Examples with SearchResultBuilder eu.etaxonomy.cdm.api.service.search.SearchResultBuilder used on opensource projects

Example 1 with SearchResultBuilder

use of eu.etaxonomy.cdm.api.service.search.SearchResultBuilder in project cdmlib by cybertaxonomy.

the class TaxonServiceImpl method findTaxaAndNamesByFullText.

@Override
public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(EnumSet<TaxaAndNamesSearchMode> searchModes, String queryString, Classification classification, TaxonNode subtree, Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> distributionStatus, List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException {
    // this requires building a special sort column by a special classBridge
    if (highlightFragments) {
        logger.warn("findTaxaAndNamesByFullText() : fragment highlighting is " + "currently not fully supported by this method and thus " + "may not work with common names and misapplied names.");
    }
    // convert sets to lists
    List<NamedArea> namedAreaList = null;
    List<PresenceAbsenceTerm> distributionStatusList = null;
    if (namedAreas != null) {
        namedAreaList = new ArrayList<>(namedAreas.size());
        namedAreaList.addAll(namedAreas);
    }
    if (distributionStatus != null) {
        distributionStatusList = new ArrayList<>(distributionStatus.size());
        distributionStatusList.addAll(distributionStatus);
    }
    // set default if parameter is null
    if (searchModes == null) {
        searchModes = EnumSet.of(TaxaAndNamesSearchMode.doTaxa);
    }
    // defined by prepare*Search methods
    if (orderHints == null) {
        orderHints = OrderHint.NOMENCLATURAL_SORT_ORDER.asList();
    }
    SortField[] sortFields = new SortField[orderHints.size()];
    int i = 0;
    for (OrderHint oh : orderHints) {
        sortFields[i++] = oh.toSortField();
    }
    // SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("id", SortField.STRING, false)};
    // SortField[] sortFields = new SortField[]{new SortField(NomenclaturalSortOrderBrigde.NAME_SORT_FIELD_NAME, SortField.STRING, false)};
    boolean addDistributionFilter = namedAreas != null && namedAreas.size() > 0;
    List<LuceneSearch> luceneSearches = new ArrayList<>();
    Map<CdmBaseType, String> idFieldMap = new HashMap<>();
    /*
          ======== filtering by distribution , HOWTO ========

           - http://www.javaranch.com/journal/2009/02/filtering-a-lucene-search.html
           - http://stackoverflow.com/questions/17709256/lucene-solr-using-complex-filters -> QueryWrapperFilter
          add Filter to search as http://lucene.apache.org/core/3_6_0/api/all/org/apache/lucene/search/Filter.html
          which will be put into a FilteredQuersy  in the end ?


          3. how does it work in spatial?
          see
           - http://www.nsshutdown.com/projects/lucene/whitepaper/locallucene_v2.html
           - http://www.infoq.com/articles/LuceneSpatialSupport
           - http://www.mhaller.de/archives/156-Spatial-search-with-Lucene.html
          ------------------------------------------------------------------------

          filter strategies:
          A) use a separate distribution filter per index sub-query/search:
           - byTaxonSyonym (query TaxaonBase):
               use a join area filter (Distribution -> TaxonBase)
           - byCommonName (query DescriptionElementBase): use an area filter on
               DescriptionElementBase !!! PROBLEM !!!
               This cannot work since the distributions are different entities than the
               common names and thus these are different lucene documents.
           - byMisaplliedNames (join query TaxonRelationship -> TaxonBase):
               use a join area filter (Distribution -> TaxonBase)

          B) use a common distribution filter for all index sub-query/searches:
           - use a common join area filter (Distribution -> TaxonBase)
           - also implement the byCommonName as join query (CommonName -> TaxonBase)
           PROBLEM in this case: we are losing the fragment highlighting for the
           common names, since the returned documents are always TaxonBases
        */
    /* The QueryFactory for creating filter queries on Distributions should
         * The query factory used for the common names query cannot be reused
         * for this case, since we want to only record the text fields which are
         * actually used in the primary query
         */
    QueryFactory distributionFilterQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(Distribution.class);
    Builder multiIndexByAreaFilterBuilder = new Builder();
    boolean includeUnpublished = searchModes.contains(TaxaAndNamesSearchMode.includeUnpublished);
    // search for taxa or synonyms
    if (searchModes.contains(TaxaAndNamesSearchMode.doTaxa) || searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {
        @SuppressWarnings("rawtypes") Class<? extends TaxonBase> taxonBaseSubclass = TaxonBase.class;
        String className = null;
        if (searchModes.contains(TaxaAndNamesSearchMode.doTaxa) && !searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {
            taxonBaseSubclass = Taxon.class;
        } else if (!searchModes.contains(TaxaAndNamesSearchMode.doTaxa) && searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {
            className = "eu.etaxonomy.cdm.model.taxon.Synonym";
        }
        luceneSearches.add(prepareFindByFullTextSearch(taxonBaseSubclass, queryString, classification, subtree, className, includeUnpublished, languages, highlightFragments, sortFields));
        idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
        /* A) does not work!!!!
            if(addDistributionFilter){
                // in this case we need a filter which uses a join query
                // to get the TaxonBase documents for the DescriptionElementBase documents
                // which are matching the areas in question
                Query taxonAreaJoinQuery = createByDistributionJoinQuery(
                        namedAreaList,
                        distributionStatusList,
                        distributionFilterQueryFactory
                        );
                multiIndexByAreaFilter.add(new QueryWrapperFilter(taxonAreaJoinQuery), Occur.SHOULD);
            }
            */
        if (addDistributionFilter && searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {
            // add additional area filter for synonyms
            // in DescriptionElementBase index
            String fromField = "inDescription.taxon.id";
            // id in TaxonBase index
            String toField = "accTaxon" + AcceptedTaxonBridge.DOC_KEY_ID_SUFFIX;
            // TODO replace by createByDistributionJoinQuery
            BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory);
            Query taxonAreaJoinQuery = distributionFilterQueryFactory.newJoinQuery(Distribution.class, fromField, true, byDistributionQuery, toField, Taxon.class, ScoreMode.None);
            multiIndexByAreaFilterBuilder.add(taxonAreaJoinQuery, Occur.SHOULD);
        }
    }
    // search by CommonTaxonName
    if (searchModes.contains(TaxaAndNamesSearchMode.doTaxaByCommonNames)) {
        // B)
        QueryFactory descriptionElementQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(DescriptionElementBase.class);
        Query byCommonNameJoinQuery = descriptionElementQueryFactory.newJoinQuery(CommonTaxonName.class, "inDescription.taxon.id", true, QueryFactory.addTypeRestriction(createByDescriptionElementFullTextQuery(queryString, classification, subtree, null, languages, descriptionElementQueryFactory), CommonTaxonName.class).build(), "id", null, ScoreMode.Max);
        if (logger.isDebugEnabled()) {
            logger.debug("byCommonNameJoinQuery: " + byCommonNameJoinQuery.toString());
        }
        LuceneSearch byCommonNameSearch = new LuceneSearch(luceneIndexToolProvider, GroupByTaxonClassBridge.GROUPBY_TAXON_FIELD, Taxon.class);
        byCommonNameSearch.setCdmTypRestriction(Taxon.class);
        Builder builder = new BooleanQuery.Builder();
        builder.add(byCommonNameJoinQuery, Occur.MUST);
        if (!includeUnpublished) {
            QueryFactory taxonBaseQueryFactory = luceneIndexToolProvider.newQueryFactoryFor(TaxonBase.class);
            builder.add(taxonBaseQueryFactory.newBooleanQuery("publish", true), Occur.MUST);
        }
        byCommonNameSearch.setQuery(builder.build());
        byCommonNameSearch.setSortFields(sortFields);
        idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
        luceneSearches.add(byCommonNameSearch);
    /* A) does not work!!!!
            luceneSearches.add(
                    prepareByDescriptionElementFullTextSearch(CommonTaxonName.class,
                            queryString, classification, null, languages, highlightFragments)
                        );
            idFieldMap.put(CdmBaseType.DESCRIPTION_ELEMENT, "inDescription.taxon.id");
            if(addDistributionFilter){
                // in this case we are able to use DescriptionElementBase documents
                // which are matching the areas in question directly
                BooleanQuery byDistributionQuery = createByDistributionQuery(
                        namedAreaList,
                        distributionStatusList,
                        distributionFilterQueryFactory
                        );
                multiIndexByAreaFilter.add(new QueryWrapperFilter(byDistributionQuery), Occur.SHOULD);
            } */
    }
    // TODO merge with pro parte synonym search once #7487 is fixed
    if (searchModes.contains(TaxaAndNamesSearchMode.doMisappliedNames)) /*|| searchModes.contains(TaxaAndNamesSearchMode.doSynonyms) */
    {
        // NOTE:
        // prepareFindByTaxonRelationFullTextSearch() is making use of JoinUtil.createJoinQuery()
        // which allows doing query time joins
        // finds the misapplied name (Taxon B) which is an misapplication for
        // a related Taxon A.
        // 
        Set<TaxonRelationshipType> relTypes = new HashSet<>();
        if (searchModes.contains(TaxaAndNamesSearchMode.doMisappliedNames)) {
            relTypes.addAll(TaxonRelationshipType.allMisappliedNameTypes());
        }
        // if (searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)){
        // relTypes.addAll(TaxonRelationshipType.allSynonymTypes());
        // }
        luceneSearches.add(prepareFindByTaxonRelationFullTextSearch(new TaxonRelationshipEdge(relTypes, Direction.relatedTo), queryString, classification, subtree, includeUnpublished, languages, highlightFragments, sortFields));
        idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
        if (addDistributionFilter) {
            // in DescriptionElementBase index
            String fromField = "inDescription.taxon.id";
            /*
                 * Here I was facing a weird and nasty bug which took me bugging be really for hours until I found this solution.
                 * Maybe this is a bug in java itself.
                 *
                 * When the string toField is constructed by using the expression TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString()
                 * directly:
                 *
                 *    String toField = "relation." + TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString() +".to.id";
                 *
                 * The byDistributionQuery fails, however when the uuid is first stored in another string variable the query
                 * will execute as expected:
                 *
                 *    String misappliedNameForUuid = TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString();
                 *    String toField = "relation." + misappliedNameForUuid +".to.id";
                 *
                 * Comparing both strings by the String.equals method returns true, so both String are identical.
                 *
                 * The bug occurs when running eu.etaxonomy.cdm.api.service.TaxonServiceSearchTest in eclipse and in maven and seems to to be
                 * dependent from a specific jvm (openjdk6  6b27-1.12.6-1ubuntu0.13.04.2, openjdk7 7u25-2.3.10-1ubuntu0.13.04.2,  oracle jdk1.7.0_25 tested)
                 * The bug is persistent after a reboot of the development computer.
                 */
            // String misappliedNameForUuid = TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString();
            // String toField = "relation." + misappliedNameForUuid +".to.id";
            String toField = "relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id";
            // System.out.println("relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id".equals("relation." + misappliedNameForUuid +".to.id") ? " > identical" : " > different");
            // System.out.println("relation.1ed87175-59dd-437e-959e-0d71583d8417.to.id".equals("relation." + TaxonRelationshipType.MISAPPLIED_NAME_FOR().getUuid().toString() +".to.id") ? " > identical" : " > different");
            // TODO replace by createByDistributionJoinQuery
            BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory);
            Query taxonAreaJoinQuery = distributionFilterQueryFactory.newJoinQuery(Distribution.class, fromField, true, byDistributionQuery, toField, null, ScoreMode.None);
            // debug code for bug described above
            // does not compile anymore since changing from lucene 3.6.2 to lucene 4.10+
            // DocIdSet filterMatchSet = filter.getDocIdSet(luceneIndexToolProvider.getIndexReaderFor(Taxon.class));
            // System.err.println(DocIdBitSetPrinter.docsAsString(filterMatchSet, 100));
            multiIndexByAreaFilterBuilder.add(taxonAreaJoinQuery, Occur.SHOULD);
        }
    }
    // search by pro parte synonyms
    if (searchModes.contains(TaxaAndNamesSearchMode.doSynonyms)) {
        // TODO merge with misapplied name search once #7487 is fixed
        Set<TaxonRelationshipType> relTypes = new HashSet<>();
        relTypes.addAll(TaxonRelationshipType.allSynonymTypes());
        luceneSearches.add(prepareFindByTaxonRelationFullTextSearch(new TaxonRelationshipEdge(relTypes, Direction.relatedTo), queryString, classification, subtree, includeUnpublished, languages, highlightFragments, sortFields));
        idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
        if (addDistributionFilter) {
            // in DescriptionElementBase index
            String fromField = "inDescription.taxon.id";
            String toField = "relation.8a896603-0fa3-44c6-9cd7-df2d8792e577.to.id";
            BooleanQuery byDistributionQuery = createByDistributionQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory);
            Query taxonAreaJoinQuery = distributionFilterQueryFactory.newJoinQuery(Distribution.class, fromField, true, byDistributionQuery, toField, null, ScoreMode.None);
            multiIndexByAreaFilterBuilder.add(taxonAreaJoinQuery, Occur.SHOULD);
        }
    }
    // end pro parte synonyms
    LuceneMultiSearch multiSearch = new LuceneMultiSearch(luceneIndexToolProvider, luceneSearches.toArray(new LuceneSearch[luceneSearches.size()]));
    if (addDistributionFilter) {
        // B)
        // in this case we need a filter which uses a join query
        // to get the TaxonBase documents for the DescriptionElementBase documents
        // which are matching the areas in question
        // 
        // for doTaxa, doByCommonName
        Query taxonAreaJoinQuery = createByDistributionJoinQuery(namedAreaList, distributionStatusList, distributionFilterQueryFactory, Taxon.class, true);
        multiIndexByAreaFilterBuilder.add(taxonAreaJoinQuery, Occur.SHOULD);
    }
    if (addDistributionFilter) {
        multiSearch.setFilter(multiIndexByAreaFilterBuilder.build());
    }
    // --- execute search
    TopGroups<BytesRef> topDocsResultSet;
    try {
        topDocsResultSet = multiSearch.executeSearch(pageSize, pageNumber);
    } catch (ParseException e) {
        LuceneParseException luceneParseException = new LuceneParseException(e.getMessage());
        luceneParseException.setStackTrace(e.getStackTrace());
        throw luceneParseException;
    }
    // --- initialize taxa, highlight matches ....
    ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(multiSearch, multiSearch.getQuery());
    List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(topDocsResultSet, multiSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
    long totalHits = (topDocsResultSet != null) ? Long.valueOf(topDocsResultSet.totalGroupCount) : 0;
    return new DefaultPagerImpl<>(pageNumber, totalHits, pageSize, searchResults);
}

Example 2 with SearchResultBuilder

use of eu.etaxonomy.cdm.api.service.search.SearchResultBuilder in project cdmlib by cybertaxonomy.

the class TaxonServiceImpl method findByDistribution.

@Override
public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter, Classification classification, TaxonNode subtree, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException {
    LuceneSearch luceneSearch = prepareByDistributionSearch(areaFilter, statusFilter, classification, subtree);
    // --- execute search
    TopGroups<BytesRef> topDocsResultSet;
    try {
        topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
    } catch (ParseException e) {
        LuceneParseException luceneParseException = new LuceneParseException(e.getMessage());
        luceneParseException.setStackTrace(e.getStackTrace());
        throw luceneParseException;
    }
    Map<CdmBaseType, String> idFieldMap = new HashMap<>();
    idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
    // ---  initialize taxa, thighlight matches ....
    ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
    List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
    long totalHits = topDocsResultSet != null ? Long.valueOf(topDocsResultSet.totalGroupCount) : 0;
    return new DefaultPagerImpl<>(pageNumber, totalHits, pageSize, searchResults);
}

Example 3 with SearchResultBuilder

use of eu.etaxonomy.cdm.api.service.search.SearchResultBuilder in project cdmlib by cybertaxonomy.

the class TaxonServiceImpl method findByEverythingFullText.

@Override
public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString, Classification classification, TaxonNode subtree, boolean includeUnpublished, List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException {
    LuceneSearch luceneSearchByDescriptionElement = prepareByDescriptionElementFullTextSearch(null, queryString, classification, subtree, null, languages, highlightFragments);
    LuceneSearch luceneSearchByTaxonBase = prepareFindByFullTextSearch(null, queryString, classification, subtree, null, includeUnpublished, languages, highlightFragments, null);
    LuceneMultiSearch multiSearch = new LuceneMultiSearch(luceneIndexToolProvider, luceneSearchByDescriptionElement, luceneSearchByTaxonBase);
    // --- execute search
    TopGroups<BytesRef> topDocsResultSet;
    try {
        topDocsResultSet = multiSearch.executeSearch(pageSize, pageNumber);
    } catch (ParseException e) {
        LuceneParseException luceneParseException = new LuceneParseException(e.getMessage());
        luceneParseException.setStackTrace(e.getStackTrace());
        throw luceneParseException;
    }
    // --- initialize taxa, highlight matches ....
    ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(multiSearch, multiSearch.getQuery());
    Map<CdmBaseType, String> idFieldMap = new HashMap<>();
    idFieldMap.put(CdmBaseType.TAXON_BASE, "id");
    idFieldMap.put(CdmBaseType.DESCRIPTION_ELEMENT, "inDescription.taxon.id");
    List<SearchResult<TaxonBase>> searchResults = searchResultBuilder.createResultSet(topDocsResultSet, multiSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
    int totalHits = topDocsResultSet != null ? topDocsResultSet.totalGroupCount : 0;
    return new DefaultPagerImpl<>(pageNumber, Long.valueOf(totalHits), pageSize, searchResults);
}

Example 4 with SearchResultBuilder

use of eu.etaxonomy.cdm.api.service.search.SearchResultBuilder in project cdmlib by cybertaxonomy.

the class NameServiceImpl method findByNameExactSearch.

@Override
public List<DocumentSearchResult> findByNameExactSearch(String name, boolean wildcard, List<Language> languages, boolean highlightFragments, int maxNoOfResults) throws IOException, LuceneParseException {
    logger.info("Name to exact search for : " + name);
    LuceneSearch luceneSearch = prepareFindByExactNameSearch(null, name, wildcard, languages, highlightFragments);
    // --- execute search
    TopDocs topDocs = luceneSearch.executeSearch(maxNoOfResults);
    // --- initialize taxa, highlight matches ....
    ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
    List<DocumentSearchResult> searchResults = searchResultBuilder.createResultSet(topDocs, luceneSearch.getHighlightFields());
    return searchResults;
}

Example 5 with SearchResultBuilder

use of eu.etaxonomy.cdm.api.service.search.SearchResultBuilder in project cdmlib by cybertaxonomy.

the class NameServiceImpl method findByNameFuzzySearch.

@Override
public List<DocumentSearchResult> findByNameFuzzySearch(String name, float accuracy, List<Language> languages, boolean highlightFragments, int maxNoOfResults) throws IOException, LuceneParseException {
    logger.info("Name to fuzzy search for : " + name);
    // parse the input name
    NonViralNameParserImpl parser = new NonViralNameParserImpl();
    INonViralName nvn = parser.parseFullName(name);
    if (name != null && !name.equals("") && nvn == null) {
        throw new LuceneParseException("Could not parse name " + name);
    }
    LuceneSearch luceneSearch = prepareFindByFuzzyNameSearch(null, nvn, accuracy, maxNoOfResults, languages, highlightFragments);
    // --- execute search
    TopDocs topDocs = luceneSearch.executeSearch(maxNoOfResults);
    Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
    // --- initialize taxa, highlight matches ....
    ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
    @SuppressWarnings("rawtypes") List<DocumentSearchResult> searchResults = searchResultBuilder.createResultSet(topDocs, luceneSearch.getHighlightFields());
    return searchResults;
}