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

Example 16 with PartData

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

the class TransferredParts method saveTransferred.

private Entry saveTransferred(PartData part) {
    Entry entry = dao.getByRecordId(part.getRecordId());
    if (entry != null) {
        Logger.info("Transferred entry found locally " + part.getRecordId());
        part.setId(entry.getId());
    } else {
        entry = InfoToModelFactory.infoToEntry(part);
        entry.setVisibility(Visibility.TRANSFERRED.getValue());
        entry = dao.create(entry);
        part.setId(entry.getId());
        part.setRecordId(entry.getRecordId());
    }
    // transfer and linked
    for (PartData data : part.getLinkedParts()) {
        Entry linked = saveTransferred(data);
        data.setId(linked.getId());
        data.setRecordId(linked.getRecordId());
        entry.getLinkedEntries().add(linked);
        dao.update(entry);
    }
    return entry;
}

Example 17 with PartData

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

the class PartnerResource method getWebEntryTooltip.

@GET
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/entries/{entryId}/tooltip")
public Response getWebEntryTooltip(@PathParam("id") final long partnerId, @PathParam("entryId") final long entryId) {
    final String userId = super.getUserId();
    RemoteEntries remoteEntries = new RemoteEntries();
    final PartData result = remoteEntries.getPublicEntryTooltip(userId, partnerId, entryId);
    return super.respond(Response.Status.OK, result);
}

Example 18 with PartData

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

the class BulkEntryCreator method createOrUpdateEntries.

public BulkUploadInfo createOrUpdateEntries(String userId, long draftId, List<PartData> data) {
    BulkUpload draft = dao.get(draftId);
    if (draft == null)
        return null;
    // check permissions
    authorization.expectWrite(userId, draft);
    BulkUploadInfo uploadInfo = draft.toDataTransferObject();
    for (PartData datum : data) {
        if (datum == null)
            continue;
        int index = datum.getIndex();
        Entry entry = entryDAO.get(datum.getId());
        if (entry != null) {
            if (draft.getStatus() != BulkUploadStatus.BULK_EDIT)
                entry.setVisibility(Visibility.DRAFT.getValue());
            datum = doUpdate(userId, entry, datum);
        } else
            datum = createEntryForUpload(userId, datum, draft);
        if (datum == null)
            return null;
        datum.setIndex(index);
        uploadInfo.getEntryList().add(datum);
    }
    return uploadInfo;
}

Example 19 with PartData

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

the class FolderContents method getContents.

/**
     * Retrieves the folder specified in the parameter and contents
     *
     * @param userId         unique identifier for user making request. If null, folder must have public read privs
     * @param folderId       unique identifier for folder to be retrieved
     * @param pageParameters paging parameters
     * @return wrapper around list of folder entries if folder is found, null otherwise
     * @throws PermissionException if user does not have read permissions on folder
     */
public FolderDetails getContents(String userId, long folderId, PageParameters pageParameters) {
    Folder folder = folderDAO.get(folderId);
    if (folder == null)
        return null;
    // should have permission to read folder
    folderAuthorization.expectRead(userId, folder);
    if (folder.getType() == FolderType.REMOTE)
        return getRemoteContents(userId, folder, pageParameters);
    boolean visibleOnly = folder.getType() != FolderType.TRANSFERRED;
    FolderDetails details = folder.toDataTransferObject();
    // all local entries at this point
    long folderSize = folderDAO.getFolderSize(folderId, pageParameters.getFilter(), visibleOnly);
    details.setCount(folderSize);
    if (userId != null) {
        List<AccessPermission> permissions = getAndFilterFolderPermissions(userId, folder);
        details.setAccessPermissions(permissions);
        boolean canEdit = permissionsController.hasWritePermission(userId, folder);
        details.setCanEdit(canEdit);
    }
    details.setPublicReadAccess(permissionsController.isPublicVisible(folder));
    Account owner = DAOFactory.getAccountDAO().getByEmail(folder.getOwnerEmail());
    if (owner != null)
        details.setOwner(owner.toDataTransferObject());
    // retrieve folder contents
    List<Entry> results = folderDAO.retrieveFolderContents(folderId, pageParameters, visibleOnly);
    for (Entry entry : results) {
        PartData info = ModelToInfoFactory.createTableViewData(userId, entry, false);
        details.getEntries().add(info);
    }
    return details;
}

Example 20 with PartData

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

the class FolderController method getPublicEntries.

/**
     * Retrieves entries that are made available publicly
     *
     * @param sort   order of retrieval for the entries
     * @param offset start of retrieval
     * @param limit  maximum number of entries to retrieve
     * @param asc    whether to retrieve the entries in ascending order
     * @return wrapper around the retrieved entries
     */
public FolderDetails getPublicEntries(ColumnField sort, int offset, int limit, boolean asc) {
    Group publicGroup = new GroupController().createOrRetrievePublicGroup();
    Set<Group> groups = new HashSet<>();
    groups.add(publicGroup);
    EntryDAO entryDAO = DAOFactory.getEntryDAO();
    List<Entry> results = entryDAO.retrieveVisibleEntries(null, groups, sort, asc, offset, limit, null);
    long visibleCount = entryDAO.visibleEntryCount(null, groups, null);
    FolderDetails details = new FolderDetails();
    details.setCount(visibleCount);
    for (Entry entry : results) {
        try {
            PartData info = ModelToInfoFactory.createTableViewData(null, entry, false);
            info.setPublicRead(true);
            details.getEntries().add(info);
        } catch (Exception e) {
            Logger.error(e);
        }
    }
    return details;
}