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