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 import io.github.classgraph.ClassGraph;
  40 import io.github.classgraph.ScanResult;
  41
  42 public class CommandLineOperations
  43 {
  44
  45   @BeforeClass(alwaysRun = true)
  46   public void setUpJvOptionPane()
  47   {
  48     JvOptionPane.setInteractiveMode(false);
  49     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  50   }
  51
  52   private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
  53                                                 // full test run than on
  54                                                 // individual tests
  55
  56   private static final int SETUP_TIMEOUT = 9000;
  57
  58   private static final int MINFILESIZE_SMALL = 2096;
  59
  60   private static final int MINFILESIZE_BIG = 4096;
  61
  62   private ArrayList<String> successfulCMDs = new ArrayList<>();
  63
  64
  65   private static ClassGraph scanner = null;
  66
  67   private static String classpath = null;
  68
  69   public synchronized static String getClassPath()
  70   {
  71     if (scanner == null)
  72     {
  73       scanner = new ClassGraph();
  74       ScanResult scan = scanner.scan();
  75       classpath = scan.getClasspath();
  76     }
  77     while (classpath == null)
  78     {
  79       try
  80       {
  81         Thread.sleep(10);
  82       } catch (InterruptedException x)
  83       {
  84
  85       }
  86     }
  87     return classpath;
  88   }
  89   private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
  90           int timeout)
  91   {
  92     // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
  93     // not expanded by the shell
  94     String classpath = getClassPath();
  95     String _cmd = "java "
  96             + (withAwt ? "-Djava.awt.headless=true" : "")
  97             + " -classpath " + classpath + " jalview.bin.Jalview ";
  98     Process ls2_proc = null;
  99     Worker worker = null;
 100     try
 101     {
 102       ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
 103     } catch (IOException e1)
 104     {
 105       e1.printStackTrace();
 106     }
 107     if (ls2_proc != null)
 108     {
 109       BufferedReader outputReader = new BufferedReader(
 110               new InputStreamReader(ls2_proc.getInputStream()));
 111       BufferedReader errorReader = new BufferedReader(
 112               new InputStreamReader(ls2_proc.getErrorStream()));
 113       worker = new Worker(ls2_proc);
 114       worker.start();
 115       try
 116       {
 117         worker.join(timeout);
 118       } catch (InterruptedException e)
 119       {
 120         // e.printStackTrace();
 121       }
 122       worker.setOutputReader(outputReader);
 123       worker.setErrorReader(errorReader);
 124     }
 125     return worker;
 126   }
 127
 128   @BeforeTest(alwaysRun = true)
 129   public void initialize()
 130   {
 131     new CommandLineOperations();
 132   }
 133
 134   @BeforeTest(alwaysRun = true)
 135   public void setUpForHeadlessCommandLineInputOperations()
 136           throws IOException
 137   {
 138     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
 139             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
 140             + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
 141     Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
 142     String ln = null;
 143     while ((ln = worker.getOutputReader().readLine()) != null)
 144     {
 145       System.out.println(ln);
 146       successfulCMDs.add(ln);
 147     }
 148   }
 149
 150   @BeforeTest(alwaysRun = true)
 151   public void setUpForCommandLineInputOperations() throws IOException
 152   {
 153     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
 154     Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
 155     String ln = null;
 156     int count = 0;
 157     while ((ln = worker.getErrorReader().readLine()) != null)
 158     {
 159       System.out.println(ln);
 160       successfulCMDs.add(ln);
 161       if (++count > 5)
 162       {
 163         break;
 164       }
 165     }
 166     if (worker != null && worker.getExitValue() == null)
 167     {
 168       worker.destroyProcess();
 169
 170     }
 171   }
 172
 173   @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
 174   public void testAllInputOperations(String expectedString,
 175           String failureMsg)
 176   {
 177     Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
 178   }
 179
 180   @Test(
 181     groups = { "Functional" },
 182     dataProvider = "headlessModeOutputOperationsData")
 183   public void testHeadlessModeOutputOperations(String harg, String type,
 184           String fileName, boolean withAWT, int expectedMinFileSize,
 185           int timeout)
 186   {
 187     String cmd = harg + type + " " + fileName;
 188     // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
 189     File file = new File(fileName);
 190     Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
 191
 192     FileAssert.assertFile(file, "Didn't create an output" + type
 193             + " file.[" + harg + "]");
 194     FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
 195     if (worker != null && worker.getExitValue() == null)
 196     {
 197       worker.destroyProcess();
 198       Assert.fail("Jalview did not exit after "
 199               + type
 200               + " generation (try running test again to verify - timeout at "
 201               + SETUP_TIMEOUT + "ms). ["
 202               + harg + "]");
 203     }
 204     new File(fileName).delete();
 205   }
 206
 207   @DataProvider(name = "allInputOpearationsData")
 208   public Object[][] getHeadlessModeInputParams()
 209   {
 210     return new Object[][] {
 211         // headless mode input operations
 212         { "CMD [-color zappo] executed successfully!",
 213             "Failed command : -color zappo" },
 214         { "CMD [-props FILE] executed successfully!",
 215             "Failed command : -props File" },
 216         { "CMD [-sortbytree] executed successfully!",
 217             "Failed command : -sortbytree" },
 218         {
 219             "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
 220             "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
 221         { "CMD [-open examples/uniref50.fa] executed successfully!",
 222             "Failed command : -open examples/uniref50.fa" },
 223         { "CMD [-nosortbytree] executed successfully!",
 224             "Failed command : -nosortbytree" },
 225         { "CMD [-dasserver nickname=www.test.com] executed successfully!",
 226             "Failed command : -dasserver nickname=www.test.com" },
 227         {
 228             "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
 229             "Failed command : -features examples/testdata/plantfdx.features" },
 230         {
 231             "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
 232             "Failed command : -annotations examples/testdata/plantfdx.annotations" },
 233         {
 234             "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
 235             "Failed command : -tree examples/testdata/uniref50_test_tree" },
 236         // non headless mode input operations
 237         { "CMD [-nousagestats] executed successfully!",
 238             "Failed command : -nousagestats" },
 239         { "CMD [-noquestionnaire] executed successfully!",
 240             "Failed command : -noquestionnaire nickname=www.test.com" } };
 241
 242   }
 243
 244   @DataProvider(name = "headlessModeOutputOperationsData")
 245   public static Object[][] getHeadlessModeOutputParams()
 246   {
 247     return new Object[][] {
 248         { "nodisplay -open examples/uniref50.fa", " -eps",
 249             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 250         { "nodisplay -open examples/uniref50.fa", " -eps",
 251             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 252         { "nogui -open examples/uniref50.fa", " -eps",
 253             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 254         { "nogui -open examples/uniref50.fa", " -eps",
 255             "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 256         { "headless -open examples/uniref50.fa", " -eps",
 257             "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 258         { "headless -open examples/uniref50.fa", " -svg",
 259             "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
 260         { "headless -open examples/uniref50.fa", " -png",
 261             "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 262         { "headless -open examples/uniref50.fa", " -html",
 263             "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
 264         { "headless -open examples/uniref50.fa", " -fasta",
 265             "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 266         { "headless -open examples/uniref50.fa", " -clustal",
 267             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 268         { "headless -open examples/uniref50.fa", " -msf",
 269             "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 270         { "headless -open examples/uniref50.fa", " -pileup",
 271             "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 272         { "headless -open examples/uniref50.fa", " -pir",
 273             "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 274         { "headless -open examples/uniref50.fa", " -pfam",
 275             "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 276         { "headless -open examples/uniref50.fa", " -blc",
 277             "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
 278         { "headless -open examples/uniref50.fa", " -jalview",
 279             "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
 280   }
 281 }