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.ModuleRef;
  43 import io.github.classgraph.ScanResult;
  44
  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
  56                                                 // on
  57                                                 // full test run than on
  58                                                 // individual tests
  59
  60   private static final int SETUP_TIMEOUT = 9000;
  61
  62   private static final int MINFILESIZE_SMALL = 2096;
  63
  64   private static final int MINFILESIZE_BIG = 4096;
  65
  66   private ArrayList<String> successfulCMDs = new ArrayList<>();
  67
  68   /***
  69    * from
  70    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
  71    * -using-javas-runtime-exec
  72    *
  73    * @author jimp
  74    *
  75    */
  76   private static class Worker extends Thread
  77   {
  78     private final Process process;
  79
  80     private BufferedReader outputReader;
  81
  82     private BufferedReader errorReader;
  83
  84     private Integer exit;
  85
  86     private Worker(Process process)
  87     {
  88       this.process = process;
  89     }
  90
  91     @Override
  92     public void run()
  93     {
  94       try
  95       {
  96         exit = process.waitFor();
  97       } catch (InterruptedException ignore)
  98       {
  99         return;
 100       }
 101     }
 102
 103     public BufferedReader getOutputReader()
 104     {
 105       return outputReader;
 106     }
 107
 108     public void setOutputReader(BufferedReader outputReader)
 109     {
 110       this.outputReader = outputReader;
 111     }
 112
 113     public BufferedReader getErrorReader()
 114     {
 115       return errorReader;
 116     }
 117
 118     public void setErrorReader(BufferedReader errorReader)
 119     {
 120       this.errorReader = errorReader;
 121     }
 122   }
 123
 124   private static ClassGraph scanner = null;
 125
 126   private static String classpath = null;
 127
 128   private static String modules = null;
 129
 130   public synchronized static String getClassPath()
 131   {
 132     if (scanner == null)
 133     {
 134       scanner = new ClassGraph();
 135       ScanResult scan = scanner.scan();
 136       classpath = scan.getClasspath();
 137       modules = "";
 138       for (ModuleRef mr : scan.getModules())
 139       {
 140         modules.concat(mr.getName());
 141       }
 142     }
 143     while (classpath == null)
 144     {
 145       try
 146       {
 147         Thread.sleep(10);
 148       } catch (InterruptedException x)
 149       {
 150
 151       }
 152     }
 153     return classpath;
 154   }
 155
 156   private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
 157           int timeout)
 158   {
 159     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
 160     // not expanded by the shell
 161     String classpath = getClassPath();
 162     String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
 163             + " -classpath " + classpath
 164             + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
 165                     : "")
 166             + " jalview.bin.Jalview ";
 167     Process ls2_proc = null;
 168     Worker worker = null;
 169     try
 170     {
 171       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 172     } catch (Throwable e1)
 173     {
 174       e1.printStackTrace();
 175     }
 176     if (ls2_proc != null)
 177     {
 178       BufferedReader outputReader = new BufferedReader(
 179               new InputStreamReader(ls2_proc.getInputStream()));
 180       BufferedReader errorReader = new BufferedReader(
 181               new InputStreamReader(ls2_proc.getErrorStream()));
 182       worker = new Worker(ls2_proc);
 183       worker.start();
 184       try
 185       {
 186         worker.join(timeout);
 187       } catch (InterruptedException e)
 188       {
 189         System.err.println("Thread interrupted");
 190       }
 191       worker.setOutputReader(outputReader);
 192       worker.setErrorReader(errorReader);
 193     }
 194     return worker;
 195   }
 196
 197   @BeforeTest(alwaysRun = true)
 198   public void initialize()
 199   {
 200     new CommandLineOperations();
 201   }
 202
 203   @BeforeTest(alwaysRun = true)
 204   public void setUpForHeadlessCommandLineInputOperations()
 205           throws IOException
 206   {
 207     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
 208             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
 209             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 210     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 211     String ln = null;
 212     while ((ln = worker.getOutputReader().readLine()) != null)
 213     {
 214       System.out.println(ln);
 215       successfulCMDs.add(ln);
 216     }
 217     while ((ln = worker.getErrorReader().readLine()) != null)
 218     {
 219       System.err.println(ln);
 220     }
 221   }
 222
 223   @BeforeTest(alwaysRun = true)
 224   public void setUpForCommandLineInputOperations() throws IOException
 225   {
 226     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 227     Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 228     String ln = null;
 229     int count = 0;
 230     while ((ln = worker.getErrorReader().readLine()) != null)
 231     {
 232       System.out.println(ln);
 233       successfulCMDs.add(ln);
 234       if (++count > 5)
 235       {
 236         break;
 237       }
 238     }
 239     if (worker != null && worker.exit == null)
 240     {
 241       worker.interrupt();
 242       Thread.currentThread().interrupt();
 243       worker.process.destroy();
 244     }
 245   }
 246
 247   @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
 248   public void testAllInputOperations(String expectedString,
 249           String failureMsg)
 250   {
 251     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 252   }
 253
 254   @Test(
 255     groups =
 256     { "Functional", "testben" },
 257     dataProvider = "headlessModeOutputOperationsData")
 258   public void testHeadlessModeOutputOperations(String harg, String type,
 259           String fileName, boolean withAWT, int expectedMinFileSize,
 260           int timeout)
 261   {
 262     String cmd = harg + type + " " + fileName;
 263     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 264     File file = new File(fileName);
 265     file.deleteOnExit();
 266     Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
 267     assertNotNull(worker, "worker is null");
 268     String msg = "Didn't create an output" + type + " file.[" + harg + "]";
 269     assertTrue(file.exists(), msg);
 270     FileAssert.assertFile(file, msg);
 271     FileAssert.assertMinLength(file, expectedMinFileSize);
 272     if (worker != null && worker.exit == null)
 273     {
 274       worker.interrupt();
 275       Thread.currentThread().interrupt();
 276       worker.process.destroy();
 277       Assert.fail("Jalview did not exit after " + type
 278               + " generation (try running test again to verify - timeout at "
 279               + timeout + "ms). [" + harg + "]");
 280     }
 281     file.delete();
 282   }
 283
 284   @DataProvider(name = "allInputOperationsData")
 285   public Object[][] getHeadlessModeInputParams()
 286   {
 287     return new Object[][] {
 288         // headless mode input operations
 289         { "CMD [-color zappo] executed successfully!",
 290             "Failed command : -color zappo" },
 291         { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
 292             "Failed command : -props File" },
 293         { "CMD [-sortbytree] executed successfully!",
 294             "Failed command : -sortbytree" },
 295         { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 296             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 297         { "CMD [-open examples/uniref50.fa] executed successfully!",
 298             "Failed command : -open examples/uniref50.fa" },
 299         { "CMD [-nosortbytree] executed successfully!",
 300             "Failed command : -nosortbytree" },
 301         { "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 302             "Failed command : -features examples/testdata/plantfdx.features" },
 303         { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 304             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 305         { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 306             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 307         // non headless mode input operations
 308         { "CMD [-nousagestats] executed successfully!",
 309             "Failed command : -nousagestats" },
 310         { "CMD [-noquestionnaire] executed successfully!",
 311             "Failed command : -noquestionnaire" } };
 312   }
 313
 314   @DataProvider(name = "headlessModeOutputOperationsData")
 315   public static Object[][] getHeadlessModeOutputParams()
 316   {
 317     return new Object[][] { { "nodisplay -open examples/uniref50.fa",
 318         " -eps", "test/jalview/bin/test_uniref50_out.eps", true,
 319         MINFILESIZE_BIG, TEST_TIMEOUT },
 320         { "nodisplay -open examples/uniref50.fa", " -eps",
 321             "test/jalview/bin/test_uniref50_out.eps", false,
 322             MINFILESIZE_BIG, TEST_TIMEOUT },
 323         { "nogui -open examples/uniref50.fa", " -eps",
 324             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 325             TEST_TIMEOUT },
 326         { "nogui -open examples/uniref50.fa", " -eps",
 327             "test/jalview/bin/test_uniref50_out.eps", false,
 328             MINFILESIZE_BIG, TEST_TIMEOUT },
 329         { "headless -open examples/uniref50.fa", " -eps",
 330             "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
 331             TEST_TIMEOUT },
 332         { "headless -open examples/uniref50.fa", " -svg",
 333             "test/jalview/bin/test_uniref50_out.svg", false,
 334             MINFILESIZE_BIG, TEST_TIMEOUT },
 335         { "headless -open examples/uniref50.fa", " -png",
 336             "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
 337             TEST_TIMEOUT },
 338         { "headless -open examples/uniref50.fa", " -html",
 339             "test/jalview/bin/test_uniref50_out.html", true,
 340             MINFILESIZE_BIG, TEST_TIMEOUT },
 341         { "headless -open examples/uniref50.fa", " -fasta",
 342             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
 343             TEST_TIMEOUT },
 344         { "headless -open examples/uniref50.fa", " -clustal",
 345             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 346             TEST_TIMEOUT },
 347         { "headless -open examples/uniref50.fa", " -msf",
 348             "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
 349             TEST_TIMEOUT },
 350         { "headless -open examples/uniref50.fa", " -pileup",
 351             "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
 352             TEST_TIMEOUT },
 353         { "headless -open examples/uniref50.fa", " -pir",
 354             "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
 355             TEST_TIMEOUT },
 356         { "headless -open examples/uniref50.fa", " -pfam",
 357             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
 358             TEST_TIMEOUT },
 359         { "headless -open examples/uniref50.fa", " -blc",
 360             "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
 361             TEST_TIMEOUT },
 362         { "headless -open examples/uniref50.fa", " -jalview",
 363             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
 364             TEST_TIMEOUT }, };
 365   }
 366 }