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 public class CommandLineOperations
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54 private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
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 " + (withAwt ? "-Djava.awt.headless=true" : "")
155 + " -classpath " + classpath + " jalview.bin.Jalview ";
156 Process ls2_proc = null;
157 Worker worker = null;
160 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
161 } catch (Throwable e1)
163 e1.printStackTrace();
165 if (ls2_proc != null)
167 BufferedReader outputReader = new BufferedReader(
168 new InputStreamReader(ls2_proc.getInputStream()));
169 BufferedReader errorReader = new BufferedReader(
170 new InputStreamReader(ls2_proc.getErrorStream()));
171 worker = new Worker(ls2_proc);
175 worker.join(timeout);
176 } catch (InterruptedException e)
178 System.err.println("Thread interrupted");
180 worker.setOutputReader(outputReader);
181 worker.setErrorReader(errorReader);
186 @BeforeTest(alwaysRun = true)
187 public void initialize()
189 new CommandLineOperations();
192 @BeforeTest(alwaysRun = true)
193 public void setUpForHeadlessCommandLineInputOperations()
196 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
197 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
198 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
199 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
201 while ((ln = worker.getOutputReader().readLine()) != null)
203 System.out.println(ln);
204 successfulCMDs.add(ln);
206 while ((ln = worker.getErrorReader().readLine()) != null)
208 System.err.println(ln);
212 @BeforeTest(alwaysRun = true)
213 public void setUpForCommandLineInputOperations() throws IOException
215 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
216 Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
219 while ((ln = worker.getErrorReader().readLine()) != null)
221 System.out.println(ln);
222 successfulCMDs.add(ln);
228 if (worker != null && worker.exit == null)
231 Thread.currentThread().interrupt();
232 worker.process.destroy();
236 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
237 public void testAllInputOperations(String expectedString,
240 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
245 { "Functional", "testben" },
246 dataProvider = "headlessModeOutputOperationsData")
247 public void testHeadlessModeOutputOperations(String harg, String type,
248 String fileName, boolean withAWT, int expectedMinFileSize,
251 String cmd = harg + type + " " + fileName;
252 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
253 File file = new File(fileName);
255 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
256 assertNotNull(worker, "worker is null");
257 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
258 assertTrue(file.exists(), msg);
259 FileAssert.assertFile(file, msg);
260 FileAssert.assertMinLength(file, expectedMinFileSize);
261 if (worker != null && worker.exit == null)
264 Thread.currentThread().interrupt();
265 worker.process.destroy();
266 Assert.fail("Jalview did not exit after " + type
267 + " generation (try running test again to verify - timeout at "
268 + timeout + "ms). [" + harg + "]");
273 @DataProvider(name = "allInputOperationsData")
274 public Object[][] getHeadlessModeInputParams()
276 return new Object[][] {
277 // headless mode input operations
278 { "CMD [-color zappo] executed successfully!",
279 "Failed command : -color zappo" },
280 { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
281 "Failed command : -props File" },
282 { "CMD [-sortbytree] executed successfully!",
283 "Failed command : -sortbytree" },
284 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
285 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
286 { "CMD [-open examples/uniref50.fa] executed successfully!",
287 "Failed command : -open examples/uniref50.fa" },
288 { "CMD [-nosortbytree] executed successfully!",
289 "Failed command : -nosortbytree" },
290 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
291 "Failed command : -features examples/testdata/plantfdx.features" },
292 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
293 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
294 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
295 "Failed command : -tree examples/testdata/uniref50_test_tree" },
296 // non headless mode input operations
297 { "CMD [-nousagestats] executed successfully!",
298 "Failed command : -nousagestats" },
299 { "CMD [-noquestionnaire] executed successfully!",
300 "Failed command : -noquestionnaire" } };
303 @DataProvider(name = "headlessModeOutputOperationsData")
304 public static Object[][] getHeadlessModeOutputParams()
306 return new Object[][] { { "nodisplay -open examples/uniref50.fa",
307 " -eps", "test/jalview/bin/test_uniref50_out.eps", true,
308 MINFILESIZE_BIG, TEST_TIMEOUT },
309 { "nodisplay -open examples/uniref50.fa", " -eps",
310 "test/jalview/bin/test_uniref50_out.eps", false,
311 MINFILESIZE_BIG, TEST_TIMEOUT },
312 { "nogui -open examples/uniref50.fa", " -eps",
313 "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
315 { "nogui -open examples/uniref50.fa", " -eps",
316 "test/jalview/bin/test_uniref50_out.eps", false,
317 MINFILESIZE_BIG, TEST_TIMEOUT },
318 { "headless -open examples/uniref50.fa", " -eps",
319 "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
321 { "headless -open examples/uniref50.fa", " -svg",
322 "test/jalview/bin/test_uniref50_out.svg", false,
323 MINFILESIZE_BIG, TEST_TIMEOUT },
324 { "headless -open examples/uniref50.fa", " -png",
325 "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
327 { "headless -open examples/uniref50.fa", " -html",
328 "test/jalview/bin/test_uniref50_out.html", true,
329 MINFILESIZE_BIG, TEST_TIMEOUT },
330 { "headless -open examples/uniref50.fa", " -fasta",
331 "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
333 { "headless -open examples/uniref50.fa", " -clustal",
334 "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
336 { "headless -open examples/uniref50.fa", " -msf",
337 "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
339 { "headless -open examples/uniref50.fa", " -pileup",
340 "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
342 { "headless -open examples/uniref50.fa", " -pir",
343 "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
345 { "headless -open examples/uniref50.fa", " -pfam",
346 "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
348 { "headless -open examples/uniref50.fa", " -blc",
349 "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
351 { "headless -open examples/uniref50.fa", " -jalview",
352 "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,