Examples with AttachmentData org.sagebionetworks.repo.model.attachment.AttachmentData used on opensource projects

Example 1 with AttachmentData

use of org.sagebionetworks.repo.model.attachment.AttachmentData in project Synapse-Repository-Services by Sage-Bionetworks.

the class StorageLocationUtilsTest method before.

@Before
public void before() {
    Long nodeId = Long.valueOf(111L);
    Long userId = Long.valueOf(333L);
    List<AttachmentData> attachmentList = new ArrayList<AttachmentData>();
    AttachmentData ad = new AttachmentData();
    ad.setName("ad1");
    ad.setTokenId("ad1Token");
    ad.setContentType("ad1Code");
    ad.setMd5("ad1Md5");
    ad.setUrl("ad1Url");
    ad.setPreviewId("ad1Preview");
    attachmentList.add(ad);
    ad = new AttachmentData();
    ad.setName("ad2");
    ad.setTokenId("ad2Token");
    ad.setContentType("ad2Code");
    ad.setMd5("ad2Md5");
    ad.setUrl("ad2Url");
    ad.setPreviewId("ad2Preview");
    attachmentList.add(ad);
    List<LocationData> locationList = new ArrayList<LocationData>();
    LocationData ld = new LocationData();
    ld.setPath("/ld1Path");
    ld.setType(LocationTypeNames.external);
    locationList.add(ld);
    ld = new LocationData();
    ld.setPath("/abc/xyz");
    ld.setType(LocationTypeNames.awss3);
    locationList.add(ld);
    Map<String, List<String>> strAnnotations = new HashMap<String, List<String>>();
    List<String> md5List = new ArrayList<String>();
    md5List.add("ldMd5");
    strAnnotations.put("md5", md5List);
    List<String> ctList = new ArrayList<String>();
    ctList.add("ldContentType");
    strAnnotations.put("contentType", ctList);
    locations = new StorageLocations(nodeId, userId, attachmentList, locationList, strAnnotations);
    List<S3ObjectSummary> objList1 = new ArrayList<S3ObjectSummary>();
    S3ObjectSummary objSummary = mock(S3ObjectSummary.class);
    when(objSummary.getKey()).thenReturn("111/ad1Token");
    when(objSummary.getSize()).thenReturn(12345L);
    objList1.add(objSummary);
    ObjectListing objListing1 = mock(ObjectListing.class);
    when(objListing1.getObjectSummaries()).thenReturn(objList1);
    when(objListing1.isTruncated()).thenReturn(true);
    List<S3ObjectSummary> objList2 = new ArrayList<S3ObjectSummary>();
    objSummary = mock(S3ObjectSummary.class);
    when(objSummary.getKey()).thenReturn("abc/xyz");
    when(objSummary.getSize()).thenReturn(54321L);
    objList2.add(objSummary);
    objSummary = mock(S3ObjectSummary.class);
    when(objSummary.getKey()).thenReturn("ld1Path");
    when(objSummary.getSize()).thenReturn(99999L);
    objList2.add(objSummary);
    ObjectListing objListing2 = mock(ObjectListing.class);
    when(objListing2.getObjectSummaries()).thenReturn(objList2);
    when(objListing2.isTruncated()).thenReturn(false);
    s3Client = mock(AmazonS3Client.class);
    String bucket = StackConfiguration.getS3Bucket();
    when(s3Client.listObjects(bucket, "111/")).thenReturn(objListing1);
    when(s3Client.listNextBatchOfObjects(objListing1)).thenReturn(objListing2);
}

Example 2 with AttachmentData

use of org.sagebionetworks.repo.model.attachment.AttachmentData in project Synapse-Repository-Services by Sage-Bionetworks.

the class Synapse method uploadAttachmentToSynapse.

/**
 * Upload an attachment to Synapse.
 * @param attachmentType
 * @param userId
 * @param dataFile
 * @param md5
 * @return
 * @throws JSONObjectAdapterException
 * @throws SynapseException
 * @throws IOException
 */
public AttachmentData uploadAttachmentToSynapse(String id, AttachmentType attachmentType, File dataFile, String fileName) throws JSONObjectAdapterException, SynapseException, IOException {
    // First we need to get an S3 token
    S3AttachmentToken token = new S3AttachmentToken();
    token.setFileName(fileName);
    String md5 = MD5ChecksumHelper.getMD5Checksum(dataFile.getAbsolutePath());
    token.setMd5(md5);
    // Create the token
    token = createAttachmentS3Token(id, attachmentType, token);
    // Upload the file
    dataUploader.uploadDataSingle(token, dataFile);
    // We are now done
    AttachmentData newData = new AttachmentData();
    newData.setContentType(token.getContentType());
    newData.setName(fileName);
    newData.setTokenId(token.getTokenId());
    newData.setMd5(token.getMd5());
    return newData;
}

Example 3 with AttachmentData

use of org.sagebionetworks.repo.model.attachment.AttachmentData in project Synapse-Repository-Services by Sage-Bionetworks.

the class IT500SynapseJavaClient method testAttachmentsImageRoundTrip.

/**
 * Test that we can add an attachment to a project and then get it back.
 *
 * @throws IOException
 * @throws JSONObjectAdapterException
 * @throws SynapseException
 */
@Test
public void testAttachmentsImageRoundTrip() throws IOException, JSONObjectAdapterException, SynapseException {
    // First load an image from the classpath
    String fileName = "images/IMAG0019.jpg";
    URL url = IT500SynapseJavaClient.class.getClassLoader().getResource(fileName);
    assertNotNull("Failed to find: " + fileName + " on the classpath", url);
    File originalFile = new File(url.getFile());
    File attachmentDownload = File.createTempFile("AttachmentTestDownload", ".tmp");
    File previewDownload = File.createTempFile("AttachmentPreviewDownload", ".png");
    FileOutputStream writer = null;
    FileInputStream reader = null;
    try {
        // We are now ready to add this file as an attachment on the project
        String finalName = "iamgeFile.jpg";
        AttachmentData data = synapse.uploadAttachmentToSynapse(project.getId(), originalFile, finalName);
        assertEquals(finalName, data.getName());
        // Save this this attachment on the entity.
        project.setAttachments(new ArrayList<AttachmentData>());
        project.getAttachments().add(data);
        // Save this attachment to the project
        project = synapse.putEntity(project);
        assertNotNull(project.getAttachments());
        assertEquals(1, project.getAttachments().size());
        AttachmentData clone = project.getAttachments().get(0);
        assertEquals(data.getName(), clone.getName());
        assertEquals(data.getMd5(), clone.getMd5());
        assertEquals(data.getContentType(), clone.getContentType());
        assertEquals(data.getTokenId(), clone.getTokenId());
        // the attachment should have preview
        assertNotNull(clone.getPreviewId());
        // Now make sure we can download our
        synapse.downloadEntityAttachment(project.getId(), clone, attachmentDownload);
        assertTrue(attachmentDownload.exists());
        System.out.println(attachmentDownload.getAbsolutePath());
        assertEquals(originalFile.length(), attachmentDownload.length());
        // Now make sure we can get the preview image
        // Before we download the preview make sure it exists
        synapse.waitForPreviewToBeCreated(project.getId(), clone.getPreviewId(), PREVIEW_TIMOUT);
        synapse.downloadEntityAttachmentPreview(project.getId(), clone.getPreviewId(), previewDownload);
        assertTrue(previewDownload.exists());
        System.out.println(previewDownload.getAbsolutePath());
        assertTrue(previewDownload.length() > 0);
        assertTrue("A preview size should not exceed 100KB.  This one is " + previewDownload.length(), previewDownload.length() < 100 * 1000);
    } finally {
        if (writer != null) {
            writer.close();
        }
        if (reader != null) {
            reader.close();
        }
        attachmentDownload.delete();
        previewDownload.delete();
    }
}

Example 4 with AttachmentData

use of org.sagebionetworks.repo.model.attachment.AttachmentData in project Synapse-Repository-Services by Sage-Bionetworks.

the class AttachmentManagerImplTest method testCreatePreviewImageLocalUrl.

@Test
public void testCreatePreviewImageLocalUrl() throws NotFoundException, DatastoreException, UnauthorizedException, InvalidModelException, InterruptedException {
    AttachmentData data = new AttachmentData();
    data.setName("shortWide.gif");
    String fileName = "images/shortWide.gif";
    URL url = AttachmentManagerUnitTest.class.getClassLoader().getResource(fileName);
    assertNotNull("Could not find: " + fileName + " on the classpath", url);
    data.setUrl(url.toString());
    String entityId = "123";
    ExampleEntity entity = new ExampleEntity();
    entity.setId(entityId);
    entity.setAttachments(new ArrayList<AttachmentData>());
    entity.getAttachments().add(data);
    // Make sure we can create a preview
    attachmentManager.checkAttachmentsForPreviews(entity);
    // Validate that an image was upload to S3.
    assertEquals(PreviewState.PREVIEW_EXISTS, data.getPreviewState());
    assertNotNull(data.getPreviewId());
    // Make sure we can download the preview
    String key = S3TokenManagerImpl.createAttachmentPathNoSlash(entity.getId(), data.getPreviewId());
    waitForPreview(key);
    // Make sure this preview gets deleted
    keysToDelete.add(key);
    // Wait for the key file to be finsihed
    File temp = s3Utility.downloadFromS3(key);
    assertNotNull(temp);
    System.out.println(temp.getAbsolutePath());
    assertTrue("The preview image should be larger than zero bytes", temp.length() > 0);
    assertTrue("The preview image should be smaller than 100K bytes", temp.length() < 100 * 1000);
    temp.delete();
}

Example 5 with AttachmentData

use of org.sagebionetworks.repo.model.attachment.AttachmentData in project Synapse-Repository-Services by Sage-Bionetworks.

the class AttachmentManagerImplTest method testCreatePreviewImageS3.

@Ignore
@Test
public void testCreatePreviewImageS3() throws NotFoundException, DatastoreException, UnauthorizedException, InvalidModelException, InterruptedException {
    String entityId = idGenerator.generateNewId().toString();
    AttachmentData data = new AttachmentData();
    data.setName("shortWide.gif");
    String fileName = "images/shortWide.gif";
    URL url = AttachmentManagerUnitTest.class.getClassLoader().getResource(fileName);
    assertNotNull("Could not find: " + fileName + " on the classpath", url);
    File toUpload = new File(url.getFile());
    String tokenId = S3TokenManagerImpl.createTokenId(idGenerator.generateNewId(), data.getName());
    String attachmentS3Key = S3TokenManagerImpl.createAttachmentPathNoSlash(entityId, tokenId);
    // Upload this file
    s3Utility.uploadToS3(toUpload, attachmentS3Key);
    // Make sure this file gets deleted
    keysToDelete.add(attachmentS3Key);
    // Now create the preview
    data.setTokenId(tokenId);
    ExampleEntity entity = new ExampleEntity();
    entity.setId(entityId);
    entity.setAttachments(new ArrayList<AttachmentData>());
    entity.getAttachments().add(data);
    // Make sure we can create a preview
    attachmentManager.checkAttachmentsForPreviews(entity);
    // Validate that an image was upload to S3.
    assertEquals(PreviewState.PREVIEW_EXISTS, data.getPreviewState());
    assertNotNull(data.getPreviewId());
    // Make sure we can download the preview
    String previewKey = S3TokenManagerImpl.createAttachmentPathNoSlash(entity.getId(), data.getPreviewId());
    // Wait for the preview
    waitForPreview(previewKey);
    // Make sure this preview gets deleted
    keysToDelete.add(previewKey);
    File temp = s3Utility.downloadFromS3(previewKey);
    assertNotNull(temp);
    System.out.println(temp.getAbsolutePath());
    assertTrue("The preview image should be larger than zero bytes", temp.length() > 0);
    assertTrue("The preview image should be smaller than 100K bytes", temp.length() < 100 * 1000);
    temp.delete();
}