ElasticSearch

pom.xml

@@ -337,6 +337,12 @@
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-search</artifactId>
 			<version>4.5.1.Final</version>
+			<exclusions>
+				<exclusion>
+					<artifactId>solr-analysis-extras</artifactId>
+					<groupId>org.apache.solr</groupId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.tomcat</groupId>
@@ -419,6 +425,66 @@
 			<version>${jetty.version}</version>
 			<scope>runtime</scope>
 		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.data</groupId>
+			<artifactId>spring-data-elasticsearch</artifactId>
+			<version>1.0.2.RELEASE</version>
+			<exclusions>
+				<exclusion>
+					<artifactId>lucene-core</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-sandbox</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-queries</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-codecs</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-grouping</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-memory</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-spatial</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-suggest</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-queryparser</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-misc</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-join</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-highlighter</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>lucene-analyzers-common</artifactId>
+					<groupId>org.apache.lucene</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
 		
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>

src/main/java/org/apache/lucene/util/Version.java

+package org.apache.lucene.util;
+
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You 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.
+ */
+
+import java.util.Locale;
+
+/**
+ * Use by certain classes to match version compatibility across releases of
+ * Lucene.
+ * 
+ * <p>
+ * <b>WARNING</b>: When changing the version parameter that you supply to
+ * components in Lucene, do not simply change the version at search-time, but
+ * instead also adjust your indexing code to match, and re-index.
+ */
+public enum Version {
+
+	/**
+	 * Match settings and bugs in Lucene's 2.0 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_20,
+
+	/**
+	 * Match settings and bugs in Lucene's 2.1 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_21,
+
+	/**
+	 * Match settings and bugs in Lucene's 2.2 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_22,
+
+	/**
+	 * Match settings and bugs in Lucene's 2.3 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_23,
+
+	/**
+	 * Match settings and bugs in Lucene's 2.4 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_24,
+
+	/**
+	 * Match settings and bugs in Lucene's 2.9 release.
+	 * 
+	 * @deprecated (3.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_29,
+	/**
+	 * Match settings and bugs in Lucene's 3.0 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_30,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.1 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_31,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.2 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_32,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.3 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_33,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.4 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_34,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.5 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_35,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.6 release.
+	 * 
+	 * @deprecated (4.0) Use latest
+	 */
+	@Deprecated
+	LUCENE_36,
+
+	/**
+	 * Match settings and bugs in Lucene's 3.6 release.
+	 * 
+	 * @deprecated (4.1) Use latest
+	 */
+	@Deprecated
+	LUCENE_40,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.1 release.
+	 * 
+	 * @deprecated (4.2) Use latest
+	 */
+	@Deprecated
+	LUCENE_41,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.2 release.
+	 * 
+	 * @deprecated (4.3) Use latest
+	 */
+	@Deprecated
+	LUCENE_42,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.3 release.
+	 * 
+	 * @deprecated (4.4) Use latest
+	 */
+	@Deprecated
+	LUCENE_43,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.4 release.
+	 * 
+	 * @deprecated (4.5) Use latest
+	 */
+	@Deprecated
+	LUCENE_44,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.5 release.
+	 * 
+	 * @deprecated (4.6) Use latest
+	 */
+	@Deprecated
+	LUCENE_45,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.6 release.
+	 * 
+	 * @deprecated (4.7) Use latest
+	 */
+	@Deprecated
+	LUCENE_46,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.7 release.
+	 * 
+	 * @deprecated (4.8) Use latest
+	 */
+	@Deprecated
+	LUCENE_47,
+
+	/**
+	 * Match settings and bugs in Lucene's 4.8 release.
+	 * <p>
+	 * Use this to get the latest &amp; greatest settings, bug fixes, etc, for
+	 * Lucene.
+	 */
+	LUCENE_48,
+
+	/* Add new constants for later versions **here** to respect order! */
+
+	/**
+	 * <p>
+	 * <b>WARNING</b>: if you use this setting, and then upgrade to a newer
+	 * release of Lucene, sizable changes may happen. If backwards compatibility
+	 * is important then you should instead explicitly specify an actual
+	 * version.
+	 * <p>
+	 * If you use this constant then you may need to <b>re-index all of your
+	 * documents</b> when upgrading Lucene, as the way text is indexed may have
+	 * changed. Additionally, you may need to <b>re-test your entire
+	 * application</b> to ensure it behaves as expected, as some defaults may
+	 * have changed and may break functionality in your application.
+	 * 
+	 * @deprecated Use an actual version instead.
+	 */
+	@Deprecated
+	LUCENE_CURRENT;
+
+	public boolean onOrAfter(Version other) {
+		return compareTo(other) >= 0;
+	}
+
+	public static Version parseLeniently(String version) {
+		String parsedMatchVersion = version.toUpperCase(Locale.ROOT);
+		return Version.valueOf(parsedMatchVersion.replaceFirst("^(\\d)\\.(\\d)$", "LUCENE_$1$2"));
+	}
+}

src/main/java/org/genesys2/server/model/elastic/AccessionEsTrait.java

+package org.genesys2.server.model.elastic;
+
+import java.math.BigDecimal;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.genesys2.server.model.genesys.ExperimentTrait;
+import org.genesys2.server.model.genesys.Method;
+import org.springframework.data.annotation.Id;
+import org.springframework.data.annotation.Version;
+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 org.springframework.data.elasticsearch.annotations.Parent;
+
+@Document(indexName = "genesys", type = "trait", refreshInterval = "-1")
+public class AccessionEsTrait {
+	private static final Logger LOG = Logger.getLogger(AccessionDetails.class);
+
+	@Id
+	private Long id;
+	@Version
+	private Long version;
+
+	@Parent(type = "mcpd")
+	private long accessionId;
+
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.Long)
+	private long methodId;
+
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private Set<String> sval = new HashSet<String>();
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.Long)
+	private Set<Long> ival = new HashSet<Long>();
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.Double)
+	private Set<Double> dval = new HashSet<Double>();
+
+	public static List<AccessionEsTrait> traits(List<Method> listMethods, Map<Long, List<ExperimentTrait>> accessionTraitValues) {
+		ArrayList<AccessionEsTrait> accessionEsTraits = new ArrayList<AccessionEsTrait>();
+
+		if (listMethods == null || listMethods.isEmpty())
+			return accessionEsTraits;
+		if (accessionTraitValues == null || accessionTraitValues.isEmpty())
+			return accessionEsTraits;
+
+		for (Method m : listMethods) {
+			List<ExperimentTrait> vals = accessionTraitValues.get(m.getId());
+			if (vals != null && !vals.isEmpty())
+				accessionEsTraits.add(AccessionEsTrait.from(m, vals));
+		}
+		return accessionEsTraits;
+	}
+
+	public static AccessionEsTrait from(Method m, List<ExperimentTrait> vals) {
+		AccessionEsTrait t = new AccessionEsTrait();
+		t.methodId = m.getId();
+
+		t.sval = new HashSet<String>();
+		for (ExperimentTrait et : vals) {
+			Object value = et.getValue();
+			if (et == null || value == null)
+				continue;
+
+			if (value instanceof String)
+				t.sval.add((String) value);
+			else if (value instanceof Integer)
+				t.ival.add(((Integer) value).longValue());
+			else if (value instanceof Long)
+				t.ival.add((Long) value);
+			else if (value instanceof Double)
+				t.dval.add((Double) value);
+			else if (value instanceof Float)
+				t.dval.add(((Float) value).doubleValue());
+			else if (value instanceof BigDecimal)
+				t.dval.add(((BigDecimal) value).doubleValue());
+			else
+				LOG.warn("Unsupported value type " + value.getClass());
+		}
+
+		return t;
+	}
+
+	public Long getId() {
+		return id;
+	}
+
+	public void setId(Long id) {
+		this.id = id;
+	}
+
+	public Long getVersion() {
+		return version;
+	}
+
+	public void setVersion(Long version) {
+		this.version = version;
+	}
+
+	public long getAccessionId() {
+		return accessionId;
+	}
+
+	public void setAccessionId(long accessionId) {
+		this.accessionId = accessionId;
+	}
+
+	public long getMethodId() {
+		return methodId;
+	}
+
+	public void setMethodId(long methodId) {
+		this.methodId = methodId;
+	}
+
+	public Set<String> getSval() {
+		return sval;
+	}
+
+	public void setSval(Set<String> sval) {
+		this.sval = sval;
+	}
+
+	public Set<Long> getIval() {
+		return ival;
+	}
+
+	public void setIval(Set<Long> ival) {
+		this.ival = ival;
+	}
+
+	public Set<Double> getDval() {
+		return dval;
+	}
+
+	public void setDval(Set<Double> dval) {
+		this.dval = dval;
+	}
+
+}
\ No newline at end of file

src/main/java/org/genesys2/server/model/elastic/Alias.java

+package org.genesys2.server.model.elastic;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.AccessionAlias;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldIndex;
+import org.springframework.data.elasticsearch.annotations.FieldType;
+
+public class Alias {
+
+	private String name;
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private String lang;
+	private String usedBy;
+
+	public static Alias from(AccessionAlias aa) {
+		Alias a = new Alias();
+		a.name = aa.getName();
+		a.lang = StringUtils.defaultIfBlank(aa.getLang(), null);
+		a.usedBy = StringUtils.defaultIfBlank(aa.getUsedBy(), null);
+		return a;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getLang() {
+		return lang;
+	}
+
+	public void setLang(String lang) {
+		this.lang = lang;
+	}
+
+	public String getUsedBy() {
+		return usedBy;
+	}
+
+	public void setUsedBy(String usedBy) {
+		this.usedBy = usedBy;
+	}
+
+}
\ No newline at end of file

src/main/java/org/genesys2/server/model/elastic/Collect.java

+package org.genesys2.server.model.elastic;
+
+import java.util.Date;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
+
+public class Collect {
+
+	public String collCode;
+	@Field(searchAnalyzer = "keyword", type = FieldType.String)
+	public String collDate;
+	public String collInstAddr;
+	public String collMissId;
+	public String collName;
+	@Field(searchAnalyzer = "keyword", type = FieldType.String)
+	public String collNumb;
+	public String collSite;
+	public Integer collSrc;
+	public Date collectingDate;
+
+	public static Collect from(AccessionCollect collect) {
+		if (collect == null)
+			return null;
+
+		Collect c = new Collect();
+		c.collCode = StringUtils.defaultIfBlank(collect.getCollCode(), null);
+		c.collDate = StringUtils.defaultIfBlank(collect.getCollDate(), null);
+		c.collInstAddr = StringUtils.defaultIfBlank(collect.getCollInstAddress(), null);
+		c.collMissId = StringUtils.defaultIfBlank(collect.getCollMissId(), null);
+		c.collName = StringUtils.defaultIfBlank(collect.getCollName(), null);
+		c.collNumb = StringUtils.defaultIfBlank(collect.getCollNumb(), null);
+		c.collSite = StringUtils.defaultIfBlank(collect.getCollSite(), null);
+		c.collSrc = collect.getCollSrc();
+		return c;
+	}
+
+}
\ No newline at end of file

src/main/java/org/genesys2/server/model/elastic/Country.java

+package org.genesys2.server.model.elastic;
+
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldIndex;
+import org.springframework.data.elasticsearch.annotations.FieldType;
+
+public class Country {
+
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private String iso3;
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private String iso2;
+	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
+	private String name;
+
+	public static Country from(org.genesys2.server.model.impl.Country country) {
+		Country c = new Country();
+		if (country != null) {
+			c.iso3 = country.getCode3();
+			c.iso2 = country.getCode2();
+			c.name = country.getName();
+		}
+		return c;
+	}
+
+	public String getIso3() {
+		return iso3;
+	}
+
+	public void setIso3(String iso3) {
+		this.iso3 = iso3;
+	}
+
+	public String getIso2() {
+		return iso2;
+	}
+
+	public void setIso2(String iso2) {
+		this.iso2 = iso2;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+	
+	
+}
\ No newline at end of file

src/main/java/org/genesys2/server/model/elastic/Geo.java

+package org.genesys2.server.model.elastic;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.AccessionGeo;
+
+public class Geo {
+
+	private String method;
+	private Double uncertainty;
+	private Double latitude;
+	private Double longitude;
+	private Double[] coordinates;
+	private Double elevation;
+	private String datum;
+
+	public static Geo from(AccessionGeo ag) {