update Elasticsearch, migrate services and components from Catalog

pom.xml

@@ -412,17 +412,10 @@
 			<scope>runtime</scope>
 		</dependency>
 
-
-		<dependency>
-			<groupId>org.elasticsearch</groupId>
-			<artifactId>elasticsearch</artifactId>
-			<version>1.7.6</version>
-		</dependency>
-
 		<dependency>
 			<groupId>org.springframework.data</groupId>
 			<artifactId>spring-data-elasticsearch</artifactId>
-			<version>1.3.2.RELEASE</version>
+			<version>2.1.12.RELEASE</version>
 		</dependency>
 
 		<dependency>

src/main/java/org/genesys/catalog/api/EsDatasetFilter.java

+/*
+ * Copyright 2018 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.genesys.catalog.api;
+
+import org.elasticsearch.index.query.QueryBuilder;
+import org.genesys.catalog.model.filters.DatasetFilter;
+import org.genesys.catalog.service.ElasticsearchFilter;
+
+/**
+ * Wrapper for {@link DatasetFilter} to produce ES queries.
+ *
+ * @author Matija Obreza
+ */
+public class EsDatasetFilter extends DatasetFilter implements ElasticsearchFilter {
+
+	/*
+	 * (non-Javadoc)
+	 * @see org.genesys.catalog.server.service.ElasticsearchFilter#elasticQuery()
+	 */
+	@Override
+	public QueryBuilder elasticQuery() {
+		return null;
+	}
+
+}

src/main/java/org/genesys/catalog/api/v0/SearchController.java

+/*
+ * Copyright 2018 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.genesys.catalog.api.v0;
+
+import com.fasterxml.jackson.annotation.JsonView;
+import org.apache.commons.lang3.StringUtils;
+import org.elasticsearch.index.query.BoolQueryBuilder;
+import org.elasticsearch.index.query.QueryBuilder;
+import org.genesys.blocks.model.BasicModel;
+import org.genesys.blocks.model.JsonViews;
+import org.genesys.catalog.api.EsDatasetFilter;
+import org.genesys.catalog.exceptions.InvalidApiUsageException;
+import org.genesys.catalog.model.Partner;
+import org.genesys.catalog.model.dataset.AccessionIdentifier;
+import org.genesys.catalog.model.dataset.Dataset;
+import org.genesys.catalog.model.traits.Descriptor;
+import org.genesys.catalog.service.ElasticsearchService;
+import org.genesys2.server.model.impl.Crop;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.*;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static com.google.common.collect.Sets.newHashSet;
+import static org.elasticsearch.index.query.QueryBuilders.boolQuery;
+import static org.elasticsearch.index.query.QueryBuilders.termsQuery;
+
+/**
+ * API to search the Catalog.
+ *
+ * @author Matija Obreza
+ */
+@RestController("catalogSearchApi0")
+@RequestMapping(value = { "/api/v0/search" })
+public class SearchController {
+
+	private static final Logger LOG = LoggerFactory.getLogger(SearchController.class);
+
+	@Autowired(required = false)
+	private ElasticsearchService elasticsearch;
+
+	/**
+	 * Get suggestions for dataset filters .
+	 *
+	 * @param filters the filters
+	 * @param searchQuery the search query
+	 * @return the map
+	 */
+	@JsonView({ JsonViews.Minimal.class })
+	@PostMapping(value = "/dataset/suggest", produces = MediaType.APPLICATION_JSON_VALUE)
+	public Map<String, SearchResults> datasets(@RequestBody(required = false) final EsDatasetFilter filters, @RequestParam(value = "q", required = true) String searchQuery) {
+		LOG.trace("Incoming {}", searchQuery);
+		searchQuery = sanitizeQuery(searchQuery);
+		LOG.info("Suggestions for datasets for: {}", searchQuery);
+
+		if (StringUtils.isBlank(searchQuery)) {
+			throw new InvalidApiUsageException("No search query provided");
+		}
+
+		QueryBuilder extraFilters = filtersFromDataset(filters);
+
+		Map<Class<?>, List<BasicModel>> hitsByEntity = elasticsearch.search(extraFilters, searchQuery, newHashSet(Crop.class, Partner.class,
+			AccessionIdentifier.class, Descriptor.class));
+
+		Map<String, SearchResults> suggestions = new HashMap<>();
+		suggestions.put("search.group.crop", SearchResults.from("code", Arrays.asList("crop"), hitsByEntity.get(Crop.class)));
+		suggestions.put("search.group.partner", SearchResults.from("uuid", Arrays.asList("owner.uuid"), hitsByEntity.get(Partner.class)));
+		suggestions.put("search.group.accession", SearchResults.from("doi", Arrays.asList("accessionIdentifier.doi"), hitsByEntity.get(AccessionIdentifier.class)));
+		suggestions.put("search.group.descriptor", SearchResults.from("uuid", Arrays.asList("descriptor.uuid"), hitsByEntity.get(Descriptor.class)));
+		
+		// Search datasets
+		suggestions.put("search.matches", SearchResults.from("uuid", Arrays.asList("uuid"), elasticsearch.search(extraFilters, searchQuery, Dataset.class)));
+
+		return suggestions;
+	}
+
+	/// Try to enhance the search by adding known Dataset filters
+	private QueryBuilder filtersFromDataset(EsDatasetFilter filters) {
+		if (filters == null) {
+			return null;
+		}
+		BoolQueryBuilder q = boolQuery();
+		if (filters.crop != null && !filters.crop.isEmpty()) {
+			q.must(termsQuery("crop", filters.crop));
+		}
+		q.boost(3.0f);
+		
+		return q.hasClauses() ? q : null;
+	}
+
+	/**
+	 * Sanitize incoming search query
+	 * 
+	 * @param searchQuery incoming
+	 * @return sanitized search query
+	 */
+	private String sanitizeQuery(String searchQuery) {
+		if (StringUtils.isBlank(searchQuery)) {
+			return null;
+		}
+		return searchQuery.replaceAll("[^\\w\\d\\s]+", "").replaceAll("\\s\\s+", " ").trim();
+	}
+}
+
+/**
+ * Wrapper for search results
+ */
+class SearchResults {
+	public List<String> filters;
+	public String key = "uuid";
+	public List<BasicModel> hits;
+
+	public static SearchResults from(String key, List<String> filters, List<BasicModel> list) {
+		if (list == null || list.isEmpty())
+			return null;
+
+		SearchResults sr = new SearchResults();
+		sr.filters = filters;
+		sr.key = key;
+		sr.hits = list;
+		return sr;
+	}
+
+}

src/main/java/org/genesys/catalog/component/ElasticJPAListener.java

+/*
+ * Copyright 2018 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.genesys.catalog.component;
+
+import com.hazelcast.core.IQueue;
+import org.aspectj.lang.JoinPoint;
+import org.aspectj.lang.annotation.AfterReturning;
+import org.aspectj.lang.annotation.Aspect;
+import org.aspectj.lang.annotation.Before;
+import org.genesys.blocks.model.BasicModel;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.Resource;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * AspectJ powered listener on repository save and delete operations
+ * adds indexed entities to re-index queue, handled by {@link ElasticReindexProcessor}.
+ */
+@Aspect
+@Component
+public class ElasticJPAListener {
+	private final static Logger LOG = LoggerFactory.getLogger(ElasticJPAListener.class);
+
+	private Set<Object> includedClasses;
+	private Set<Object> ignoredClasses;
+	
+	@Resource
+	private IQueue<ElasticReindex> elasticReindexQueue;
+
+	/**
+	 * Instantiates a new elastic JPA listener.
+	 */
+	public ElasticJPAListener() {
+		System.err.println("Making ElasticJPAListener");
+		ignoredClasses = Collections.synchronizedSet(new HashSet<>());
+		includedClasses = Collections.synchronizedSet(new HashSet<>());
+	}
+
+	/**
+	 * After persist.
+	 *
+	 * @param joinPoint the join point
+	 * @param result the result
+	 */
+	@AfterReturning(value = "execution(* org.springframework.data.jpa.repository.JpaRepository.save(..))", returning = "result")
+	public void afterPersist(final JoinPoint joinPoint, final Object result) {
+		LOG.debug("JPA afterPersist {} {}", joinPoint.toLongString(), joinPoint.getTarget());
+
+		try {
+			scheduleReindexing(result);
+		} catch (Throwable e) {
+			LOG.error(e.getMessage(), e);
+		}
+	}
+
+	/**
+	 * Before remove.
+	 *
+	 * @param joinPoint the join point
+	 */
+	@Before(value = "execution(* org.springframework.data.jpa.repository.JpaRepository.delete(..)) || execution(* org.springframework.data.jpa.repository.JpaRepository.deleteInBatch(..))")
+	public void beforeRemove(final JoinPoint joinPoint) {
+		final Object[] args = joinPoint.getArgs();
+		try {
+			final Object removed = args[0];
+			LOG.debug("JPA afterRemove: {} {}", joinPoint.toLongString(), joinPoint.getTarget());
+			scheduleReindexing(removed);
+		} catch (Throwable e) {
+			LOG.error(e.getMessage(), e);
+		}
+	}
+
+	/**
+	 * Flatten collections (if Iterable) and check each object class if indexed
+	 * 
+	 * @param toReindex
+	 */
+	private void scheduleReindexing(Object toReindex) {
+		if (toReindex == null) {
+			return;
+		}
+
+		if (toReindex instanceof Iterable<?>) {
+			// Iterate and test
+			Iterable<?> it = (Iterable<?>) toReindex;
+			for (Object obj : it) {
+				scheduleReindexing(obj);
+			}
+		} else {
+			Class<?> clazz = toReindex.getClass();
+			if (isIndexed(clazz)) {
+				LOG.warn("Reindexing {} {}", clazz.getName(), toReindex);
+				if (toReindex instanceof BasicModel) {
+					BasicModel entity = (BasicModel) toReindex;
+					elasticReindexQueue.add(new ElasticReindex(clazz.getName(), entity.getId()));
+				} else {
+					LOG.warn("Don't know how to index {}. Not a BasicModel.", clazz.getName());
+				}
+			}
+		}
+	}
+
+	private boolean isIndexed(Class<?> clazz) {
+		if (ignoredClasses.contains(clazz)) {
+			return false;
+		}
+
+		if (includedClasses.contains(clazz)) {
+			return true;
+		}
+
+		Document esDocumentAnnotation = clazz.getAnnotation(Document.class);
+		if (esDocumentAnnotation == null) {
+			ignoredClasses.add(clazz);
+			return false;
+		} else {
+			includedClasses.add(clazz);
+			return true;
+		}
+	}
+}

src/main/java/org/genesys/catalog/component/ElasticReindex.java

+/*
+ * Copyright 2018 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.genesys.catalog.component;
+
+import java.io.Serializable;
+
+/**
+ * The Class ElasticReindex.
+ */
+public class ElasticReindex implements Serializable {
+
+	private static final long serialVersionUID = -7779348224175021304L;
+	private String clazz;
+	private Long id;
+
+	/**
+	 * Instantiates a new elastic reindex.
+	 *
+	 * @param clazz the clazz
+	 * @param id the id
+	 */
+	public ElasticReindex(String clazz, Long id) {
+		this.clazz = clazz;
+		this.id = id;
+	}
+
+	/**
+	 * Gets the clazz.
+	 *
+	 * @return the clazz
+	 */
+	public String getClazz() {
+		return clazz;
+	}
+	
+	/**
+	 * Gets the id.
+	 *
+	 * @return the id
+	 */
+	public Long getId() {
+		return id;
+	}
+	
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((clazz == null) ? 0 : clazz.hashCode());
+		result = prime * result + ((id == null) ? 0 : id.hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		ElasticReindex other = (ElasticReindex) obj;
+		if (clazz == null) {
+			if (other.clazz != null)
+				return false;
+		} else if (!clazz.equals(other.clazz))
+			return false;
+		if (id == null) {
+			if (other.id != null)
+				return false;
+		} else if (!id.equals(other.id))
+			return false;
+		return true;
+	}
+}

src/main/java/org/genesys/catalog/component/ElasticReindexProcessor.java

+/*
+ * Copyright 2018 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.genesys.catalog.component;
+
+import com.hazelcast.core.IQueue;
+import org.genesys.blocks.model.BasicModel;
+import org.genesys.catalog.service.ElasticsearchService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.Resource;
+import java.util.*;
+
+/**
+ * ES Processor component uses Spring's @Scheduled annotation to scan queues
+ * with 2000ms delay measured from the completion time of each preceding
+ * invocation.
+ */
+@Component
+public class ElasticReindexProcessor {
+	
+	/** The Constant LOG. */
+	public static final Logger LOG = LoggerFactory.getLogger(ElasticReindexProcessor.class);
+
+	private static final int BATCH_SIZE = 100;
+
+	@Resource
+	private IQueue<ElasticReindex> elasticReindexQueue;
+	
+	@Autowired
+	private ElasticsearchService elasticsearch;
+	
+	/**
+	 * Process queues.
+	 */
+	@Scheduled(fixedDelay = 2000)
+	public void processQueues() {
+		if (LOG.isTraceEnabled()) {
+			LOG.trace("Scanning ES remove queue");
+		}
+
+		List<ElasticReindex> forReindexing = new ArrayList<>();
+		Map<String, Set<Long>> buckets = Collections.synchronizedMap(new HashMap<String, Set<Long>>());
+
+		while (elasticReindexQueue.drainTo(forReindexing, 100) > 0) {
+			LOG.info("Remaining for reindex={}", elasticReindexQueue.size());
+			forReindexing.stream().forEach(er -> bucketize(buckets, er));
+			forReindexing.clear();
+		}
+
+		if (!buckets.isEmpty()) {
+			for (String className : buckets.keySet()) {
+				try {
+					@SuppressWarnings("unchecked")
+					Class<? extends BasicModel> clazz = (Class<? extends BasicModel>) Class.forName(className);
+					Set<Long> bucket = buckets.get(className);
+					elasticsearch.asyncUpdate(clazz, bucket);
+					bucket.clear();
+				} catch (ClassNotFoundException e) {
+					LOG.error(e.getMessage(), e);
+				}
+			}
+			buckets.clear();
+		}
+	}
+
+	private void bucketize(final Map<String, Set<Long>> buckets, final ElasticReindex toReindex) {
+		if (toReindex == null)
+			return;
+
+		Set<Long> bucket = buckets.get(toReindex.getClazz());
+		if (bucket == null) {
+			buckets.put(toReindex.getClazz(), bucket = Collections.synchronizedSet(new HashSet<Long>()));
+		}
+		bucket.add(toReindex.getId());
+
+		if (bucket.size() >= BATCH_SIZE) {
+			try {
+				@SuppressWarnings("unchecked")
+				Class<? extends BasicModel> clazz = (Class<? extends BasicModel>) Class.forName(toReindex.getClazz());
+				elasticsearch.asyncUpdate(clazz, bucket);
+				bucket.clear();
+			} catch (ClassNotFoundException e) {
+				LOG.error(e.getMessage(), e);
+			}
+		}
+	}
+
+}
\ No newline at end of file

src/main/java/org/genesys/catalog/custom/elasticsearch/CustomMapping.java

+/*
+ * Copyright 2018 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.genesys.catalog.custom.elasticsearch;
+
+import org.elasticsearch.common.xcontent.XContentBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.data.elasticsearch.ElasticsearchException;
+
+import java.io.IOException;
+
+import static org.genesys.catalog.custom.elasticsearch.CustomMappingBuilder.buildMapping;
+
+
+/**
+ * Used to access the package-protected buildMapping functions.
+ */
+public class CustomMapping {
+	
+	/** The Constant LOG. */
+	public static final Logger LOG