Examples with Upload org.sagebionetworks.bridge.models.upload.Upload used on opensource projects

Example 1 with Upload

use of org.sagebionetworks.bridge.models.upload.Upload in project BridgeServer2 by Sage-Bionetworks.

the class Exporter3ServiceTest method completeUpload_NoSharing.

@Test
public void completeUpload_NoSharing() {
    // Set up inputs.
    Upload upload = Upload.create();
    upload.setHealthCode(TestConstants.HEALTH_CODE);
    upload.setUploadId(RECORD_ID);
    // Mock AccountService.
    Account account = Account.create();
    account.setSharingScope(SharingScope.NO_SHARING);
    when(mockAccountService.getAccount(any())).thenReturn(Optional.of(account));
    // Mock HealthDataEx3Service.
    HealthDataRecordEx3 createdRecord = HealthDataRecordEx3.create();
    createdRecord.setId(RECORD_ID);
    when(mockHealthDataEx3Service.createOrUpdateRecord(any())).thenReturn(createdRecord);
    // Execute.
    exporter3Service.completeUpload(app, upload);
    // No call to SQS.
    verifyZeroInteractions(mockSqsClient);
}

Example 2 with Upload

use of org.sagebionetworks.bridge.models.upload.Upload in project BridgeServer2 by Sage-Bionetworks.

the class UploadService method createUpload.

public UploadSession createUpload(String appId, StudyParticipant participant, UploadRequest uploadRequest) {
    Validate.entityThrowingException(UploadValidator.INSTANCE, uploadRequest);
    // Check to see if upload is a dupe, and if it is, get the upload status.
    String uploadMd5 = uploadRequest.getContentMd5();
    DateTime uploadRequestedOn = DateUtils.getCurrentDateTime();
    String originalUploadId = null;
    UploadStatus originalUploadStatus = null;
    // same uploads over and over again with each test run.
    if (!API_APP_ID.equals(appId)) {
        try {
            originalUploadId = uploadDedupeDao.getDuplicate(participant.getHealthCode(), uploadMd5, uploadRequestedOn);
            if (originalUploadId != null) {
                Upload originalUpload = uploadDao.getUpload(originalUploadId);
                originalUploadStatus = originalUpload.getStatus();
            }
        } catch (RuntimeException ex) {
            // Don't want dedupe logic to fail the upload. Log an error and swallow the exception.
            logger.error("Error deduping upload: " + ex.getMessage(), ex);
        }
    }
    String uploadId;
    if (originalUploadId != null && originalUploadStatus == UploadStatus.REQUESTED) {
        // This is a dupe of a previous upload, and that previous upload is incomplete (REQUESTED). Instead of
        // creating a new upload in the upload table, reactivate the old one.
        uploadId = originalUploadId;
    } else {
        // This is a new upload.
        Upload upload = uploadDao.createUpload(uploadRequest, appId, participant.getHealthCode(), originalUploadId);
        uploadId = upload.getUploadId();
        if (originalUploadId != null) {
            // We had a dupe of a previous completed upload. Log this for future analysis.
            logger.info("Detected dupe: App " + appId + ", upload " + uploadId + " is a dupe of " + originalUploadId);
        } else {
            try {
                // Not a dupe. Register this dupe so we can detect dupes of this.
                uploadDedupeDao.registerUpload(participant.getHealthCode(), uploadMd5, uploadRequestedOn, uploadId);
            } catch (RuntimeException ex) {
                // Don't want dedupe logic to fail the upload. Log an error and swallow the exception.
                logger.error("Error registering upload " + uploadId + " in dedupe table: " + ex.getMessage(), ex);
            }
        }
    }
    // Upload ID in DynamoDB is the same as the S3 Object ID
    GeneratePresignedUrlRequest presignedUrlRequest = new GeneratePresignedUrlRequest(uploadBucket, uploadId, HttpMethod.PUT);
    // Expiration
    final Date expiration = DateTime.now(DateTimeZone.UTC).toDate();
    expiration.setTime(expiration.getTime() + EXPIRATION);
    presignedUrlRequest.setExpiration(expiration);
    // Temporary session credentials
    AWSStaticCredentialsProvider credentialsProvider = new AWSStaticCredentialsProvider(uploadCredentailsService.getSessionCredentials());
    presignedUrlRequest.setRequestCredentialsProvider(credentialsProvider);
    // Ask for server-side encryption
    presignedUrlRequest.addRequestParameter(SERVER_SIDE_ENCRYPTION, AES_256_SERVER_SIDE_ENCRYPTION);
    // Additional headers for signing
    presignedUrlRequest.setContentMd5(uploadMd5);
    presignedUrlRequest.setContentType(uploadRequest.getContentType());
    URL url = s3UploadClient.generatePresignedUrl(presignedUrlRequest);
    return new UploadSession(uploadId, url, expiration.getTime());
}

Example 3 with Upload

use of org.sagebionetworks.bridge.models.upload.Upload in project BridgeServer2 by Sage-Bionetworks.

the class UploadService method getUploadValidationStatus.

/**
 * <p>
 * Gets validation status and messages for the given upload ID. This includes the health data record, if one was
 * created for the upload.
 * </p>
 * <p>
 * user comes from the controller, and is guaranteed to be present. However, uploadId is user input and must be
 * validated.
 * </p>
 *
 * @param uploadId
 *         ID of upload to fetch, must be non-null and non-empty
 * @return upload validation status, which includes the health data record if one was created
 */
public UploadValidationStatus getUploadValidationStatus(@Nonnull String uploadId) {
    Upload upload = getUpload(uploadId);
    // get record, if it exists
    HealthDataRecord record = null;
    String recordId = upload.getRecordId();
    if (!Strings.isNullOrEmpty(recordId)) {
        try {
            record = healthDataService.getRecordById(recordId);
        } catch (RuntimeException ex) {
            // Underlying service failed to get the health data record. Log a warning, but move on.
            logger.warn("Error getting record ID " + recordId + " for upload ID " + uploadId + ": " + ex.getMessage(), ex);
        }
    }
    UploadValidationStatus validationStatus = UploadValidationStatus.from(upload, record);
    return validationStatus;
}

Example 4 with Upload

use of org.sagebionetworks.bridge.models.upload.Upload in project BridgeServer2 by Sage-Bionetworks.

the class UploadValidationContextTest method shallowCopy.

@Test
public void shallowCopy() {
    // dummy objects to test against
    App app = TestUtils.getValidApp(UploadValidationContextTest.class);
    Upload upload = new DynamoUpload2();
    File tempDir = mock(File.class);
    File dataFile = mock(File.class);
    File decryptedDataFile = mock(File.class);
    Map<String, File> unzippedDataFileMap = ImmutableMap.<String, File>builder().put("foo", mock(File.class)).put("bar", mock(File.class)).put("baz", mock(File.class)).build();
    JsonNode infoJsonNode = BridgeObjectMapper.get().createObjectNode();
    HealthDataRecord record = HealthDataRecord.create();
    // create original
    UploadValidationContext original = new UploadValidationContext();
    original.setHealthCode(HEALTH_CODE);
    original.setAppId(app.getIdentifier());
    original.setUpload(upload);
    original.setSuccess(false);
    original.addMessage("common message");
    original.setTempDir(tempDir);
    original.setDataFile(dataFile);
    original.setDecryptedDataFile(decryptedDataFile);
    original.setUnzippedDataFileMap(unzippedDataFileMap);
    original.setInfoJsonNode(infoJsonNode);
    original.setHealthDataRecord(record);
    original.setRecordId("test-record");
    // copy and validate
    UploadValidationContext copy = original.shallowCopy();
    assertEquals(copy.getHealthCode(), HEALTH_CODE);
    assertSame(copy.getAppId(), app.getIdentifier());
    assertSame(copy.getUpload(), upload);
    assertFalse(copy.getSuccess());
    assertSame(copy.getTempDir(), tempDir);
    assertSame(copy.getDataFile(), dataFile);
    assertSame(copy.getDecryptedDataFile(), decryptedDataFile);
    assertEquals(copy.getUnzippedDataFileMap(), unzippedDataFileMap);
    assertSame(copy.getInfoJsonNode(), infoJsonNode);
    assertSame(copy.getHealthDataRecord(), record);
    assertEquals(copy.getRecordId(), "test-record");
    assertEquals(copy.getMessageList().size(), 1);
    assertEquals(copy.getMessageList().get(0), "common message");
    // modify original and validate copy unchanged
    original.setHealthCode("new-health-code");
    original.addMessage("original message");
    assertEquals(copy.getHealthCode(), HEALTH_CODE);
    assertEquals(copy.getMessageList().size(), 1);
    assertEquals(copy.getMessageList().get(0), "common message");
    // modify copy and validate original unchanged
    copy.setRecordId("new-record-id");
    copy.addMessage("copy message");
    assertEquals(original.getRecordId(), "test-record");
    assertEquals(original.getMessageList().size(), 2);
    assertEquals(original.getMessageList().get(0), "common message");
    assertEquals(original.getMessageList().get(1), "original message");
}

Example 5 with Upload

use of org.sagebionetworks.bridge.models.upload.Upload in project BridgeServer2 by Sage-Bionetworks.

the class UploadValidationTaskFactoryTest method test.

@Test
public void test() {
    // test dao and handlers
    List<UploadValidationHandler> handlerList = Collections.emptyList();
    UploadDao dao = mock(UploadDao.class);
    FileHelper fileHelper = new FileHelper();
    HealthDataService healthDataService = new HealthDataService();
    // set up task factory
    UploadValidationTaskFactory taskFactory = new UploadValidationTaskFactory();
    taskFactory.setFileHelper(fileHelper);
    taskFactory.setHandlerList(handlerList);
    taskFactory.setUploadDao(dao);
    taskFactory.setHealthDataService(healthDataService);
    // inputs
    App app = TestUtils.getValidApp(UploadValidationTaskFactoryTest.class);
    Upload upload = Upload.create();
    upload.setHealthCode(HEALTH_CODE);
    // execute and validate
    UploadValidationTask task = taskFactory.newTask(app.getIdentifier(), upload);
    assertEquals(task.getContext().getHealthCode(), HEALTH_CODE);
    assertSame(task.getContext().getAppId(), app.getIdentifier());
    assertSame(task.getContext().getUpload(), upload);
    assertSame(task.getFileHelper(), fileHelper);
    assertSame(task.getHandlerList(), handlerList);
    assertSame(task.getUploadDao(), dao);
    assertSame(task.getHealthDataService(), healthDataService);
}