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<String>();
  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 _cmd = "java "
 120             + (withAwt ? "-Djava.awt.headless=true" : "")
 121             + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
 122     System.out.println("CMD [" + cmd + "]");
 123     Process ls2_proc = null;
 124     Worker worker = null;
 125     try
 126     {
 127       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 128     } catch (IOException e1)
 129     {
 130       e1.printStackTrace();
 131     }
 132     if (ls2_proc != null)
 133     {
 134       BufferedReader outputReader = new BufferedReader(
 135               new InputStreamReader(ls2_proc.getInputStream()));
 136       BufferedReader errorReader = new BufferedReader(
 137               new InputStreamReader(ls2_proc.getErrorStream()));
 138       worker = new Worker(ls2_proc);
 139       worker.start();
 140       try
 141       {
 142         worker.join(timeout);
 143       } catch (InterruptedException e)
 144       {
 145         // e.printStackTrace();
 146       }
 147       worker.setOutputReader(outputReader);
 148       worker.setErrorReader(errorReader);
 149     }
 150     return worker;
 151   }
 152
 153   @BeforeTest(alwaysRun = true)
 154   public void initialize()
 155   {
 156     new CommandLineOperations();
 157   }
 158
 159   @BeforeTest(alwaysRun = true)
 160   public void setUpForHeadlessCommandLineInputOperations()
 161           throws IOException
 162   {
 163     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 164             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 165             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 166     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 167     String ln = null;
 168     while ((ln = worker.getOutputReader().readLine()) != null)
 169     {
 170       System.out.println(ln);
 171       successfulCMDs.add(ln);
 172     }
 173   }
 174
 175   @BeforeTest(alwaysRun = true)
 176   public void setUpForCommandLineInputOperations() throws IOException
 177   {
 178     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 179     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 180     String ln = null;
 181     int count = 0;
 182     while ((ln = worker.getErrorReader().readLine()) != null)
 183     {
 184       System.out.println(ln);
 185       successfulCMDs.add(ln);
 186       if (++count > 5)
 187       {
 188         break;
 189       }
 190     }
 191     if (worker != null && worker.exit == null)
 192     {
 193       worker.interrupt();
 194       Thread.currentThread().interrupt();
 195       worker.process.destroy();
 196     }
 197   }
 198
 199   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 200   public void testAllInputOperations(String expectedString,
 201           String failureMsg)
 202   {
 203     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 204   }
 205
 206   @Test(
 207     groups = { "Functional" },
 208     dataProvider = "headlessModeOutputOperationsData")
 209   public void testHeadlessModeOutputOperations(String harg, String type,
 210           String fileName, boolean withAWT, int expectedMinFileSize,
 211           int timeout)
 212   {
 213     String cmd = harg + type + " " + fileName;
 214     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 215     File file = new File(fileName);
 216     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 217
 218     FileAssert.assertFile(file, "Didn't create an output" + type
 219             + " file.[" + harg + "]");
 220     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 221     if (worker != null && worker.exit == null)
 222     {
 223       worker.interrupt();
 224       Thread.currentThread().interrupt();
 225       worker.process.destroy();
 226       Assert.fail("Jalview did not exit after "
 227               + type
 228               + " generation (try running test again to verify - timeout at "
 229               + SETUP_TIMEOUT + "ms). ["
 230               + harg + "]");
 231     }
 232     new File(fileName).delete();
 233   }
 234
 235   @DataProvider(name = "allInputOpearationsData")
 236   public Object[][] getHeadlessModeInputParams()
 237   {
 238     return new Object[][] {
 239         // headless mode input operations
 240         { "CMD [-color zappo] executed successfully!",
 241             "Failed command : -color zappo" },
 242         { "CMD [-props FILE] executed successfully!",
 243             "Failed command : -props File" },
 244         { "CMD [-sortbytree] executed successfully!",
 245             "Failed command : -sortbytree" },
 246         {
 247             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 248             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 249         { "CMD [-open examples/uniref50.fa] executed successfully!",
 250             "Failed command : -open examples/uniref50.fa" },
 251         { "CMD [-nosortbytree] executed successfully!",
 252             "Failed command : -nosortbytree" },
 253         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 254             "Failed command : -dasserver nickname=www.test.com" },
 255         {
 256             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 257             "Failed command : -features examples/testdata/plantfdx.features" },
 258         {
 259             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 260             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 261         {
 262             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 263             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 264         // non headless mode input operations
 265         { "CMD [-nousagestats] executed successfully!",
 266             "Failed command : -nousagestats" },
 267         { "CMD [-noquestionnaire] executed successfully!",
 268             "Failed command : -noquestionnaire nickname=www.test.com" } };
 269
 270   }
 271
 272   @DataProvider(name = "headlessModeOutputOperationsData")
 273   public static Object[][] getHeadlessModeOutputParams()
 274   {
 275     return new Object[][] {
 276         { "nodisplay -open examples/uniref50.fa", " -eps",
 277             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 278         { "nodisplay -open examples/uniref50.fa", " -eps",
 279             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 280         { "nogui -open examples/uniref50.fa", " -eps",
 281             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 282         { "nogui -open examples/uniref50.fa", " -eps",
 283             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 284         { "headless -open examples/uniref50.fa", " -eps",
 285             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 286         { "headless -open examples/uniref50.fa", " -svg",
 287             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 288         { "headless -open examples/uniref50.fa", " -png",
 289             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 290         { "headless -open examples/uniref50.fa", " -html",
 291             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 292         { "headless -open examples/uniref50.fa", " -fasta",
 293             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 294         { "headless -open examples/uniref50.fa", " -clustal",
 295             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 296         { "headless -open examples/uniref50.fa", " -msf",
 297             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 298         { "headless -open examples/uniref50.fa", " -pileup",
 299             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 300         { "headless -open examples/uniref50.fa", " -pir",
 301             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 302         { "headless -open examples/uniref50.fa", " -pfam",
 303             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 304         { "headless -open examples/uniref50.fa", " -blc",
 305             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 306         { "headless -open examples/uniref50.fa", " -jalview",
 307             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 308   }
 309 }