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

Example 1 with EntryType

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

the class BulkUploadResource method post.

/**
     * @return Response with the id of the imported bulk upload
     */
@POST
@Path("file")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
public Response post(@FormDataParam("file") InputStream fileInputStream, @FormDataParam("type") String type, @FormDataParam("file") FormDataContentDisposition contentDispositionHeader) {
    try {
        String userId = getUserId();
        String fileName = userId + "-" + System.currentTimeMillis() + "-" + contentDispositionHeader.getFileName();
        File file = Paths.get(Utils.getConfigValue(ConfigurationKey.DATA_DIRECTORY), "bulk-import", fileName).toFile();
        FileUtils.copyInputStreamToFile(fileInputStream, file);
        EntryType addType = EntryType.valueOf(type.toUpperCase());
        FileBulkUpload bulkUpload = new FileBulkUpload(userId, file.toPath(), addType);
        ProcessedBulkUpload processedBulkUpload = bulkUpload.process();
        if (processedBulkUpload.isSuccess())
            return Response.status(Response.Status.OK).entity(processedBulkUpload).build();
        return Response.status(Response.Status.BAD_REQUEST).entity(processedBulkUpload).build();
    } catch (IOException e) {
        Logger.error(e);
        ProcessedBulkUpload processedBulkUpload = new ProcessedBulkUpload();
        processedBulkUpload.setUserMessage(e.getCause().getMessage());
        processedBulkUpload.setSuccess(false);
        return Response.status(Response.Status.BAD_REQUEST).entity(processedBulkUpload).build();
    }
}

Example 2 with EntryType

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

the class BulkUploadControllerTest method testAutoUpdateBulkUpload.

@Test
public void testAutoUpdateBulkUpload() throws Exception {
    EntryType type = EntryType.STRAIN;
    Account account = AccountCreator.createTestAccount("testAutoUpdateBulkUpload", false);
    BulkUploadAutoUpdate autoUpdate = new BulkUploadAutoUpdate(EntryType.STRAIN);
    autoUpdate.getKeyValue().put(EntryField.LINKS, "google");
    // first auto update. expect it to create a new bulk upload and entry
    autoUpdate = controller.autoUpdateBulkUpload(account.getEmail(), autoUpdate, type);
    Assert.assertNotNull(autoUpdate);
    long entryId = autoUpdate.getEntryId();
    long bulkId = autoUpdate.getBulkUploadId();
    Assert.assertTrue(entryId > 0);
    Assert.assertTrue(bulkId > 0);
    BulkUploadInfo bulkUploadInfo = controller.getBulkImport(account.getEmail(), bulkId, 0, 1000);
    Assert.assertNotNull(bulkUploadInfo);
    EntryDAO dao = DAOFactory.getEntryDAO();
    Entry entry = dao.get(entryId);
    Assert.assertNotNull(entry);
    Assert.assertNotNull(entry.getLinks());
    Assert.assertEquals(1, entry.getLinks().size());
    autoUpdate = new BulkUploadAutoUpdate(EntryType.PLASMID);
    // auto update: expect plasmid and bulk upload with no fields set
    autoUpdate = controller.autoUpdateBulkUpload(account.getEmail(), autoUpdate, type);
    Assert.assertNotNull(autoUpdate);
    entryId = autoUpdate.getEntryId();
    bulkId = autoUpdate.getBulkUploadId();
    Assert.assertTrue(entryId > 0);
    Assert.assertTrue(bulkId > 0);
    entry = dao.get(entryId);
    Assert.assertNotNull(entry);
}

Example 3 with EntryType

use of org.jbei.ice.lib.dto.entry.EntryType 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 4 with EntryType

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

the class BulkUploadValidation method validateEntry.

protected void validateEntry(Entry entry) {
    EntryType type = EntryType.nameToType(entry.getRecordType());
    if (type == null)
        return;
    validateCommonFields(entry);
    if (entry.getLinkedEntries() != null) {
        for (Entry linked : entry.getLinkedEntries()) {
            validateEntry(linked);
        }
    }
    switch(type) {
        default:
        case PART:
            break;
        case STRAIN:
            validateStrain((Strain) entry);
            break;
        case PLASMID:
            validatePlasmid((Plasmid) entry);
            break;
        case SEED:
            validateSeedFields((ArabidopsisSeed) entry);
            break;
        case PROTEIN:
            break;
    }
}

Example 5 with EntryType

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

the class EntriesAsCSV method getEntryFields.

private EntryFieldLabel[] getEntryFields() {
    Set<String> recordTypes = new HashSet<>(dao.getRecordTypes(entries));
    List<EntryFieldLabel> fields = EntryFields.getCommonFields();
    for (String recordType : recordTypes) {
        EntryType type = EntryType.nameToType(recordType);
        if (type == null) {
            Logger.error("Could not convert entry type " + recordType);
            continue;
        }
        switch(type) {
            case SEED:
                EntryFields.addArabidopsisSeedHeaders(fields);
                break;
            case STRAIN:
                EntryFields.addStrainHeaders(fields);
                break;
            case PLASMID:
                EntryFields.addPlasmidHeaders(fields);
                break;
            case PROTEIN:
                EntryFields.addProteinHeaders(fields);
                break;
        }
    }
    return fields.toArray(new EntryFieldLabel[0]);
}