test/jalview/bin/CommandLineOperations.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.bin;
  22
  23 import jalview.gui.JvOptionPane;
  24
  25 import java.io.BufferedReader;
  26 import java.io.File;
  27 import java.io.IOException;
  28 import java.io.InputStreamReader;
  29 import java.util.ArrayList;
  30
  31 import org.testng.Assert;
  32 import org.testng.FileAssert;
  33 import org.testng.annotations.BeforeClass;
  34 import org.testng.annotations.BeforeTest;
  35 import org.testng.annotations.DataProvider;
  36 import org.testng.annotations.Test;
  37
  38 public class CommandLineOperations
  39 {
  40
  41   @BeforeClass(alwaysRun = true)
  42   public void setUpJvOptionPane()
  43   {
  44     JvOptionPane.setInteractiveMode(false);
  45     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  46   }
  47
  48   private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
  49                                                 // full test run than on
  50                                                 // individual tests
  51
  52   private static final int SETUP_TIMEOUT = 9000;
  53
  54   private static final int MINFILESIZE_SMALL = 2096;
  55
  56   private static final int MINFILESIZE_BIG = 4096;
  57
  58   private ArrayList<String> successfulCMDs = new ArrayList<>();
  59
  60   /***
  61    * from
  62    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  63    * -using-javas-runtime-exec
  64    *
  65    * @author jimp
  66    *
  67    */
  68   private static class Worker extends Thread
  69   {
  70     private final Process process;
  71
  72     private BufferedReader outputReader;
  73
  74     private BufferedReader errorReader;
  75
  76     private Integer exit;
  77
  78     private Worker(Process process)
  79     {
  80       this.process = process;
  81     }
  82
  83     @Override
  84     public void run()
  85     {
  86       try
  87       {
  88         exit = process.waitFor();
  89       } catch (InterruptedException ignore)
  90       {
  91         return;
  92       }
  93     }
  94
  95     public BufferedReader getOutputReader()
  96     {
  97       return outputReader;
  98     }
  99
 100     public void setOutputReader(BufferedReader outputReader)
 101     {
 102       this.outputReader = outputReader;
 103     }
 104
 105     public BufferedReader getErrorReader()
 106     {
 107       return errorReader;
 108     }
 109
 110     public void setErrorReader(BufferedReader errorReader)
 111     {
 112       this.errorReader = errorReader;
 113     }
 114   }
 115
 116   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
 117           int timeout)
 118   {
 119     String cp_sep = ":";
 120     if (System.getProperty("os.name").indexOf("Windows") >= 0)
 121     {
 122       cp_sep = ";";
 123     }
 124     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
 125     // not expanded by the shell
 126     String _cmd = "java "
 127             + (withAwt ? "-Djava.awt.headless=true" : "")
 128             + " -classpath ./classes" + cp_sep
 129             + "./lib/* jalview.bin.Jalview ";
 130     System.out.println("CMD [" + cmd + "]");
 131     Process ls2_proc = null;
 132     Worker worker = null;
 133     try
 134     {
 135       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 136     } catch (IOException e1)
 137     {
 138       e1.printStackTrace();
 139     }
 140     if (ls2_proc != null)
 141     {
 142       BufferedReader outputReader = new BufferedReader(
 143               new InputStreamReader(ls2_proc.getInputStream()));
 144       BufferedReader errorReader = new BufferedReader(
 145               new InputStreamReader(ls2_proc.getErrorStream()));
 146       worker = new Worker(ls2_proc);
 147       worker.start();
 148       try
 149       {
 150         worker.join(timeout);
 151       } catch (InterruptedException e)
 152       {
 153         // e.printStackTrace();
 154       }
 155       worker.setOutputReader(outputReader);
 156       worker.setErrorReader(errorReader);
 157     }
 158     return worker;
 159   }
 160
 161   @BeforeTest(alwaysRun = true)
 162   public void initialize()
 163   {
 164     new CommandLineOperations();
 165   }
 166
 167   @BeforeTest(alwaysRun = true)
 168   public void setUpForHeadlessCommandLineInputOperations()
 169           throws IOException
 170   {
 171     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 172             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 173             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 174     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 175     String ln = null;
 176     while ((ln = worker.getOutputReader().readLine()) != null)
 177     {
 178       System.out.println(ln);
 179       successfulCMDs.add(ln);
 180     }
 181   }
 182
 183   @BeforeTest(alwaysRun = true)
 184   public void setUpForCommandLineInputOperations() throws IOException
 185   {
 186     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 187     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 188     String ln = null;
 189     int count = 0;
 190     while ((ln = worker.getErrorReader().readLine()) != null)
 191     {
 192       System.out.println(ln);
 193       successfulCMDs.add(ln);
 194       if (++count > 5)
 195       {
 196         break;
 197       }
 198     }
 199     if (worker != null && worker.exit == null)
 200     {
 201       worker.interrupt();
 202       Thread.currentThread().interrupt();
 203       worker.process.destroy();
 204     }
 205   }
 206
 207   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 208   public void testAllInputOperations(String expectedString,
 209           String failureMsg)
 210   {
 211     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 212   }
 213
 214   @Test(
 215     groups = { "Functional" },
 216     dataProvider = "headlessModeOutputOperationsData")
 217   public void testHeadlessModeOutputOperations(String harg, String type,
 218           String fileName, boolean withAWT, int expectedMinFileSize,
 219           int timeout)
 220   {
 221     String cmd = harg + type + " " + fileName;
 222     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 223     File file = new File(fileName);
 224     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 225
 226     FileAssert.assertFile(file, "Didn't create an output" + type
 227             + " file.[" + harg + "]");
 228     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 229     if (worker != null && worker.exit == null)
 230     {
 231       worker.interrupt();
 232       Thread.currentThread().interrupt();
 233       worker.process.destroy();
 234       Assert.fail("Jalview did not exit after "
 235               + type
 236               + " generation (try running test again to verify - timeout at "
 237               + SETUP_TIMEOUT + "ms). ["
 238               + harg + "]");
 239     }
 240     new File(fileName).delete();
 241   }
 242
 243   @DataProvider(name = "allInputOpearationsData")
 244   public Object[][] getHeadlessModeInputParams()
 245   {
 246     return new Object[][] {
 247         // headless mode input operations
 248         { "CMD [-color zappo] executed successfully!",
 249             "Failed command : -color zappo" },
 250         { "CMD [-props FILE] executed successfully!",
 251             "Failed command : -props File" },
 252         { "CMD [-sortbytree] executed successfully!",
 253             "Failed command : -sortbytree" },
 254         {
 255             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 256             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 257         { "CMD [-open examples/uniref50.fa] executed successfully!",
 258             "Failed command : -open examples/uniref50.fa" },
 259         { "CMD [-nosortbytree] executed successfully!",
 260             "Failed command : -nosortbytree" },
 261         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 262             "Failed command : -dasserver nickname=www.test.com" },
 263         {
 264             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 265             "Failed command : -features examples/testdata/plantfdx.features" },
 266         {
 267             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 268             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 269         {
 270             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 271             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 272         // non headless mode input operations
 273         { "CMD [-nousagestats] executed successfully!",
 274             "Failed command : -nousagestats" },
 275         { "CMD [-noquestionnaire] executed successfully!",
 276             "Failed command : -noquestionnaire nickname=www.test.com" } };
 277
 278   }
 279
 280   @DataProvider(name = "headlessModeOutputOperationsData")
 281   public static Object[][] getHeadlessModeOutputParams()
 282   {
 283     return new Object[][] {
 284         { "nodisplay -open examples/uniref50.fa", " -eps",
 285             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 286         { "nodisplay -open examples/uniref50.fa", " -eps",
 287             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 288         { "nogui -open examples/uniref50.fa", " -eps",
 289             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 290         { "nogui -open examples/uniref50.fa", " -eps",
 291             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 292         { "headless -open examples/uniref50.fa", " -eps",
 293             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 294         { "headless -open examples/uniref50.fa", " -svg",
 295             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 296         { "headless -open examples/uniref50.fa", " -png",
 297             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 298         { "headless -open examples/uniref50.fa", " -html",
 299             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 300         { "headless -open examples/uniref50.fa", " -fasta",
 301             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 302         { "headless -open examples/uniref50.fa", " -clustal",
 303             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 304         { "headless -open examples/uniref50.fa", " -msf",
 305             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 306         { "headless -open examples/uniref50.fa", " -pileup",
 307             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 308         { "headless -open examples/uniref50.fa", " -pir",
 309             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 310         { "headless -open examples/uniref50.fa", " -pfam",
 311             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 312         { "headless -open examples/uniref50.fa", " -blc",
 313             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 314         { "headless -open examples/uniref50.fa", " -jalview",
 315             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 316   }
 317 }