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 import io.github.classgraph.ClassGraph;
  39 import io.github.classgraph.ScanResult;
  40
  41 public class CommandLineOperations
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
  52                                                 // on
  53                                                 // full test run than on
  54                                                 // individual tests
  55
  56   private static final int SETUP_TIMEOUT = 9000;
  57
  58   private static final int MINFILESIZE_SMALL = 2096;
  59
  60   private static final int MINFILESIZE_BIG = 4096;
  61
  62   private ArrayList<String> successfulCMDs = new ArrayList<>();
  63
  64   /***
  65    * from
  66    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  67    * -using-javas-runtime-exec
  68    *
  69    * @author jimp
  70    *
  71    */
  72   private static class Worker extends Thread
  73   {
  74     private final Process process;
  75
  76     private BufferedReader outputReader;
  77
  78     private BufferedReader errorReader;
  79
  80     private Integer exit;
  81
  82     private Worker(Process process)
  83     {
  84       this.process = process;
  85     }
  86
  87     @Override
  88     public void run()
  89     {
  90       try
  91       {
  92         exit = process.waitFor();
  93       } catch (InterruptedException ignore)
  94       {
  95         return;
  96       }
  97     }
  98
  99     public BufferedReader getOutputReader()
 100     {
 101       return outputReader;
 102     }
 103
 104     public void setOutputReader(BufferedReader outputReader)
 105     {
 106       this.outputReader = outputReader;
 107     }
 108
 109     public BufferedReader getErrorReader()
 110     {
 111       return errorReader;
 112     }
 113
 114     public void setErrorReader(BufferedReader errorReader)
 115     {
 116       this.errorReader = errorReader;
 117     }
 118   }
 119
 120   private static ClassGraph scanner = null;
 121
 122   private static String classpath = null;
 123
 124   public synchronized static String getClassPath()
 125   {
 126     if (scanner == null)
 127     {
 128       scanner = new ClassGraph();
 129       ScanResult scan = scanner.scan();
 130       classpath = scan.getClasspath();
 131     }
 132     while (classpath == null)
 133     {
 134       try
 135       {
 136         Thread.sleep(10);
 137       } catch (InterruptedException x)
 138       {
 139
 140       }
 141     }
 142     return classpath;
 143   }
 144
 145   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
 146           int timeout)
 147   {
 148     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
 149     // not expanded by the shell
 150     String classpath = getClassPath();
 151     String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
 152             + " -classpath " + classpath + " jalview.bin.Jalview ";
 153     Process ls2_proc = null;
 154     Worker worker = null;
 155     try
 156     {
 157       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 158     } catch (IOException e1)
 159     {
 160       e1.printStackTrace();
 161     }
 162     if (ls2_proc != null)
 163     {
 164       BufferedReader outputReader = new BufferedReader(
 165               new InputStreamReader(ls2_proc.getInputStream()));
 166       BufferedReader errorReader = new BufferedReader(
 167               new InputStreamReader(ls2_proc.getErrorStream()));
 168       worker = new Worker(ls2_proc);
 169       worker.start();
 170       try
 171       {
 172         worker.join(timeout);
 173       } catch (InterruptedException e)
 174       {
 175         // e.printStackTrace();
 176       }
 177       worker.setOutputReader(outputReader);
 178       worker.setErrorReader(errorReader);
 179     }
 180     return worker;
 181   }
 182
 183   @BeforeTest(alwaysRun = true)
 184   public void initialize()
 185   {
 186     new CommandLineOperations();
 187   }
 188
 189   @BeforeTest(alwaysRun = true)
 190   public void setUpForHeadlessCommandLineInputOperations()
 191           throws IOException
 192   {
 193     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 194             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 195             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 196     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 197     String ln = null;
 198     while ((ln = worker.getOutputReader().readLine()) != null)
 199     {
 200       System.out.println(ln);
 201       successfulCMDs.add(ln);
 202     }
 203   }
 204
 205   @BeforeTest(alwaysRun = true)
 206   public void setUpForCommandLineInputOperations() throws IOException
 207   {
 208     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 209     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 210     String ln = null;
 211     int count = 0;
 212     while ((ln = worker.getErrorReader().readLine()) != null)
 213     {
 214       System.out.println(ln);
 215       successfulCMDs.add(ln);
 216       if (++count > 5)
 217       {
 218         break;
 219       }
 220     }
 221     if (worker != null && worker.exit == null)
 222     {
 223       worker.interrupt();
 224       Thread.currentThread().interrupt();
 225       worker.process.destroy();
 226     }
 227   }
 228
 229   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 230   public void testAllInputOperations(String expectedString,
 231           String failureMsg)
 232   {
 233     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 234   }
 235
 236   @Test(
 237     groups =
 238     { "Functional", "testben" },
 239     dataProvider = "headlessModeOutputOperationsData")
 240   public void testHeadlessModeOutputOperations(String harg, String type,
 241           String fileName, boolean withAWT, int expectedMinFileSize,
 242           int timeout)
 243   {
 244     String cmd = harg + type + " " + fileName;
 245     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 246     File file = new File(fileName);
 247     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 248
 249     FileAssert.assertFile(file,
 250             "Didn't create an output" + type + " file.[" + harg + "]");
 251     // System.out.println( "File '" + file.getName() + "' has size " +
 252     // file.length());
 253     // FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 254     FileAssert.assertMinLength(file, expectedMinFileSize);
 255     if (worker != null && worker.exit == null)
 256     {
 257       worker.interrupt();
 258       Thread.currentThread().interrupt();
 259       worker.process.destroy();
 260       Assert.fail("Jalview did not exit after " + type
 261               + " generation (try running test again to verify - timeout at "
 262               + timeout + "ms). [" + harg + "]");
 263     }
 264     new File(fileName).delete();
 265   }
 266
 267   @DataProvider(name = "allInputOpearationsData")
 268   public Object[][] getHeadlessModeInputParams()
 269   {
 270     return new Object[][] {
 271         // headless mode input operations
 272         { "CMD [-color zappo] executed successfully!",
 273             "Failed command : -color zappo" },
 274         { "CMD [-props FILE] executed successfully!",
 275             "Failed command : -props File" },
 276         { "CMD [-sortbytree] executed successfully!",
 277             "Failed command : -sortbytree" },
 278         { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 279             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 280         { "CMD [-open examples/uniref50.fa] executed successfully!",
 281             "Failed command : -open examples/uniref50.fa" },
 282         { "CMD [-nosortbytree] executed successfully!",
 283             "Failed command : -nosortbytree" },
 284         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 285             "Failed command : -dasserver nickname=www.test.com" },
 286         { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 287             "Failed command : -features examples/testdata/plantfdx.features" },
 288         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 289             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 290         { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 291             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 292         // non headless mode input operations
 293         { "CMD [-nousagestats] executed successfully!",
 294             "Failed command : -nousagestats" },
 295         { "CMD [-noquestionnaire] executed successfully!",
 296             "Failed command : -noquestionnaire nickname=www.test.com" } };
 297
 298   }
 299
 300   @DataProvider(name = "headlessModeOutputOperationsData")
 301   public static Object[][] getHeadlessModeOutputParams()
 302   {
 303     return new Object[][] {
 304         { "nodisplay -open examples/uniref50.fa", " -eps",
 305             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 306         { "nodisplay -open examples/uniref50.fa", " -eps",
 307             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 308         { "nogui -open examples/uniref50.fa", " -eps",
 309             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 310         { "nogui -open examples/uniref50.fa", " -eps",
 311             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 312         { "headless -open examples/uniref50.fa", " -eps",
 313             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 314         { "headless -open examples/uniref50.fa", " -svg",
 315             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 316         { "headless -open examples/uniref50.fa", " -png",
 317             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 318         { "headless -open examples/uniref50.fa", " -html",
 319             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 320         { "headless -open examples/uniref50.fa", " -fasta",
 321             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
 322             TEST_TIMEOUT },
 323         { "headless -open examples/uniref50.fa", " -clustal",
 324             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 325             TEST_TIMEOUT },
 326         { "headless -open examples/uniref50.fa", " -msf",
 327             "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
 328             TEST_TIMEOUT },
 329         { "headless -open examples/uniref50.fa", " -pileup",
 330             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 331             TEST_TIMEOUT },
 332         { "headless -open examples/uniref50.fa", " -pir",
 333             "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
 334             TEST_TIMEOUT },
 335         { "headless -open examples/uniref50.fa", " -pfam",
 336             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
 337             TEST_TIMEOUT },
 338         { "headless -open examples/uniref50.fa", " -blc",
 339             "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
 340             TEST_TIMEOUT },
 341         { "headless -open examples/uniref50.fa", " -jalview",
 342             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
 343             TEST_TIMEOUT }, };
 344   }
 345 }