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.io.*; import java.util.*; import java.util.logging.Level; import java.util.logging.Logger; import java.util.regex.Matcher; import java.util.regex.Pattern; import net.sourceforge.seqware.common.module.ReturnValue; import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator; import static net.sourceforge.seqware.pipeline.plugins.PluginTest.metadata; import org.apache.commons.dbutils.handlers.ArrayHandler; import org.junit.*; import org.junit.contrib.java.lang.system.ExpectedSystemExit; import org.junit.rules.TestRule; import org.junit.rules.TestWatcher; import org.junit.runner.Description; /** * Runs the tests for the GenericMetadataSaver plugin * * @author dyuen */ public class GenericMetadataSaverTest extends PluginTest { private ByteArrayOutputStream outStream = null; private ByteArrayOutputStream errStream = null; private Pattern swidPattern = Pattern.compile("SWID: ([\\d]+)"); private Pattern errorPattern = Pattern.compile("ERROR|error|Error|FATAL|fatal|Fatal|WARN|warn|Warn"); private PrintStream systemErr = System.err; /** * This allows us to intercept and ignore the various System.exit calls within runner * so they don't take down the tests as well */ @Rule public final ExpectedSystemExit exit = ExpectedSystemExit.none(); @BeforeClass public static void beforeClass() { BasicTestDatabaseCreator.resetDatabaseWithUsers(); } @Before @Override public void setUp() { super.setUp(); instance = new ModuleRunner(); instance.setMetadata(metadata); outStream = new ByteArrayOutputStream(); errStream = new ByteArrayOutputStream(); PrintStream pso = new PrintStream(outStream); PrintStream pse = new PrintStream(errStream) { @Override public PrintStream append(CharSequence csq) { return super.append(csq); } @Override public void print(String s) { super.print(s); } }; System.setOut(pso); System.setErr(pse); } @Override public void tearDown() { super.tearDown(); } public GenericMetadataSaverTest() { } private String getOut() { return parsePrintStream(outStream); } private String getErr() { return parsePrintStream(errStream); } private String parsePrintStream(ByteArrayOutputStream stream) { StringBuilder sb = new StringBuilder(); BufferedReader r = null; try { ByteArrayInputStream inStream = new ByteArrayInputStream(stream.toByteArray()); r = new BufferedReader(new InputStreamReader(inStream)); String s = r.readLine(); while (s != null) { s = s.trim(); //remove any blank lines if (s.isEmpty()) { s = r.readLine(); continue; } if (s.endsWith("[")) { while (s != null && !s.contains("]")) { sb.append(s); s = r.readLine(); } } sb.append(s).append("\n"); s = r.readLine(); } } catch (IOException ex) { Logger.getLogger(GenericMetadataSaverTest.class.getName()).log(Level.SEVERE, null, ex); } finally { if (r != null) { try { r.close(); } catch (IOException ex) { systemErr.println("Couldn't close System.out reader" + ex.getMessage()); } } } return sb.toString(); } private void checkErrors(String s) { Matcher matcher = errorPattern.matcher(s); systemErr.println("~~~~~~~~~~" + s); Assert.assertFalse("Output contains errors:" + s, matcher.find()); } @Test public void testMatcher() { String string = "[SeqWare Pipeline] ERROR [2012/11/01 15:53:51] | " + "MetadataWS.findObject with search string /288023 encountered error " + "Internal Server Error\nExperiment: null\nSWID: 6740"; Matcher match = swidPattern.matcher(string); Assert.assertTrue(match.find()); Assert.assertEquals("6740", match.group(1)); match = errorPattern.matcher(string); Assert.assertTrue(match.find()); Assert.assertEquals("ERROR", match.group(0)); } @Test public void testSaveNonExistingFileFail() { exit.expectSystemExitWithStatus(ReturnValue.FILENOTREADABLE); instance.setParams( Arrays.asList("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver", "--metadata-parent-accession", "10", "--", "--gms-output-file", "text::text/plain::/abcdefghijklmnop/test.txt", "--gms-algorithm", "UploadText")); String s = getOut(); checkExpectedFailure(); } @Test public void testSaveNonExistingFile() throws IOException { exit.expectSystemExitWithStatus(ReturnValue.SUCCESS); launchPlugin("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver", "--metadata-parent-accession", "10", "--", "--gms-output-file", "text::text/plain::/tmp/abcdefghijklmnop/xyz", "--gms-algorithm", "UploadText", "--gms-suppress-output-file-check"); String s = getOut(); String swid = getAndCheckSwid(s); int accession = Integer.valueOf(swid); // check that file records and processing were created properly BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); Object[] runQuery = dbCreator.runQuery(new ArrayHandler(), "select file_path, meta_type, algorithm from file f, processing_files pf, processing p WHERE f.file_id = pf.file_id AND pf.processing_id = p.processing_id AND p.sw_accession == ?", accession); Assert.assertTrue("values not found", runQuery.length == 3); Assert.assertTrue("file_path value incorrect", runQuery[0].equals("/tmp/abcdefghijklmnop/xyz")); Assert.assertTrue("meta_type value incorrect", runQuery[1].equals("text/plain")); Assert.assertTrue("algorithm value incorrect", runQuery[2].equals("UploadText")); } @Test public void testSaveExistingFile() throws IOException { exit.expectSystemExitWithStatus(ReturnValue.SUCCESS); File createTempFile = File.createTempFile("output", "txt"); createTempFile.createNewFile(); launchPlugin("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver", "--metadata-parent-accession", "10", "--", "--gms-output-file", "text::text/plain::" + createTempFile.getAbsolutePath(), "--gms-algorithm", "UploadText"); String s = getOut(); String swid = getAndCheckSwid(s); int accession = Integer.valueOf(swid); // check that file records and processing were created properly BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator(); Object[] runQuery = dbCreator.runQuery(new ArrayHandler(), "select file_path, meta_type, algorithm from file f, processing_files pf, processing p WHERE f.file_id = pf.file_id AND pf.processing_id = p.processing_id AND p.sw_accession == ?", accession); Assert.assertTrue("values not found", runQuery.length == 3); Assert.assertTrue("file_path value incorrect", runQuery[0].equals(createTempFile.getAbsolutePath())); Assert.assertTrue("meta_type value incorrect", runQuery[1].equals("text/plain")); Assert.assertTrue("algorithm value incorrect", runQuery[2].equals("UploadText")); } //////////////////////////////////////////////////////////////////////////// private String getAndCheckSwid(String s) throws NumberFormatException { Matcher match = swidPattern.matcher(s); Assert.assertTrue("SWID not found in output.", match.find()); String swid = match.group(1); Assert.assertFalse("The SWID was empty", swid.trim().isEmpty()); Integer.parseInt(swid.trim()); return swid; } @Rule public TestRule watchman = new TestWatcher() { //This doesn't catch logs that are sent to Log4J @Override protected void succeeded(Description d) { // do not fail on tests that intend on failing if (!d.getMethodName().endsWith("Fail")) { checkErrors(getErr()); checkErrors(getOut()); } } }; /** * Run an instance with an error and/or failure expected */ private void checkExpectedFailure() { checkReturnValue(ReturnValue.SUCCESS, instance.parse_parameters()); checkReturnValue(ReturnValue.SUCCESS, instance.init()); checkReturnValue(ReturnValue.FAILURE, instance.do_run()); } /** * Run an instance with incorrect parameters expected. */ private void checkExpectedIncorrectParameters() { checkReturnValue(ReturnValue.SUCCESS, instance.parse_parameters()); checkReturnValue(ReturnValue.SUCCESS, instance.init()); checkReturnValue(ReturnValue.INVALIDPARAMETERS, instance.do_run()); } }