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

Example 21 with PartData

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

the class FolderContents method getRemotelySharedContents.

// remote request for shared contents
public FolderDetails getRemotelySharedContents(String remoteUserId, String token, RegistryPartner partner, long folderId, PageParameters pageParameters) {
    RemotePartner remotePartner = DAOFactory.getRemotePartnerDAO().getByUrl(partner.getUrl());
    if (remotePartner == null) {
        Logger.error("Cannot retrieve remote partner " + partner.getUrl());
        return null;
    }
    Folder folder = folderDAO.get(folderId);
    if (folder == null) {
        Logger.error("Cannot retrieve folder with id " + folderId);
        return null;
    }
    RemoteShareModelDAO shareModelDAO = DAOFactory.getRemoteShareModelDAO();
    RemoteShareModel shareModel = shareModelDAO.get(remoteUserId, remotePartner, folder);
    if (shareModel == null) {
        Logger.error("Could not retrieve share model");
        return null;
    }
    //verify access
    TokenHash tokenHash = new TokenHash();
    String secret = tokenHash.encrypt(folderId + remotePartner.getUrl() + remoteUserId, token);
    if (!secret.equals(shareModel.getSecret())) {
        Logger.error("Authorization failed for remote folder retrieve");
        return null;
    }
    boolean canEdit = shareModel.getPermission().isCanWrite();
    // todo : move everything above to folder permissions and folder authorization
    FolderDetails details = folder.toDataTransferObject();
    details.setCanEdit(canEdit);
    long folderSize = folderDAO.getFolderSize(folderId, pageParameters.getFilter(), true);
    details.setCount(folderSize);
    // retrieve folder contents
    List<Entry> results = folderDAO.retrieveFolderContents(folderId, pageParameters, true);
    for (Entry entry : results) {
        PartData info = ModelToInfoFactory.createTableViewData(null, entry, false);
        info.setCanEdit(canEdit);
        details.getEntries().add(info);
    }
    return details;
}

Example 22 with PartData

use of org.jbei.ice.lib.dto.entry.PartData 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 23 with PartData

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

the class BulkUploadResource method createEntry.

/**
     * @param uploadId
     * @param data
     * @return Response with created part data
     */
@PUT
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/entry")
public Response createEntry(@PathParam("id") long uploadId, PartData data) {
    String userId = getUserId();
    Logger.info(userId + ": adding entry to upload \"" + uploadId + "\"");
    PartData result = creator.createEntry(userId, uploadId, data);
    return respond(result);
}

Example 24 with PartData

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

the class BulkUploadResource method updateEntry.

/**
     * @param uploadId
     * @param entryId
     * @param data
     * @return Response with updated part data
     */
@POST
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/entry/{entryId}")
public Response updateEntry(@PathParam("id") long uploadId, @PathParam("entryId") long entryId, PartData data) {
    String userId = getUserId();
    Logger.info(userId + ": updating entry \"" + entryId + "\" for upload \"" + uploadId + "\"");
    PartData result = creator.updateEntry(userId, uploadId, entryId, data);
    return respond(result);
}

Example 25 with PartData

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

the class WebResource 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();
    final PartData result = remoteEntries.getPublicEntryTooltip(userId, partnerId, entryId);
    return super.respond(Response.Status.OK, result);
}