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 java.io.BufferedReader;
  24 import java.io.File;
  25 import java.io.IOException;
  26 import java.io.InputStreamReader;
  27 import java.util.ArrayList;
  28
  29 import org.testng.Assert;
  30 import org.testng.FileAssert;
  31 import org.testng.annotations.BeforeTest;
  32 import org.testng.annotations.DataProvider;
  33 import org.testng.annotations.Test;
  34
  35 public class CommandLineOperations
  36 {
  37   private static final int TEST_TIMEOUT = 4000;
  38
  39   private static final int SETUP_TIMEOUT = 9000;
  40
  41   private static final int MINFILESIZE_SMALL = 2096;
  42
  43   private static final int MINFILESIZE_BIG = 4096;
  44
  45   private ArrayList<String> successfulCMDs = new ArrayList<String>();
  46
  47   /***
  48    * from
  49    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  50    * -using-javas-runtime-exec
  51    *
  52    * @author jimp
  53    *
  54    */
  55   private static class Worker extends Thread
  56   {
  57     private final Process process;
  58
  59     private BufferedReader outputReader;
  60
  61     private BufferedReader errorReader;
  62
  63     private Integer exit;
  64
  65     private Worker(Process process)
  66     {
  67       this.process = process;
  68     }
  69
  70     @Override
  71     public void run()
  72     {
  73       try
  74       {
  75         exit = process.waitFor();
  76       } catch (InterruptedException ignore)
  77       {
  78         return;
  79       }
  80     }
  81
  82     public BufferedReader getOutputReader()
  83     {
  84       return outputReader;
  85     }
  86
  87     public void setOutputReader(BufferedReader outputReader)
  88     {
  89       this.outputReader = outputReader;
  90     }
  91
  92     public BufferedReader getErrorReader()
  93     {
  94       return errorReader;
  95     }
  96
  97     public void setErrorReader(BufferedReader errorReader)
  98     {
  99       this.errorReader = errorReader;
 100     }
 101   }
 102
 103   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
 104           int timeout)
 105   {
 106     String _cmd = "java "
 107             + (withAwt ? "-Djava.awt.headless=true" : "")
 108             + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
 109     System.out.println("CMD [" + cmd + "]");
 110     Process ls2_proc = null;
 111     Worker worker = null;
 112     try
 113     {
 114       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 115     } catch (IOException e1)
 116     {
 117       e1.printStackTrace();
 118     }
 119     if (ls2_proc != null)
 120     {
 121       BufferedReader outputReader = new BufferedReader(
 122               new InputStreamReader(ls2_proc.getInputStream()));
 123       BufferedReader errorReader = new BufferedReader(
 124               new InputStreamReader(ls2_proc.getErrorStream()));
 125       worker = new Worker(ls2_proc);
 126       worker.start();
 127       try
 128       {
 129         worker.join(timeout);
 130       } catch (InterruptedException e)
 131       {
 132         // e.printStackTrace();
 133       }
 134       worker.setOutputReader(outputReader);
 135       worker.setErrorReader(errorReader);
 136     }
 137     return worker;
 138   }
 139
 140   @BeforeTest(alwaysRun = true)
 141   public void initialize()
 142   {
 143     new CommandLineOperations();
 144   }
 145
 146   @BeforeTest(alwaysRun = true)
 147   public void setUpForHeadlessCommandLineInputOperations()
 148           throws IOException
 149   {
 150     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 151             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 152             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 153     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 154     String ln = null;
 155     while ((ln = worker.getOutputReader().readLine()) != null)
 156     {
 157       System.out.println(ln);
 158       successfulCMDs.add(ln);
 159     }
 160   }
 161
 162   @BeforeTest(alwaysRun = true)
 163   public void setUpForCommandLineInputOperations() throws IOException
 164   {
 165     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 166     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 167     String ln = null;
 168     int count = 0;
 169     while ((ln = worker.getErrorReader().readLine()) != null)
 170     {
 171       System.out.println(ln);
 172       successfulCMDs.add(ln);
 173       if (++count > 5)
 174       {
 175         break;
 176       }
 177     }
 178     if (worker != null && worker.exit == null)
 179     {
 180       worker.interrupt();
 181       Thread.currentThread().interrupt();
 182       worker.process.destroy();
 183     }
 184   }
 185
 186   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 187   public void testAllInputOperations(String expectedString,
 188           String failureMsg)
 189   {
 190     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 191   }
 192
 193   @Test(
 194     groups = { "Functional" },
 195     dataProvider = "headlessModeOutputOperationsData")
 196   public void testHeadlessModeOutputOperations(String harg, String type,
 197           String fileName, boolean withAWT, int expectedMinFileSize,
 198           int timeout)
 199   {
 200     String cmd = harg + type + " " + fileName;
 201     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 202     File file = new File(fileName);
 203     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 204
 205     FileAssert.assertFile(file, "Didn't create an output" + type
 206             + " file.[" + harg + "]");
 207     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 208     if (worker != null && worker.exit == null)
 209     {
 210       worker.interrupt();
 211       Thread.currentThread().interrupt();
 212       worker.process.destroy();
 213       Assert.fail("Jalview did not exit after "
 214               + type
 215               + " generation (try running test again to verify - timeout at "
 216               + SETUP_TIMEOUT + "ms). ["
 217               + harg + "]");
 218     }
 219     new File(fileName).delete();
 220   }
 221
 222   @DataProvider(name = "allInputOpearationsData")
 223   public Object[][] getHeadlessModeInputParams()
 224   {
 225     return new Object[][] {
 226         // headless mode input operations
 227         { "CMD [-color zappo] executed successfully!",
 228             "Failed command : -color zappo" },
 229         { "CMD [-props FILE] executed successfully!",
 230             "Failed command : -props File" },
 231         { "CMD [-sortbytree] executed successfully!",
 232             "Failed command : -sortbytree" },
 233         {
 234             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 235             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 236         { "CMD [-open examples/uniref50.fa] executed successfully!",
 237             "Failed command : -open examples/uniref50.fa" },
 238         { "CMD [-nosortbytree] executed successfully!",
 239             "Failed command : -nosortbytree" },
 240         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 241             "Failed command : -dasserver nickname=www.test.com" },
 242         {
 243             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 244             "Failed command : -features examples/testdata/plantfdx.features" },
 245         {
 246             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 247             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 248         {
 249             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 250             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 251         // non headless mode input operations
 252         { "CMD [-nousagestats] executed successfully!",
 253             "Failed command : -nousagestats" },
 254         { "CMD [-noquestionnaire] executed successfully!",
 255             "Failed command : -noquestionnaire nickname=www.test.com" } };
 256
 257   }
 258
 259   @DataProvider(name = "headlessModeOutputOperationsData")
 260   public static Object[][] getHeadlessModeOutputParams()
 261   {
 262     return new Object[][] {
 263         { "nodisplay -open examples/uniref50.fa", " -eps",
 264             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 265         { "nodisplay -open examples/uniref50.fa", " -eps",
 266             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 267         { "nogui -open examples/uniref50.fa", " -eps",
 268             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 269         { "nogui -open examples/uniref50.fa", " -eps",
 270             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 271         { "headless -open examples/uniref50.fa", " -eps",
 272             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 273         { "headless -open examples/uniref50.fa", " -svg",
 274             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 275         { "headless -open examples/uniref50.fa", " -png",
 276             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 277         { "headless -open examples/uniref50.fa", " -html",
 278             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 279         { "headless -open examples/uniref50.fa", " -fasta",
 280             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 281         { "headless -open examples/uniref50.fa", " -clustal",
 282             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 283         { "headless -open examples/uniref50.fa", " -msf",
 284             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 285         { "headless -open examples/uniref50.fa", " -pileup",
 286             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 287         { "headless -open examples/uniref50.fa", " -pir",
 288             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 289         { "headless -open examples/uniref50.fa", " -pfam",
 290             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 291         { "headless -open examples/uniref50.fa", " -blc",
 292             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 293         { "headless -open examples/uniref50.fa", " -jalview",
 294             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 295   }
 296 }