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

Example 6 with EntryType

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

the class FileResource method uploadSequence.

/**
     * this creates an entry if an id is not specified in the form data
     */
@POST
@Path("sequence")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public Response uploadSequence(@FormDataParam("file") InputStream fileInputStream, @FormDataParam("entryRecordId") String recordId, @FormDataParam("entryType") String entryType, @FormDataParam("file") FormDataContentDisposition contentDispositionHeader) {
    try {
        final String fileName = contentDispositionHeader.getFileName();
        String userId = getUserId();
        PartSequence partSequence;
        if (StringUtils.isEmpty(recordId)) {
            if (entryType == null) {
                entryType = "PART";
            }
            EntryType type = EntryType.nameToType(entryType);
            partSequence = new PartSequence(userId, type);
        } else {
            partSequence = new PartSequence(userId, recordId);
        }
        SequenceInfo info = partSequence.parseSequenceFile(fileInputStream, fileName);
        if (info == null)
            throw new WebApplicationException(Response.serverError().build());
        return Response.status(Response.Status.OK).entity(info).build();
    } catch (Exception e) {
        Logger.error(e);
        ErrorResponse response = new ErrorResponse();
        response.setMessage(e.getMessage());
        throw new WebApplicationException(Response.serverError().entity(response).build());
    }
}

Example 7 with EntryType

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

the class FileResource method getUploadCSV.

@GET
@Path("upload/{type}")
public Response getUploadCSV(@PathParam("type") final String type, @QueryParam("link") final String linkedType) {
    EntryType entryAddType = EntryType.nameToType(type);
    EntryType linked;
    if (linkedType != null) {
        linked = EntryType.nameToType(linkedType);
    } else {
        linked = null;
    }
    final StreamingOutput stream = output -> {
        byte[] template = FileBulkUpload.getCSVTemplateBytes(entryAddType, linked, "existing".equalsIgnoreCase(linkedType));
        ByteArrayInputStream input = new ByteArrayInputStream(template);
        ByteStreams.copy(input, output);
    };
    String filename = type.toLowerCase();
    if (linkedType != null) {
        filename += ("_" + linkedType.toLowerCase());
    }
    return addHeaders(Response.ok(stream), filename + "_csv_upload.csv");
}

Example 8 with EntryType

use of org.jbei.ice.lib.dto.entry.EntryType 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 9 with EntryType

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

the class Entries method getEntriesFromSelectionContext.

public List<Long> getEntriesFromSelectionContext(EntrySelection context) {
    boolean all = context.isAll();
    EntryType entryType = context.getEntryType();
    if (context.getSelectionType() == null)
        return context.getEntries();
    switch(context.getSelectionType()) {
        default:
        case FOLDER:
            if (!context.getEntries().isEmpty()) {
                return context.getEntries();
            } else {
                long folderId = Long.decode(context.getFolderId());
                return getFolderEntries(folderId, all, entryType);
            }
        case SEARCH:
            return getSearchResults(context.getSearchQuery());
        case COLLECTION:
            if (!context.getEntries().isEmpty()) {
                return context.getEntries();
            } else {
                return getCollectionEntries(context.getFolderId(), all, entryType);
            }
    }
}

Example 10 with EntryType

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

the class SearchFieldFactory method entryFields.

public static HashSet<String> entryFields(List<EntryType> types) {
    HashSet<String> fields = new HashSet<>();
    for (EntryType type : types) {
        switch(type) {
            case STRAIN:
                fields.addAll(strainFields);
                break;
            case PLASMID:
                fields.addAll(plasmidFields);
                break;
            case ARABIDOPSIS:
                fields.addAll(seedFields);
                break;
        }
    }
    fields.addAll(commonFields);
    return fields;
}