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

Example 1 with SearchResult

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

the class BlastPlus method parseBlastOutputLine.

/**
     * Parses a blast output that represents a single hit
     *
     * @param line blast output for hit
     * @return object wrapper around details of the hit
     */
private static SearchResult parseBlastOutputLine(String[] line) {
    // extract part information
    PartData view = new PartData(EntryType.nameToType(line[1]));
    view.setId(Long.decode(line[0]));
    view.setName(line[2]);
    view.setPartId(line[3]);
    String summary = DAOFactory.getEntryDAO().getEntrySummary(view.getId());
    view.setShortDescription(summary);
    //search result object
    SearchResult searchResult = new SearchResult();
    searchResult.setEntryInfo(view);
    searchResult.seteValue(line[9]);
    searchResult.setScore(Float.valueOf(line[11]));
    searchResult.setAlignment(line[13]);
    searchResult.setQueryLength(Integer.parseInt(line[12]));
    searchResult.setNident(Integer.parseInt(line[13]));
    return searchResult;
}

Example 2 with SearchResult

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

the class BlastPlus method processBlastOutput.

/**
     * Processes the result of a blast search
     *
     * @param blastOutput result output from running blast on the command line
     * @param queryLength length of query sequence
     * @return mapping of entryId to search result object containing information about the blast search for that particular hit
     */
private static LinkedHashMap<String, SearchResult> processBlastOutput(String blastOutput, int queryLength) {
    LinkedHashMap<String, SearchResult> hashMap = new LinkedHashMap<>();
    try (CSVReader reader = new CSVReader(new StringReader(blastOutput))) {
        List<String[]> lines = reader.readAll();
        reader.close();
        for (String[] line : lines) {
            SearchResult info = parseBlastOutputLine(line);
            info.setQueryLength(queryLength);
            String idString = Long.toString(info.getEntryInfo().getId());
            SearchResult currentResult = hashMap.get(idString);
            // if there is an existing record for same entry with a lower relative score then replace
            if (currentResult == null)
                hashMap.put(idString, info);
        }
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
    return hashMap;
}

Example 3 with SearchResult

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

the class StandardBlastDatabase method processBlastOutput.

/**
 * Processes the result of a blast search
 *
 * @param blastOutput result output from running blast on the command line
 * @param queryLength length of query sequence
 * @return mapping of entryId to search result object containing information about the blast search for that particular hit
 */
private LinkedHashMap<String, SearchResult> processBlastOutput(String blastOutput, int queryLength) {
    LinkedHashMap<String, SearchResult> hashMap = new LinkedHashMap<>();
    try (CSVReader reader = new CSVReader(new StringReader(blastOutput))) {
        List<String[]> lines = reader.readAll();
        reader.close();
        for (String[] line : lines) {
            SearchResult info = parseBlastOutputLine(line);
            if (info == null)
                continue;
            info.setQueryLength(queryLength);
            String idString = Long.toString(info.getEntryInfo().getId());
            // if there is an existing record for same entry with a lower relative score then replace
            hashMap.putIfAbsent(idString, info);
        }
    } catch (IOException | CsvException e) {
        Logger.error(e);
        return null;
    }
    return hashMap;
}

Example 4 with SearchResult

use of org.jbei.ice.lib.dto.search.SearchResult 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 5 with SearchResult

use of org.jbei.ice.lib.dto.search.SearchResult 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;
}