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       }
 180       worker.setOutputReader(outputReader);
 181       worker.setErrorReader(errorReader);
 182     }
 183     return worker;
 184   }
 185
 186   @BeforeTest(alwaysRun = true)
 187   public void initialize()
 188   {
 189     new CommandLineOperations();
 190   }
 191
 192   @BeforeTest(alwaysRun = true)
 193   public void setUpForHeadlessCommandLineInputOperations()
 194           throws IOException
 195   {
 196     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
 197             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
 198             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 199     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 200     String ln = null;
 201     while ((ln = worker.getOutputReader().readLine()) != null)
 202     {
 203       System.out.println(ln);
 204       successfulCMDs.add(ln);
 205     }
 206     while ((ln = worker.getErrorReader().readLine()) != null)
 207     {
 208       System.err.println(ln);
 209     }
 210   }
 211
 212   @BeforeTest(alwaysRun = true)
 213   public void setUpForCommandLineInputOperations() throws IOException
 214   {
 215     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 216     Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 217     String ln = null;
 218     int count = 0;
 219     while ((ln = worker.getErrorReader().readLine()) != null)
 220     {
 221       System.out.println(ln);
 222       successfulCMDs.add(ln);
 223       if (++count > 5)
 224       {
 225         break;
 226       }
 227     }
 228     if (worker != null && worker.exit == null)
 229     {
 230       worker.interrupt();
 231       Thread.currentThread().interrupt();
 232       worker.process.destroy();
 233     }
 234   }
 235
 236   @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
 237   public void testAllInputOperations(String expectedString,
 238           String failureMsg)
 239   {
 240     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 241   }
 242
 243   @Test(
 244     groups = { "Functional" },
 245     dataProvider = "headlessModeOutputOperationsData")
 246   public void testHeadlessModeOutputOperations(String harg, String type,
 247           String fileName, boolean withAWT, int expectedMinFileSize,
 248           int timeout)
 249   {
 250     String cmd = harg + type + " " + fileName;
 251     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 252     File file = new File(fileName);
 253     file.deleteOnExit();
 254     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
 255     assertNotNull(worker, "worker is null");
 256     String msg = "Didn't create an output" + type + " file.[" + harg + "]";
 257     assertTrue(file.exists(), msg);
 258     FileAssert.assertFile(file, msg);
 259     FileAssert.assertMinLength(file, expectedMinFileSize);
 260     if (worker != null && worker.exit == null)
 261     {
 262       worker.interrupt();
 263       Thread.currentThread().interrupt();
 264       worker.process.destroy();
 265       Assert.fail("Jalview did not exit after "
 266               + type
 267               + " generation (try running test again to verify - timeout at "
 268               + SETUP_TIMEOUT + "ms). ["
 269               + harg + "]");
 270     }
 271     file.delete();
 272   }
 273
 274   @DataProvider(name = "allInputOperationsData")
 275   public Object[][] getHeadlessModeInputParams()
 276   {
 277     return new Object[][] {
 278         // headless mode input operations
 279         { "CMD [-color zappo] executed successfully!",
 280             "Failed command : -color zappo" },
 281         { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
 282             "Failed command : -props File" },
 283         { "CMD [-sortbytree] executed successfully!",
 284             "Failed command : -sortbytree" },
 285         { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 286             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 287         { "CMD [-open examples/uniref50.fa] executed successfully!",
 288             "Failed command : -open examples/uniref50.fa" },
 289         { "CMD [-nosortbytree] executed successfully!",
 290             "Failed command : -nosortbytree" },
 291         { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 292             "Failed command : -features examples/testdata/plantfdx.features" },
 293         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 294             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 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   @DataProvider(name = "headlessModeOutputOperationsData")
 305   public static Object[][] getHeadlessModeOutputParams()
 306   {
 307     return new Object[][] {
 308         { "nodisplay -open examples/uniref50.fa", " -eps",
 309             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 310             TEST_TIMEOUT },
 311         { "nodisplay -open examples/uniref50.fa", " -eps",
 312             "test/jalview/bin/test_uniref50_out.eps", false,
 313             MINFILESIZE_BIG, TEST_TIMEOUT },
 314         { "nogui -open examples/uniref50.fa", " -eps",
 315             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 316             TEST_TIMEOUT },
 317         { "nogui -open examples/uniref50.fa", " -eps",
 318             "test/jalview/bin/test_uniref50_out.eps", false,
 319             MINFILESIZE_BIG, TEST_TIMEOUT },
 320         { "headless -open examples/uniref50.fa", " -eps",
 321             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 322             TEST_TIMEOUT },
 323         { "headless -open examples/uniref50.fa", " -svg",
 324             "test/jalview/bin/test_uniref50_out.svg", false,
 325             MINFILESIZE_BIG, TEST_TIMEOUT },
 326         { "headless -open examples/uniref50.fa", " -png",
 327             "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
 328             TEST_TIMEOUT },
 329         { "headless -open examples/uniref50.fa", " -html",
 330             "test/jalview/bin/test_uniref50_out.html", true,
 331             MINFILESIZE_BIG, TEST_TIMEOUT },
 332         { "headless -open examples/uniref50.fa", " -fasta",
 333             "test/jalview/bin/test_uniref50_out.mfa", true,
 334             MINFILESIZE_SMALL, TEST_TIMEOUT },
 335         { "headless -open examples/uniref50.fa", " -clustal",
 336             "test/jalview/bin/test_uniref50_out.aln", true,
 337             MINFILESIZE_SMALL, TEST_TIMEOUT },
 338         { "headless -open examples/uniref50.fa", " -msf",
 339             "test/jalview/bin/test_uniref50_out.msf", true,
 340             MINFILESIZE_SMALL, TEST_TIMEOUT },
 341         { "headless -open examples/uniref50.fa", " -pileup",
 342             "test/jalview/bin/test_uniref50_out.aln", true,
 343             MINFILESIZE_SMALL, TEST_TIMEOUT },
 344         { "headless -open examples/uniref50.fa", " -pir",
 345             "test/jalview/bin/test_uniref50_out.pir", true,
 346             MINFILESIZE_SMALL, TEST_TIMEOUT },
 347         { "headless -open examples/uniref50.fa", " -pfam",
 348             "test/jalview/bin/test_uniref50_out.pfam", true,
 349             MINFILESIZE_SMALL, TEST_TIMEOUT },
 350         { "headless -open examples/uniref50.fa", " -blc",
 351             "test/jalview/bin/test_uniref50_out.blc", true,
 352             MINFILESIZE_SMALL, TEST_TIMEOUT },
 353         { "headless -open examples/uniref50.fa", " -jalview",
 354             "test/jalview/bin/test_uniref50_out.jvp", true,
 355             MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 356   }
 357 }