Examples with PartSequence org.jbei.ice.lib.entry.sequence.PartSequence used on opensource projects

Example 11 with PartSequence

use of org.jbei.ice.lib.entry.sequence.PartSequence in project ice by JBEI.

the class BulkUploadController method addSequence.

public SequenceInfo addSequence(String userId, long bulkUploadId, long entryId, String sequenceString, String fileName) {
    BulkUpload upload = dao.get(bulkUploadId);
    if (upload == null)
        return null;
    authorization.expectWrite(userId, upload);
    PartSequence partSequence = new PartSequence(userId, Long.toString(entryId));
    try {
        ByteArrayInputStream inputStream = new ByteArrayInputStream(sequenceString.getBytes(StandardCharsets.UTF_8));
        return partSequence.parseSequenceFile(inputStream, fileName);
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
}

Example 12 with PartSequence

use of org.jbei.ice.lib.entry.sequence.PartSequence 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 13 with PartSequence

use of org.jbei.ice.lib.entry.sequence.PartSequence in project ice by JBEI.

the class Entries method copy.

/**
 * Creates a copy of referenced part
 *
 * @param sourceId unique identifier for part acting as source of copy. Can be the part id, uuid or id
 * @return wrapper around the id and record id of the newly created entry
 * @throws IllegalArgumentException if the source part for the copy cannot be located using the identifier
 */
public PartData copy(String sourceId) {
    Entry entry = getEntry(sourceId);
    if (entry == null)
        throw new IllegalArgumentException("Could not retrieve entry \"" + sourceId + "\" for copy");
    // check permission (expecting read permission)
    authorization.expectRead(userId, entry);
    Sequence sequence = null;
    if (sequenceDAO.hasSequence(entry.getId())) {
        sequence = sequenceDAO.getByEntry(entry);
    }
    // copy to data model and back ??
    PartData partData = ModelToInfoFactory.getInfo(entry);
    entry = InfoToModelFactory.infoToEntry(partData);
    // create entry
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    entry.setName(entry.getName() + " (copy)");
    entry.setRecordId(Utils.generateUUID());
    entry.setVersionId(entry.getRecordId());
    entry.setOwnerEmail(account.getEmail());
    entry.setOwner(account.getFullName());
    entry = createEntry(account, entry, new ArrayList<>());
    // check sequence
    if (sequence != null) {
        PartSequence partSequence = new PartSequence(userId, sourceId);
        new PartSequence(userId, entry.getPartNumber()).save(partSequence.get(true));
    }
    PartData copy = new PartData(EntryType.nameToType(entry.getRecordType()));
    copy.setId(entry.getId());
    copy.setRecordId(entry.getRecordId());
    return copy;
}

Example 14 with PartSequence

use of org.jbei.ice.lib.entry.sequence.PartSequence in project ice by JBEI.

the class BulkUploadResource method deleteEntrySequence.

/**
 * @param uploadId
 * @param entryId
 * @return OK response if sequence is deleted
 */
@DELETE
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/entry/{entryId}/sequence")
public Response deleteEntrySequence(@PathParam("id") long uploadId, @PathParam("entryId") String entryId) {
    String userId = getUserId();
    PartSequence partSequence = new PartSequence(userId, entryId);
    partSequence.delete();
    return Response.ok().build();
}

Example 15 with PartSequence

use of org.jbei.ice.lib.entry.sequence.PartSequence in project ice by JBEI.

the class PartResource method getSequence.

@GET
@Produces(MediaType.APPLICATION_JSON)
@Path("/{id}/sequence")
public Response getSequence(@PathParam("id") final String partId, @DefaultValue("false") @QueryParam("remote") boolean isRemote, @QueryParam("token") String remoteUserToken, @QueryParam("userId") String remoteUserId, @QueryParam("folderId") long fid, @DefaultValue("true") @QueryParam("annotations") boolean includeAnnotations) {
    final FeaturedDNASequence sequence;
    final String userId = getUserId();
    Sequences sequences = new Sequences(userId);
    if (isRemote) {
        // entry exists remotely
        sequence = remoteEntries.getSequence(userId, fid, partId);
    } else {
        // what request is being responded to (local or remote)
        if (StringUtils.isEmpty(userId)) {
            RegistryPartner partner = requireWebPartner();
            if (StringUtils.isEmpty(remoteUserToken) || fid == 0) {
                sequence = new PartSequence(userId, partId).get(includeAnnotations);
            } else {
                sequence = sequences.getRequestedSequence(partner, remoteUserId, remoteUserToken, partId, fid);
            }
        } else {
            // user id can be null if partId is public
            sequence = new PartSequence(userId, partId).get(includeAnnotations);
        }
    }
    return Response.status(Response.Status.OK).entity(sequence).build();
}