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package eu.dnetlib.data.dedup;
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import java.io.IOException;
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import java.util.*;
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import java.util.stream.Collectors;
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import javax.annotation.Resource;
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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.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.transform.OafEntityMerger;
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import eu.dnetlib.data.transform.SolrProtoMapper;
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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.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.modular.ui.dedup.SimilarityGroup;
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import eu.dnetlib.pace.config.DedupConfig;
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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.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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public class DedupIndexDAO {
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private static final Log log = LogFactory.getLog(DedupIndexDAO.class);
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private static final String ID_PREFIX_REGEX = "^\\d\\d\\|";
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private static final Map<String, Map<String, String>> paths = Maps.newHashMap();
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static {
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paths.put("result", new HashMap<>());
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paths.put("organization", new HashMap<>());
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paths.put("person", new HashMap<>());
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paths.get("result").put("provenance", "collectedfrom/value");
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paths.get("organization").put("provenance", "collectedfrom/value");
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paths.get("person").put("provenance", "collectedfrom/value");
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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/metadata/author/fullname");
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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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@Resource
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private UniqueServiceLocator serviceLocator;
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/**
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* The index client factory.
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*/
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@Autowired
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private ResolvingIndexClientFactory indexClientFactory;
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private IndexClient indexClient = null;
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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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public OafResult search(final String type, final String userQuery, final String actionSet, final int start, final int rows, final String fields)
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throws Exception {
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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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}
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public OafResult searchById(final String actionSet, final String type, final String objidentifier, 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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public boolean commit(final SimilarityGroup group) throws Exception {
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int commitStatus = 0;
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int addStatus = 0;
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log.info("starting index update");
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final CloudSolrServer solrServer = getSolrServer();
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try {
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final SolrProtoMapper mapper = initProtoMapper();
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final Function<Oaf, SolrInputDocument> oaf2solr = oaf2solr(group, mapper);
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final List<SolrInputDocument> buffer = Lists.newLinkedList();
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// mark as deleted all the documents in the group
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final List<Oaf> groupDocs = markDeleted(asOafBuilder(parseBase64(queryIndex(group.getGroup(), group.getActionSet()))));
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buffer.addAll(asIndexDocs(oaf2solr, groupDocs));
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// elect a new representative
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final SolrInputDocument newRoot = oaf2solr.apply(OafEntityMerger.merge(getDedupConf(group), newRootId(group), groupDocs).build());
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final String newRootId = (String) newRoot.getFieldValue("objidentifier");
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// newRoot.setField("actionset", dedupConf.getWf().getConfigurationId());
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buffer.add(newRoot);
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// mark as non deleted the documents taken away from the group
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final List<Oaf> dissimDocs = markUnDeleted(asOafBuilder(parseBase64(queryIndex(unique(group.getDissimilar()), group.getActionSet()))));
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buffer.addAll(asIndexDocs(oaf2solr, dissimDocs));
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log.debug(String.format("adding %d documents to index %s", buffer.size(), dedupIndexCollection));
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// add the changes to the server
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addStatus = solrServer.add(buffer).getStatus();
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log.debug("solr add status: " + addStatus);
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// delete the old representatives, avoiding to remove the current one (if it didn't change)
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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(), rootId -> !rootId.equals(newRootId))) {
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solrServer.deleteById(mapper.getRecordId(rootId, group.getActionSet()));
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}
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commitStatus = solrServer.commit().getStatus();
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log.debug("solr commit status: " + commitStatus);
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} finally {
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solrServer.shutdown();
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}
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return (addStatus == 0) && (commitStatus == 0);
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}
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private Iterable<Oaf> toOaf(final LookupResponse rsp) {
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return Iterables.transform(rsp.getRecords(), getXml2OafFunction());
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}
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private Iterable<Oaf> parseBase64(final Iterable<String> r) {
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return Iterables.transform(r, getXml2OafFunction());
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}
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private Function<String, Oaf> getXml2OafFunction() {
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return s -> {
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// final String base64 = s.replaceAll("<record.*>", "").replace("</record>", "");
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final String base64 = StringUtils.substringBefore(StringUtils.substringAfter(s, ">"), "<");
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try {
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final byte[] oafBytes = Base64.decodeBase64(base64);
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final Oaf oaf = OafDecoder.decode(oafBytes).getOaf();
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return oaf;
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} catch (final Throwable e) {
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throw new IllegalArgumentException("unable to decode base64 encoded Oaf object: " + base64);
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}
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};
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}
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private SolrProtoMapper initProtoMapper() throws DocumentException, ISLookUpException, ISLookUpDocumentNotFoundException {
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return new SolrProtoMapper(
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serviceLocator
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.getService(ISLookUpService.class)
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.getResourceProfileByQuery(
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"collection('')//RESOURCE_PROFILE[.//RESOURCE_TYPE/@value = 'MDFormatDSResourceType' and .//NAME='" + indexFormat
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+ "']//LAYOUT[@name='index']/FIELDS"));
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}
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private CloudSolrServer getSolrServer() {
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final String zk = getIndexSolrUrlZk();
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log.info(String.format("initializing solr client for collection %s, zk url: %s", dedupIndexCollection, zk));
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final CloudSolrServer solrServer = new CloudSolrServer(zk);
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solrServer.setDefaultCollection(dedupIndexCollection);
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return solrServer;
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}
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private String getIndexSolrUrlZk() {
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try {
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return getResourceProfileByQuery(
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"for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()");
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} catch (final ISLookUpException e) {
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throw new IllegalStateException("unable to read solr ZK url from service profile", e);
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}
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}
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private String getResourceProfileByQuery(final String xquery) throws ISLookUpException {
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log.debug("quering for service property: " + xquery);
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final String res = serviceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xquery);
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if (StringUtils.isBlank(res)) throw new IllegalStateException("unable to find unique service property, xquery: " + xquery);
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return res;
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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 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 = oaf.getEntity().getChildrenList().stream()
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.map(e -> e.getId())
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.map(s -> cleanId(s))
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.collect(Collectors.toList());
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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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private String cleanId(final String id) {
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return id.replaceFirst(ID_PREFIX_REGEX, "");
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}
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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 Iterable<String> queryIndex(final Iterable<String> ids, final String actionset) {
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return Iterables.transform(ids, id -> {
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260 |
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try {
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final String cql = "objidentifier exact \"" + id + "\" and actionset exact \"" + actionset + "\"";
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final LookupResponse rsp = getIndexClient().lookup(cql, null, 0, 1);
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log.debug(String.format("query index for id '%s', found '%d'", id, rsp.getTotal()));
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return Iterables.getOnlyElement(rsp.getRecords());
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} catch (final Throwable e) {
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log.error(e);
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throw new RuntimeException("unable to query id: " + id, e);
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}
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});
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}
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private List<Oaf> markDeleted(final Iterable<Oaf.Builder> builders) {
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return Lists.newArrayList(Iterables.transform(builders, builder -> {
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// TODO add more changes to the Oaf object here as needed.
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builder.getDataInfoBuilder().setDeletedbyinference(true);
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return builder.build();
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}));
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}
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private List<Oaf> markUnDeleted(final Iterable<Oaf.Builder> builders) {
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return Lists.newArrayList(Iterables.transform(builders, builder -> {
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// TODO add more changes to the Oaf object here as needed.
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builder.getDataInfoBuilder().setDeletedbyinference(false);
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return builder.build();
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}));
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}
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private Iterable<Oaf.Builder> asOafBuilder(final Iterable<Oaf> oaf) {
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return Iterables.transform(oaf, oaf1 -> Oaf.newBuilder(oaf1));
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}
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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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}
|
298 |
|
|
|
299 |
|
|
private List<SolrInputDocument> asIndexDocs(final Function<Oaf, SolrInputDocument> mapper, final Iterable<Oaf> protos) {
|
300 |
|
|
return Lists.newArrayList(Iterables.transform(protos, mapper));
|
301 |
|
|
}
|
302 |
|
|
|
303 |
|
|
private Function<Oaf, SolrInputDocument> oaf2solr(final SimilarityGroup group, final SolrProtoMapper mapper) {
|
304 |
48920
|
claudio.at
|
return oaf -> {
|
305 |
|
|
try {
|
306 |
|
|
return mapper.map(oaf, group.getDate(), "", group.getActionSet());
|
307 |
|
|
} catch (final Throwable e) {
|
308 |
|
|
throw new IllegalArgumentException("unable to map proto to index document", e);
|
309 |
39358
|
claudio.at
|
}
|
310 |
|
|
};
|
311 |
|
|
}
|
312 |
|
|
|
313 |
|
|
private Set<String> unique(final Map<String, Set<String>> map) {
|
314 |
|
|
final Set<String> res = Sets.newHashSet();
|
315 |
|
|
for (final Set<String> ids : map.values()) {
|
316 |
|
|
res.addAll(ids);
|
317 |
|
|
}
|
318 |
|
|
|
319 |
|
|
return res;
|
320 |
|
|
}
|
321 |
|
|
|
322 |
|
|
private DedupConfig getDedupConf(final SimilarityGroup group) throws IOException {
|
323 |
|
|
final Map<String, String> config = Maps.newHashMap();
|
324 |
|
|
config.put("entityType", group.getEntityType().getType());
|
325 |
|
|
config.put("configurationId", group.getActionSet());
|
326 |
|
|
final DedupConfig dedupConf = DedupConfig.loadDefault(config);
|
327 |
|
|
return dedupConf;
|
328 |
|
|
}
|
329 |
|
|
|
330 |
|
|
}
|