Added licensing headers and updated obsolete fragments

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

+/**
+ * Copyright 2016 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
 package org.genesys2.server.service;
 
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;

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

+/**
+ * Copyright 2016 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
 package org.genesys2.server.service;
 
 public interface IndexAliasConstants {

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

+/**
+ * Copyright 2016 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
 package org.genesys2.server.service.impl;
 
 import com.hazelcast.core.ILock;
@@ -129,7 +145,7 @@ public class ElasticSearchManagementServiceImpl implements ElasticSearchManageme
 	 */
 	@Override
 	public void regenerateIndexes(final String indexName) throws ElasticsearchException {
-		Class clazz = null;
+		Class<?> clazz = null;
 		String readAlias = null;
 		String writeAlias = null;
 		if (IndexAliasConstants.INDEX_FULLTEXT.equals(indexName)) {

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

+/**
+ * Copyright 2016 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ **/
+
 package org.genesys2.server.service.impl;
 
 import java.sql.ResultSet;
@@ -85,7 +101,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 	@Override
 	public Page<AccessionDetails> search(String query, Pageable pageable) throws SearchException {
 		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(IndexAliasConstants.INDEXALIAS_PASSPORT_READ).withTypes(IndexAliasConstants.PASSPORT_TYPE)
-				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryString(query).defaultOperator(Operator.AND)).withPageable(pageable).build();
+				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryStringQuery(query).defaultOperator(Operator.AND)).withPageable(pageable).build();
 
 		try {
 			Page<AccessionDetails> sampleEntities = elasticsearchTemplate.queryForPage(searchQuery, AccessionDetails.class);
@@ -98,7 +114,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 	@Override
 	public List<String> autocompleteSearch(String query) throws SearchException {
 		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(IndexAliasConstants.INDEXALIAS_PASSPORT_READ).withTypes(IndexAliasConstants.PASSPORT_TYPE)
-				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryString("acceNumb:(" + query + "*)").defaultOperator(Operator.AND))
+				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryStringQuery("acceNumb:(" + query + "*)").defaultOperator(Operator.AND))
 				.withSort(SortBuilders.fieldSort(FilterConstants.ACCENUMB).order(SortOrder.ASC)).withPageable(new PageRequest(0, 10)).build();
 
 		try {
@@ -243,9 +259,9 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 						if (FilterConstants.ALIAS.equals(key)) {
 							// Nested
-							orFilter.add(FilterBuilders.nestedFilter("aliases", QueryBuilders.queryString("aliases.name" + ":(" + sb.toString() + ")")));
+							orFilter.add(FilterBuilders.nestedFilter("aliases", QueryBuilders.queryStringQuery("aliases.name" + ":(" + sb.toString() + ")")));
 						} else {
-							orFilter.add(FilterBuilders.queryFilter(QueryBuilders.queryString(key + ":(" + sb.toString() + ")")));
+							orFilter.add(FilterBuilders.queryFilter(QueryBuilders.queryStringQuery(key + ":(" + sb.toString() + ")")));
 						}
 					} else {
 						// terms
@@ -280,9 +296,9 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 						if (genesysFilter.isAnalyzed()) {
 							if (FilterConstants.ALIAS.equals(key)) {
 								orFilter.add(FilterBuilders.nestedFilter("aliases",
-										QueryBuilders.queryString("aliases.name" + ":" + startsWith.getStartsWith() + "*")));
+										QueryBuilders.queryStringQuery("aliases.name" + ":" + startsWith.getStartsWith() + "*")));
 							} else {
-								orFilter.add(FilterBuilders.queryFilter(QueryBuilders.queryString(key + ":" + startsWith.getStartsWith() + "*")));
+								orFilter.add(FilterBuilders.queryFilter(QueryBuilders.queryStringQuery(key + ":" + startsWith.getStartsWith() + "*")));
 							}
 						} else {
 							orFilter.add(FilterBuilders.prefixFilter(key, startsWith.getStartsWith()));

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

@@ -18,7 +18,7 @@ package org.genesys2.server.service.impl;
 import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
 import static org.elasticsearch.index.query.QueryBuilders.functionScoreQuery;
 import static org.elasticsearch.index.query.QueryBuilders.matchQuery;
-import static org.elasticsearch.index.query.QueryBuilders.queryString;
+import static org.elasticsearch.index.query.QueryBuilders.queryStringQuery;
 import static org.elasticsearch.index.query.functionscore.ScoreFunctionBuilders.fieldValueFactorFunction;
 
 import java.util.ArrayList;
@@ -144,7 +144,7 @@ public class FullTextSearchServiceImpl implements FullTextSearchService, Initial
 				.withQuery(
 						functionScoreQuery(
 								boolQuery().must(matchQuery(CLASSPK_SHORTNAME, classPK.getShortName())).must(
-										queryString(query).defaultOperator(QueryStringQueryBuilder.Operator.AND))).add(
+										queryStringQuery(query).defaultOperator(QueryStringQueryBuilder.Operator.AND))).add(
 								fieldValueFactorFunction("score").factor(1.0f))).withPageable(pageable).build();
 
 		try {
@@ -156,7 +156,7 @@ public class FullTextSearchServiceImpl implements FullTextSearchService, Initial
 	}
 
 	private Page<?> toEntities(FacetedPage<FullTextDocument> fulltextResults, Pageable pageable) {
-		List content = new ArrayList(fulltextResults.getSize());
+		List<Object> content = new ArrayList<>(fulltextResults.getSize());
 		for (FullTextDocument document : fulltextResults.getContent()) {
 			content.add(toEntity(document.getClassPK().getClassName(), document.getId()));
 		}
@@ -185,7 +185,7 @@ public class FullTextSearchServiceImpl implements FullTextSearchService, Initial
 		}
 
 		SearchQuery searchQuery;
-		Class clazz;
+		Class<?> clazz;
 
 		if (section.equals(ACCESSION_SECTION)) {
 			throw new UnsupportedOperationException("Use ElasticsearchServiceImpl for accession search");
@@ -195,7 +195,7 @@ public class FullTextSearchServiceImpl implements FullTextSearchService, Initial
 					.withQuery(
 							functionScoreQuery(
 									boolQuery().must(matchQuery(CLASSPK_SHORTNAME, section)).must(
-											queryString(query).defaultOperator(QueryStringQueryBuilder.Operator.AND))).add(
+											queryStringQuery(query).defaultOperator(QueryStringQueryBuilder.Operator.AND))).add(
 									fieldValueFactorFunction("score").factor(1.0f))).withPageable(pageable).build();
 			clazz = FullTextDocument.class;
 		}