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     String _cmd = "java "
 125             + (withAwt ? "-Djava.awt.headless=true" : "")
 126             + " -classpath \"./lib/*" + cp_sep
 127             + "./classes\" jalview.bin.Jalview ";
 128     System.out.println("CMD [" + cmd + "]");
 129     Process ls2_proc = null;
 130     Worker worker = null;
 131     try
 132     {
 133       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 134     } catch (IOException e1)
 135     {
 136       e1.printStackTrace();
 137     }
 138     if (ls2_proc != null)
 139     {
 140       BufferedReader outputReader = new BufferedReader(
 141               new InputStreamReader(ls2_proc.getInputStream()));
 142       BufferedReader errorReader = new BufferedReader(
 143               new InputStreamReader(ls2_proc.getErrorStream()));
 144       worker = new Worker(ls2_proc);
 145       worker.start();
 146       try
 147       {
 148         worker.join(timeout);
 149       } catch (InterruptedException e)
 150       {
 151         // e.printStackTrace();
 152       }
 153       worker.setOutputReader(outputReader);
 154       worker.setErrorReader(errorReader);
 155     }
 156     return worker;
 157   }
 158
 159   @BeforeTest(alwaysRun = true)
 160   public void initialize()
 161   {
 162     new CommandLineOperations();
 163   }
 164
 165   @BeforeTest(alwaysRun = true)
 166   public void setUpForHeadlessCommandLineInputOperations()
 167           throws IOException
 168   {
 169     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 170             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 171             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 172     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 173     String ln = null;
 174     while ((ln = worker.getOutputReader().readLine()) != null)
 175     {
 176       System.out.println(ln);
 177       successfulCMDs.add(ln);
 178     }
 179   }
 180
 181   @BeforeTest(alwaysRun = true)
 182   public void setUpForCommandLineInputOperations() throws IOException
 183   {
 184     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 185     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 186     String ln = null;
 187     int count = 0;
 188     while ((ln = worker.getErrorReader().readLine()) != null)
 189     {
 190       System.out.println(ln);
 191       successfulCMDs.add(ln);
 192       if (++count > 5)
 193       {
 194         break;
 195       }
 196     }
 197     if (worker != null && worker.exit == null)
 198     {
 199       worker.interrupt();
 200       Thread.currentThread().interrupt();
 201       worker.process.destroy();
 202     }
 203   }
 204
 205   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 206   public void testAllInputOperations(String expectedString,
 207           String failureMsg)
 208   {
 209     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 210   }
 211
 212   @Test(
 213     groups = { "Functional" },
 214     dataProvider = "headlessModeOutputOperationsData")
 215   public void testHeadlessModeOutputOperations(String harg, String type,
 216           String fileName, boolean withAWT, int expectedMinFileSize,
 217           int timeout)
 218   {
 219     String cmd = harg + type + " " + fileName;
 220     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 221     File file = new File(fileName);
 222     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 223
 224     FileAssert.assertFile(file, "Didn't create an output" + type
 225             + " file.[" + harg + "]");
 226     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 227     if (worker != null && worker.exit == null)
 228     {
 229       worker.interrupt();
 230       Thread.currentThread().interrupt();
 231       worker.process.destroy();
 232       Assert.fail("Jalview did not exit after "
 233               + type
 234               + " generation (try running test again to verify - timeout at "
 235               + SETUP_TIMEOUT + "ms). ["
 236               + harg + "]");
 237     }
 238     new File(fileName).delete();
 239   }
 240
 241   @DataProvider(name = "allInputOpearationsData")
 242   public Object[][] getHeadlessModeInputParams()
 243   {
 244     return new Object[][] {
 245         // headless mode input operations
 246         { "CMD [-color zappo] executed successfully!",
 247             "Failed command : -color zappo" },
 248         { "CMD [-props FILE] executed successfully!",
 249             "Failed command : -props File" },
 250         { "CMD [-sortbytree] executed successfully!",
 251             "Failed command : -sortbytree" },
 252         {
 253             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 254             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 255         { "CMD [-open examples/uniref50.fa] executed successfully!",
 256             "Failed command : -open examples/uniref50.fa" },
 257         { "CMD [-nosortbytree] executed successfully!",
 258             "Failed command : -nosortbytree" },
 259         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 260             "Failed command : -dasserver nickname=www.test.com" },
 261         {
 262             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 263             "Failed command : -features examples/testdata/plantfdx.features" },
 264         {
 265             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 266             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 267         {
 268             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 269             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 270         // non headless mode input operations
 271         { "CMD [-nousagestats] executed successfully!",
 272             "Failed command : -nousagestats" },
 273         { "CMD [-noquestionnaire] executed successfully!",
 274             "Failed command : -noquestionnaire nickname=www.test.com" } };
 275
 276   }
 277
 278   @DataProvider(name = "headlessModeOutputOperationsData")
 279   public static Object[][] getHeadlessModeOutputParams()
 280   {
 281     return new Object[][] {
 282         { "nodisplay -open examples/uniref50.fa", " -eps",
 283             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 284         { "nodisplay -open examples/uniref50.fa", " -eps",
 285             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 286         { "nogui -open examples/uniref50.fa", " -eps",
 287             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 288         { "nogui -open examples/uniref50.fa", " -eps",
 289             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 290         { "headless -open examples/uniref50.fa", " -eps",
 291             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 292         { "headless -open examples/uniref50.fa", " -svg",
 293             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 294         { "headless -open examples/uniref50.fa", " -png",
 295             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 296         { "headless -open examples/uniref50.fa", " -html",
 297             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 298         { "headless -open examples/uniref50.fa", " -fasta",
 299             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 300         { "headless -open examples/uniref50.fa", " -clustal",
 301             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 302         { "headless -open examples/uniref50.fa", " -msf",
 303             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 304         { "headless -open examples/uniref50.fa", " -pileup",
 305             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 306         { "headless -open examples/uniref50.fa", " -pir",
 307             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 308         { "headless -open examples/uniref50.fa", " -pfam",
 309             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 310         { "headless -open examples/uniref50.fa", " -blc",
 311             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 312         { "headless -open examples/uniref50.fa", " -jalview",
 313             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 314   }
 315 }