Examples with SearchQuery org.jbei.ice.lib.dto.search.SearchQuery used on opensource projects

Example 1 with SearchQuery

use of org.jbei.ice.lib.dto.search.SearchQuery in project ice by JBEI.

the class HibernateSearch method filterBlastResults.

/**
     * Intended to be called after running a blast search to filter the results. Blast search runs
     * on a fasta file which contains all the sequences. Hibernate search has a security filter for permissions
     * and is therefore used to filter out the blast results, as well as to filter based on the entry
     * attributes not handled by blast; such as "has sequence" and "bio-safety level"
     *
     * @param userId       identifier for account of user performing search
     * @param start        paging start
     * @param count        maximum number of results to return
     * @param blastResults raw results of the blast search
     * @return wrapper around list of filtered results
     */
public SearchResults filterBlastResults(String userId, int start, int count, SearchQuery searchQuery, final HashMap<String, SearchResult> blastResults) {
    Session session = HibernateUtil.getSessionFactory().getCurrentSession();
    FullTextSession fullTextSession = Search.getFullTextSession(session);
    QueryBuilder qb = fullTextSession.getSearchFactory().buildQueryBuilder().forEntity(Entry.class).get();
    Query query = qb.keyword().onField("visibility").matching(Visibility.OK.getValue()).createQuery();
    // todo : there is a limit of 1024 boolean clauses so return only return top blast results
    BooleanQuery.Builder builder = new BooleanQuery.Builder();
    builder.add(query, BooleanClause.Occur.FILTER);
    // wrap Lucene query in a org.hibernate.Query
    Class<?>[] classes = SearchFieldFactory.classesForTypes(searchQuery.getEntryTypes());
    FullTextQuery fullTextQuery = fullTextSession.createFullTextQuery(builder.build(), classes);
    // enable security filter if an admin
    checkEnableSecurityFilter(userId, fullTextQuery);
    // enable has attachment/sequence/sample (if needed)
    checkEnableHasAttribute(fullTextQuery, searchQuery.getParameters());
    // bio-safety level
    if (searchQuery.getBioSafetyOption() != null) {
        TermContext levelContext = qb.keyword();
        Query biosafetyQuery = levelContext.onField("bioSafetyLevel").ignoreFieldBridge().matching(searchQuery.getBioSafetyOption().getValue()).createQuery();
        builder.add(biosafetyQuery, BooleanClause.Occur.MUST);
    }
    // execute search
    fullTextQuery.setProjection("id");
    // list contains an object array with one Long object
    List luceneResult = fullTextQuery.list();
    HashSet<String> resultSet = new HashSet<>();
    // page
    for (Object object : luceneResult) {
        Long result = (Long) ((Object[]) object)[0];
        resultSet.add(result.toString());
    }
    Iterator<String> iterator = blastResults.keySet().iterator();
    while (iterator.hasNext()) {
        String key = iterator.next();
        if (!resultSet.contains(key))
            iterator.remove();
    }
    SearchResult[] searchResults = new SearchResult[count];
    int limit = (start + count) > blastResults.size() ? blastResults.size() : (start + count);
    LinkedList<SearchResult> list = new LinkedList<>(Arrays.asList(blastResults.values().toArray(searchResults)).subList(start, limit));
    SearchResults results = new SearchResults();
    results.setResultCount(blastResults.size());
    results.setResults(list);
    return results;
}

Example 2 with SearchQuery

use of org.jbei.ice.lib.dto.search.SearchQuery in project ice by JBEI.

the class HibernateSearch method executeSearchNoTerms.

public SearchResults executeSearchNoTerms(String userId, HashMap<String, SearchResult> blastResults, SearchQuery searchQuery) {
    ArrayList<EntryType> entryTypes = searchQuery.getEntryTypes();
    if (entryTypes == null || entryTypes.isEmpty()) {
        entryTypes = new ArrayList<>();
        entryTypes.addAll(Arrays.asList(EntryType.values()));
    }
    Session session = HibernateUtil.getSessionFactory().getCurrentSession();
    int resultCount;
    FullTextSession fullTextSession = Search.getFullTextSession(session);
    BooleanQuery.Builder builder = new BooleanQuery.Builder();
    QueryBuilder qb = fullTextSession.getSearchFactory().buildQueryBuilder().forEntity(Entry.class).get();
    ArrayList<Query> except = new ArrayList<>();
    for (EntryType type : EntryType.values()) {
        if (entryTypes.contains(type))
            continue;
        except.add(qb.keyword().onField("recordType").matching(type.getName()).createQuery());
    }
    // add terms for record types
    Query[] queries = new Query[] {};
    Query recordTypeQuery = qb.all().except(except.toArray(queries)).createQuery();
    builder.add(recordTypeQuery, BooleanClause.Occur.FILTER);
    // visibility
    Query visibilityQuery = qb.keyword().onField("visibility").matching(Visibility.OK.getValue()).createQuery();
    builder.add(visibilityQuery, BooleanClause.Occur.FILTER);
    // bio safety level
    BioSafetyOption option = searchQuery.getBioSafetyOption();
    if (option != null) {
        TermContext bslContext = qb.keyword();
        Query biosafetyQuery = bslContext.onField("bioSafetyLevel").ignoreFieldBridge().matching(option.getIntValue()).createQuery();
        builder.add(biosafetyQuery, BooleanClause.Occur.FILTER);
    }
    // check filter filters
    if (searchQuery.getFieldFilters() != null && !searchQuery.getFieldFilters().isEmpty()) {
        for (FieldFilter fieldFilter : searchQuery.getFieldFilters()) {
            String searchField = SearchFieldFactory.searchFieldForEntryField(fieldFilter.getField());
            if (StringUtils.isEmpty(searchField))
                continue;
            Query filterQuery = qb.keyword().onField(searchField).matching(fieldFilter.getFilter()).createQuery();
            builder.add(filterQuery, BooleanClause.Occur.MUST);
        }
    }
    // check if there is a blast results
    createBlastFilterQuery(fullTextSession, blastResults, builder);
    // wrap Lucene query in a org.hibernate.Query
    FullTextQuery fullTextQuery = fullTextSession.createFullTextQuery(builder.build(), Entry.class);
    // get sorting values
    Sort sort = getSort(searchQuery.getParameters().isSortAscending(), searchQuery.getParameters().getSortField());
    fullTextQuery.setSort(sort);
    // enable security filter if needed
    checkEnableSecurityFilter(userId, fullTextQuery);
    // enable has attachment/sequence/sample (if needed)
    checkEnableHasAttribute(fullTextQuery, searchQuery.getParameters());
    // set paging params
    fullTextQuery.setFirstResult(searchQuery.getParameters().getStart());
    fullTextQuery.setMaxResults(searchQuery.getParameters().getRetrieveCount());
    resultCount = fullTextQuery.getResultSize();
    List result = fullTextQuery.list();
    LinkedList<SearchResult> searchResults = new LinkedList<>();
    for (Object object : result) {
        Entry entry = (Entry) object;
        SearchResult searchResult;
        if (blastResults != null) {
            searchResult = blastResults.get(Long.toString(entry.getId()));
            if (// this should not really happen since we already filter
            searchResult == null)
                continue;
        } else {
            searchResult = new SearchResult();
            searchResult.setScore(1f);
            PartData info = ModelToInfoFactory.createTableViewData(userId, entry, true);
            searchResult.setEntryInfo(info);
        }
        searchResult.setMaxScore(1f);
        searchResults.add(searchResult);
    }
    SearchResults results = new SearchResults();
    results.setResultCount(resultCount);
    results.setResults(searchResults);
    Logger.info(userId + ": obtained " + resultCount + " results for empty query");
    return results;
}

Example 3 with SearchQuery

use of org.jbei.ice.lib.dto.search.SearchQuery in project ice by JBEI.

the class SearchResource method search.

/**
     * Keyword search
     *
     * @param queryString keywords to search on
     * @param searchWeb   whether to perform a web of registry search or not
     * @param offset      result start
     * @param limit       result count upper limit
     * @param sort        result sort
     * @param asc         true if return results in ascending order, false otherwise
     * @return wrapper around list of search results conforming to query params
     */
@GET
@Produces(MediaType.APPLICATION_JSON)
public Response search(@QueryParam("q") final String queryString, @DefaultValue("false") @QueryParam("webSearch") final boolean searchWeb, @DefaultValue("0") @QueryParam("offset") final int offset, @DefaultValue("15") @QueryParam("limit") final int limit, @DefaultValue("relevance") @QueryParam("sort") final String sort, @DefaultValue("false") @QueryParam("asc") final boolean asc) {
    final String userId = getUserId();
    if (StringUtils.isEmpty(userId) && !searchWeb) {
        return super.respond(Response.Status.FORBIDDEN);
    }
    log(userId, "query \'" + queryString + '\'');
    final SearchQuery query = new SearchQuery();
    query.setQueryString(queryString);
    final SearchQuery.Parameters parameters = query.getParameters();
    parameters.setRetrieveCount(limit);
    parameters.setStart(offset);
    parameters.setSortAscending(asc);
    parameters.setSortField(ColumnField.valueOf(sort.toUpperCase()));
    final List<EntryType> types = Arrays.asList(EntryType.values());
    query.setEntryTypes(types);
    return super.respond(controller.runSearch(userId, query));
}

Example 4 with SearchQuery

use of org.jbei.ice.lib.dto.search.SearchQuery in project ice by JBEI.

the class SearchControllerTest method testRunSearch.

@Test
public void testRunSearch() throws Exception {
    Account account = AccountCreator.createTestAccount("testRunSearch", false);
    Assert.assertNotNull(account);
    // create entry
    PlasmidData plasmidData = new PlasmidData();
    plasmidData.setCircular(true);
    plasmidData.setPromoters("pTet");
    plasmidData.setOriginOfReplication("oRep");
    PartData partData = new PartData(EntryType.PLASMID);
    partData.setBioSafetyLevel(BioSafetyOption.LEVEL_ONE.ordinal());
    partData.setStatus("Complete");
    partData.setName("testPlasmid");
    partData.setFundingSource("DOE");
    partData.setPrincipalInvestigator("Nathan");
    partData.setPlasmidData(plasmidData);
    Entry entry = InfoToModelFactory.infoToEntry(partData);
    entry = new EntryCreator().createEntry(account, entry, null);
    Assert.assertNotNull(entry);
    Assert.assertTrue(entry.getId() > 0);
    // commit triggers indexing
    HibernateUtil.commitTransaction();
    HibernateUtil.beginTransaction();
    SearchQuery query = new SearchQuery();
    query.setQueryString("testPlasmid");
    SearchResults results = controller.runSearch(account.getEmail(), query);
    Assert.assertNotNull(results);
    Assert.assertEquals(1, results.getResultCount());
    // search for promoters
    query.setQueryString("pTet");
    results = controller.runSearch(account.getEmail(), query);
    Assert.assertNotNull(results);
    Assert.assertEquals(1, results.getResultCount());
    // search email
    query.setQueryString(account.getEmail());
    results = controller.runSearch(account.getEmail(), query);
    Assert.assertNotNull(results);
    Assert.assertEquals(1, results.getResultCount());
    // fake search
    query.setQueryString("FAKE_SEARCH");
    results = controller.runSearch(account.getEmail(), query);
    Assert.assertNotNull(results);
    Assert.assertEquals(0, results.getResultCount());
}