	@RequestMapping(value = "/10.{dummy:[0-9]+}/**", method=RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	@RequestMapping(value = "/10.{dummy:[0-9]+}/**", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
 	@JsonView({ JsonViews.Protected.class })
 	public Accession getByDoi(HttpServletRequest request) {
 		final String fullpath = (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
-		final String doi = fullpath.substring(API_BASE.length()+1);
+		final String doi = fullpath.substring(API_BASE.length() + 1);
 
 		return accessionService.getByDoi(doi);
 	}
 
-	
 	/**
 	 * List accessions by filterCode or filter
 	 *
@@ -106,17 +122,16 @@ public class AccessionController {
 	 * @param filterCode short filter code
 	 * @param filter the filter
 	 * @return the page
-	 * @throws IOException 
+	 * @throws IOException
 	 */
 	@PostMapping(value = "/list", produces = { MediaType.APPLICATION_JSON_VALUE })
 	@JsonView({ JsonViews.Public.class })
 	public FilteredPage<Accession> list(@RequestParam(name = "p", required = false, defaultValue = "0") final int page,
-            @RequestParam(name = "l", required = false, defaultValue = "50") final int pageSize,
-            @RequestParam(name = "d", required = false, defaultValue = "ASC") final Sort.Direction direction,
-            @RequestParam(name = "s", required = false, defaultValue = "id") final String[] sort,
-			@RequestParam(name = "f", required = false) String filterCode,
+			@RequestParam(name = "l", required = false, defaultValue = "50") final int pageSize,
+			@RequestParam(name = "d", required = false, defaultValue = "ASC") final Sort.Direction direction,
+			@RequestParam(name = "s", required = false, defaultValue = "id") final String[] sort, @RequestParam(name = "f", required = false) String filterCode,
 			@RequestBody(required = false) AccessionFilter filter) throws IOException {
-		
+
 		if (filterCode != null) {
 			filter = shortFilterService.filterByCode(filterCode, AccessionFilter.class);
 		} else {
@@ -125,4 +140,88 @@ public class AccessionController {
 		return new FilteredPage<>(filterCode, filter, accessionService.list(filter, new PageRequest(page, Integer.min(pageSize, 100), direction, sort)));
 	}
 
+	/**
+	 * Get term overview for filters
+	 *
+	 * @param filterCode short filter code
+	 * @param filter the filter
+	 * @return the page
+	 * @throws SearchException
+	 */
+	@PostMapping(value = "/overview", produces = { MediaType.APPLICATION_JSON_VALUE })
+	@JsonView({ JsonViews.Public.class })
+	public Map<String, TermResult> overview(@RequestParam(name = "f", required = false) String filterCode, @RequestBody(required = false) AccessionFilter filter)
+			throws IOException, SearchException {
+
+		if (filterCode != null) {
+			filter = shortFilterService.filterByCode(filterCode, AccessionFilter.class);
+		} else {
+			filterCode = shortFilterService.getCode(filter);
+		}
+
+		return elasticsearchService.termStatisticsAuto(Accession.class, filter, 10, terms.toArray(new String[] {}));
+	}
+
+	/**
+	 * Get term overview for filters
+	 *
+	 * @param filterCode short filter code
+	 * @param filter the filter
+	 * @return the page
+	 * @throws SearchException
+	 */
+	@PostMapping(value = "/filter-suggest", produces = { MediaType.APPLICATION_JSON_VALUE })
+	@JsonView({ JsonViews.Public.class })
+	public Map<String, TermResult> filterSuggestions(@RequestParam(name = "f", required = false) String filterCode, @RequestBody(required = false) AccessionFilter filter)
+			throws IOException, SearchException {
+
+		if (filterCode != null) {
+			filter = shortFilterService.filterByCode(filterCode, AccessionFilter.class);
+		} else {
+			filterCode = shortFilterService.getCode(filter);
+		}
+
+		Map<String, TermResult> termResults = elasticsearchService.termStatisticsAuto(Accession.class, filter, 10, terms.toArray(new String[] {}));
+
+		// "institute.code", "institute.country.code3", "cropName", "crop.shortName",
+		// "taxonomy.genus", "taxonomy.genusSpecies", "taxonomy.species",
+		// "countryOfOrigin.code3", "sampStat", "available", "mlsStatus", "donorCode",
+		// "sgsv", "storage", "duplSite", "breederCode"
+		if (filter.taxa != null) {
+			if (CollectionUtil.isNotEmpty(filter.taxa.species)) {
+				AccessionFilter modifiedFilter = copyFilter(filter);
+				modifiedFilter.taxa.species.clear();
+				termResults.put("taxonomy.species", elasticsearchService.termStatisticsAuto(Accession.class, modifiedFilter, 10, "taxonomy.species"));
+			}
+			if (CollectionUtil.isNotEmpty(filter.taxa.genus)) {
+				AccessionFilter modifiedFilter = copyFilter(filter);
+				modifiedFilter.taxa.genus.clear();
+				termResults.put("taxonomy.genus", elasticsearchService.termStatisticsAuto(Accession.class, modifiedFilter, 10, "taxonomy.genus"));
+			}
+		}
+		if (filter.origin != null) {
+			AccessionFilter modifiedFilter = copyFilter(filter);
+			modifiedFilter.origin = null;
+			termResults.put("countryOfOrigin.code3", elasticsearchService.termStatisticsAuto(Accession.class, modifiedFilter, 10, "countryOfOrigin.code3"));
+		}
+
+		if (filter.holder != null) {
+			AccessionFilter modifiedFilter =  copyFilter(filter);
+			modifiedFilter.holder = null;
+			termResults.putAll(elasticsearchService.termStatisticsAuto(Accession.class, modifiedFilter, 10, "institute.code", "institute.country.code3"));
+		}
+
+		if (filter.crop != null) {
+			AccessionFilter modifiedFilter = copyFilter(filter);
+			modifiedFilter.crop = null;
+			termResults.putAll(elasticsearchService.termStatisticsAuto(Accession.class, modifiedFilter, 10, "cropName", "crop.shortName"));
+		}
+
+		return termResults;
+	}
+
+	private AccessionFilter copyFilter(AccessionFilter filter) throws JsonParseException, JsonMappingException, JsonProcessingException, IOException {
+		return objectMapper.readValue(objectMapper.writeValueAsString(filter), AccessionFilter.class);
+	}
+
 }

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

@@ -20,6 +20,7 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.elasticsearch.index.query.QueryBuilder;
 import org.genesys.blocks.model.BasicModel;
@@ -123,13 +124,18 @@ public interface ElasticsearchService {
 	public static class TermResult {
 
 		private List<Term> terms;
+		
 		private Long total;
 		private long other;
+		
+		/**
+		 * @deprecated This number is useless here and needs to be calculated based matches - total - other
+		 */
 		private Long missing;
 
 		public TermResult(String name, List<Term> terms, long other, Long missing) {
 			this.terms = terms;
-			this.total = (long) terms.size();
+			this.total = terms.stream().map(Term::getCount).mapToLong(Long::longValue).sum();
 			this.other = other;
 			this.missing = missing;
 		}