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

Example 1 with PartSequence

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

the class AnnotationsTest method testCurate.

@Test
public void testCurate() throws Exception {
    Account account = AccountCreator.createTestAccount("AnnotationsTest.testCurate", true);
    Plasmid plasmid = TestEntryCreator.createTestPlasmid(account);
    Assert.assertNotNull(plasmid);
    SequenceDAO sequenceDAO = new SequenceDAO();
    Assert.assertFalse(sequenceDAO.hasSequence(plasmid.getId()));
    FeaturedDNASequence dnaSequence = GeneralParser.parse(sequenceString);
    PartSequence partSequence = new PartSequence(account.getEmail(), plasmid.getRecordId());
    partSequence.save(dnaSequence);
    SequenceFeatureDAO sequenceFeatureDAO = new SequenceFeatureDAO();
    List<SequenceFeature> sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    Assert.assertEquals(1, sequenceFeatures.size());
    Feature feature = sequenceFeatures.get(0).getFeature();
    DNAFeature dnaFeature = feature.toDataTransferObject();
    Curation curation = new Curation();
    curation.setExclude(true);
    dnaFeature.setCuration(curation);
    List<DNAFeature> features = new ArrayList<>();
    features.add(dnaFeature);
    Annotations annotations = new Annotations(account.getEmail());
    annotations.curate(features);
    sequenceFeatures = sequenceFeatureDAO.getEntrySequenceFeatures(plasmid);
    feature = sequenceFeatures.get(0).getFeature();
    Assert.assertTrue(feature.getCuration().isExclude());
}

Example 2 with PartSequence

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

the class PartResource method deleteSequence.

@DELETE
@Path("/{id}/sequence")
public Response deleteSequence(@PathParam("id") final String partId) {
    final String userId = requireUserId();
    PartSequence partSequence = new PartSequence(userId, partId);
    partSequence.delete();
    return super.respond(true);
}

Example 3 with PartSequence

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

the class FileResource method downloadSequence.

@GET
@Path("{partId}/sequence/{type}")
public Response downloadSequence(@PathParam("partId") final String partId, @PathParam("type") final String downloadType, @DefaultValue("-1") @QueryParam("remoteId") long remoteId, @QueryParam("sid") String sid) {
    if (StringUtils.isEmpty(sessionId))
        sessionId = sid;
    final String userId = getUserId(sessionId);
    if (remoteId != -1) {
        RemoteSequence sequence = new RemoteSequence(remoteId, Long.decode(partId));
        final InputStreamWrapper wrapper = sequence.get(downloadType);
        StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
        return addHeaders(Response.ok(stream), wrapper.getName());
    } else {
        InputStreamWrapper wrapper = new PartSequence(userId, partId).toFile(SequenceFormat.fromString(downloadType), true);
        StreamingOutput stream = output -> IOUtils.copy(wrapper.getInputStream(), output);
        return addHeaders(Response.ok(stream), wrapper.getName());
    }
}

Example 4 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("extractHierarchy") @DefaultValue("false") boolean extractHierarchy, @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, extractHierarchy);
        if (info == null)
            throw new WebApplicationException(Response.serverError().build());
        return Response.status(Response.Status.OK).entity(info).build();
    } catch (IOException e) {
        Logger.error(e);
        ErrorResponse response = new ErrorResponse();
        response.setMessage(e.getMessage());
        throw new WebApplicationException(Response.serverError().entity(response).build());
    }
}

Example 5 with PartSequence

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

the class BulkUploads 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, false);
    } catch (IOException e) {
        Logger.error(e);
        return null;
    }
}