Java tutorial
/* Copyright (c) 2013, Washington University in St.Louis All rights reserved. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. */ package edu.wustl.xipHost.caGrid; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.EOFException; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.util.HashMap; import java.util.Map; import java.util.zip.ZipInputStream; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; import org.apache.log4j.Logger; import org.cagrid.transfer.context.client.TransferServiceContextClient; import org.cagrid.transfer.context.client.helper.TransferClientHelper; import org.cagrid.transfer.context.stubs.types.TransferServiceContextReference; import org.globus.gsi.GlobusCredential; import edu.osu.bmi.utils.io.zip.ZipEntryInputStream; import edu.wustl.xipHost.dicom.DicomUtil; import edu.wustl.xipHost.hostLogin.GridLogin; import edu.wustl.xipHost.hostLogin.Login; import gov.nih.nci.cagrid.ncia.client.NCIACoreServiceClient; import java.io.FileFilter; /** * @author Jaroslaw Krych * */ public class RetrieveNBIASecuredTest { final static Logger logger = Logger.getLogger(RetrieveNBIASecuredTest.class); String gridServiceUrl = "http://imaging.nci.nih.gov/wsrf/services/cagrid/NCIACoreService"; String authUrl = "https://cagrid-auth.nci.nih.gov:8443/wsrf/services/cagrid/AuthenticationService"; String dorianURL = "https://cagrid-dorian.nci.nih.gov:8443/wsrf/services/cagrid/Dorian"; File inputDir; @BeforeClass public static void setUpBeforeClass() throws Exception { } /** * @throws java.lang.Exception */ @AfterClass public static void tearDownAfterClass() throws Exception { } @Test public void test() throws Exception { System.setProperty("org.apache.commons.logging.Log", "org.apache.commons.logging.impl.NoOpLog"); Login login = new GridLogin(); String userName = "<JIRAusername>"; String password = "<JIRApassword>"; DcmFileFilter dcmFilter = new DcmFileFilter(); login.login(userName, password); GlobusCredential globusCred = login.getGlobusCredential(); boolean isConnectionSecured = login.isConnectionSecured(); logger.debug("Acquired NBIA GlobusCredential. Connection secured = " + isConnectionSecured); if (!isConnectionSecured) { fail("Unable to acquire NBIA GlobusCredential. Check username and password."); return; } NCIACoreServiceClient client = new NCIACoreServiceClient(gridServiceUrl, globusCred); client.setAnonymousPrefered(false); TransferServiceContextReference tscr = client.retrieveDicomDataBySeriesUID("1.3.6.1.4.1.9328.50.1.4718"); TransferServiceContextClient tclient = new TransferServiceContextClient(tscr.getEndpointReference(), globusCred); InputStream istream = TransferClientHelper.getData(tclient.getDataTransferDescriptor(), globusCred); ZipInputStream zis = new ZipInputStream(istream); ZipEntryInputStream zeis = null; BufferedInputStream bis = null; File importDir = new File("./test-content/NBIA5"); if (!importDir.exists()) { importDir.mkdirs(); } else { File[] files = importDir.listFiles(dcmFilter); for (int j = 0; j < files.length; j++) { File file = files[j]; file.delete(); } } while (true) { try { zeis = new ZipEntryInputStream(zis); } catch (EOFException e) { break; } catch (IOException e) { logger.error(e, e); } String unzzipedFile = null; try { unzzipedFile = importDir.getCanonicalPath(); } catch (IOException e) { logger.error(e, e); } logger.debug(" filename: " + zeis.getName()); bis = new BufferedInputStream(zeis); byte[] data = new byte[8192]; int bytesRead = 0; String retrievedFilePath = unzzipedFile + File.separator + zeis.getName(); try { BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(retrievedFilePath)); while ((bytesRead = (bis.read(data, 0, data.length))) != -1) { bos.write(data, 0, bytesRead); } bos.flush(); bos.close(); } catch (IOException e) { logger.error(e, e); } } try { zis.close(); tclient.destroy(); } catch (IOException e) { logger.error(e, e); } File[] retrievedFiles = importDir.listFiles(dcmFilter); int numbOfRetreivedFiles = retrievedFiles.length; assertEquals("Number of retrieved files should be 2 but is. " + numbOfRetreivedFiles, numbOfRetreivedFiles, 2); //Assert file names. They should be equal to items' SeriesInstanceUIDs Map<String, File> mapRetrievedFiles = new HashMap<String, File>(); for (int i = 0; i < numbOfRetreivedFiles; i++) { File file = retrievedFiles[i]; mapRetrievedFiles.put(file.getName(), file); } boolean retrievedFilesCorrect = false; if (mapRetrievedFiles.containsKey("1.3.6.1.4.1.9328.50.1.4716.dcm") && mapRetrievedFiles.containsKey("1.3.6.1.4.1.9328.50.1.4720.dcm")) { retrievedFilesCorrect = true; } assertTrue("Retrieved files are not as expected.", retrievedFilesCorrect); } class DcmFileFilter implements FileFilter { @Override public boolean accept(File file) { try { if (DicomUtil.mimeType(file).equalsIgnoreCase("application/dicom")) { return true; } else { return false; } } catch (IOException e) { return false; } } } }