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package eu.dnetlib.functionality.modular.ui.dedup;
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import java.io.IOException;
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import java.util.Collections;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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import javax.annotation.Resource;
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import org.apache.commons.codec.binary.Base64;
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import org.apache.commons.lang.StringUtils;
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import org.apache.commons.lang.exception.ExceptionUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.solr.client.solrj.impl.CloudSolrServer;
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import org.apache.solr.common.SolrInputDocument;
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import org.dom4j.DocumentException;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.stereotype.Controller;
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import org.springframework.web.bind.annotation.RequestBody;
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import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RequestParam;
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import org.springframework.web.bind.annotation.ResponseBody;
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import com.google.common.base.Function;
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import com.google.common.base.Joiner;
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import com.google.common.base.Predicate;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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import eu.dnetlib.data.mapreduce.util.OafDecoder;
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import eu.dnetlib.data.mapreduce.util.OafEntityDecoder;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.Oaf.Builder;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.transform.OafEntityMerger;
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import eu.dnetlib.data.transform.SolrProtoMapper;
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import eu.dnetlib.enabling.database.rmi.DatabaseService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.locators.UniqueServiceLocator;
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import eu.dnetlib.enabling.resultset.client.ResultSetClientFactory;
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import eu.dnetlib.functionality.index.client.IndexClient;
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import eu.dnetlib.functionality.index.client.IndexClientException;
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import eu.dnetlib.functionality.index.client.ResolvingIndexClientFactory;
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import eu.dnetlib.functionality.index.client.response.LookupResponse;
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import eu.dnetlib.functionality.index.solr.feed.InputDocumentFactory;
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import eu.dnetlib.functionality.modular.ui.AbstractAjaxController;
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import eu.dnetlib.miscutils.datetime.DateUtils;
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import eu.dnetlib.pace.config.DedupConfig;
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@Controller
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public class DedupServiceInternalController extends AbstractAjaxController {
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private static final String ID_PREFIX_REGEX = "^\\d\\d\\|";
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private static final Log log = LogFactory.getLog(DedupServiceInternalController.class);
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@Resource
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private UniqueServiceLocator serviceLocator;
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@Autowired
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private ResultSetClientFactory resultSetClientFactory;
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@Value("${dnet.dedup.db.name}")
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private String dbName;
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/** The index client factory. */
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@Autowired
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private ResolvingIndexClientFactory indexClientFactory;
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@Value("${dnet.dedup.index.format}")
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private String indexFormat;
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@Value("${dnet.dedup.index.collection}")
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private String dedupIndexCollection;
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private IndexClient indexClient = null;
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public class OafResult {
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private long total;
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private List<Map<String, String>> results;
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public OafResult(final long total, final List<Map<String, String>> results) {
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super();
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this.setTotal(total);
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this.setResults(results);
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}
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public long getTotal() {
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return total;
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}
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public void setTotal(final long total) {
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this.total = total;
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}
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public List<Map<String, String>> getResults() {
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return results;
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}
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public void setResults(final List<Map<String, String>> results) {
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this.results = results;
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}
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}
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@ResponseBody
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@RequestMapping(value = "/ui/dedup/lookupConfigurations.do")
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public Map<String, List<String>> lookupConfigurations() throws ISLookUpException {
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final Map<String, List<String>> res = Maps.newHashMap();
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final ISLookUpService lookUpService = serviceLocator.getService(ISLookUpService.class);
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final String listEntityTypesXQuery =
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"distinct-values(for $x in //RESOURCE_PROFILE["
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+ ".//RESOURCE_TYPE/@value = 'DedupOrchestrationDSResourceType' and "
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+ ".//CONFIGURATION/@enabled='true'] return $x//ENTITY/@name/string())";
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for (final String entityType : lookUpService.quickSearchProfile(listEntityTypesXQuery)) {
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final String xquery =
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String.format(
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"for $x in //RESOURCE_PROFILE[" +
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".//RESOURCE_TYPE/@value = 'DedupOrchestrationDSResourceType' and .//ENTITY/@name='%s' ] " +
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"return $x//ACTION_SET/@id/string()", entityType);
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res.put(entityType, lookUpService.quickSearchProfile(xquery));
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}
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return res;
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}
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@ResponseBody
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@RequestMapping(value = "/ui/dedup/search.do")
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public OafResult search(@RequestParam(value = "entityType", required = true) final String type,
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@RequestParam(value = "query", required = true) final String userQuery,
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@RequestParam(value = "actionSet", required = true) final String actionSet,
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@RequestParam(value = "start", required = true) final int start,
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@RequestParam(value = "rows", required = true) final int rows,
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@RequestParam(value = "fields", required = true) final String fields) throws Exception {
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try {
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final String cqlQuery =
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String.format("(>s=SOLR s.q.op=AND) and oaftype = %s and actionset exact \"%s\" and deletedbyinference = false and %s", type, actionSet,
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userQuery);
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final LookupResponse rsp = getIndexClient().lookup(cqlQuery, null, start, (start + rows) - 1);
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final List<String> fieldList = Lists.newLinkedList(Splitter.on(",").omitEmptyStrings().trimResults().split(fields));
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final List<Map<String, String>> resList = Lists.newLinkedList(Iterables.transform(toOaf(rsp), getOaf2FieldMapFunction(type, fieldList)));
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return new OafResult(rsp.getTotal(), resList);
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} catch (final Exception e) {
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log.error("search error", e);
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throw e;
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}
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}
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@ResponseBody
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@RequestMapping(value = "/ui/dedup/searchById.do")
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public OafResult searchById(@RequestParam(value = "actionSet", required = true) final String actionSet,
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@RequestParam(value = "entityType", required = true) final String type,
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@RequestParam(value = "objidentifier", required = true) final String objidentifier,
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@RequestParam(value = "fields", required = true) final List<String> fields) throws Exception {
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final String cqlQuery = "objidentifier exact \"" + objidentifier + "\" and actionset exact \"" + actionSet + "\"";
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final LookupResponse rsp = getIndexClient().lookup(cqlQuery, null, 0, 1);
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final Iterable<Oaf> oafList = toOaf(rsp);
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final List<Map<String, String>> resList = Lists.newLinkedList(Iterables.transform(oafList, getOaf2FieldMapFunction(type, fields)));
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return new OafResult(rsp.getTotal(), resList);
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}
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@ResponseBody
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@RequestMapping(value = "/ui/dedup/commit.do")
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public boolean addSimRels(@RequestBody(required = true) final SimilarityGroup group) throws Exception {
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try {
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if (StringUtils.isBlank(group.getActionSet())) throw new IllegalArgumentException("missing actionset");
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final DatabaseService dbService = serviceLocator.getService(DatabaseService.class);
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final String version = InputDocumentFactory.getParsedDateField(DateUtils.now_ISO8601());
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group.setId(UUID.randomUUID().toString());
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group.setDate(version);
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// relational DB update
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log.info("adding similarities: " + group.getGroup());
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updateGroupSql(dbService, group, version);
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log.info("adding dissimilarities: " + group.getDissimilar());
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dissimilaritiesSql(dbService, group);
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// index update
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log.info("starting index update");
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final CloudSolrServer solrServer = getSolrServer();
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final SolrProtoMapper mapper = initProtoMapper();
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final Function<Oaf, SolrInputDocument> oaf2solr = oaf2solr(version, group.getActionSet(), mapper);
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final List<SolrInputDocument> buffer = Lists.newLinkedList();
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final List<Oaf> groupDocs = Lists.newArrayList(markDeleted(asOafBuilder(parseBase64(queryIndex(group.getGroup(), group.getActionSet())))));
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buffer.addAll(Lists.newArrayList(asIndexDocs(oaf2solr, groupDocs)));
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final DedupConfig dedupConf = getDedupConfig(group);
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final SolrInputDocument newRoot = oaf2solr.apply(OafEntityMerger.merge(dedupConf, newRootId(group), groupDocs).build());
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// newRoot.setField("actionset", dedupConf.getWf().getConfigurationId());
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buffer.add(newRoot);
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final Set<String> dissimIds = getUniqueDissimilarIds(group.getDissimilar());
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final List<Oaf> dissimDocs =
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Lists.newArrayList(markUnDeleted(asOafBuilder(parseBase64(queryIndex(dissimIds, group.getActionSet())))));
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buffer.addAll(Lists.newArrayList(asIndexDocs(oaf2solr, dissimDocs)));
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log.debug(String.format("adding %d documents to index %s", buffer.size(), dedupIndexCollection));
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final int addStatus = solrServer.add(buffer).getStatus();
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log.debug("solr add status: " + addStatus);
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log.debug(String.format("deleting %d documents from index %s", group.getRootIds().size(), dedupIndexCollection));
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for (final String rootId : Iterables.filter(group.getRootIds(), new Predicate<String>() {
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final String newRootId = (String) newRoot.getFieldValue("objidentifier");
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@Override
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public boolean apply(final String rootId) {
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return !rootId.equals(newRootId);
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}
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})) {
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solrServer.deleteById(mapper.getRecordId(rootId, group.getActionSet()));
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}
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final int commitStatus = solrServer.commit().getStatus();
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log.debug("solr commit status: " + commitStatus);
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return (addStatus == 0) && (commitStatus == 0);
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} catch (final Exception e) {
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log.error(e);
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throw e;
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}
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}
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private Set<String> getUniqueDissimilarIds(final Map<String, Set<String>> map) {
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final Set<String> res = Sets.newHashSet();
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for (final Set<String> ids : map.values()) {
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res.addAll(ids);
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}
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return res;
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}
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private DedupConfig getDedupConfig(final SimilarityGroup group) throws IOException {
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final Map<String, String> config = Maps.newHashMap();
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config.put("entityType", group.getEntityType().getType());
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config.put("configurationId", group.getActionSet());
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final DedupConfig dedupConf = DedupConfig.loadDefault(config);
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return dedupConf;
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}
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// helpers
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private IndexClient getIndexClient() throws IndexClientException, ISLookUpDocumentNotFoundException, ISLookUpException {
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if (indexClient == null) {
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indexClient = indexClientFactory.getClient(indexFormat, "index", "dedup", "solr");
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}
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return indexClient;
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}
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private static Map<String, Map<String, String>> paths = Maps.newHashMap();
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static {
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paths.put("result", new HashMap<String, String>());
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paths.put("organization", new HashMap<String, String>());
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paths.put("person", new HashMap<String, String>());
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paths.get("result").put("title", "result/metadata/title/value");
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paths.get("result").put("dateofacceptance", "result/metadata/dateofacceptance/value");
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paths.get("result").put("description", "result/metadata/description/value");
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paths.get("result").put("author", "result/author/metadata/fullname/value");
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paths.get("organization").put("legalname", "organization/metadata/legalname/value");
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paths.get("organization").put("legalshortname", "organization/metadata/legalshortname/value");
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paths.get("organization").put("websiteurl", "organization/metadata/websiteurl/value");
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paths.get("organization").put("country", "organization/metadata/country/classid");
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paths.get("person").put("fullname", "person/metadata/fullname/value");
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}
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private Function<Oaf, Map<String, String>> getOaf2FieldMapFunction(final String type, final List<String> fields) {
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return new Function<Oaf, Map<String, String>>() {
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301
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302
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@Override
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public Map<String, String> apply(final Oaf oaf) {
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final OafEntityDecoder ed = OafDecoder.decode(oaf).decodeEntity();
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final Map<String, String> res = Maps.newHashMap();
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final String oafId = cleanId(oaf.getEntity().getId());
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final List<String> idList = Lists.newArrayList(Iterables.transform(oaf.getEntity().getChildrenList(), new Function<OafEntity, String>() {
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@Override
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public String apply(final OafEntity e) {
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return cleanId(e.getId());
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}
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}));
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if (idList.isEmpty()) {
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idList.add(oafId);
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}
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res.put("id", oafId);
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res.put("idList", Joiner.on(",").join(idList));
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res.put("groupSize", idList.isEmpty() ? "1" : idList.size() + "");
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for (final String fieldName : fields) {
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res.put(fieldName, Joiner.on("; ").skipNulls().join(ed.getFieldValues(paths.get(type).get(fieldName))));
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}
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return res;
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}
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};
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}
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private String cleanId(final String id) {
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return id.replaceFirst(ID_PREFIX_REGEX, "");
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}
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334
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private String newRootId(final SimilarityGroup group) {
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return "dedup_wf_001::" + Collections.min(group.getGroup()).replaceFirst("^.*::", "");
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// else return Collections.min(group.getRootIds());
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}
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340
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private Iterable<SolrInputDocument> asIndexDocs(final Function<Oaf, SolrInputDocument> mapper, final Iterable<Oaf> protos) {
|
|
341
|
return Iterables.transform(protos, mapper);
|
|
342
|
}
|
|
343
|
|
|
344
|
private Function<Oaf, SolrInputDocument> oaf2solr(final String version, final String actionSetId, final SolrProtoMapper mapper) {
|
|
345
|
return new Function<Oaf, SolrInputDocument>() {
|
|
346
|
|
|
347
|
@Override
|
|
348
|
public SolrInputDocument apply(final Oaf oaf) {
|
|
349
|
try {
|
|
350
|
return mapper.map(oaf, version, "", actionSetId);
|
|
351
|
} catch (final Throwable e) {
|
|
352
|
throw new IllegalArgumentException("unable to map proto to index document", e);
|
|
353
|
}
|
|
354
|
}
|
|
355
|
};
|
|
356
|
}
|
|
357
|
|
|
358
|
private Iterable<String> queryIndex(final Iterable<String> ids, final String actionset) {
|
|
359
|
return Iterables.transform(ids, idToIndexDocumentMapper(actionset));
|
|
360
|
}
|
|
361
|
|
|
362
|
private Function<String, String> idToIndexDocumentMapper(final String actionset) {
|
|
363
|
return new Function<String, String>() {
|
|
364
|
|
|
365
|
@Override
|
|
366
|
public String apply(final String id) {
|
|
367
|
try {
|
|
368
|
final String cql = "objidentifier exact \"" + id + "\" and actionset exact \"" + actionset + "\"";
|
|
369
|
final LookupResponse rsp = getIndexClient().lookup(cql, null, 0, 1);
|
|
370
|
|
|
371
|
log.debug(String.format("query index for id '%s', found '%d'", id, rsp.getTotal()));
|
|
372
|
|
|
373
|
return Iterables.getOnlyElement(rsp.getRecords());
|
|
374
|
} catch (final Throwable e) {
|
|
375
|
log.error(e);
|
|
376
|
throw new RuntimeException("unable to query id: " + id, e);
|
|
377
|
}
|
|
378
|
}
|
|
379
|
};
|
|
380
|
}
|
|
381
|
|
|
382
|
private Iterable<Oaf> parseBase64(final Iterable<String> r) {
|
|
383
|
return Iterables.transform(r, getXml2OafFunction());
|
|
384
|
}
|
|
385
|
|
|
386
|
private SolrProtoMapper initProtoMapper() throws DocumentException, ISLookUpException, ISLookUpDocumentNotFoundException {
|
|
387
|
return new SolrProtoMapper(
|
|
388
|
serviceLocator
|
|
389
|
.getService(ISLookUpService.class)
|
|
390
|
.getResourceProfileByQuery(
|
|
391
|
"collection('')//RESOURCE_PROFILE[.//RESOURCE_TYPE/@value = 'MDFormatDSResourceType' and .//NAME='" + indexFormat
|
|
392
|
+ "']//LAYOUT[@name='index']/FIELDS"));
|
|
393
|
}
|
|
394
|
|
|
395
|
private Iterable<Oaf> markDeleted(final Iterable<Oaf.Builder> builders) {
|
|
396
|
return Iterables.transform(builders, new Function<Oaf.Builder, Oaf>() {
|
|
397
|
|
|
398
|
@Override
|
|
399
|
public Oaf apply(final Oaf.Builder builder) {
|
|
400
|
// TODO add more changes to the Oaf object here as needed.
|
|
401
|
builder.getDataInfoBuilder().setDeletedbyinference(true);
|
|
402
|
return builder.build();
|
|
403
|
}
|
|
404
|
});
|
|
405
|
}
|
|
406
|
|
|
407
|
private Iterable<Oaf> markUnDeleted(final Iterable<Oaf.Builder> builders) {
|
|
408
|
return Iterables.transform(builders, new Function<Oaf.Builder, Oaf>() {
|
|
409
|
|
|
410
|
@Override
|
|
411
|
public Oaf apply(final Oaf.Builder builder) {
|
|
412
|
// TODO add more changes to the Oaf object here as needed.
|
|
413
|
builder.getDataInfoBuilder().setDeletedbyinference(false);
|
|
414
|
return builder.build();
|
|
415
|
}
|
|
416
|
});
|
|
417
|
}
|
|
418
|
|
|
419
|
private Iterable<Oaf.Builder> asOafBuilder(final Iterable<Oaf> oaf) {
|
|
420
|
return Iterables.transform(oaf, new Function<Oaf, Oaf.Builder>() {
|
|
421
|
|
|
422
|
@Override
|
|
423
|
public Builder apply(final Oaf oaf) {
|
|
424
|
return Oaf.newBuilder(oaf);
|
|
425
|
}
|
|
426
|
});
|
|
427
|
}
|
|
428
|
|
|
429
|
private Function<String, Oaf> getXml2OafFunction() {
|
|
430
|
return new Function<String, Oaf>() {
|
|
431
|
|
|
432
|
@Override
|
|
433
|
public Oaf apply(final String s) {
|
|
434
|
// final String base64 = s.replaceAll("<record.*>", "").replace("</record>", "");
|
|
435
|
final String base64 = StringUtils.substringBefore(StringUtils.substringAfter(s, ">"), "<");
|
|
436
|
try {
|
|
437
|
final byte[] oaf = Base64.decodeBase64(base64);
|
|
438
|
return OafDecoder.decode(oaf).getOaf();
|
|
439
|
} catch (final Throwable e) {
|
|
440
|
throw new IllegalArgumentException("unable to decode base64 encoded Oaf object: " + base64);
|
|
441
|
}
|
|
442
|
}
|
|
443
|
};
|
|
444
|
}
|
|
445
|
|
|
446
|
private Iterable<Oaf> toOaf(final LookupResponse rsp) {
|
|
447
|
return Iterables.transform(rsp.getRecords(), getXml2OafFunction());
|
|
448
|
}
|
|
449
|
|
|
450
|
private void updateGroupSql(final DatabaseService dbService, final SimilarityGroup group, final String version) throws Exception {
|
|
451
|
for (final String id : group.getGroup()) {
|
|
452
|
// sql.append(String.format("DELETE FROM entities WHERE objidentifier = '%s'; ", id));
|
|
453
|
safeUpdateSql(dbService, String.format("DELETE FROM similarity_groups WHERE objidentifier = '%s'; ", id));
|
|
454
|
}
|
|
455
|
final String type = group.getEntityType().getType();
|
|
456
|
safeUpdateSql(dbService,
|
|
457
|
String.format("INSERT INTO groups(id, entitytype, date, actionsetid) VALUES('%s', '%s', '%s', '%s'); ", group.getId(), type, version,
|
|
458
|
group.getActionSet()));
|
|
459
|
for (final String id : group.getGroup()) {
|
|
460
|
if (!dbService.contains(dbName, "entities", "id", id)) {
|
|
461
|
safeUpdateSql(dbService, String.format("INSERT INTO entities(id, entitytype) VALUES('%s', '%s'); ", id, type));
|
|
462
|
}
|
|
463
|
|
|
464
|
// throw new Exception("id already defined in a similarity group.");
|
|
465
|
safeUpdateSql(dbService, String.format("INSERT INTO similarity_groups(groupid, objidentifier) VALUES('%s', '%s'); ", group.getId(), id));
|
|
466
|
}
|
|
467
|
}
|
|
468
|
|
|
469
|
private void dissimilaritiesSql(final DatabaseService dbService, final SimilarityGroup group) {
|
|
470
|
|
|
471
|
final String type = group.getEntityType().getType();
|
|
472
|
|
|
473
|
for (final Entry<String, Set<String>> e : group.getDissimilar().entrySet()) {
|
|
474
|
if (!dbService.contains(dbName, "entities", "id", e.getKey())) {
|
|
475
|
safeUpdateSql(dbService, String.format("INSERT INTO entities(id, entitytype) VALUES('%s', '%s'); ", e.getKey(), type));
|
|
476
|
}
|
|
477
|
for (final String id : e.getValue()) {
|
|
478
|
if (!dbService.contains(dbName, "entities", "id", id)) {
|
|
479
|
safeUpdateSql(dbService, String.format("INSERT INTO entities(id, entitytype) VALUES('%s', '%s'); ", id, type));
|
|
480
|
}
|
|
481
|
}
|
|
482
|
}
|
|
483
|
|
|
484
|
for (final Entry<String, Set<String>> e : group.getDissimilar().entrySet()) {
|
|
485
|
for (final String id : e.getValue()) {
|
|
486
|
safeUpdateSql(dbService,
|
|
487
|
String.format("INSERT INTO dissimilarities(id1, id2, actionsetid) VALUES('%s', '%s', '%s'); ", e.getKey(), id, group.getActionSet()));
|
|
488
|
}
|
|
489
|
}
|
|
490
|
}
|
|
491
|
|
|
492
|
private boolean safeUpdateSql(final DatabaseService dbService, final String sql) {
|
|
493
|
try {
|
|
494
|
log.info(sql);
|
|
495
|
return dbService.updateSQL(dbName, sql);
|
|
496
|
} catch (final Throwable e) {
|
|
497
|
log.error(e.getMessage());
|
|
498
|
log.debug(ExceptionUtils.getFullStackTrace(e));
|
|
499
|
return false;
|
|
500
|
}
|
|
501
|
}
|
|
502
|
|
|
503
|
private CloudSolrServer getSolrServer() {
|
|
504
|
final String zk = getIndexSolrUrlZk();
|
|
505
|
log.info(String.format("initializing solr client for collection %s, zk url: %s", dedupIndexCollection, zk));
|
|
506
|
final CloudSolrServer solrServer = new CloudSolrServer(zk);
|
|
507
|
solrServer.setDefaultCollection(dedupIndexCollection);
|
|
508
|
|
|
509
|
return solrServer;
|
|
510
|
}
|
|
511
|
|
|
512
|
private String getIndexSolrUrlZk() {
|
|
513
|
try {
|
|
514
|
return getResourceProfileByQuery("for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()");
|
|
515
|
} catch (final ISLookUpException e) {
|
|
516
|
throw new IllegalStateException("unable to read solr ZK url from service profile", e);
|
|
517
|
}
|
|
518
|
}
|
|
519
|
|
|
520
|
private String getResourceProfileByQuery(final String xquery) throws ISLookUpException {
|
|
521
|
log.debug("quering for service property: " + xquery);
|
|
522
|
final String res = serviceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xquery);
|
|
523
|
if (StringUtils.isBlank(res)) throw new IllegalStateException("unable to find unique service property, xquery: " + xquery);
|
|
524
|
return res;
|
|
525
|
}
|
|
526
|
|
|
527
|
}
|