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

Example 6 with SequenceInfo

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

the class PartSequenceTest method testGet.

@Test
public void testGet() throws Exception {
    Account account = AccountCreator.createTestAccount("PartSequenceTest.testGet", false);
    Strain strain = TestEntryCreator.createTestStrain(account);
    PartSequence partSequence = new PartSequence(account.getEmail(), strain.getRecordId());
    FeaturedDNASequence sequence = partSequence.get();
    Assert.assertNull(sequence);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(genbank.getBytes());
    SequenceInfo sequenceInfo = partSequence.parseSequenceFile(inputStream, "testFile.gb");
    Assert.assertNotNull(sequenceInfo);
    FeaturedDNASequence featuredDNASequence = (FeaturedDNASequence) sequenceInfo.getSequence();
    Assert.assertNotNull(featuredDNASequence);
    Assert.assertEquals(1, featuredDNASequence.getFeatures().size());
    sequence = partSequence.get();
    Assert.assertNotNull(sequence);
    Assert.assertEquals(234, sequence.getSequence().length());
    Assert.assertEquals(1, sequence.getFeatures().size());
}

Example 7 with SequenceInfo

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

the class PartSequence method save.

protected SequenceInfo save(DNASequence dnaSequence, String sequenceString, String fileName) {
    Sequence sequence = SequenceController.dnaSequenceToSequence(dnaSequence);
    sequence.setSequenceUser(sequenceString);
    sequence.setEntry(entry);
    if (!StringUtils.isBlank(fileName))
        sequence.setFileName(fileName);
    Sequence result = sequenceDAO.saveSequence(sequence);
    BlastPlus.scheduleBlastIndexRebuildTask(true);
    SequenceInfo info = result.toDataTransferObject();
    info.setSequence(dnaSequence);
    return info;
}

Example 8 with SequenceInfo

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

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

the class BulkUploadResource method uploadSequenceFile.

@POST
@Path("/{id}/sequence")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public Response uploadSequenceFile(@PathParam("id") long uploadId, @FormDataParam("file") InputStream fileInputStream, @FormDataParam("entryId") long entryId, @FormDataParam("file") FormDataContentDisposition contentDispositionHeader) {
    try {
        String fileName = contentDispositionHeader.getFileName();
        String userId = requireUserId();
        String sequence = Utils.getString(fileInputStream);
        SequenceInfo sequenceInfo = controller.addSequence(userId, uploadId, entryId, sequence, fileName);
        if (sequenceInfo == null) {
            return Response.status(Response.Status.INTERNAL_SERVER_ERROR).build();
        }
        return Response.status(Response.Status.OK).entity(sequenceInfo).build();
    } catch (IOException e) {
        Logger.error(e);
        return Response.status(Response.Status.INTERNAL_SERVER_ERROR).build();
    }
}