Examples with PartData org.jbei.ice.lib.dto.entry.PartData used on opensource projects

Example 56 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class CollectionEntries method getPersonalEntries.

/**
     * Retrieves entries owned by user
     *
     * @param field  sort field
     * @param asc    sort order
     * @param offset paging start
     * @param limit  maximum number of entries to retrieve
     * @param filter optional text to filter entries by
     * @return wrapper around list of parts that conform to the parameters and the maximum number
     * of such entries that are available
     * @throws PermissionException on null user id which is required for owner entries
     */
protected Results<PartData> getPersonalEntries(ColumnField field, boolean asc, int offset, int limit, String filter) {
    if (userId == null || userId.isEmpty())
        throw new PermissionException("User id is required to retrieve owner entries");
    OwnerEntries ownerEntries = new OwnerEntries(userId, userId);
    final List<PartData> entries = ownerEntries.retrieveOwnerEntries(field, asc, offset, limit, filter);
    final long count = ownerEntries.getNumberOfOwnerEntries();
    Results<PartData> results = new Results<>();
    results.setResultCount(count);
    results.setData(entries);
    return results;
}

Example 57 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class UserResource method getProfileEntries.

/**
     * @return collection for user's part entries
     */
@GET
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/entries")
public FolderDetails getProfileEntries(@PathParam("id") long userId, @DefaultValue("0") @QueryParam("offset") int offset, @DefaultValue("15") @QueryParam("limit") int limit, @DefaultValue("created") @QueryParam("sort") String sort, @DefaultValue("false") @QueryParam("asc") boolean asc, @DefaultValue("") @QueryParam("filter") String filter) {
    String userIdString = getUserId();
    ColumnField field = ColumnField.valueOf(sort.toUpperCase());
    OwnerEntries ownerEntries = new OwnerEntries(userIdString, userId);
    List<PartData> entries = ownerEntries.retrieveOwnerEntries(field, asc, offset, limit, filter);
    long count = ownerEntries.getNumberOfOwnerEntries();
    FolderDetails details = new FolderDetails();
    details.getEntries().addAll(entries);
    details.setCount(count);
    return details;
}

Example 58 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class HibernateSearch method executeSearch.

@SuppressWarnings("unchecked")
public SearchResults executeSearch(String userId, HashMap<String, QueryType> terms, SearchQuery searchQuery, HashMap<String, SearchResult> blastResults) {
    Session session = HibernateUtil.getSessionFactory().getCurrentSession();
    int resultCount;
    FullTextSession fullTextSession = Search.getFullTextSession(session);
    BooleanQuery.Builder builder = new BooleanQuery.Builder();
    // get classes for search
    HashSet<String> fields = new HashSet<>();
    fields.addAll(SearchFieldFactory.entryFields(searchQuery.getEntryTypes()));
    Class<?>[] classes = SearchFieldFactory.classesForTypes(searchQuery.getEntryTypes());
    // generate queries for terms filtering stop words
    for (Map.Entry<String, QueryType> entry : terms.entrySet()) {
        String term = cleanQuery(entry.getKey());
        if (term.trim().isEmpty() || StandardAnalyzer.STOP_WORDS_SET.contains(term))
            continue;
        BioSafetyOption safetyOption = searchQuery.getBioSafetyOption();
        generateQueriesForType(fullTextSession, fields, builder, term, entry.getValue(), safetyOption);
    }
    // check for blast search results filter
    createBlastFilterQuery(fullTextSession, blastResults, builder);
    // wrap Lucene query in a org.hibernate.Query
    FullTextQuery fullTextQuery = fullTextSession.createFullTextQuery(builder.build(), classes);
    // get max score
    fullTextQuery.setFirstResult(0);
    fullTextQuery.setMaxResults(1);
    fullTextQuery.setProjection(FullTextQuery.SCORE);
    List result = fullTextQuery.list();
    float maxScore = -1f;
    if (result.size() == 1) {
        maxScore = (Float) ((Object[]) (result.get(0)))[0];
    }
    // end get max score
    // get sorting values
    Sort sort = getSort(searchQuery.getParameters().isSortAscending(), searchQuery.getParameters().getSortField());
    fullTextQuery.setSort(sort);
    // projection (specified properties must be stored in the index @Field(store=Store.YES))
    fullTextQuery.setProjection(FullTextQuery.SCORE, FullTextQuery.THIS);
    // enable security filter if needed
    fullTextQuery = checkEnableSecurityFilter(userId, fullTextQuery);
    // check sample
    checkEnableHasAttribute(fullTextQuery, searchQuery.getParameters());
    // set paging params
    fullTextQuery.setFirstResult(searchQuery.getParameters().getStart());
    fullTextQuery.setMaxResults(searchQuery.getParameters().getRetrieveCount());
    resultCount = fullTextQuery.getResultSize();
    // execute search
    result = fullTextQuery.list();
    Logger.info(resultCount + " results for \"" + searchQuery.getQueryString() + "\"");
    LinkedList<SearchResult> searchResults = new LinkedList<>();
    for (Object[] objects : (Iterable<Object[]>) result) {
        float score = (Float) objects[0];
        Entry entry = (Entry) objects[1];
        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(score);
            PartData info = ModelToInfoFactory.createTableViewData(userId, entry, true);
            if (info == null)
                continue;
            searchResult.setEntryInfo(info);
        }
        searchResult.setMaxScore(maxScore);
        searchResults.add(searchResult);
    }
    SearchResults results = new SearchResults();
    results.setResultCount(resultCount);
    results.setResults(searchResults);
    return results;
}

Example 59 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class BulkEntryCreatorTest method testUpdateEntry.

@Test
public void testUpdateEntry() throws Exception {
    Account account = AccountCreator.createTestAccount("testUpdateEntry", false);
    PartData strainData = new PartData(EntryType.STRAIN);
    PartData plasmidData = new PartData(EntryType.PLASMID);
    strainData.setPrincipalInvestigator("test 1");
    plasmidData.setPrincipalInvestigator("test 2");
    // create bulk upload
    BulkUploadController controller = new BulkUploadController();
    BulkUploadInfo info = new BulkUploadInfo();
    info.setAccount(account.toDataTransferObject());
    info = controller.create(account.getEmail(), info);
    Assert.assertNotNull(info);
    Assert.assertEquals(info.getStatus(), BulkUploadStatus.IN_PROGRESS);
    // create strain entry
    strainData = creator.createEntry(account.getEmail(), info.getId(), strainData);
    Assert.assertNotNull(strainData);
    Assert.assertTrue(strainData.getId() > 0);
    // link plasmid
    strainData.getLinkedParts().add(plasmidData);
    strainData = creator.updateEntry(account.getEmail(), info.getId(), strainData.getId(), strainData);
    Assert.assertNotNull(strainData);
    // retrieve
    BulkUploadInfo retrieved = controller.getBulkImport(account.getEmail(), info.getId(), 0, 10);
    Assert.assertNotNull(retrieved);
    Assert.assertEquals(retrieved.getEntryList().size(), 1);
    PartData retrievedPart = retrieved.getEntryList().get(0);
    Assert.assertTrue(retrievedPart.getLinkedParts().size() == 1);
}

Example 60 with PartData

use of org.jbei.ice.lib.dto.entry.PartData in project ice by JBEI.

the class TestEntryCreator method createTestPart.

public static long createTestPart(String userId) throws Exception {
    PartData data = new PartData(EntryType.PART);
    data.setShortDescription("summary for test");
    data.setName("pTest " + userId);
    data.setBioSafetyLevel(1);
    return new EntryCreator().createPart(userId, data).getId();
}