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 import jalview.ws.utils.Worker;
  25
  26 import java.io.BufferedReader;
  27 import java.io.File;
  28 import java.io.IOException;
  29 import java.io.InputStreamReader;
  30 import java.util.ArrayList;
  31
  32 import org.testng.Assert;
  33 import org.testng.FileAssert;
  34 import org.testng.annotations.BeforeClass;
  35 import org.testng.annotations.BeforeTest;
  36 import org.testng.annotations.DataProvider;
  37 import org.testng.annotations.Test;
  38
  39 public class CommandLineOperations
  40 {
  41
  42   @BeforeClass(alwaysRun = true)
  43   public void setUpJvOptionPane()
  44   {
  45     JvOptionPane.setInteractiveMode(false);
  46     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  47   }
  48
  49   private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
  50                                                 // full test run than on
  51                                                 // individual tests
  52
  53   private static final int SETUP_TIMEOUT = 9000;
  54
  55   private static final int MINFILESIZE_SMALL = 2096;
  56
  57   private static final int MINFILESIZE_BIG = 4096;
  58
  59   private ArrayList<String> successfulCMDs = new ArrayList<>();
  60
  61   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
  62           int timeout)
  63   {
  64     String cp_sep = ":";
  65     if (System.getProperty("os.name").indexOf("Windows") >= 0)
  66     {
  67       cp_sep = ";";
  68     }
  69     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
  70     // not expanded by the shell
  71     String _cmd = "java "
  72             + (withAwt ? "-Djava.awt.headless=true" : "")
  73             + " -classpath ./classes" + cp_sep
  74             + "./lib/* jalview.bin.Jalview ";
  75     System.out.println("CMD [" + cmd + "]");
  76     Process ls2_proc = null;
  77     Worker worker = null;
  78     try
  79     {
  80       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
  81     } catch (IOException e1)
  82     {
  83       e1.printStackTrace();
  84     }
  85     if (ls2_proc != null)
  86     {
  87       BufferedReader outputReader = new BufferedReader(
  88               new InputStreamReader(ls2_proc.getInputStream()));
  89       BufferedReader errorReader = new BufferedReader(
  90               new InputStreamReader(ls2_proc.getErrorStream()));
  91       worker = new Worker(ls2_proc);
  92       worker.start();
  93       try
  94       {
  95         worker.join(timeout);
  96       } catch (InterruptedException e)
  97       {
  98         // e.printStackTrace();
  99       }
 100       worker.setOutputReader(outputReader);
 101       worker.setErrorReader(errorReader);
 102     }
 103     return worker;
 104   }
 105
 106   @BeforeTest(alwaysRun = true)
 107   public void initialize()
 108   {
 109     new CommandLineOperations();
 110   }
 111
 112   @BeforeTest(alwaysRun = true)
 113   public void setUpForHeadlessCommandLineInputOperations()
 114           throws IOException
 115   {
 116     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 117             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 118             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 119     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 120     String ln = null;
 121     while ((ln = worker.getOutputReader().readLine()) != null)
 122     {
 123       System.out.println(ln);
 124       successfulCMDs.add(ln);
 125     }
 126   }
 127
 128   @BeforeTest(alwaysRun = true)
 129   public void setUpForCommandLineInputOperations() throws IOException
 130   {
 131     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 132     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 133     String ln = null;
 134     int count = 0;
 135     while ((ln = worker.getErrorReader().readLine()) != null)
 136     {
 137       System.out.println(ln);
 138       successfulCMDs.add(ln);
 139       if (++count > 5)
 140       {
 141         break;
 142       }
 143     }
 144     if (worker != null && worker.getExitValue() == null)
 145     {
 146       worker.destroyProcess();
 147
 148     }
 149   }
 150
 151   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 152   public void testAllInputOperations(String expectedString,
 153           String failureMsg)
 154   {
 155     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 156   }
 157
 158   @Test(
 159     groups = { "Functional" },
 160     dataProvider = "headlessModeOutputOperationsData")
 161   public void testHeadlessModeOutputOperations(String harg, String type,
 162           String fileName, boolean withAWT, int expectedMinFileSize,
 163           int timeout)
 164   {
 165     String cmd = harg + type + " " + fileName;
 166     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 167     File file = new File(fileName);
 168     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 169
 170     FileAssert.assertFile(file, "Didn't create an output" + type
 171             + " file.[" + harg + "]");
 172     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 173     if (worker != null && worker.getExitValue() == null)
 174     {
 175       worker.destroyProcess();
 176       Assert.fail("Jalview did not exit after "
 177               + type
 178               + " generation (try running test again to verify - timeout at "
 179               + SETUP_TIMEOUT + "ms). ["
 180               + harg + "]");
 181     }
 182     new File(fileName).delete();
 183   }
 184
 185   @DataProvider(name = "allInputOpearationsData")
 186   public Object[][] getHeadlessModeInputParams()
 187   {
 188     return new Object[][] {
 189         // headless mode input operations
 190         { "CMD [-color zappo] executed successfully!",
 191             "Failed command : -color zappo" },
 192         { "CMD [-props FILE] executed successfully!",
 193             "Failed command : -props File" },
 194         { "CMD [-sortbytree] executed successfully!",
 195             "Failed command : -sortbytree" },
 196         {
 197             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 198             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 199         { "CMD [-open examples/uniref50.fa] executed successfully!",
 200             "Failed command : -open examples/uniref50.fa" },
 201         { "CMD [-nosortbytree] executed successfully!",
 202             "Failed command : -nosortbytree" },
 203         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 204             "Failed command : -dasserver nickname=www.test.com" },
 205         {
 206             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 207             "Failed command : -features examples/testdata/plantfdx.features" },
 208         {
 209             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 210             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 211         {
 212             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 213             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 214         // non headless mode input operations
 215         { "CMD [-nousagestats] executed successfully!",
 216             "Failed command : -nousagestats" },
 217         { "CMD [-noquestionnaire] executed successfully!",
 218             "Failed command : -noquestionnaire nickname=www.test.com" } };
 219
 220   }
 221
 222   @DataProvider(name = "headlessModeOutputOperationsData")
 223   public static Object[][] getHeadlessModeOutputParams()
 224   {
 225     return new Object[][] {
 226         { "nodisplay -open examples/uniref50.fa", " -eps",
 227             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 228         { "nodisplay -open examples/uniref50.fa", " -eps",
 229             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 230         { "nogui -open examples/uniref50.fa", " -eps",
 231             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 232         { "nogui -open examples/uniref50.fa", " -eps",
 233             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 234         { "headless -open examples/uniref50.fa", " -eps",
 235             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 236         { "headless -open examples/uniref50.fa", " -svg",
 237             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 238         { "headless -open examples/uniref50.fa", " -png",
 239             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 240         { "headless -open examples/uniref50.fa", " -html",
 241             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 242         { "headless -open examples/uniref50.fa", " -fasta",
 243             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 244         { "headless -open examples/uniref50.fa", " -clustal",
 245             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 246         { "headless -open examples/uniref50.fa", " -msf",
 247             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 248         { "headless -open examples/uniref50.fa", " -pileup",
 249             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 250         { "headless -open examples/uniref50.fa", " -pir",
 251             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 252         { "headless -open examples/uniref50.fa", " -pfam",
 253             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 254         { "headless -open examples/uniref50.fa", " -blc",
 255             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 256         { "headless -open examples/uniref50.fa", " -jalview",
 257             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 258   }
 259 }