Java tutorial
/* * Copyright (C) 2012 SeqWare * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package io.seqware.pipeline.plugins; import io.seqware.Engines; import io.seqware.common.model.WorkflowRunStatus; import java.io.File; import java.io.IOException; import java.util.Arrays; import java.util.List; import java.util.Map; import net.sourceforge.seqware.common.model.WorkflowRun; import net.sourceforge.seqware.common.util.filetools.FileTools; import net.sourceforge.seqware.common.util.maptools.MapTools; import net.sourceforge.seqware.common.util.maptools.ReservedIniKeys; import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator; import net.sourceforge.seqware.pipeline.plugins.ExtendedPluginTest; import org.apache.commons.dbutils.handlers.ArrayListHandler; import org.apache.commons.io.FileUtils; import org.junit.Assert; import org.junit.Before; import org.junit.BeforeClass; import org.junit.Test; /** * Runs the tests for the FileLinker * * @author dyuen */ public class WorkflowSchedulerTest extends ExtendedPluginTest { @BeforeClass public static void beforeClass() { BasicTestDatabaseCreator.resetDatabaseWithUsers(); } @Before @Override public void setUp() { instance = new WorkflowScheduler(); super.setUp(); } @Test public void testNormalSchedule() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); } @Test public void testOozieWorkflowEngine() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--workflow-engine", Engines.TYPES.oozie.toString()); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.workflow_engine from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); Assert.assertTrue("schedule workflow engine is incorrect " + runQuery.get(0)[2].toString(), runQuery.get(0)[2].equals(Engines.TYPES.oozie.toString())); } @Test public void testOozieSGEWorkflowEngine() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--workflow-engine", Engines.TYPES.oozie_sge.toString()); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.workflow_engine from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); Assert.assertTrue("schedule workflow engine is incorrect " + runQuery.get(0)[2].toString(), runQuery.get(0)[2].equals(Engines.TYPES.oozie_sge.toString())); } @Test public void testParentAccessions() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--parent-accessions", "4765,4789"); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); String iniFile = runQuery.get(0)[2].toString(); Map<String, String> iniMap = MapTools.iniString2Map(iniFile); testIniKey(iniMap, ReservedIniKeys.PARENT_DASH_ACCESSIONS.getKey(), "4765"); testIniKey(iniMap, ReservedIniKeys.PARENT_DASH_ACCESSIONS.getKey(), "4789"); testIniKey(iniMap, ReservedIniKeys.PARENT_ACCESSION.getKey(), "4765"); testIniKey(iniMap, ReservedIniKeys.PARENT_ACCESSION.getKey(), "4789"); testIniKey(iniMap, ReservedIniKeys.PARENT_UNDERSCORE_ACCESSIONS.getKey(), "4765"); testIniKey(iniMap, ReservedIniKeys.PARENT_UNDERSCORE_ACCESSIONS.getKey(), "4789"); } private void testIniKey(Map<String, String> iniMap, String key, String value) { Assert.assertTrue(key + " incorrect", iniMap.get(key).contains(value)); } @Test public void testLinkWorkflowRunToParents() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--link-workflow-run-to-parents", "4765,4789"); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); List<Object[]> runQuery2 = dbCreator.runQuery(new ArrayListHandler(), "select i.sw_accession from ius_workflow_runs ir join workflow_run r on ir.workflow_run_id=r.workflow_run_id join ius i on i.ius_id=ir.ius_id where r.sw_accession = ? order by sw_accession;", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "ius links are incorrect " + runQuery2.get(0)[0].toString() + " " + runQuery2.get(1)[0].toString(), runQuery2.get(0)[0].equals(4765) && runQuery2.get(1)[0].equals(4789)); } @Test public void testInputFiles() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--input-files", "835,838"); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun)); Assert.assertTrue("input file links incorrect", workflowRun.getInputFileAccessions().contains(835) && workflowRun.getInputFileAccessions().contains(838)); } @Test public void testDefaultIniFromBundle() { launchPlugin("--workflow-accession", "2861", "--host", FileTools.getLocalhost(null).hostname); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(16)); WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun)); // check that default keys are present Map<String, String> baseMap = MapTools.iniString2Map(workflowRun.getIniFile()); Assert.assertTrue("base map is missing variables", baseMap.containsKey("min_qual_score") && baseMap.containsKey("inputs_read_1") && baseMap.containsKey("inputs_read_2") && baseMap.containsKey("cat") && baseMap.containsKey("output_prefix") && baseMap.containsKey("output_dir") && baseMap.containsKey("min_percent_bases")); Assert.assertTrue("base map has incorrect values", baseMap.get("min_qual_score").equals("20") && baseMap.get("cat").equals("zcat") && baseMap.get("min_percent_bases").equals("90")); } @Test public void testLeftToRightOverrideByIniFiles() throws IOException { String[] iniFileContents1 = { "min_qual_score=30", "min_percent_bases=90", "cat=dog" }; String[] iniFileContents2 = { "min_qual_score=40", "min_percent_bases=100" }; String[] iniFileContents3 = { "min_qual_score=50" }; File ini1 = File.createTempFile("ini", "ini"); File ini2 = File.createTempFile("ini", "ini"); File ini3 = File.createTempFile("ini", "ini"); ini1.deleteOnExit(); ini2.deleteOnExit(); ini3.deleteOnExit(); FileUtils.writeLines(ini1, Arrays.asList(iniFileContents1)); FileUtils.writeLines(ini2, Arrays.asList(iniFileContents2)); FileUtils.writeLines(ini3, Arrays.asList(iniFileContents3)); launchPlugin("--workflow-accession", "2861", "--host", FileTools.getLocalhost(null).hostname, "--ini-files", ini1.getAbsolutePath() + "," + ini2.getAbsolutePath() + "," + ini3.getAbsolutePath()); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(16)); WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun)); // check that default keys are present Map<String, String> baseMap = MapTools.iniString2Map(workflowRun.getIniFile()); Assert.assertTrue("overridden map is missing variables", baseMap.containsKey("min_qual_score") && baseMap.containsKey("inputs_read_1") && baseMap.containsKey("inputs_read_2") && baseMap.containsKey("cat") && baseMap.containsKey("output_prefix") && baseMap.containsKey("output_dir") && baseMap.containsKey("min_percent_bases")); Assert.assertTrue("overridden map has incorrect values", baseMap.get("min_qual_score").equals("50") && baseMap.get("cat").equals("dog") && baseMap.get("min_percent_bases").equals("100") && baseMap.get("output_dir").equals("results")); } @Test public void testLeftToRightOverrideByCLI() throws IOException { String[] iniFileContents1 = { "min_qual_score=30", "min_percent_bases=90", "cat=dog" }; String[] iniFileContents2 = { "min_qual_score=40", "min_percent_bases=100" }; String[] iniFileContents3 = { "min_qual_score=50" }; File ini1 = File.createTempFile("ini", "ini"); File ini2 = File.createTempFile("ini", "ini"); File ini3 = File.createTempFile("ini", "ini"); ini1.deleteOnExit(); ini2.deleteOnExit(); ini3.deleteOnExit(); FileUtils.writeLines(ini1, Arrays.asList(iniFileContents1)); FileUtils.writeLines(ini2, Arrays.asList(iniFileContents2)); FileUtils.writeLines(ini3, Arrays.asList(iniFileContents3)); launchPlugin("--workflow-accession", "2861", "--host", FileTools.getLocalhost(null).hostname, "--ini-files", ini1.getAbsolutePath() + "," + ini2.getAbsolutePath() + "," + ini3.getAbsolutePath(), "--", "--output_dir", "zebra", "--min_qual_score", "0"); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.ini_file from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(16)); WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun)); // check that default keys are present Map<String, String> baseMap = MapTools.iniString2Map(workflowRun.getIniFile()); Assert.assertTrue("overridden map is missing variables", baseMap.containsKey("min_qual_score") && baseMap.containsKey("inputs_read_1") && baseMap.containsKey("inputs_read_2") && baseMap.containsKey("cat") && baseMap.containsKey("output_prefix") && baseMap.containsKey("output_dir") && baseMap.containsKey("min_percent_bases")); Assert.assertTrue("overridden map has incorrect values", baseMap.get("min_qual_score").equals("0") && baseMap.get("cat").equals("dog") && baseMap.get("min_percent_bases").equals("100") && baseMap.get("output_dir").equals("zebra")); } @Test public void testMetadataOff() { launchPlugin("--workflow-accession", "2860", "--host", FileTools.getLocalhost(null).hostname, "--no-metadata"); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select r.status, r.workflow_id, r.workflow_engine from workflow_run r\n" + "WHERE \n" + "r.sw_accession = ?\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue( "schedule workflow is incorrect " + runQuery.get(0)[0].toString() + " " + runQuery.get(0)[1].toString(), runQuery.get(0)[0].equals(WorkflowRunStatus.submitted.toString()) && runQuery.get(0)[1].equals(15)); WorkflowRun workflowRun = metadata.getWorkflowRun(Integer.valueOf(firstWorkflowRun)); // check that default keys are present Map<String, String> baseMap = MapTools.iniString2Map(workflowRun.getIniFile()); Assert.assertTrue("base map is metadata", baseMap.containsKey("metadata")); Assert.assertTrue("base map has incorrect values", baseMap.get("metadata").equals("no-metadata")); } }