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 = 4500; // Note longer timeout needed on
  38                                                 // full test run than on
  39                                                 // individual tests
  40
  41   private static final int SETUP_TIMEOUT = 9000;
  42
  43   private static final int MINFILESIZE_SMALL = 2096;
  44
  45   private static final int MINFILESIZE_BIG = 4096;
  46
  47   private ArrayList<String> successfulCMDs = new ArrayList<String>();
  48
  49   /***
  50    * from
  51    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  52    * -using-javas-runtime-exec
  53    *
  54    * @author jimp
  55    *
  56    */
  57   private static class Worker extends Thread
  58   {
  59     private final Process process;
  60
  61     private BufferedReader outputReader;
  62
  63     private BufferedReader errorReader;
  64
  65     private Integer exit;
  66
  67     private Worker(Process process)
  68     {
  69       this.process = process;
  70     }
  71
  72     @Override
  73     public void run()
  74     {
  75       try
  76       {
  77         exit = process.waitFor();
  78       } catch (InterruptedException ignore)
  79       {
  80         return;
  81       }
  82     }
  83
  84     public BufferedReader getOutputReader()
  85     {
  86       return outputReader;
  87     }
  88
  89     public void setOutputReader(BufferedReader outputReader)
  90     {
  91       this.outputReader = outputReader;
  92     }
  93
  94     public BufferedReader getErrorReader()
  95     {
  96       return errorReader;
  97     }
  98
  99     public void setErrorReader(BufferedReader errorReader)
 100     {
 101       this.errorReader = errorReader;
 102     }
 103   }
 104
 105   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
 106           int timeout)
 107   {
 108     String _cmd = "java "
 109             + (withAwt ? "-Djava.awt.headless=true" : "")
 110             + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
 111     System.out.println("CMD [" + cmd + "]");
 112     Process ls2_proc = null;
 113     Worker worker = null;
 114     try
 115     {
 116       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 117     } catch (IOException e1)
 118     {
 119       e1.printStackTrace();
 120     }
 121     if (ls2_proc != null)
 122     {
 123       BufferedReader outputReader = new BufferedReader(
 124               new InputStreamReader(ls2_proc.getInputStream()));
 125       BufferedReader errorReader = new BufferedReader(
 126               new InputStreamReader(ls2_proc.getErrorStream()));
 127       worker = new Worker(ls2_proc);
 128       worker.start();
 129       try
 130       {
 131         worker.join(timeout);
 132       } catch (InterruptedException e)
 133       {
 134         // e.printStackTrace();
 135       }
 136       worker.setOutputReader(outputReader);
 137       worker.setErrorReader(errorReader);
 138     }
 139     return worker;
 140   }
 141
 142   @BeforeTest(alwaysRun = true)
 143   public void initialize()
 144   {
 145     new CommandLineOperations();
 146   }
 147
 148   @BeforeTest(alwaysRun = true)
 149   public void setUpForHeadlessCommandLineInputOperations()
 150           throws IOException
 151   {
 152     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 153             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 154             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 155     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 156     String ln = null;
 157     while ((ln = worker.getOutputReader().readLine()) != null)
 158     {
 159       System.out.println(ln);
 160       successfulCMDs.add(ln);
 161     }
 162   }
 163
 164   @BeforeTest(alwaysRun = true)
 165   public void setUpForCommandLineInputOperations() throws IOException
 166   {
 167     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 168     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 169     String ln = null;
 170     int count = 0;
 171     while ((ln = worker.getErrorReader().readLine()) != null)
 172     {
 173       System.out.println(ln);
 174       successfulCMDs.add(ln);
 175       if (++count > 5)
 176       {
 177         break;
 178       }
 179     }
 180     if (worker != null && worker.exit == null)
 181     {
 182       worker.interrupt();
 183       Thread.currentThread().interrupt();
 184       worker.process.destroy();
 185     }
 186   }
 187
 188   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 189   public void testAllInputOperations(String expectedString,
 190           String failureMsg)
 191   {
 192     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 193   }
 194
 195   @Test(
 196     groups = { "Functional" },
 197     dataProvider = "headlessModeOutputOperationsData")
 198   public void testHeadlessModeOutputOperations(String harg, String type,
 199           String fileName, boolean withAWT, int expectedMinFileSize,
 200           int timeout)
 201   {
 202     String cmd = harg + type + " " + fileName;
 203     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 204     File file = new File(fileName);
 205     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 206
 207     FileAssert.assertFile(file, "Didn't create an output" + type
 208             + " file.[" + harg + "]");
 209     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 210     if (worker != null && worker.exit == null)
 211     {
 212       worker.interrupt();
 213       Thread.currentThread().interrupt();
 214       worker.process.destroy();
 215       Assert.fail("Jalview did not exit after "
 216               + type
 217               + " generation (try running test again to verify - timeout at "
 218               + SETUP_TIMEOUT + "ms). ["
 219               + harg + "]");
 220     }
 221     new File(fileName).delete();
 222   }
 223
 224   @DataProvider(name = "allInputOpearationsData")
 225   public Object[][] getHeadlessModeInputParams()
 226   {
 227     return new Object[][] {
 228         // headless mode input operations
 229         { "CMD [-color zappo] executed successfully!",
 230             "Failed command : -color zappo" },
 231         { "CMD [-props FILE] executed successfully!",
 232             "Failed command : -props File" },
 233         { "CMD [-sortbytree] executed successfully!",
 234             "Failed command : -sortbytree" },
 235         {
 236             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 237             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 238         { "CMD [-open examples/uniref50.fa] executed successfully!",
 239             "Failed command : -open examples/uniref50.fa" },
 240         { "CMD [-nosortbytree] executed successfully!",
 241             "Failed command : -nosortbytree" },
 242         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 243             "Failed command : -dasserver nickname=www.test.com" },
 244         {
 245             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 246             "Failed command : -features examples/testdata/plantfdx.features" },
 247         {
 248             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 249             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 250         {
 251             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 252             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 253         // non headless mode input operations
 254         { "CMD [-nousagestats] executed successfully!",
 255             "Failed command : -nousagestats" },
 256         { "CMD [-noquestionnaire] executed successfully!",
 257             "Failed command : -noquestionnaire nickname=www.test.com" } };
 258
 259   }
 260
 261   @DataProvider(name = "headlessModeOutputOperationsData")
 262   public static Object[][] getHeadlessModeOutputParams()
 263   {
 264     return new Object[][] {
 265         { "nodisplay -open examples/uniref50.fa", " -eps",
 266             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 267         { "nodisplay -open examples/uniref50.fa", " -eps",
 268             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 269         { "nogui -open examples/uniref50.fa", " -eps",
 270             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 271         { "nogui -open examples/uniref50.fa", " -eps",
 272             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 273         { "headless -open examples/uniref50.fa", " -eps",
 274             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 275         { "headless -open examples/uniref50.fa", " -svg",
 276             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 277         { "headless -open examples/uniref50.fa", " -png",
 278             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 279         { "headless -open examples/uniref50.fa", " -html",
 280             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 281         { "headless -open examples/uniref50.fa", " -fasta",
 282             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 283         { "headless -open examples/uniref50.fa", " -clustal",
 284             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 285         { "headless -open examples/uniref50.fa", " -msf",
 286             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 287         { "headless -open examples/uniref50.fa", " -pileup",
 288             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 289         { "headless -open examples/uniref50.fa", " -pir",
 290             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 291         { "headless -open examples/uniref50.fa", " -pfam",
 292             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 293         { "headless -open examples/uniref50.fa", " -blc",
 294             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 295         { "headless -open examples/uniref50.fa", " -jalview",
 296             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 297   }
 298 }