package gov.nih.ncgc.bard.search;
import gov.nih.ncgc.bard.entity.Assay;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServer;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.impl.CommonsHttpSolrServer;
import org.apache.solr.client.solrj.response.FacetField;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.net.MalformedURLException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
/**
* Full text search for assay entities.
*
* @author Rajarshi Guha
*/
public class AssaySearch extends SolrSearch {
private final String HL_FIELD = "text";
private final String PKEY_ASSAY_DOC = "bardAssayId";
Logger log;
public AssaySearch(String query, String coreName) {
super(query);
CORE_NAME = coreName;
log = LoggerFactory.getLogger(this.getClass());
try {
db.closeConnection();
} catch (SQLException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
}
public void run(boolean detailed, String filter, Integer top, Integer skip) throws MalformedURLException, SolrServerException {
facets = new ArrayList<Facet>();
results = new SearchResult();
SolrServer solr = new CommonsHttpSolrServer
(getSolrURL() + CORE_NAME);
SolrQuery sq = new SolrQuery(query);
sq = setFilterQueries(sq, filter);
sq.setRows(10000);
sq.setShowDebugInfo(true);
sq.setFacet(true);
sq.setFacetMinCount(1);
QueryResponse response = solr.query(sq);
List<SolrDocument> docs = getHighlightedDocuments(response, PKEY_ASSAY_DOC, HL_FIELD);
// get facet counts
long start = System.currentTimeMillis();
// pull in field facets
List<FacetField> solrf = response.getFacetFields();
for (FacetField f : solrf) {
Facet bardFacet = new Facet(f.getName());
List<FacetField.Count> values = f.getValues();
if (values != null) {
for (FacetField.Count value : values) bardFacet.counts.put(value.getName(), (int) value.getCount());
}
facets.add(bardFacet);
}
long end = System.currentTimeMillis();
log.info("Facet summary calculated in " + (end - start) / 1000.0 + "s");
List<Long> aids = new ArrayList<Long>();
for (SolrDocument doc : docs) {
Object id = doc.getFieldValue(PKEY_ASSAY_DOC);
try {
long aid = Long.parseLong(id.toString());
if (aid > 0l) {
aids.add(aid);
}
} catch (Exception ex) {
log.warn("Bogus bardAssayid " + id);
}
}
SearchMeta meta = new SearchMeta();
meta.setNhit(response.getResults().getNumFound());
meta.setFacets(facets);
meta.setQueryTime(response.getQTime());
meta.setElapsedTime(response.getElapsedTime());
try {
putEtag(aids, Assay.class);
} catch (Exception e) {
log.error("Can't process ETag", e);
}
// only return the requested number of docs, from the requested starting point
// and generate reduced representation if required
//
// Also extract the matching field names for the docs we do return
Map<String, String> xplainMap = response.getExplainMap();
Map<String, Map<String, Object>> matchFields = new HashMap<String, Map<String, Object>>();
Map<String, Float> scores = new LinkedHashMap<String, Float>(); // to maintain doc id ordering
// first set up field match details & document scores
int size = Math.min(skip + top, docs.size());
for (int i = skip; i < size; i++) {
SolrDocument doc = docs.get(i);
String assayId = (String) doc.getFieldValue(PKEY_ASSAY_DOC);
Map<String, Object> value = new HashMap<String, Object>();
List<String> fns = SearchUtil.getMatchingFieldNames(xplainMap.get(assayId));
for (String fn : fns) {
Object obj = doc.getFieldValue(fn);
value.put(fn, obj);
}
matchFields.put(assayId, value);
scores.put(assayId, (Float) doc.getFieldValue("score"));
}
meta.setMatchingFields(matchFields);
meta.setScores(scores);
List ret;
if (!detailed) {
ret = copyRange(docs, skip, top, detailed, PKEY_ASSAY_DOC, "name");
} else {
ret = new ArrayList();
try {
for (int i = skip; i < size; i++) {
SolrDocument doc = docs.get(i);
String assayId = (String) doc.getFieldValue(PKEY_ASSAY_DOC);
Assay a = db.getAssayByAid(Long.parseLong(assayId));
if (a != null) ret.add(a);
}
db.closeConnection();
} catch (SQLException e) {
e.printStackTrace();
}
}
results.setDocs(ret);
results.setMetaData(meta);
}
}