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