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

Example 1 with SearchResults

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

the class SearchIndexesTest 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);
    partData = new Entries(account.getEmail()).create(partData);
    Entry entry = DAOFactory.getEntryDAO().get(partData.getId());
    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());
    // case insensentive
    results = controller.runSearch(account.getEmail().toLowerCase(), 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());
}

Example 2 with SearchResults

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

the class WebSearch method run.

/**
 * Searches all registries in the web of registries configuration with this
 * registry. Without some sort of indexing locally or in some central location,
 * this will be slow for large numbers of results
 *
 * @param query               wrapper around search query
 * @param includeThisInstance whether to include results from this instance of ICE
 * @return list of search results
 */
public WebSearchResults run(SearchQuery query, boolean includeThisInstance) {
    List<RemotePartner> partners = this.remotePartnerDAO.getRegistryPartners();
    if (partners == null)
        return null;
    List<SearchTask> searchTasks = new LinkedList<>();
    // for each approved partner run the search task
    for (RemotePartner partner : partners) {
        if (partner.getUrl() == null || partner.getPartnerStatus() != RemotePartnerStatus.APPROVED)
            continue;
        SearchTask task = runSearchThread(partner, query);
        searchTasks.add(task);
    }
    WebSearchResults searchResults = new WebSearchResults(searchTasks.size() + 1);
    // String inWWoR = Utils.getConfigValue(ConfigurationKey.JOIN_WEB_OF_REGISTRIES);
    if (includeThisInstance) {
        SearchIndexes searchIndexes = new SearchIndexes();
        SearchResults results = searchIndexes.runSearch(null, query);
        searchResults.setQuery(query);
        WebResult thisResult = new WebResult();
        thisResult.getResults().addAll(results.getResults());
        thisResult.setCount(results.getResultCount());
        String url = Utils.getConfigValue(ConfigurationKey.URI_PREFIX);
        String projectName = Utils.getConfigValue(ConfigurationKey.PROJECT_NAME);
        RegistryPartner thisPartner = new RegistryPartner();
        thisPartner.setUrl(url);
        thisPartner.setName(projectName);
        thisResult.setPartner(thisPartner);
        searchResults.getResults().add(thisResult);
        searchResults.setTotalCount(thisResult.getCount());
    }
    // go through tasks and check if completed
    while (!searchTasks.isEmpty()) {
        Iterator<SearchTask> iterator = searchTasks.iterator();
        // todo : set time limit and abandon task (shutdown) if exceeded (or after give it till after this instance is searched)
        while (iterator.hasNext()) {
            SearchTask task = iterator.next();
            TaskStatus status = task.getStatus();
            if (status == TaskStatus.COMPLETED || status == TaskStatus.EXCEPTION) {
                iterator.remove();
                if (status == TaskStatus.COMPLETED) {
                    WebResult webResult = new WebResult();
                    webResult.setPartner(task.getPartner().toDataTransferObject());
                    SearchResults partnerResults = task.getResults();
                    webResult.setCount(partnerResults.getResultCount());
                    webResult.getResults().addAll(partnerResults.getResults());
                    searchResults.getResults().add(webResult);
                    searchResults.setTotalCount(searchResults.getTotalCount() + partnerResults.getResultCount());
                }
            }
        }
    }
    return searchResults;
}

Example 3 with SearchResults

use of org.jbei.ice.lib.dto.search.SearchResults 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());
    }
    blastResults.keySet().removeIf(key -> !resultSet.contains(key));
    SearchResult[] searchResults = new SearchResult[count];
    int limit = Math.min((start + count), blastResults.size());
    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 4 with SearchResults

use of org.jbei.ice.lib.dto.search.SearchResults 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());
}

Example 5 with SearchResults

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

the class Entries method getSearchResults.

private List<Long> getSearchResults(SearchQuery searchQuery) {
    SearchIndexes searchIndexes = new SearchIndexes();
    SearchResults searchResults = searchIndexes.runSearch(userId, searchQuery);
    // todo : inefficient: have search return ids only
    List<Long> results = new LinkedList<>();
    for (SearchResult result : searchResults.getResults()) {
        results.add(result.getEntryInfo().getId());
    }
    return results;
}