2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.gui.JvOptionPane;
25 import java.io.BufferedReader;
27 import java.io.IOException;
28 import java.io.InputStreamReader;
29 import java.util.ArrayList;
31 import org.testng.Assert;
32 import org.testng.FileAssert;
33 import org.testng.annotations.BeforeClass;
34 import org.testng.annotations.BeforeTest;
35 import org.testng.annotations.DataProvider;
36 import org.testng.annotations.Test;
38 public class CommandLineOperations
41 @BeforeClass(alwaysRun = true)
42 public void setUpJvOptionPane()
44 JvOptionPane.setInteractiveMode(false);
45 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48 private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
49 // full test run than on
52 private static final int SETUP_TIMEOUT = 9000;
54 private static final int MINFILESIZE_SMALL = 2096;
56 private static final int MINFILESIZE_BIG = 4096;
58 private ArrayList<String> successfulCMDs = new ArrayList<>();
62 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
63 * -using-javas-runtime-exec
68 private static class Worker extends Thread
70 private final Process process;
72 private BufferedReader outputReader;
74 private BufferedReader errorReader;
78 private Worker(Process process)
80 this.process = process;
88 exit = process.waitFor();
89 } catch (InterruptedException ignore)
95 public BufferedReader getOutputReader()
100 public void setOutputReader(BufferedReader outputReader)
102 this.outputReader = outputReader;
105 public BufferedReader getErrorReader()
110 public void setErrorReader(BufferedReader errorReader)
112 this.errorReader = errorReader;
116 private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
120 if (System.getProperty("os.name").indexOf("Windows") >= 0)
124 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
125 // not expanded by the shell
126 String _cmd = "java "
127 + (withAwt ? "-Djava.awt.headless=true" : "")
128 + " -classpath ./classes" + cp_sep
129 + "./lib/* jalview.bin.Jalview ";
130 System.out.println("CMD [" + cmd + "]");
131 Process ls2_proc = null;
132 Worker worker = null;
135 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
136 } catch (IOException e1)
138 e1.printStackTrace();
140 if (ls2_proc != null)
142 BufferedReader outputReader = new BufferedReader(
143 new InputStreamReader(ls2_proc.getInputStream()));
144 BufferedReader errorReader = new BufferedReader(
145 new InputStreamReader(ls2_proc.getErrorStream()));
146 worker = new Worker(ls2_proc);
150 worker.join(timeout);
151 } catch (InterruptedException e)
153 // e.printStackTrace();
155 worker.setOutputReader(outputReader);
156 worker.setErrorReader(errorReader);
161 @BeforeTest(alwaysRun = true)
162 public void initialize()
164 new CommandLineOperations();
167 @BeforeTest(alwaysRun = true)
168 public void setUpForHeadlessCommandLineInputOperations()
171 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
172 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
173 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
174 Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
176 while ((ln = worker.getOutputReader().readLine()) != null)
178 System.out.println(ln);
179 successfulCMDs.add(ln);
183 @BeforeTest(alwaysRun = true)
184 public void setUpForCommandLineInputOperations() throws IOException
186 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
187 Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
190 while ((ln = worker.getErrorReader().readLine()) != null)
192 System.out.println(ln);
193 successfulCMDs.add(ln);
199 if (worker != null && worker.exit == null)
202 Thread.currentThread().interrupt();
203 worker.process.destroy();
207 @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
208 public void testAllInputOperations(String expectedString,
211 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
215 groups = { "Functional" },
216 dataProvider = "headlessModeOutputOperationsData")
217 public void testHeadlessModeOutputOperations(String harg, String type,
218 String fileName, boolean withAWT, int expectedMinFileSize,
221 String cmd = harg + type + " " + fileName;
222 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
223 File file = new File(fileName);
224 Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
226 FileAssert.assertFile(file, "Didn't create an output" + type
227 + " file.[" + harg + "]");
228 FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
229 if (worker != null && worker.exit == null)
232 Thread.currentThread().interrupt();
233 worker.process.destroy();
234 Assert.fail("Jalview did not exit after "
236 + " generation (try running test again to verify - timeout at "
237 + SETUP_TIMEOUT + "ms). ["
240 new File(fileName).delete();
243 @DataProvider(name = "allInputOpearationsData")
244 public Object[][] getHeadlessModeInputParams()
246 return new Object[][] {
247 // headless mode input operations
248 { "CMD [-color zappo] executed successfully!",
249 "Failed command : -color zappo" },
250 { "CMD [-props FILE] executed successfully!",
251 "Failed command : -props File" },
252 { "CMD [-sortbytree] executed successfully!",
253 "Failed command : -sortbytree" },
255 "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
256 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
257 { "CMD [-open examples/uniref50.fa] executed successfully!",
258 "Failed command : -open examples/uniref50.fa" },
259 { "CMD [-nosortbytree] executed successfully!",
260 "Failed command : -nosortbytree" },
261 { "CMD [-dasserver nickname=www.test.com] executed successfully!",
262 "Failed command : -dasserver nickname=www.test.com" },
264 "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
265 "Failed command : -features examples/testdata/plantfdx.features" },
267 "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
268 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
270 "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
271 "Failed command : -tree examples/testdata/uniref50_test_tree" },
272 // non headless mode input operations
273 { "CMD [-nousagestats] executed successfully!",
274 "Failed command : -nousagestats" },
275 { "CMD [-noquestionnaire] executed successfully!",
276 "Failed command : -noquestionnaire nickname=www.test.com" } };
280 @DataProvider(name = "headlessModeOutputOperationsData")
281 public static Object[][] getHeadlessModeOutputParams()
283 return new Object[][] {
284 { "nodisplay -open examples/uniref50.fa", " -eps",
285 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
286 { "nodisplay -open examples/uniref50.fa", " -eps",
287 "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
288 { "nogui -open examples/uniref50.fa", " -eps",
289 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
290 { "nogui -open examples/uniref50.fa", " -eps",
291 "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
292 { "headless -open examples/uniref50.fa", " -eps",
293 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
294 { "headless -open examples/uniref50.fa", " -svg",
295 "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
296 { "headless -open examples/uniref50.fa", " -png",
297 "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
298 { "headless -open examples/uniref50.fa", " -html",
299 "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
300 { "headless -open examples/uniref50.fa", " -fasta",
301 "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
302 { "headless -open examples/uniref50.fa", " -clustal",
303 "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
304 { "headless -open examples/uniref50.fa", " -msf",
305 "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
306 { "headless -open examples/uniref50.fa", " -pileup",
307 "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
308 { "headless -open examples/uniref50.fa", " -pir",
309 "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
310 { "headless -open examples/uniref50.fa", " -pfam",
311 "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
312 { "headless -open examples/uniref50.fa", " -blc",
313 "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
314 { "headless -open examples/uniref50.fa", " -jalview",
315 "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };