Java tutorial
/* * Copyright (c) 2012 The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.jna.drmaa.v1_0; import org.apache.commons.io.FileUtils; import org.broadinstitute.sting.BaseTest; import org.ggf.drmaa.*; import org.testng.Assert; import org.testng.annotations.Test; import java.io.File; import java.util.*; public class JnaSessionPipelineTest extends BaseTest { private String implementation = null; private static final SessionFactory factory = new JnaSessionFactory(); @Test public void testDrmaa() throws Exception { Session session = factory.getSession(); Version version = session.getVersion(); System.out.println(String.format("DRMAA version: %d.%d", version.getMajor(), version.getMinor())); System.out.println(String.format("DRMAA contact(s): %s", session.getContact())); System.out.println(String.format("DRM system(s): %s", session.getDrmSystem())); System.out.println(String.format("DRMAA implementation(s): %s", session.getDrmaaImplementation())); this.implementation = session.getDrmaaImplementation(); } @Test(dependsOnMethods = { "testDrmaa" }) public void testSubmitEcho() throws Exception { if (implementation.contains("LSF")) { System.err.println(" ***********************************************************"); System.err.println(" *************************************************************"); System.err.println(" **** ****"); System.err.println(" **** Skipping JnaSessionIntegrationTest.testSubmitEcho() ****"); System.err.println(" **** Are you using the dotkit .combined_LSF_SGE? ****"); System.err.println(" **** ****"); System.err.println(" *************************************************************"); System.err.println(" ***********************************************************"); return; } File outFile = tryCreateNetworkTempFile("JnaSessionIntegrationTest.out"); Session session = factory.getSession(); session.init(null); try { JobTemplate template = session.createJobTemplate(); template.setRemoteCommand("sh"); template.setOutputPath(":" + outFile.getAbsolutePath()); template.setJoinFiles(true); template.setArgs(Arrays.asList("-c", "echo \"Hello world.\"")); String jobId = session.runJob(template); System.out.println(String.format("Job id %s", jobId)); session.deleteJobTemplate(template); System.out.println("Waiting for job to run: " + jobId); int remotePs = Session.QUEUED_ACTIVE; List<Integer> runningStatuses = Arrays.asList(Session.QUEUED_ACTIVE, Session.RUNNING); while (runningStatuses.contains(remotePs)) { Thread.sleep(30 * 1000L); remotePs = session.getJobProgramStatus(jobId); } Assert.assertEquals(remotePs, Session.DONE, "Job status is not DONE."); JobInfo jobInfo = session.wait(jobId, Session.TIMEOUT_NO_WAIT); Assert.assertTrue(jobInfo.hasExited(), String.format("Job did not exit cleanly: %s", jobId)); Assert.assertEquals(jobInfo.getExitStatus(), 0, String.format("Exit status for jobId %s is non-zero", jobId)); if (jobInfo.hasSignaled()) Assert.fail(String.format("JobId %s exited with signal %s and core dump flag %s", jobId, jobInfo.getTerminatingSignal(), jobInfo.hasCoreDump())); Assert.assertFalse(jobInfo.wasAborted(), String.format("Job was aborted: %s", jobId)); } finally { session.exit(); } Assert.assertTrue(FileUtils.waitFor(outFile, 120), "File not found: " + outFile.getAbsolutePath()); System.out.println("--- output ---"); System.out.println(FileUtils.readFileToString(outFile)); System.out.println("--- output ---"); Assert.assertTrue(outFile.delete(), "Unable to delete " + outFile.getAbsolutePath()); System.out.println("Validating that we reached the end of the test without exit."); } @Test public void testCollectionConversions() { Collection<String> list = Arrays.asList("a=1", "foo=bar", "empty="); Map<String, String> map = new LinkedHashMap<String, String>(); map.put("a", "1"); map.put("foo", "bar"); map.put("empty", ""); Assert.assertEquals(JnaSession.collectionToMap(list), map); Assert.assertEquals(JnaSession.mapToCollection(map), list); } @Test public void testLimitConversions() { Assert.assertEquals(JnaSession.formatLimit(0), "0:00:00"); Assert.assertEquals(JnaSession.formatLimit(59), "0:00:59"); Assert.assertEquals(JnaSession.formatLimit(60), "0:01:00"); Assert.assertEquals(JnaSession.formatLimit(3540), "0:59:00"); Assert.assertEquals(JnaSession.formatLimit(3599), "0:59:59"); Assert.assertEquals(JnaSession.formatLimit(7200), "2:00:00"); Assert.assertEquals(JnaSession.formatLimit(7260), "2:01:00"); Assert.assertEquals(JnaSession.formatLimit(7261), "2:01:01"); Assert.assertEquals(JnaSession.parseLimit("0"), 0); Assert.assertEquals(JnaSession.parseLimit("00"), 0); Assert.assertEquals(JnaSession.parseLimit("0:00"), 0); Assert.assertEquals(JnaSession.parseLimit("00:00"), 0); Assert.assertEquals(JnaSession.parseLimit("0:00:00"), 0); Assert.assertEquals(JnaSession.parseLimit("1"), 1); Assert.assertEquals(JnaSession.parseLimit("01"), 1); Assert.assertEquals(JnaSession.parseLimit("0:01"), 1); Assert.assertEquals(JnaSession.parseLimit("00:01"), 1); Assert.assertEquals(JnaSession.parseLimit("0:00:01"), 1); Assert.assertEquals(JnaSession.parseLimit("10"), 10); Assert.assertEquals(JnaSession.parseLimit("0:10"), 10); Assert.assertEquals(JnaSession.parseLimit("00:10"), 10); Assert.assertEquals(JnaSession.parseLimit("0:00:10"), 10); Assert.assertEquals(JnaSession.parseLimit("1:0"), 60); Assert.assertEquals(JnaSession.parseLimit("1:00"), 60); Assert.assertEquals(JnaSession.parseLimit("01:00"), 60); Assert.assertEquals(JnaSession.parseLimit("0:01:00"), 60); Assert.assertEquals(JnaSession.parseLimit("1:00:00"), 3600); Assert.assertEquals(JnaSession.parseLimit("1:02:03"), 3723); } }