Retrieving selected _source fields from a search using Java API

Output_Java.txt

{"query":{"field":{"organism_id":1}}}
region1
{"uniqueName":"region1","organism_id":1,"sequence":"atgc"}
region2
{"uniqueName":"region2","organism_id":1,"sequence":"atgcatgc"}
region3
{"uniqueName":"region3","organism_id":1,"sequence":"atgcatgcatgc"}
{"query":{"field":{"organism_id":1}},"fields":["uniqueName","organism_id"]}
region1
null
region2
null
region3
null

Output_ommand_line.json

{
  "took" : 400,
  "timed_out" : false,
  "_shards" : {
    "total" : 5,
    "successful" : 5,
    "failed" : 0
  },
  "hits" : {
    "total" : 3,
    "max_score" : 1.0,
    "hits" : [ {
      "_index" : "annotations",
      "_type" : "region",
      "_id" : "region1",
      "_score" : 1.0,
      "fields" : {
        "organism_id" : 1,
        "uniqueName" : "region1"
      }
    }, {
      "_index" : "annotations",
      "_type" : "region",
      "_id" : "region2",
      "_score" : 1.0,
      "fields" : {
        "organism_id" : 1,
        "uniqueName" : "region2"
      }
    }, {
      "_index" : "annotations",
      "_type" : "region",
      "_id" : "region3",
      "_score" : 1.0,
      "fields" : {
        "organism_id" : 1,
        "uniqueName" : "region3"
      }
    } ]
  }
}

search_on_command_line.sh

curl -XGET 'http://localhost:9200/annotations/region/_search?pretty=true' -d '{"query":{"field":{"organism_id":1}},"fields":["uniqueName","organism_id"]}'

TestES.java

package org.genedb.test;

import java.io.IOException;

import org.elasticsearch.ElasticSearchException;
import org.elasticsearch.action.search.SearchResponse;
import org.elasticsearch.client.action.search.SearchRequestBuilder;
import org.elasticsearch.client.transport.TransportClient;
import org.elasticsearch.index.query.xcontent.FieldQueryBuilder;
import org.elasticsearch.index.query.xcontent.QueryBuilders;
import org.elasticsearch.search.SearchHit;
import org.elasticsearch.search.SearchHits;
import org.elasticsearch.client.Client;
import org.elasticsearch.common.transport.InetSocketTransportAddress;
import org.elasticsearch.common.xcontent.ToXContent;
import org.elasticsearch.common.xcontent.json.JsonXContent;

import static org.elasticsearch.common.xcontent.XContentFactory.*;

public class TestES {

	Client client;
	
	public static void main(String[] args) throws ElasticSearchException, IOException {
		TestES test = new TestES();
		
		test.index("region1", 1, "atgc");
		test.index("region2", 1, "atgcatgc");
		test.index("region3", 1, "atgcatgcatgc");
		
		// works, will bring back the source
		test.search(1, null);
		
		// specifying fields results in an empty source
		test.search(1, new String[]{"uniqueName", "organism_id"});
		
	}
	
	TestES() {
		client = new TransportClient().addTransportAddress(new InetSocketTransportAddress("localhost", 9300));
	}
	
	void index(String key, int organism_id, String sequence) throws ElasticSearchException, IOException {
		client.prepareIndex("annotations", "region", key)
        .setSource(jsonBuilder()
                    .startObject()
                        .field("uniqueName", key)
                        .field("organism_id", organism_id)
                        .field("sequence", sequence)
                    .endObject()
                  )
        .execute()
        .actionGet();
	}
	
	void search(int organism_id, String[] fields) {
		
		FieldQueryBuilder organismQuery = 
			QueryBuilders.fieldQuery("organism_id", organism_id);
		
		
		SearchRequestBuilder srb = client
			.prepareSearch("annotations")
			.setTypes("region")
			.setQuery(organismQuery);
		
		// if any fields are specified, the source is not returned
		if (fields != null) {
			srb.addFields(fields);
		}
		
		System.out.println(toString(srb.internalBuilder()));
		
		SearchResponse response = srb.execute()
			.actionGet();
		
		SearchHits hits = response.getHits();
		
		for (SearchHit hit : hits) {
			
			// always returns fine
			System.out.println(hit.getId());
			
			// will be null if any fields specified
			System.out.println(hit.sourceAsString());
		}
	}
	
	static String toString(ToXContent tmp) {
		try {
			return tmp.toXContent(JsonXContent.unCachedContentBuilder(),
							ToXContent.EMPTY_PARAMS).prettyPrint().string();
		} catch (Exception ex) {
			return "<ERROR:" + ex.getMessage() + ">";
		}
	}
	
}