Java tutorial
/* * Copyright 2012-2016 Broad Institute, Inc. * * 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.gatk.utils.jna.lsf.v7_0_6; import com.sun.jna.*; import com.sun.jna.ptr.IntByReference; import org.apache.commons.io.FileUtils; import org.broadinstitute.gatk.utils.Utils; import org.testng.Assert; import org.testng.SkipException; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import org.broadinstitute.gatk.utils.BaseTest; import org.broadinstitute.gatk.utils.jna.lsf.v7_0_6.LibBat.*; import java.io.File; /** * Really unit tests, but these tests will only run on systems with LSF set up. */ public class LibBatQueueTest extends BaseTest { @BeforeClass(enabled = false) public void initLibBat() { Assert.assertFalse(LibBat.lsb_init("LibBatQueueTest") < 0, LibBat.lsb_sperror("lsb_init() failed")); } @Test(enabled = false) public void testClusterName() { String clusterName = LibLsf.ls_getclustername(); System.out.println("Cluster name: " + clusterName); Assert.assertNotNull(clusterName); } @Test(enabled = false) public void testReadConfEnv() { LibLsf.config_param[] configParams = (LibLsf.config_param[]) new LibLsf.config_param().toArray(4); configParams[0].paramName = "LSF_UNIT_FOR_LIMITS"; configParams[1].paramName = "LSF_CONFDIR"; configParams[2].paramName = "MADE_UP_PARAMETER"; Structure.autoWrite(configParams); if (LibLsf.ls_readconfenv(configParams[0], null) != 0) { Assert.fail(LibLsf.ls_sysmsg()); } Structure.autoRead(configParams); System.out.println("LSF_UNIT_FOR_LIMITS: " + configParams[0].paramValue); Assert.assertNotNull(configParams[1].paramValue); Assert.assertNull(configParams[2].paramValue); Assert.assertNull(configParams[3].paramName); Assert.assertNull(configParams[3].paramValue); } @Test(enabled = false) public void testReadQueueLimits() { String queue = "hour"; StringArray queues = new StringArray(new String[] { queue }); IntByReference numQueues = new IntByReference(1); queueInfoEnt queueInfo = LibBat.lsb_queueinfo(queues, numQueues, null, null, 0); Assert.assertEquals(numQueues.getValue(), 1); Assert.assertNotNull(queueInfo); Assert.assertEquals(queueInfo.queue, queue); int runLimit = queueInfo.rLimits[LibLsf.LSF_RLIMIT_RUN]; Assert.assertTrue(runLimit > 0, "LSF run limit is not greater than zero: " + runLimit); } @Test(enabled = false) public void testSubmitEcho() throws Exception { if (!queueTestRunModeIsSet) { throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode"); } String queue = "hour"; File outFile = tryCreateNetworkTempFile("LibBatQueueTest.out"); submit req = new submit(); for (int i = 0; i < LibLsf.LSF_RLIM_NLIMITS; i++) req.rLimits[i] = LibLsf.DEFAULT_RLIMIT; req.projectName = "LibBatQueueTest"; req.options |= LibBat.SUB_PROJECT_NAME; req.queue = queue; req.options |= LibBat.SUB_QUEUE; req.outFile = outFile.getPath(); req.options |= LibBat.SUB_OUT_FILE; req.userPriority = 100; req.options2 |= LibBat.SUB2_JOB_PRIORITY; req.command = "echo \"Hello world.\""; String[] argv = { "", "-a", "tv" }; int setOptionResult = LibBat.setOption_(argv.length, new StringArray(argv), "a:", req, ~0, ~0, ~0, null); Assert.assertTrue(setOptionResult != -1, "setOption_ returned -1"); submitReply reply = new submitReply(); long jobId = LibBat.lsb_submit(req, reply); Assert.assertFalse(jobId < 0, LibBat.lsb_sperror("Error dispatching")); System.out.println("Waiting for job to run: " + jobId); int jobStatus = LibBat.JOB_STAT_PEND; while (Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_PEND) || Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_RUN)) { Thread.sleep(30 * 1000L); int numJobs = LibBat.lsb_openjobinfo(jobId, null, null, null, null, LibBat.ALL_JOB); try { Assert.assertEquals(numJobs, 1); IntByReference more = new IntByReference(); jobInfoEnt jobInfo = LibBat.lsb_readjobinfo(more); Assert.assertNotNull(jobInfo, "Job info is null"); Assert.assertEquals(more.getValue(), 0, "More job info results than expected"); jobStatus = jobInfo.status; } finally { LibBat.lsb_closejobinfo(); } } Assert.assertTrue(Utils.isFlagSet(jobStatus, LibBat.JOB_STAT_DONE), String.format("Unexpected job status: 0x%02x", jobStatus)); 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()); Assert.assertEquals(reply.queue, req.queue, "LSF reply queue does not match requested queue."); System.out.println("Validating that we reached the end of the test without exit."); } }