Cleanup

src/main/java/org/genesys2/server/model/elastic/FullTextDocument.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.model.elastic;
 
-import com.eclipsesource.json.JsonObject;
-import com.eclipsesource.json.JsonValue;
-import com.eclipsesource.json.ParseException;
-import org.apache.log4j.Logger;
-import org.genesys2.server.model.impl.*;
+import java.util.Date;
+import java.util.Locale;
+
+import org.genesys2.server.model.impl.ClassPK;
 import org.springframework.data.annotation.Id;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
 import org.springframework.data.elasticsearch.annotations.FieldIndex;
 import org.springframework.data.elasticsearch.annotations.FieldType;
 
-import java.util.Date;
-import java.util.Locale;
+import com.eclipsesource.json.JsonObject;
+import com.eclipsesource.json.JsonValue;
+import com.eclipsesource.json.ParseException;
 
 /**
  * <code>FullTextDocument</code> is used in Elasticsearch mapping
  */
 @Document(indexName = "fulltext", refreshInterval = "60s")
 public class FullTextDocument {
-	private static final Logger LOG = Logger.getLogger(FullTextDocument.class);
+	// FIXME Revisit!
 	private static final String ENGLISH_LOCALE = "en";
 
 	@Id
@@ -47,81 +62,81 @@ public class FullTextDocument {
 	private Date lastModifiedDate;
 
 	public Long getId() {
-		return id;
+		return this.id;
 	}
 
-	public void setId(Long id) {
+	public void setId(final Long id) {
 		this.id = id;
 	}
 
 	public String getUrlToContent() {
-		return urlToContent;
+		return this.urlToContent;
 	}
 
-	public void setUrlToContent(String urlToContent) {
+	public void setUrlToContent(final String urlToContent) {
 		this.urlToContent = urlToContent;
 	}
 
 	public ClassPK getClassPK() {
-		return classPK;
+		return this.classPK;
 	}
 
-	public void setClassPK(ClassPK classPK) {
+	public void setClassPK(final ClassPK classPK) {
 		this.classPK = classPK;
 	}
 
 	public String getBody() {
-		return body;
+		return this.body;
 	}
 
-	public void setBody(String body) {
+	public void setBody(final String body) {
 		this.body = body;
 	}
 
 	public String getSummary() {
-		return summary;
+		return this.summary;
 	}
 
-	public void setSummary(String summary) {
+	public void setSummary(final String summary) {
 		this.summary = summary;
 	}
 
-	public String getTextByLocale(Locale locale) {
+	public String getTextByLocale(final Locale locale) {
 		try {
-			JsonObject json = JsonObject.readFrom(body);
+			final JsonObject json = JsonObject.readFrom(this.body);
 			JsonValue value = json.get(locale.getLanguage());
 			if (value == null) {
 				value = json.get(ENGLISH_LOCALE);
 			}
 
 			return value.toString().replace("\"", "");
-		} catch (ParseException ignored) {
+		} catch (final ParseException ignored) {
 		}
 
 		return getBody();
 	}
 
 	public String getLanguage() {
-		return language;
+		return this.language;
 	}
 
-	public void setLanguage(String language) {
+	public void setLanguage(final String language) {
 		this.language = language;
 	}
 
 	public Date getCreatedDate() {
-		return createdDate;
+		return this.createdDate;
 	}
 
-	public void setCreatedDate(Date createdDate) {
+	public void setCreatedDate(final Date createdDate) {
 		this.createdDate = createdDate;
 	}
 
 	public Date getLastModifiedDate() {
-		return lastModifiedDate;
+		return this.lastModifiedDate;
 	}
 
-	public void setLastModifiedDate(Date lastModifiedDate) {
+	public void setLastModifiedDate(final Date lastModifiedDate) {
 		this.lastModifiedDate = lastModifiedDate;
 	}
 }

src/main/java/org/genesys2/server/service/FullTextSearchService.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 java.util.Collection;
+import java.util.List;
+
 import org.genesys2.server.model.elastic.FullTextDocument;
 import org.genesys2.server.service.impl.SearchException;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.elasticsearch.ElasticsearchException;
 
-import java.util.Collection;
-import java.util.List;
-
 public interface FullTextSearchService {
 
 	Page<?> search(String query, Pageable pageable, String section) throws SearchException;

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

@@ -74,8 +74,9 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 	private static final Log LOG = LogFactory.getLog(ElasticsearchSearchServiceImpl.class);
 
-	private static final String INDEXALIAS_PASSPORT_READ = "passport";
+	public static final String INDEXALIAS_PASSPORT_READ = "passport";
 	private static final String INDEXALIAS_PASSPORT_WRITE = "passportWrite";
+	public static final String PASSPORT_TYPE = "mcpd";
 
 	@Autowired
 	private Client client;
@@ -108,7 +109,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 	@Override
 	public Page<AccessionDetails> search(String query, Pageable pageable) throws SearchException {
-		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes("mcpd")
+		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes(PASSPORT_TYPE)
 				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryString(query).defaultOperator(Operator.AND)).withPageable(pageable).build();
 
 		try {
@@ -121,7 +122,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 	@Override
 	public List<String> autocompleteSearch(String query) throws SearchException {
-		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes("mcpd")
+		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes(PASSPORT_TYPE)
 				.withQuery(org.elasticsearch.index.query.QueryBuilders.queryString("acceNumb:(" + query + "*)").defaultOperator(Operator.AND))
 				.withSort(SortBuilders.fieldSort(FilterConstants.ACCENUMB).order(SortOrder.ASC)).withPageable(new PageRequest(0, 10)).build();
 
@@ -143,7 +144,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 		AndFilterBuilder filterBuilder = getFilterBuilder(appliedFilters);
 
 		SortBuilder sortBuilder = SortBuilders.fieldSort(FilterConstants.ACCENUMB).order(SortOrder.ASC);
-		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes("mcpd")
+		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes(PASSPORT_TYPE)
 				.withFilter(filterBuilder).withSort(sortBuilder).withPageable(pageable).build();
 
 		try {
@@ -167,7 +168,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 		} else {
 			termFacetRequest = new TermFacetRequestBuilder("f").applyQueryFilter().fields(term).size(size).build();
 		}
-		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes("mcpd")
+		SearchQuery searchQuery = new NativeSearchQueryBuilder().withIndices(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ).withTypes(PASSPORT_TYPE)
 				.withFilter(filterBuilder).withFacet(termFacetRequest).build();
 
 		try {
@@ -348,7 +349,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 			IndexQuery iq = new IndexQuery();
 			iq.setIndexName(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE);
-			iq.setType("mcpd");
+			iq.setType(PASSPORT_TYPE);
 			iq.setId(String.valueOf(ad.getId()));
 			iq.setObject(ad);
 
@@ -373,7 +374,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 		LOG.info("Removing from index " + clazz2 + " id=" + id);
 
 		if (clazz2.equals(AccessionDetails.class)) {
-			elasticsearchTemplate.delete(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE, "mcpd", String.valueOf(id));
+			elasticsearchTemplate.delete(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE, PASSPORT_TYPE, String.valueOf(id));
 		} else {
 			// Default
 			elasticsearchTemplate.delete(clazz2, String.valueOf(id));
@@ -411,7 +412,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 			LOG.info("Initializing genesysarchive");
 			elasticsearchTemplate.createIndex("genesysarchive");
 			LOG.info("Copying mapping to genesysarchive");
-			elasticsearchTemplate.putMapping("genesysarchive", "mcpd", indexMapping);
+			elasticsearchTemplate.putMapping("genesysarchive", PASSPORT_TYPE, indexMapping);
 		}
 
 		if (!aliasExists(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_READ)) {
@@ -525,7 +526,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 			}
 		}
 	}
-	
+
 	/**
 	 * Delete an index
 	 */
@@ -540,7 +541,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 		LOG.info("Creating index " + indexName);
 		elasticsearchTemplate.createIndex(indexName, settings);
 		LOG.info("Copying mapping to genesysarchive");
-		elasticsearchTemplate.putMapping(indexName, "mcpd", indexMapping);
+		elasticsearchTemplate.putMapping(indexName, PASSPORT_TYPE, indexMapping);
 	}
 
 	@Override
@@ -588,10 +589,10 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 			try {
 
 				IndexRequest indexRequest = new IndexRequest();
-				indexRequest.index(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE).type("mcpd");
+				indexRequest.index(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE).type(PASSPORT_TYPE);
 				indexRequest.source("seqNo", o[2]);
 				UpdateQuery updateQuery = new UpdateQueryBuilder().withClass(AccessionDetails.class)
-						.withIndexName(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE).withType("mcpd").withId(o[0].toString())
+						.withIndexName(ElasticsearchSearchServiceImpl.INDEXALIAS_PASSPORT_WRITE).withType(PASSPORT_TYPE).withId(o[0].toString())
 						.withIndexRequest(indexRequest).build();
 				queries.add(updateQuery);
 				// LOG.debug("ES added seqNo to " + o[0].toString());

src/main/java/org/genesys2/server/servlet/controller/admin/ElasticSearchController.java

@@ -101,9 +101,19 @@ public class ElasticSearchController {
 	 *
 	 * @return
 	 */
-	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "regenerate" })
+	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "regenerate=accn" })
 	public String regenerateElastic() {
 		elasticService.regenerateIndexes();
+		return "redirect:/admin/elastic/";
+	}
+	
+	/**
+	 * Completely recreate Elasticsearch indexes: create, index, re-alias.
+	 *
+	 * @return
+	 */
+	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "regenerate=content" })
+	public String regenerateElasticContent() {
 		fullTextSearchService.regenerateIndexes();
 		return "redirect:/admin/elastic/";
 	}
@@ -115,7 +125,7 @@ public class ElasticSearchController {
 	 * @param jsonFilter
 	 * @throws IOException
 	 */
-	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "reindex", "filter" })
+	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "reindex=accn", "filter" })
 	public String reindexElasticFiltered(@RequestParam(value = "filter", required = true) String jsonFilter,
 										 @RequestParam(value = "type", required = true) String type) throws IOException {
 
@@ -133,6 +143,27 @@ public class ElasticSearchController {
 		return "redirect:/admin/elastic/";
 	}
 
+
+	/**
+	 * This method refreshes data in the currently active index. It is very
+	 * handy when having to refresh part of ES after direct database update.
+	 *
+	 * @param jsonFilter
+	 * @throws IOException
+	 */
+	@RequestMapping(method = RequestMethod.POST, value = "/action", params = { "reindex=content", "type" })
+	public String reindexElasticContent(@RequestParam(value = "type", required = true) String type) throws IOException {
+
+		if (type.equals("All")) {
+			fullTextSearchService.regenerateIndexes();
+		} else {
+			fullTextSearchService.reindex(type);
+		}
+
+		return "redirect:/admin/elastic/";
+	}
+
+	
 	/**
 	 * Clear ES queue
 	 *

src/main/webapp/WEB-INF/jsp/admin/elastic/index.jsp

@@ -9,25 +9,33 @@
   <body>
     <%@ include file="/WEB-INF/jsp/admin/menu.jsp"%>
 
+		<h3>Accession data</h3>
 		<form method="post" action="<c:url value="/admin/elastic/action" />">
 			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
-
 			<input type="text" name="filter" placeholder="Genesys filter {}" value="{}" />
-
-            <select name="type">
-              <option value="All" selected>All entities</option>
-              <c:forEach items="${reindexTypes}" var="type">
-                <option value="${type.value}">${type.key}</option>
-              </c:forEach>
-            </select>
-
-			<button type="submit" class="btn btn-default" name="reindex">Reindex</button>
-			<button type="submit" class="btn btn-default" name="regenerate">Regenerate</button>
+			<button type="submit" class="btn btn-default" value="accn" name="reindex">Reindex</button>
+			<button type="submit" class="btn btn-default" value="accn" name="regenerate">Regenerate</button>
+		</form>
+		
+		<h3>Content</h3>
+		<form method="post" action="<c:url value="/admin/elastic/action" />">
+			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
+			<select name="type">
+				<option value="All" selected>All content entities</option>
+				<c:forEach items="${reindexTypes}" var="type">
+					<option value="${type.value}">${type.key}</option>
+				</c:forEach>
+			</select>
+			<button type="submit" class="btn btn-default" value="content" name="reindex">Reindex</button>
+			<button type="submit" class="btn btn-default" value="content" name="regenerate">Regenerate</button>
 		</form>
+		
 		<form method="post" action="<c:url value="/admin/elastic/action" />">
 			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
 			<button type="submit" class="btn btn-default" name="clear-queues">Clear ES update queues</button>
 		</form>
+		
+		<h3>Index alias management</h3>
 		<form method="post" action="<c:url value="/admin/elastic/action" />">
 			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
 			Alias:<input type="text" name="aliasName" />
@@ -37,7 +45,7 @@
 			<button type="submit" class="btn btn-default" value="delete-index" name="action">Delete index</button>
 		</form>
 
-	<h3>Indexes and their aliases</h3>
+	<h3>Indexes and aliases</h3>
     <c:if test="${empty indexes}">
       <h5>No indexes found.</h5>
     </c:if>