X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=7e775d856fb3fb842d2f451255ffad3d10bbda62;hb=04c8f7bff663aa469127e9eed4164e02933782f1;hp=40263c3e81ec1564a33752a4cfb1ad8c9af4ad12;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index 40263c3..7e775d8 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,121 +20,408 @@ */ package jalview.bin; -import static org.junit.Assert.*; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStreamReader; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; -import org.junit.AfterClass; -import org.junit.BeforeClass; -import org.junit.Test; +import org.testng.Assert; +import org.testng.FileAssert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeTest; +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; + +import io.github.classgraph.ClassGraph; +import io.github.classgraph.ModuleRef; +import io.github.classgraph.ScanResult; +import jalview.gui.JvOptionPane; public class CommandLineOperations { - @BeforeClass - public static void setUpBeforeClass() throws Exception + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - @AfterClass - public static void tearDownAfterClass() throws Exception + private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed + // on + // full test run than on + // individual tests + + private static final int SETUP_TIMEOUT = 9500; + + private static final int MINFILESIZE_SMALL = 2096; + + private static final int MINFILESIZE_BIG = 4096; + + private ArrayList successfulCMDs = new ArrayList<>(); + + /*** + * from + * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when + * -using-javas-runtime-exec + * + * @author jimp + * + */ + private static class Worker extends Thread { + private final Process process; + + private BufferedReader outputReader; + + private BufferedReader errorReader; + + private Integer exit; + + private Worker(Process process) + { + this.process = process; + } + + @Override + public void run() + { + try + { + exit = process.waitFor(); + } catch (InterruptedException ignore) + { + return; + } + } + + public BufferedReader getOutputReader() + { + return outputReader; + } + + public void setOutputReader(BufferedReader outputReader) + { + this.outputReader = outputReader; + } + + public BufferedReader getErrorReader() + { + return errorReader; + } + + public void setErrorReader(BufferedReader errorReader) + { + this.errorReader = errorReader; + } } -/*** - * from http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when-using-javas-runtime-exec - * @author jimp - * - */ -private static class Worker extends Thread { - private final Process process; - private Integer exit; - private Worker(Process process) { - this.process = process; + + private static ClassGraph scanner = null; + + private static String classpath = null; + + private static String modules = null; + + private static String java_exe = null; + + public synchronized static String getClassPath() + { + if (scanner == null) + { + scanner = new ClassGraph(); + ScanResult scan = scanner.scan(); + classpath = scan.getClasspath(); + modules = ""; + for (ModuleRef mr : scan.getModules()) + { + modules.concat(mr.getName()); + } + java_exe = System.getProperty("java.home") + File.separator + "bin" + + File.separator + "java"; + + } + while (classpath == null) + { + try + { + Thread.sleep(10); + } catch (InterruptedException x) + { + + } + } + return classpath; } - public void run() { - try { - exit = process.waitFor(); - } catch (InterruptedException ignore) { - return; + + private Worker getJalviewDesktopRunner(boolean withAwt, String cmd, + int timeout) + { + // Note: JAL-3065 - don't include quotes for lib/* because the arguments are + // not expanded by the shell + String classpath = getClassPath(); + String _cmd = java_exe + " " + + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath " + + classpath + + (modules.length() > 2 ? "--add-modules=\"" + modules + "\"" + : "") + + " jalview.bin.Jalview "; + Process ls2_proc = null; + Worker worker = null; + try + { + ls2_proc = Runtime.getRuntime().exec(_cmd + cmd); + } catch (Throwable e1) + { + e1.printStackTrace(); + } + if (ls2_proc != null) + { + BufferedReader outputReader = new BufferedReader( + new InputStreamReader(ls2_proc.getInputStream())); + BufferedReader errorReader = new BufferedReader( + new InputStreamReader(ls2_proc.getErrorStream())); + worker = new Worker(ls2_proc); + worker.start(); + try + { + worker.join(timeout); + } catch (InterruptedException e) + { + System.err.println("Thread interrupted"); + } + worker.setOutputReader(outputReader); + worker.setErrorReader(errorReader); } + return worker; } -} -private Worker jalviewDesktopRunner(boolean withAwt, String cmd, int timeout) throws InterruptedException, IOException + + @Test(groups = { "Functional" }) + public void reportCurrentWorkingDirectory() { - String _cmd = "java "+(withAwt ? "-Djava.awt.headless=true":"")+" -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview "; - System.out.println("###############Jalview CMD: " + _cmd+cmd); - Process ls2_proc = Runtime.getRuntime().exec(_cmd+cmd); - BufferedReader outputReader = new BufferedReader(new InputStreamReader( - ls2_proc.getInputStream())); - - BufferedReader errorReader = new BufferedReader(new InputStreamReader( - ls2_proc.getErrorStream())); - Worker worker = new Worker(ls2_proc); - worker.start(); - worker.join(timeout); - System.out.println("Output: "); - String ln = null; - while ((ln = outputReader.readLine()) != null) + try { - System.out.println(ln); + Path currentRelativePath = Paths.get(""); + String s = currentRelativePath.toAbsolutePath().toString(); + System.out.println("Test CWD is " + s); + } catch (Exception q) + { + q.printStackTrace(); } + } - System.out.println("Error: "); - while ((ln = errorReader.readLine()) != null) + @BeforeTest(alwaysRun = true) + public void initialize() + { + new CommandLineOperations(); + } + + @BeforeTest(alwaysRun = true) + public void setUpForHeadlessCommandLineInputOperations() + throws IOException + { + String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo " + + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree " + + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree"; + Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT); + String ln = null; + while ((ln = worker.getOutputReader().readLine()) != null) { System.out.println(ln); + successfulCMDs.add(ln); + } + while ((ln = worker.getErrorReader().readLine()) != null) + { + System.err.println(ln); } - return worker; } - @Test - public void testHeadlessModeEPS() throws Exception + + @BeforeTest(alwaysRun = true) + public void setUpForCommandLineInputOperations() throws IOException { - String[] headlessArgs=new String[] { "nodisplay","headless","nogui"}; - for (String _harg:headlessArgs) + String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats"; + final Worker worker = getJalviewDesktopRunner(false, cmds, + SETUP_TIMEOUT); + + // number of lines expected on STDERR when Jalview starts up normally + // may need to adjust this if Jalview is excessively noisy ? + final int STDERR_SETUPLINES = 50; + + // thread monitors stderr - bails after SETUP_TIMEOUT or when + // STDERR_SETUPLINES have been read + Thread runner = new Thread(new Runnable() { - boolean _switch=false,withAwt=false; - do { - if (_switch) + @Override + public void run() + { + String ln = null; + int count = 0; + try { - withAwt=true; + while ((ln = worker.getErrorReader().readLine()) != null) + { + System.out.println(ln); + successfulCMDs.add(ln); + if (++count > STDERR_SETUPLINES) + { + break; + } + } + } catch (Exception e) + { + System.err.println( + "Unexpected Exception reading stderr from the Jalview process"); + e.printStackTrace(); } - _switch=true; - String jalview_input = "examples/uniref50.fa"; - String jalview_output = "test_uniref50_out.eps"; - String cmd = ""+_harg+" -open "+ jalview_input + " -eps " + jalview_output; - String harg = _harg+(withAwt ? "-Djava.awt.headless=true":" NO AWT.HEADLESS"); - System.out.println("Testing with Headless argument: '"+harg+"'\n"); - Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); - assertTrue("Didn't create an output EPS file.["+harg+"]", new File("test_uniref50_out.eps").exists()); - assertTrue("Didn't create an EPS file with any content["+harg+"]", new File("test_uniref50_out.eps").length()>4096); - if (worker.exit == null){ + } + }); + long t = System.currentTimeMillis() + SETUP_TIMEOUT; + runner.start(); + while (!runner.isInterrupted() && System.currentTimeMillis() < t) + { + try + { + Thread.sleep(500); + } catch (InterruptedException e) + { + } + } + runner.interrupt(); + if (worker != null && worker.exit == null) + { worker.interrupt(); Thread.currentThread().interrupt(); worker.process.destroy(); - fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]"); } - } while (!withAwt); - } } -// @Test -// public void testJalview2XMLDataset() throws Exception -// { -// String jalview_input = "examples/uniref50.fa"; -// String jalview_output = "test_uniref50_out.eps"; -// String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output; -// //String harg = _harg+(withAwt ? "-Djava.awt.headless=true":" NO AWT.HEADLESS"); -// System.out.println("Testing with Headless argument: '"+harg+"'\n"); -// Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); -// assertTrue("Didn't create an output EPS file.["+harg+"]", new File("test_uniref50_out.eps").exists()); -// assertTrue("Didn't create an EPS file with any content["+harg+"]", new File("test_uniref50_out.eps").length()>4096); -// if (worker.exit == null){ -// worker.interrupt(); -// Thread.currentThread().interrupt(); -// worker.process.destroy(); -// fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]"); -// } -// } + + @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData") + public void testAllInputOperations(String expectedString, + String failureMsg) + { + Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg); + } + + @Test( + groups = + { "Functional" }, + dataProvider = "headlessModeOutputOperationsData") + public void testHeadlessModeOutputOperations(String harg, String type, + String fileName, boolean withAWT, int expectedMinFileSize, + int timeout) + { + String cmd = harg + type + " " + fileName; + // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd); + File file = new File(fileName); + file.deleteOnExit(); + Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout); + assertNotNull(worker, "worker is null"); + String msg = "Didn't create an output" + type + " file.[" + harg + "]"; + assertTrue(file.exists(), msg); + FileAssert.assertFile(file, msg); + FileAssert.assertMinLength(file, expectedMinFileSize); + if (worker != null && worker.exit == null) + { + worker.interrupt(); + Thread.currentThread().interrupt(); + worker.process.destroy(); + Assert.fail("Jalview did not exit after " + type + + " generation (try running test again to verify - timeout at " + + timeout + "ms). [" + harg + "]"); + } + file.delete(); + } + + @DataProvider(name = "allInputOperationsData") + public Object[][] getHeadlessModeInputParams() + { + return new Object[][] { + // headless mode input operations + { "CMD [-color zappo] executed successfully!", + "Failed command : -color zappo" }, + { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!", + "Failed command : -props File" }, + { "CMD [-sortbytree] executed successfully!", + "Failed command : -sortbytree" }, + { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!", + "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" }, + { "CMD [-open examples/uniref50.fa] executed successfully!", + "Failed command : -open examples/uniref50.fa" }, + { "CMD [-nosortbytree] executed successfully!", + "Failed command : -nosortbytree" }, + { "CMD [-features examples/testdata/plantfdx.features] executed successfully!", + "Failed command : -features examples/testdata/plantfdx.features" }, + { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!", + "Failed command : -annotations examples/testdata/plantfdx.annotations" }, + { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!", + "Failed command : -tree examples/testdata/uniref50_test_tree" }, + // non headless mode input operations + { "CMD [-nousagestats] executed successfully!", + "Failed command : -nousagestats" }, + { "CMD [-noquestionnaire] executed successfully!", + "Failed command : -noquestionnaire" } }; + } + + @DataProvider(name = "headlessModeOutputOperationsData") + public static Object[][] getHeadlessModeOutputParams() + { + // JBPNote: I'm not clear why need to specify full path for output file + // when running tests on build server, but we will keep this patch for now + // since it works. + // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609 + String workingDir = "test/jalview/bin/"; + return new Object[][] { { "nodisplay -open examples/uniref50.fa", + " -eps", workingDir + "test_uniref50_out.eps", true, + MINFILESIZE_BIG, TEST_TIMEOUT }, + { "nodisplay -open examples/uniref50.fa", " -eps", + workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "nogui -open examples/uniref50.fa", " -eps", + workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "nogui -open examples/uniref50.fa", " -eps", + workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -eps", + workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -svg", + workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -png", + workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -html", + workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -fasta", + workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -clustal", + workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -msf", + workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -pileup", + workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -pir", + workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -pfam", + workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -blc", + workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + { "headless -open examples/uniref50.fa", " -jalview", + workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, }; + } }