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