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 static org.testng.Assert.assertNotNull;
  24 import static org.testng.Assert.assertTrue;
  25
  26 import jalview.gui.JvOptionPane;
  27
  28 import java.io.BufferedReader;
  29 import java.io.File;
  30 import java.io.IOException;
  31 import java.io.InputStreamReader;
  32 import java.util.ArrayList;
  33
  34 import org.testng.Assert;
  35 import org.testng.FileAssert;
  36 import org.testng.annotations.BeforeClass;
  37 import org.testng.annotations.BeforeTest;
  38 import org.testng.annotations.DataProvider;
  39 import org.testng.annotations.Test;
  40
  41 import io.github.classgraph.ClassGraph;
  42 import io.github.classgraph.ScanResult;
  43
  44 @Test(singleThreaded = true)
  45 public class CommandLineOperations
  46 {
  47
  48   @BeforeClass(alwaysRun = true)
  49   public void setUpJvOptionPane()
  50   {
  51     JvOptionPane.setInteractiveMode(false);
  52     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  53   }
  54
  55   private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
  56                                                 // full test run than on
  57                                                 // individual tests
  58
  59   private static final int SETUP_TIMEOUT = 9000;
  60
  61   private static final int MINFILESIZE_SMALL = 2096;
  62
  63   private static final int MINFILESIZE_BIG = 4096;
  64
  65   private ArrayList<String> successfulCMDs = new ArrayList<>();
  66
  67   /***
  68    * from
  69    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  70    * -using-javas-runtime-exec
  71    *
  72    * @author jimp
  73    *
  74    */
  75   private static class Worker extends Thread
  76   {
  77     private final Process process;
  78
  79     private BufferedReader outputReader;
  80
  81     private BufferedReader errorReader;
  82
  83     private Integer exit;
  84
  85     private Worker(Process process)
  86     {
  87       this.process = process;
  88     }
  89
  90     @Override
  91     public void run()
  92     {
  93       try
  94       {
  95         exit = process.waitFor();
  96       } catch (InterruptedException ignore)
  97       {
  98         return;
  99       }
 100     }
 101
 102     public BufferedReader getOutputReader()
 103     {
 104       return outputReader;
 105     }
 106
 107     public void setOutputReader(BufferedReader outputReader)
 108     {
 109       this.outputReader = outputReader;
 110     }
 111
 112     public BufferedReader getErrorReader()
 113     {
 114       return errorReader;
 115     }
 116
 117     public void setErrorReader(BufferedReader errorReader)
 118     {
 119       this.errorReader = errorReader;
 120     }
 121   }
 122
 123   private static ClassGraph scanner = null;
 124
 125   private static String classpath = null;
 126
 127   public synchronized static String getClassPath()
 128   {
 129     if (scanner == null)
 130     {
 131       scanner = new ClassGraph();
 132       ScanResult scan = scanner.scan();
 133       classpath = scan.getClasspath();
 134     }
 135     while (classpath == null)
 136     {
 137       try
 138       {
 139         Thread.sleep(10);
 140       } catch (InterruptedException x)
 141       {
 142
 143       }
 144     }
 145     return classpath;
 146   }
 147
 148   private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
 149           int timeout)
 150   {
 151     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
 152     // not expanded by the shell
 153     String classpath = getClassPath();
 154     String _cmd = "java "
 155             + (withAwt ? "-Djava.awt.headless=true" : "")
 156             + " -classpath " + classpath + " jalview.bin.Jalview ";
 157     Process ls2_proc = null;
 158     Worker worker = null;
 159     try
 160     {
 161       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 162     } catch (Throwable e1)
 163     {
 164       e1.printStackTrace();
 165     }
 166     if (ls2_proc != null)
 167     {
 168       BufferedReader outputReader = new BufferedReader(
 169               new InputStreamReader(ls2_proc.getInputStream()));
 170       BufferedReader errorReader = new BufferedReader(
 171               new InputStreamReader(ls2_proc.getErrorStream()));
 172       worker = new Worker(ls2_proc);
 173       worker.setOutputReader(outputReader);
 174       worker.setErrorReader(errorReader);
 175       worker.start();
 176       try
 177       {
 178
 179         worker.join(timeout);
 180
 181       } catch (InterruptedException e)
 182       {
 183         System.err.println("Thread interrupted");
 184       }
 185     }
 186     return worker;
 187   }
 188
 189   @BeforeTest(alwaysRun = true)
 190   public void initialize()
 191   {
 192     new CommandLineOperations();
 193   }
 194
 195   @BeforeTest(alwaysRun = true)
 196   public void setUpForHeadlessCommandLineInputOperations()
 197           throws IOException
 198   {
 199     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
 200             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
 201             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 202     System.out.println("CommandLine test " + ++ntest);
 203     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 204     String ln = null;
 205     while ((ln = worker.getOutputReader().readLine()) != null)
 206     {
 207       System.out.println(ln);
 208       successfulCMDs.add(ln);
 209       if (ln.equals(Jalview.TERMINATOR_LINE))
 210       {
 211         break;
 212       }
 213     }
 214     if (worker != null && worker.exit == null)
 215     {
 216       worker.interrupt();
 217       Thread.currentThread().interrupt();
 218       worker.process.destroy();
 219     }
 220     // while ((ln = worker.getErrorReader().readLine()) != null)
 221     // {
 222     // System.err.println(ln);
 223     // }
 224
 225   }
 226
 227   int ntest = 0;
 228
 229   @BeforeTest(alwaysRun = true)
 230   public void setUpForNonHeadlessInputOperations() throws IOException
 231   {
 232     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 233     Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 234     String ln = null;
 235     int count = 0;
 236     while ((ln = worker.getErrorReader().readLine()) != null)
 237     {
 238       System.out.println(ln);
 239       successfulCMDs.add(ln);
 240       if (ln.equals(Jalview.TERMINATOR_LINE))
 241       {
 242         break;
 243       }
 244
 245       if (++count > 5)
 246       {
 247         break;
 248       }
 249     }
 250     if (worker != null && worker.exit == null)
 251     {
 252       worker.interrupt();
 253       Thread.currentThread().interrupt();
 254       worker.process.destroy();
 255     }
 256   }
 257
 258   @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
 259   public void testAllInputOperations(String expectedString,
 260           String failureMsg)
 261   {
 262     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 263   }
 264
 265   @Test(
 266     groups =
 267     { "Functional" },
 268     dataProvider = "headlessModeOutputOperationsData")
 269   public void testHeadlessModeOutputOperations(String harg, String type,
 270           String fileName, boolean withAWT, int expectedMinFileSize,
 271           int timeout) throws IOException
 272   {
 273     File file = new File(fileName);
 274     String cmd = harg + type + " "
 275             + file.getAbsolutePath().replace('\\', '/');
 276     System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 277
 278     file.deleteOnExit();
 279     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
 280     assertNotNull(worker, "worker is null");
 281     String msg = "Didn't create an output" + type + " file: "
 282             + file.getAbsolutePath() + " [" + harg + "]";
 283     while (worker.isAlive())
 284     {
 285     }
 286     while (worker.getOutputReader().ready())
 287     {
 288       String ln = worker.getOutputReader().readLine();
 289       System.out.println(ln);
 290     }
 291     assertTrue(file.exists(), msg);
 292     FileAssert.assertFile(file, msg);
 293     FileAssert.assertMinLength(file, expectedMinFileSize);
 294     if (worker != null && worker.exit == null)
 295     {
 296       worker.interrupt();
 297       Thread.currentThread().interrupt();
 298       worker.process.destroy();
 299       // Assert.fail("Jalview did not exit after "
 300       // + type
 301       // + " generation (try running test again to verify - timeout at "
 302       // + SETUP_TIMEOUT + "ms). ["
 303       // + harg + "]");
 304     }
 305     file.delete();
 306   }
 307
 308   @DataProvider(name = "allInputOperationsData")
 309   public Object[][] getAllInputParams()
 310   {
 311     return new Object[][] {
 312         // headless mode input operations
 313         { "CMD [-color zappo] executed successfully!",
 314             "Failed command : -color zappo" },
 315         { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
 316             "Failed command : -props File" },
 317         { "CMD [-sortbytree] executed successfully!",
 318             "Failed command : -sortbytree" },
 319         { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 320             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 321         { "CMD [-open examples/uniref50.fa] executed successfully!",
 322             "Failed command : -open examples/uniref50.fa" },
 323         { "CMD [-nosortbytree] executed successfully!",
 324             "Failed command : -nosortbytree" },
 325         { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 326             "Failed command : -features examples/testdata/plantfdx.features" },
 327         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 328             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 329         { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 330             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 331         // non headless mode input operations
 332         { "CMD [-nousagestats] executed successfully!",
 333             "Failed command : -nousagestats" },
 334         { "CMD [-noquestionnaire] executed successfully!",
 335             "Failed command : -noquestionnaire" } };
 336   }
 337
 338   @DataProvider(name = "headlessModeOutputOperationsData")
 339   public static Object[][] getHeadlessModeOutputParams()
 340   {
 341     return new Object[][] {
 342         // works
 343         { "nodisplay -open examples/uniref50.fa", " -eps",
 344             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 345             TEST_TIMEOUT },
 346         { "nodisplay -open examples/uniref50.fa", " -eps",
 347             "test/jalview/bin/test_uniref50_out.eps", false,
 348             MINFILESIZE_BIG, TEST_TIMEOUT },
 349         { "nogui -open examples/uniref50.fa", " -eps",
 350             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 351             TEST_TIMEOUT },
 352         { "nogui -open examples/uniref50.fa", " -eps",
 353             "test/jalview/bin/test_uniref50_out.eps", false,
 354             MINFILESIZE_BIG, TEST_TIMEOUT },
 355         { "headless -open examples/uniref50.fa", " -eps",
 356             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 357             TEST_TIMEOUT },
 358         { "headless -open examples/uniref50.fa", " -svg",
 359             "test/jalview/bin/test_uniref50_out.svg", false,
 360             MINFILESIZE_BIG, TEST_TIMEOUT },
 361         { "headless -open examples/uniref50.fa", " -png",
 362             "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
 363             TEST_TIMEOUT },
 364         { "headless -open examples/uniref50.fa", " -html",
 365             "test/jalview/bin/test_uniref50_out.html", true,
 366             MINFILESIZE_BIG, TEST_TIMEOUT },
 367         { "headless -open examples/uniref50.fa", " -fasta",
 368             "test/jalview/bin/test_uniref50_out.mfa", true,
 369             MINFILESIZE_SMALL, TEST_TIMEOUT },
 370         { "headless -open examples/uniref50.fa", " -clustal",
 371             "test/jalview/bin/test_uniref50_out.aln", true,
 372             MINFILESIZE_SMALL, TEST_TIMEOUT },
 373         { "headless -open examples/uniref50.fa", " -msf",
 374             "test/jalview/bin/test_uniref50_out.msf", true,
 375             MINFILESIZE_SMALL, TEST_TIMEOUT },
 376         { "headless -open examples/uniref50.fa", " -pileup",
 377             "test/jalview/bin/test_uniref50_out.aln", true,
 378             MINFILESIZE_SMALL, TEST_TIMEOUT },
 379         { "headless -open examples/uniref50.fa", " -pir",
 380             "test/jalview/bin/test_uniref50_out.pir", true,
 381             MINFILESIZE_SMALL, TEST_TIMEOUT },
 382         { "headless -open examples/uniref50.fa", " -pfam",
 383             "test/jalview/bin/test_uniref50_out.pfam", true,
 384             MINFILESIZE_SMALL, TEST_TIMEOUT },
 385         { "headless -open examples/uniref50.fa", " -blc",
 386             "test/jalview/bin/test_uniref50_out.blc", true,
 387             MINFILESIZE_SMALL, TEST_TIMEOUT },
 388         { "headless -open examples/uniref50.fa", " -jalview",
 389             "test/jalview/bin/test_uniref50_out.jvp", true,
 390             MINFILESIZE_SMALL, TEST_TIMEOUT },
 391     };
 392   }
 393 }