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 static org.testng.Assert.assertNotNull;
24 import static org.testng.Assert.assertTrue;
26 import jalview.gui.JvOptionPane;
28 import java.io.BufferedReader;
30 import java.io.IOException;
31 import java.io.InputStreamReader;
32 import java.util.ArrayList;
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;
41 import io.github.classgraph.ClassGraph;
42 import io.github.classgraph.ScanResult;
44 @Test(singleThreaded = true)
45 public class CommandLineOperations
48 @BeforeClass(alwaysRun = true)
49 public void setUpJvOptionPane()
51 JvOptionPane.setInteractiveMode(false);
52 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
56 // full test run than on
59 private static final int SETUP_TIMEOUT = 9000;
61 private static final int MINFILESIZE_SMALL = 2096;
63 private static final int MINFILESIZE_BIG = 4096;
65 private ArrayList<String> successfulCMDs = new ArrayList<>();
69 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
70 * -using-javas-runtime-exec
75 private static class Worker extends Thread
77 private final Process process;
79 private BufferedReader outputReader;
81 private BufferedReader errorReader;
85 private Worker(Process process)
87 this.process = process;
95 exit = process.waitFor();
96 } catch (InterruptedException ignore)
102 public BufferedReader getOutputReader()
107 public void setOutputReader(BufferedReader outputReader)
109 this.outputReader = outputReader;
112 public BufferedReader getErrorReader()
117 public void setErrorReader(BufferedReader errorReader)
119 this.errorReader = errorReader;
123 private static ClassGraph scanner = null;
125 private static String classpath = null;
127 public synchronized static String getClassPath()
131 scanner = new ClassGraph();
132 ScanResult scan = scanner.scan();
133 classpath = scan.getClasspath();
135 while (classpath == null)
140 } catch (InterruptedException x)
148 private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
151 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
152 // not expanded by the shell
153 String classpath = getClassPath();
154 String _cmd = "java "
155 + (withAwt ? "-Djava.awt.headless=true" : "")
156 + " -classpath " + classpath + " jalview.bin.Jalview ";
157 Process ls2_proc = null;
158 Worker worker = null;
161 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
162 } catch (Throwable e1)
164 e1.printStackTrace();
166 if (ls2_proc != null)
168 BufferedReader outputReader = new BufferedReader(
169 new InputStreamReader(ls2_proc.getInputStream()));
170 BufferedReader errorReader = new BufferedReader(
171 new InputStreamReader(ls2_proc.getErrorStream()));
172 worker = new Worker(ls2_proc);
173 worker.setOutputReader(outputReader);
174 worker.setErrorReader(errorReader);
179 worker.join(timeout);
181 } catch (InterruptedException e)
183 System.err.println("Thread interrupted");
189 @BeforeTest(alwaysRun = true)
190 public void initialize()
192 new CommandLineOperations();
195 @BeforeTest(alwaysRun = true)
196 public void setUpForHeadlessCommandLineInputOperations()
199 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
200 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
201 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
202 System.out.println("CommandLine test " + ++ntest);
203 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
205 while ((ln = worker.getOutputReader().readLine()) != null)
207 System.out.println(ln);
208 successfulCMDs.add(ln);
209 if (ln.equals(Jalview.TERMINATOR_LINE))
214 if (worker != null && worker.exit == null)
217 Thread.currentThread().interrupt();
218 worker.process.destroy();
220 // while ((ln = worker.getErrorReader().readLine()) != null)
222 // System.err.println(ln);
229 @BeforeTest(alwaysRun = true)
230 public void setUpForNonHeadlessInputOperations() throws IOException
232 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
233 Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
236 while ((ln = worker.getErrorReader().readLine()) != null)
238 System.out.println(ln);
239 successfulCMDs.add(ln);
240 if (ln.equals(Jalview.TERMINATOR_LINE))
250 if (worker != null && worker.exit == null)
253 Thread.currentThread().interrupt();
254 worker.process.destroy();
258 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
259 public void testAllInputOperations(String expectedString,
262 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
268 dataProvider = "headlessModeOutputOperationsData")
269 public void testHeadlessModeOutputOperations(String harg, String type,
270 String fileName, boolean withAWT, int expectedMinFileSize,
271 int timeout) throws IOException
273 File file = new File(fileName);
274 String cmd = harg + type + " "
275 + file.getAbsolutePath().replace('\\', '/');
276 System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
279 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
280 assertNotNull(worker, "worker is null");
281 String msg = "Didn't create an output" + type + " file: "
282 + file.getAbsolutePath() + " [" + harg + "]";
283 while (worker.isAlive())
286 while (worker.getOutputReader().ready())
288 String ln = worker.getOutputReader().readLine();
289 System.out.println(ln);
291 assertTrue(file.exists(), msg);
292 FileAssert.assertFile(file, msg);
293 FileAssert.assertMinLength(file, expectedMinFileSize);
294 if (worker != null && worker.exit == null)
297 Thread.currentThread().interrupt();
298 worker.process.destroy();
299 // Assert.fail("Jalview did not exit after "
301 // + " generation (try running test again to verify - timeout at "
302 // + SETUP_TIMEOUT + "ms). ["
308 @DataProvider(name = "allInputOperationsData")
309 public Object[][] getAllInputParams()
311 return new Object[][] {
312 // headless mode input operations
313 { "CMD [-color zappo] executed successfully!",
314 "Failed command : -color zappo" },
315 { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
316 "Failed command : -props File" },
317 { "CMD [-sortbytree] executed successfully!",
318 "Failed command : -sortbytree" },
319 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
320 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
321 { "CMD [-open examples/uniref50.fa] executed successfully!",
322 "Failed command : -open examples/uniref50.fa" },
323 { "CMD [-nosortbytree] executed successfully!",
324 "Failed command : -nosortbytree" },
325 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
326 "Failed command : -features examples/testdata/plantfdx.features" },
327 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
328 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
329 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
330 "Failed command : -tree examples/testdata/uniref50_test_tree" },
331 // non headless mode input operations
332 { "CMD [-nousagestats] executed successfully!",
333 "Failed command : -nousagestats" },
334 { "CMD [-noquestionnaire] executed successfully!",
335 "Failed command : -noquestionnaire" } };
338 @DataProvider(name = "headlessModeOutputOperationsData")
339 public static Object[][] getHeadlessModeOutputParams()
341 return new Object[][] {
343 { "nodisplay -open examples/uniref50.fa", " -eps",
344 "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
346 { "nodisplay -open examples/uniref50.fa", " -eps",
347 "test/jalview/bin/test_uniref50_out.eps", false,
348 MINFILESIZE_BIG, TEST_TIMEOUT },
349 { "nogui -open examples/uniref50.fa", " -eps",
350 "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
352 { "nogui -open examples/uniref50.fa", " -eps",
353 "test/jalview/bin/test_uniref50_out.eps", false,
354 MINFILESIZE_BIG, TEST_TIMEOUT },
355 { "headless -open examples/uniref50.fa", " -eps",
356 "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
358 { "headless -open examples/uniref50.fa", " -svg",
359 "test/jalview/bin/test_uniref50_out.svg", false,
360 MINFILESIZE_BIG, TEST_TIMEOUT },
361 { "headless -open examples/uniref50.fa", " -png",
362 "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
364 { "headless -open examples/uniref50.fa", " -html",
365 "test/jalview/bin/test_uniref50_out.html", true,
366 MINFILESIZE_BIG, TEST_TIMEOUT },
367 { "headless -open examples/uniref50.fa", " -fasta",
368 "test/jalview/bin/test_uniref50_out.mfa", true,
369 MINFILESIZE_SMALL, TEST_TIMEOUT },
370 { "headless -open examples/uniref50.fa", " -clustal",
371 "test/jalview/bin/test_uniref50_out.aln", true,
372 MINFILESIZE_SMALL, TEST_TIMEOUT },
373 { "headless -open examples/uniref50.fa", " -msf",
374 "test/jalview/bin/test_uniref50_out.msf", true,
375 MINFILESIZE_SMALL, TEST_TIMEOUT },
376 { "headless -open examples/uniref50.fa", " -pileup",
377 "test/jalview/bin/test_uniref50_out.aln", true,
378 MINFILESIZE_SMALL, TEST_TIMEOUT },
379 { "headless -open examples/uniref50.fa", " -pir",
380 "test/jalview/bin/test_uniref50_out.pir", true,
381 MINFILESIZE_SMALL, TEST_TIMEOUT },
382 { "headless -open examples/uniref50.fa", " -pfam",
383 "test/jalview/bin/test_uniref50_out.pfam", true,
384 MINFILESIZE_SMALL, TEST_TIMEOUT },
385 { "headless -open examples/uniref50.fa", " -blc",
386 "test/jalview/bin/test_uniref50_out.blc", true,
387 MINFILESIZE_SMALL, TEST_TIMEOUT },
388 { "headless -open examples/uniref50.fa", " -jalview",
389 "test/jalview/bin/test_uniref50_out.jvp", true,
390 MINFILESIZE_SMALL, TEST_TIMEOUT },