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
  55                                                 // 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 " + (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 =
 245     { "Functional", "testben" },
 246     dataProvider = "headlessModeOutputOperationsData")
 247   public void testHeadlessModeOutputOperations(String harg, String type,
 248           String fileName, boolean withAWT, int expectedMinFileSize,
 249           int timeout)
 250   {
 251     String cmd = harg + type + " " + fileName;
 252     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 253     File file = new File(fileName);
 254     file.deleteOnExit();
 255     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
 256     assertNotNull(worker, "worker is null");
 257     String msg = "Didn't create an output" + type + " file.[" + harg + "]";
 258     assertTrue(file.exists(), msg);
 259     FileAssert.assertFile(file, msg);
 260     FileAssert.assertMinLength(file, expectedMinFileSize);
 261     if (worker != null && worker.exit == null)
 262     {
 263       worker.interrupt();
 264       Thread.currentThread().interrupt();
 265       worker.process.destroy();
 266       Assert.fail("Jalview did not exit after " + type
 267               + " generation (try running test again to verify - timeout at "
 268               + timeout + "ms). [" + harg + "]");
 269     }
 270     file.delete();
 271   }
 272
 273   @DataProvider(name = "allInputOperationsData")
 274   public Object[][] getHeadlessModeInputParams()
 275   {
 276     return new Object[][] {
 277         // headless mode input operations
 278         { "CMD [-color zappo] executed successfully!",
 279             "Failed command : -color zappo" },
 280         { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
 281             "Failed command : -props File" },
 282         { "CMD [-sortbytree] executed successfully!",
 283             "Failed command : -sortbytree" },
 284         { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 285             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 286         { "CMD [-open examples/uniref50.fa] executed successfully!",
 287             "Failed command : -open examples/uniref50.fa" },
 288         { "CMD [-nosortbytree] executed successfully!",
 289             "Failed command : -nosortbytree" },
 290         { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 291             "Failed command : -features examples/testdata/plantfdx.features" },
 292         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 293             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 294         { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 295             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 296         // non headless mode input operations
 297         { "CMD [-nousagestats] executed successfully!",
 298             "Failed command : -nousagestats" },
 299         { "CMD [-noquestionnaire] executed successfully!",
 300             "Failed command : -noquestionnaire" } };
 301   }
 302
 303   @DataProvider(name = "headlessModeOutputOperationsData")
 304   public static Object[][] getHeadlessModeOutputParams()
 305   {
 306     return new Object[][] { { "nodisplay -open examples/uniref50.fa",
 307         " -eps", "test/jalview/bin/test_uniref50_out.eps", true,
 308         MINFILESIZE_BIG, TEST_TIMEOUT },
 309         { "nodisplay -open examples/uniref50.fa", " -eps",
 310             "test/jalview/bin/test_uniref50_out.eps", false,
 311             MINFILESIZE_BIG, TEST_TIMEOUT },
 312         { "nogui -open examples/uniref50.fa", " -eps",
 313             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 314             TEST_TIMEOUT },
 315         { "nogui -open examples/uniref50.fa", " -eps",
 316             "test/jalview/bin/test_uniref50_out.eps", false,
 317             MINFILESIZE_BIG, TEST_TIMEOUT },
 318         { "headless -open examples/uniref50.fa", " -eps",
 319             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 320             TEST_TIMEOUT },
 321         { "headless -open examples/uniref50.fa", " -svg",
 322             "test/jalview/bin/test_uniref50_out.svg", false,
 323             MINFILESIZE_BIG, TEST_TIMEOUT },
 324         { "headless -open examples/uniref50.fa", " -png",
 325             "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
 326             TEST_TIMEOUT },
 327         { "headless -open examples/uniref50.fa", " -html",
 328             "test/jalview/bin/test_uniref50_out.html", true,
 329             MINFILESIZE_BIG, TEST_TIMEOUT },
 330         { "headless -open examples/uniref50.fa", " -fasta",
 331             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
 332             TEST_TIMEOUT },
 333         { "headless -open examples/uniref50.fa", " -clustal",
 334             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 335             TEST_TIMEOUT },
 336         { "headless -open examples/uniref50.fa", " -msf",
 337             "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
 338             TEST_TIMEOUT },
 339         { "headless -open examples/uniref50.fa", " -pileup",
 340             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 341             TEST_TIMEOUT },
 342         { "headless -open examples/uniref50.fa", " -pir",
 343             "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
 344             TEST_TIMEOUT },
 345         { "headless -open examples/uniref50.fa", " -pfam",
 346             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
 347             TEST_TIMEOUT },
 348         { "headless -open examples/uniref50.fa", " -blc",
 349             "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
 350             TEST_TIMEOUT },
 351         { "headless -open examples/uniref50.fa", " -jalview",
 352             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
 353             TEST_TIMEOUT }, };
 354   }
 355 }