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 net.sourceforge.seqware.pipeline.plugins; import java.util.List; import net.sourceforge.seqware.common.model.WorkflowRun; import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator; import static net.sourceforge.seqware.pipeline.plugins.PluginTest.metadata; import org.apache.commons.dbutils.handlers.ArrayListHandler; import org.apache.commons.lang.StringUtils; import org.junit.*; /** * Runs the tests for the FileLinker * @author dyuen */ public class FileLinkerTest extends ExtendedPluginTest { @BeforeClass public static void beforeClass() { BasicTestDatabaseCreator.resetDatabaseWithUsers(); } @Before @Override public void setUp() { instance = new FileLinker(); super.setUp(); } public FileLinkerTest() { } @Test public void testFileLinkerNormal() { String path = FileLinkerTest.class.getResource("file_linker_test.txt").getPath(); launchPlugin("--workflow-accession", "4", "--file-list-file", path); String s = getOut(); String firstWorkflowRun = getAndCheckSwid(s); BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); List<Object[]> runQuery = dbCreator.runQuery(new ArrayListHandler(), "select f.file_path, f.meta_type, i.sw_accession from workflow_run r, processing p, processing_files pf, file f, processing_ius pi, ius i\n" + "WHERE \n" + "r.sw_accession = ?\n" + "AND p.workflow_run_id = r.workflow_run_id\n" + "AND p.processing_id = pf.processing_id\n" + "AND pf.file_id = f.file_id\n" + "AND p.processing_id = pi.processing_id \n" + "AND pi.ius_id = i.ius_id\n" + "ORDER BY f.sw_accession\n" + "; ", Integer.valueOf(firstWorkflowRun)); Assert.assertTrue("first file values were incorrect", runQuery.get(0)[0].equals("funky_file1.gz") && runQuery.get(0)[1].equals("txt")); Assert.assertTrue("second file values were incorrect", runQuery.get(1)[0].equals("funky_file2.gz") && runQuery.get(1)[1].equals("txt")); Assert.assertTrue("ius links were correct", runQuery.get(0)[2].equals(4765) && runQuery.get(1)[2].equals(4765)); // check that we can get them back via metadata methods as well WorkflowRun workflowRun = metadata.getWorkflowRunWithWorkflow(firstWorkflowRun); Assert.assertTrue("could not retrieve optional fields via metadata", workflowRun.getSwAccession().equals(Integer.valueOf(firstWorkflowRun))); Assert.assertTrue("parent workflow incorrect", workflowRun.getWorkflow().getSwAccession() == 4); String workflowRunReport = metadata.getWorkflowRunReport(Integer.valueOf(firstWorkflowRun)); // look for files using the gross metadata way Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("funky_file1.gz") && workflowRunReport.contains("funky_file2.gz")); s = s.split("\n")[1]; int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s)); workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun); Assert.assertTrue("second set of files could not be found using the metadata workflow run report", workflowRunReport.contains("abc1.gz") && workflowRunReport.contains("abc2.gz")); } @Test public void testFileLinkerComma() { String path = FileLinkerTest.class.getResource("file_linker_test_comma.txt").getPath(); launchPlugin("--workflow-accession", "4", "--file-list-file", path, "--csv-separator", ","); String s = getOut(); int firstWorkflowRun = Integer.valueOf(getAndCheckSwid(s)); String workflowRunReport = metadata.getWorkflowRunReport(firstWorkflowRun); // look for files using the gross metadata way Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("cfunky_file1.gz") && workflowRunReport.contains("cfunky_file2.gz")); s = s.split("\n")[1]; int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s)); workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun); Assert.assertTrue("second set of files could not be found using the metadata workflow run report", workflowRunReport.contains("cabc1.gz") && workflowRunReport.contains("cabc2.gz")); } @Test public void testFileLinkerWithNoLanes() { String path = FileLinkerTest.class.getResource("file_linker_no_lane_test.txt").getPath(); launchPlugin("--workflow-accession", "4", "--file-list-file", path); String s = getOut(); int firstWorkflowRun = Integer.valueOf(getAndCheckSwid(s)); String workflowRunReport = metadata.getWorkflowRunReport(firstWorkflowRun); // look for files using the gross metadata way Assert.assertTrue("files could not be found using the metadata workflow run report", workflowRunReport.contains("nfunky_file1.gz") && workflowRunReport.contains("nfunky_file2.gz")); s = s.split("\n")[1]; int secondWorkflowRun = Integer.valueOf(getAndCheckSwid(s)); workflowRunReport = metadata.getWorkflowRunReport(secondWorkflowRun); Assert.assertTrue("second set of files could not be found using the metadata workflow run report", workflowRunReport.contains("nabc1.gz") && workflowRunReport.contains("nabc2.gz")); } @Test public void checkRepeatedFileImportFail() { String path = FileLinkerTest.class.getResource("file_linker_test2.txt").getPath(); launchPlugin("--workflow-accession", "4", "--file-list-file", path); launchPlugin("--workflow-accession", "4", "--file-list-file", path); String s = getOut(); Assert.assertTrue("should be no file imports possible", s.contains("SWID") && StringUtils.countMatches(s, "Ignored file") == 4); } }