Use AppliedFilters instead of ObjectNode/String jsonFilter

src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepository.java

@@ -19,10 +19,9 @@ package org.genesys2.server.persistence.domain;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.springframework.jdbc.core.RowCallbackHandler;
 
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 public interface GenesysLowlevelRepository {
 
 	void updateCountryRefs();
@@ -38,20 +37,20 @@ public interface GenesysLowlevelRepository {
 
 	void refreshMetadataMethods();
 
-	void listAccessions(ObjectNode filter, RowCallbackHandler rowCallbackHandler);
+	void listAccessions(AppliedFilters filter, RowCallbackHandler rowCallbackHandler);
 
-	void listAccessionsGeo(ObjectNode filter, RowCallbackHandler rowCallbackHandler);
+	void listAccessionsGeo(AppliedFilters filter, RowCallbackHandler rowCallbackHandler);
 
-	void listAccessionsColl(ObjectNode filter, RowCallbackHandler rowCallbackHandler);
+	void listAccessionsColl(AppliedFilters filter, RowCallbackHandler rowCallbackHandler);
 
 	void listMetadataAccessions(long id, RowCallbackHandler rowCallbackHandler);
 
-	void listAccessionsAlias(ObjectNode filter, RowCallbackHandler rowCallbackHandler);
+	void listAccessionsAlias(AppliedFilters filter, RowCallbackHandler rowCallbackHandler);
 
 	void listAccessionsAccenames(RowCallbackHandler rowCallbackHandler);
 
 	void listAccessionsAlias(RowCallbackHandler rowCallbackHandler);
 
-	int countAccessions(ObjectNode filter);
+	int countAccessions(AppliedFilters filter);
 
 }

src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepositoryImpl.java

@@ -30,6 +30,7 @@ import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.service.impl.DirectMysqlQuery;
 import org.genesys2.server.service.impl.DirectMysqlQuery.MethodResolver;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.BadSqlGrammarException;
 import org.springframework.jdbc.core.ArgumentPreparedStatementSetter;
@@ -40,8 +41,6 @@ import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Repository;
 import org.springframework.transaction.annotation.Transactional;
 
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 @Repository
 @Transactional(readOnly = true)
 public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository {
@@ -218,7 +217,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	}
 
 	@Override
-	public int countAccessions(final ObjectNode filter) {
+	public int countAccessions(final AppliedFilters filter) {
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
 		directQuery.jsonFilter(filter, new MethodResolver() {
 			@Override
@@ -231,7 +230,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	}
 
 	@Override
-	public void listAccessions(final ObjectNode filter, final RowCallbackHandler rowCallbackHandler) {
+	public void listAccessions(final AppliedFilters filter, final RowCallbackHandler rowCallbackHandler) {
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
 		directQuery.outerJoin("taxonomy2", "t", "t.id=a.taxonomyId2");
 		directQuery.jsonFilter(filter, new MethodResolver() {
@@ -258,7 +257,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	}
 
 	@Override
-	public void listAccessionsGeo(final ObjectNode filter, final RowCallbackHandler rowCallbackHandler) {
+	public void listAccessionsGeo(final AppliedFilters filter, final RowCallbackHandler rowCallbackHandler) {
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accessiongeo", "geo");
 		directQuery.innerJoin("accession", "a", "a.id=geo.accessionId");
 		directQuery.jsonFilter(filter, new MethodResolver() {
@@ -285,7 +284,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	}
 
 	@Override
-	public void listAccessionsAlias(final ObjectNode filter, final RowCallbackHandler rowCallbackHandler) {
+	public void listAccessionsAlias(final AppliedFilters filter, final RowCallbackHandler rowCallbackHandler) {
 		// from n inner join accession a on a.id=n.accessionId
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accessionalias", "n");
 		directQuery.innerJoin("accession", "a", "a.id=n.accessionId");
@@ -326,7 +325,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 	}
 
 	@Override
-	public void listAccessionsColl(final ObjectNode filter, final RowCallbackHandler rowCallbackHandler) {
+	public void listAccessionsColl(final AppliedFilters filter, final RowCallbackHandler rowCallbackHandler) {
 		// from accessioncollect coll inner join accession a on
 		// a.id=coll.accessionId
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accessioncollect", "coll");

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

@@ -19,13 +19,14 @@ package org.genesys2.server.service;
 import java.util.Collection;
 
 import org.genesys2.server.model.elastic.AccessionDetails;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.genesys2.server.service.impl.SearchException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 
 public interface ElasticService {
 
-	void reindexByFilter(String jsonFilter, boolean slow);
+	void reindexByFilter(AppliedFilters filters, boolean slow);
 
 	Page<AccessionDetails> search(String query, Pageable pageable) throws SearchException;
 
@@ -39,4 +40,5 @@ public interface ElasticService {
 
 	Page<AccessionDetails> filter(String jsonFilter, Pageable pageable) throws SearchException;
 
+
 }

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

@@ -55,4 +55,6 @@ public interface FilterConstants {
 	public static final String TAXONOMY_SPECIES = "taxonomy.species";
 
 	public static final String TAXONOMY_GENUS = "taxonomy.genus";
+
+	public static final String ID = "id";
 }

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

@@ -19,21 +19,20 @@ package org.genesys2.server.service;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.genesys2.server.service.impl.GenesysFilterServiceImpl.LabelValue;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.jdbc.core.RowCallbackHandler;
 
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 public interface GenesysFilterService {
 
-	Page<Accession> listAccessions(ObjectNode jsonTree, Pageable pageable);
+	Page<Accession> listAccessions(AppliedFilters filters, Pageable pageable);
 
-	List<LabelValue<String>> autocomplete(String filter, String ac,ObjectNode jsonTree);
+	List<LabelValue<String>> autocomplete(String filter, String ac, AppliedFilters filters);
 
-	void listGeo(ObjectNode jsonTree, Integer limit, RowCallbackHandler rowHandler);
+	void listGeo(AppliedFilters filters, Integer limit, RowCallbackHandler rowHandler);
 
-	void listGeoTile(boolean distinct, ObjectNode jsonTree, Integer limit, int zoom, int xtile, int ytile, RowCallbackHandler rowHandler);
+	void listGeoTile(boolean distinct, AppliedFilters filters, Integer limit, int zoom, int xtile, int ytile, RowCallbackHandler rowHandler);
 
 }

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

@@ -42,6 +42,7 @@ import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -149,7 +150,7 @@ public interface GenesysService {
 
 	long countDatasets(FaoInstitute faoInstitute);
 
-	void writeAccessions(String jsonFilter, OutputStream outputStream) throws IOException;
+	void writeAccessions(AppliedFilters filters, OutputStream outputStream) throws IOException;
 
 	List<AccessionAlias> saveAliases(List<AccessionAlias> aliases);
 
@@ -183,7 +184,7 @@ public interface GenesysService {
 
 	Set<Long> listAccessions(FaoInstitute holdingInstitute, Set<Long> accessionIds);
 
-	int countAccessions(String jsonFilter);
+	int countAccessions(AppliedFilters filters);
 
 	List<AccessionRemark> saveRemarks(List<AccessionRemark> toSaveRemarks);
 

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

@@ -18,15 +18,17 @@ package org.genesys2.server.service;
 
 import java.io.IOException;
 
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
+
 public interface MappingService {
 
 	void clearCache();
 
-	String filteredKml(String jsonFilter);
+	String filteredKml(AppliedFilters filters);
 
-	String filteredGeoJson(String string, Integer limit) throws IOException;
+	String filteredGeoJson(AppliedFilters filters, Integer limit) throws IOException;
 
-	byte[] getTile(String jsonFilter, int zoom, int xtile, int ytile);
+	byte[] getTile(AppliedFilters filters, int zoom, int xtile, int ytile);
 
 	public static class CoordUtil {
 		public static double tileToLon(int zoom, int xtile) {

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

@@ -21,6 +21,7 @@ import org.genesys2.server.service.ElasticService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysFilterService;
 import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -256,7 +257,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 	}
 
 	@Override
-	public void reindexByFilter(String jsonFilter, boolean slow) {
+	public void reindexByFilter(AppliedFilters filters, boolean slow) {
 
 		LOG.info("Creating index");
 		elasticsearchTemplate.createIndex(AccessionDetails.class);
@@ -265,19 +266,6 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 		LOG.info("Refreshing");
 		elasticsearchTemplate.refresh(AccessionDetails.class, true);
 
-		ObjectNode jsonTree = null;
-		try {
-			if (StringUtils.isNotBlank(jsonFilter))
-				jsonTree = (ObjectNode) objectMapper.readTree(jsonFilter);
-			else {
-				LOG.warn("No filter provided. Quitting.");
-				return;
-			}
-		} catch (IOException e) {
-			LOG.error(e.getMessage(), e);
-			return;
-		}
-
 		StopWatch stopWatch = new StopWatch();
 		stopWatch.setKeepTaskList(false);
 
@@ -288,7 +276,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 			queries.clear();
 
 			stopWatch.start("Get data by filter");
-			Page<Accession> accessions = filterService.listAccessions(jsonTree, new PageRequest(page, size));
+			Page<Accession> accessions = filterService.listAccessions(filters, new PageRequest(page, size));
 			stopWatch.stop();
 			LOG.info(stopWatch.getLastTaskName() + " took " + stopWatch.getLastTaskTimeMillis());
 

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

@@ -18,6 +18,7 @@ package org.genesys2.server.service.impl;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -241,12 +242,23 @@ public class FilterHandler {
 	}
 
 	public static interface FilterValue {
-
+		String getType();
 	}
 
 	@JsonSerialize(using = AppliedFilters.Serializer.class)
 	@JsonDeserialize(using = AppliedFilters.Deserializer.class)
 	public static class AppliedFilters extends ArrayList<AppliedFilter> {
+		private static final ObjectMapper objectMapper = new ObjectMapper();
+
+		@Override
+		public String toString() {
+			try {
+				return objectMapper.writeValueAsString(this);
+			} catch (JsonProcessingException e) {
+				throw new RuntimeException(e);
+			}
+		}
+
 		public static class Serializer extends JsonSerializer<AppliedFilters> {
 			@Override
 			public void serialize(AppliedFilters filters, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
@@ -357,6 +369,9 @@ public class FilterHandler {
 
 								if (jp.nextToken() != JsonToken.END_OBJECT)
 									throw new JsonParseException("Expecting }, got " + jp.getCurrentToken(), jp.getCurrentLocation());
+							} else if (jp.getCurrentToken() == JsonToken.END_ARRAY) {
+								// Blank array
+								break;
 							} else {
 								throw new JsonParseException("I don't know where I am.", jp.getCurrentLocation());
 							}
@@ -377,6 +392,63 @@ public class FilterHandler {
 				return appliedFilters;
 			}
 		}
+
+		/**
+		 * Get the first applied filter matching filterName
+		 * 
+		 * @param filterName
+		 * @return
+		 */
+		public AppliedFilter get(String filterName) {
+			for (AppliedFilter af : this) {
+				if (af.getFilterName().equals(filterName))
+					return af;
+			}
+			return null;
+		}
+
+		public Collection<AppliedFilter> methodFilters() {
+			return CollectionUtils.select(this, new Predicate<AppliedFilter>() {
+				@Override
+				public boolean evaluate(AppliedFilter filter) {
+					return filter.getFilterName().startsWith("gm:");
+				}
+			});
+		}
+
+		/**
+		 * Collect filterNames from AppliedFilters in this list
+		 * 
+		 * @return
+		 */
+		public String[] getFilterNames() {
+			List<String> filterNames = new ArrayList<String>();
+			for (AppliedFilter af : this) {
+				filterNames.add(af.getFilterName());
+			}
+			return filterNames.toArray(ArrayUtils.EMPTY_STRING_ARRAY);
+		}
+
+		/**
+		 * Get first literal filter value
+		 * 
+		 * @param filterName
+		 * @param class1
+		 * @return
+		 */
+		public <T> T getFirstLiteralValue(String filterName, Class<T> clazz) {
+			AppliedFilter af = get(filterName);
+			if (af != null) {
+				for (FilterValue fv : af.getValues()) {
+					if (fv instanceof LiteralValueFilter) {
+						Object obj = ((LiteralValueFilter) fv).getValue();
+						if (clazz.isAssignableFrom(obj.getClass()))
+							return (T) obj;
+					}
+				}
+			}
+			return null;
+		}
 	}
 
 	public static class AppliedFilter {
@@ -454,6 +526,10 @@ public class FilterHandler {
 				return false;
 			return true;
 		}
+
+		public int size() {
+			return values.size();
+		}
 	}
 
 	@JsonSerialize(using = LiteralValueFilter.Serializer.class)
@@ -500,6 +576,11 @@ public class FilterHandler {
 				return false;
 			return true;
 		}
+
+		@Override
+		public String getType() {
+			return "literal";
+		}
 	}
 
 	@JsonSerialize(using = ValueRangeFilter.Serializer.class)
@@ -509,7 +590,7 @@ public class FilterHandler {
 			@Override
 			public void serialize(ValueRangeFilter value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
 				jgen.writeStartObject();
-				jgen.writeArrayFieldStart("range");
+				jgen.writeArrayFieldStart(value.getType());
 				jgen.writeObject(value.getFrom());
 				jgen.writeObject(value.getTo());
 				jgen.writeEndArray();
@@ -538,6 +619,11 @@ public class FilterHandler {
 			this.to = number1.doubleValue() < number2.doubleValue() ? number2 : number1;
 		}
 
+		@Override
+		public String getType() {
+			return "range";
+		}
+
 		public Number getFrom() {
 			return from;
 		}
@@ -584,7 +670,7 @@ public class FilterHandler {
 			@Override
 			public void serialize(MaxValueFilter value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
 				jgen.writeStartObject();
-				jgen.writeObjectField("max", value.getTo());
+				jgen.writeObjectField(value.getType(), value.getTo());
 				jgen.writeEndObject();
 			}
 		}
@@ -600,6 +686,11 @@ public class FilterHandler {
 			this.to = max;
 		}
 
+		@Override
+		public String getType() {
+			return "max";
+		}
+
 		public Number getTo() {
 			return to;
 		}
@@ -636,7 +727,7 @@ public class FilterHandler {
 			@Override
 			public void serialize(MinValueFilter value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
 				jgen.writeStartObject();
-				jgen.writeObjectField("min", value.getFrom());
+				jgen.writeObjectField(value.getType(), value.getFrom());
 				jgen.writeEndObject();
 			}
 		}
@@ -652,6 +743,11 @@ public class FilterHandler {
 				this.from = min;
 		}
 
+		@Override
+		public String getType() {
+			return "min";
+		}
+
 		public Number getFrom() {
 			return from;
 		}
@@ -689,7 +785,7 @@ public class FilterHandler {
 			@Override
 			public void serialize(StartsWithFilter value, JsonGenerator jgen, SerializerProvider provider) throws IOException, JsonProcessingException {
 				jgen.writeStartObject();
-				jgen.writeObjectField("like", value.getStartsWith());
+				jgen.writeObjectField(value.getType(), value.getStartsWith());
 				jgen.writeEndObject();
 			}
 		}
@@ -700,6 +796,11 @@ public class FilterHandler {
 			this.startsWith = startsWith;
 		}
 
+		@Override
+		public String getType() {
+			return "like";
+		}
+
 		public String getStartsWith() {
 			return startsWith;
 		}

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

@@ -20,31 +20,15 @@ import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
+import java.util.Set;
 
 import javax.sql.DataSource;
 
-import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.collections4.Predicate;
-import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.genesys2.server.model.filters.AutocompleteFilter;
-import org.genesys2.server.model.filters.CodedMethodFilter;
-import org.genesys2.server.model.filters.GenesysFilter;
-import org.genesys2.server.model.filters.BasicFilter;
-import org.genesys2.server.model.filters.I18nListFilter;
-import org.genesys2.server.model.filters.MethodFilter;
-import org.genesys2.server.model.filters.ValueName;
-import org.genesys2.server.model.filters.GenesysFilter.DataType;
-import org.genesys2.server.model.filters.GenesysFilter.FilterType;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Method;
-import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
@@ -59,6 +43,10 @@ import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.impl.DirectMysqlQuery.MethodResolver;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilter;
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
+import org.genesys2.server.service.impl.FilterHandler.FilterValue;
+import org.genesys2.server.service.impl.FilterHandler.LiteralValueFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
@@ -71,10 +59,6 @@ import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
 @Service
 @Transactional(readOnly = true)
 public class GenesysFilterServiceImpl implements GenesysFilterService {
@@ -92,7 +76,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 
 	@Autowired
 	private TraitService traitService;
-	
+
 	@Autowired
 	private GeoService geoService;
 
@@ -107,24 +91,24 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	@Autowired
 	private TaxonomyService taxonomyService;
 
-    @Autowired
-    private CropService cropService;
+	@Autowired
+	private CropService cropService;
 
-    @Autowired
+	@Autowired
 	public void setDataSource(final DataSource dataSource) {
 		this.jdbcTemplate = new JdbcTemplate(dataSource);
 	}
 
 	@Override
-	public Page<Accession> listAccessions(ObjectNode jsonTree, Pageable pageable) {
-		final Iterator<Entry<String, JsonNode>> fields = jsonTree.fields();
-		while (fields.hasNext()) {
-			final Entry<String, JsonNode> entry = fields.next();
-			LOG.debug("Looking at " + entry.getKey() + " = " + entry.getValue());
+	public Page<Accession> listAccessions(AppliedFilters filters, Pageable pageable) {
+		if (LOG.isDebugEnabled()) {
+			for (AppliedFilter filter : filters) {
+				LOG.debug("Looking at " + filter.toString());
+			}
 		}
 
 		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
-		directQuery.jsonFilter(jsonTree, new MethodResolver() {
+		directQuery.jsonFilter(filters, new MethodResolver() {
 			@Override
 			public Method getMethod(long methodId) {
 				return methodRepository.findOne(methodId);
@@ -153,18 +137,18 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	 * Filtering autocompleter
 	 */
 	@Override
-	public List<LabelValue<String>> autocomplete(String filter, String ac,ObjectNode jsonTree) {
+	public List<LabelValue<String>> autocomplete(String filter, String ac, AppliedFilters filters) {
 		if (LOG.isDebugEnabled()) {
 			LOG.debug("Autocomplete " + filter + " ac=" + ac);
 		}
-        String shortName = null;
-        try {
-            shortName = jsonTree.get(FilterConstants.CROPS).get(0).asText();
-        } catch (NullPointerException e) {
-            LOG.info("Crop not selected");
-        }
 
-        Crop crop = cropService.getCrop(shortName);
+		Crop crop = null;
+
+		{
+			String shortName = filters.getFirstLiteralValue(FilterConstants.CROPS, String.class);
+			if (shortName != null)
+				crop = cropService.getCrop((String) shortName);
+		}
 
 		final List<LabelValue<String>> completed = new ArrayList<LabelValue<String>>();
 		if ("instCode".equalsIgnoreCase(filter)) {
@@ -178,24 +162,21 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 				completed.add(new LabelValue<String>(c.getCode3(), c.getCode3() + ", " + c.getName()));
 			}
 		} else if ("genus".equalsIgnoreCase(filter)) {
-			final List<String> genera = taxonomyService.autocompleteGenus(ac,crop);
+			final List<String> genera = taxonomyService.autocompleteGenus(ac, crop);
 			for (final String value : genera) {
 				completed.add(new LabelValue<String>(value, value));
 			}
 		} else if ("species".equalsIgnoreCase(filter)) {
-            List<String> genus= new ArrayList<>();
-
-            ArrayNode arrayRoot = (ArrayNode)  jsonTree.get(FilterConstants.TAXONOMY_GENUS);
-            if (arrayRoot!=null){
-                Iterator<JsonNode> elements = arrayRoot.elements();
-                JsonNode element;
-                while(elements.hasNext()){
-                    element = elements.next();
-                    genus.add(element.asText());
-                }
-            }
-
-			final List<String> species = taxonomyService.autocompleteSpecies(ac,crop, genus);
+			List<String> genus = new ArrayList<>();
+