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.nio.file.Path;
33 import java.nio.file.Paths;
34 import java.util.ArrayList;
36 import org.testng.Assert;
37 import org.testng.FileAssert;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.BeforeTest;
40 import org.testng.annotations.DataProvider;
41 import org.testng.annotations.Test;
43 import io.github.classgraph.ClassGraph;
44 import io.github.classgraph.ModuleRef;
45 import io.github.classgraph.ScanResult;
47 public class CommandLineOperations
50 @BeforeClass(alwaysRun = true)
51 public void setUpJvOptionPane()
53 JvOptionPane.setInteractiveMode(false);
54 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
59 // full test run than on
62 private static final int SETUP_TIMEOUT = 9000;
64 private static final int MINFILESIZE_SMALL = 2096;
66 private static final int MINFILESIZE_BIG = 4096;
68 private ArrayList<String> successfulCMDs = new ArrayList<>();
72 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
73 * -using-javas-runtime-exec
78 private static class Worker extends Thread
80 private final Process process;
82 private BufferedReader outputReader;
84 private BufferedReader errorReader;
88 private Worker(Process process)
90 this.process = process;
98 exit = process.waitFor();
99 } catch (InterruptedException ignore)
105 public BufferedReader getOutputReader()
110 public void setOutputReader(BufferedReader outputReader)
112 this.outputReader = outputReader;
115 public BufferedReader getErrorReader()
120 public void setErrorReader(BufferedReader errorReader)
122 this.errorReader = errorReader;
126 private static ClassGraph scanner = null;
128 private static String classpath = null;
130 private static String modules = null;
132 private static String java_exe = null;
134 public synchronized static String getClassPath()
138 scanner = new ClassGraph();
139 ScanResult scan = scanner.scan();
140 classpath = scan.getClasspath();
142 for (ModuleRef mr : scan.getModules())
144 modules.concat(mr.getName());
146 java_exe = System.getProperty("java.home") + File.separator + "bin"
147 + File.separator + "java";
150 while (classpath == null)
155 } catch (InterruptedException x)
163 private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
166 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
167 // not expanded by the shell
168 String classpath = getClassPath();
169 String _cmd = java_exe + " "
170 + (withAwt ? "-Djava.awt.headless=true" : "")
171 + " -classpath " + classpath
172 + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
174 + " jalview.bin.Jalview ";
175 Process ls2_proc = null;
176 Worker worker = null;
179 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
180 } catch (Throwable e1)
182 e1.printStackTrace();
184 if (ls2_proc != null)
186 BufferedReader outputReader = new BufferedReader(
187 new InputStreamReader(ls2_proc.getInputStream()));
188 BufferedReader errorReader = new BufferedReader(
189 new InputStreamReader(ls2_proc.getErrorStream()));
190 worker = new Worker(ls2_proc);
194 worker.join(timeout);
195 } catch (InterruptedException e)
197 System.err.println("Thread interrupted");
199 worker.setOutputReader(outputReader);
200 worker.setErrorReader(errorReader);
205 @Test(groups = { "Functional" })
206 public void reportCurrentWorkingDirectory()
210 Path currentRelativePath = Paths.get("");
211 String s = currentRelativePath.toAbsolutePath().toString();
212 System.out.println("Test CWD is " + s);
213 } catch (Exception q)
219 @BeforeTest(alwaysRun = true)
220 public void initialize()
222 new CommandLineOperations();
225 @BeforeTest(alwaysRun = true)
226 public void setUpForHeadlessCommandLineInputOperations()
229 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
230 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
231 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
232 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
234 while ((ln = worker.getOutputReader().readLine()) != null)
236 System.out.println(ln);
237 successfulCMDs.add(ln);
239 while ((ln = worker.getErrorReader().readLine()) != null)
241 System.err.println(ln);
245 @BeforeTest(alwaysRun = true)
246 public void setUpForCommandLineInputOperations() throws IOException
248 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
249 Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
252 while ((ln = worker.getErrorReader().readLine()) != null)
254 System.out.println(ln);
255 successfulCMDs.add(ln);
261 if (worker != null && worker.exit == null)
264 Thread.currentThread().interrupt();
265 worker.process.destroy();
269 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
270 public void testAllInputOperations(String expectedString,
273 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
278 { "Functional", "testben" },
279 dataProvider = "headlessModeOutputOperationsData")
280 public void testHeadlessModeOutputOperations(String harg, String type,
281 String fileName, boolean withAWT, int expectedMinFileSize,
284 String cmd = harg + type + " " + fileName;
285 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
286 File file = new File(fileName);
288 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
289 assertNotNull(worker, "worker is null");
290 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
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 " + type
300 + " generation (try running test again to verify - timeout at "
301 + timeout + "ms). [" + harg + "]");
306 @DataProvider(name = "allInputOperationsData")
307 public Object[][] getHeadlessModeInputParams()
309 return new Object[][] {
310 // headless mode input operations
311 { "CMD [-color zappo] executed successfully!",
312 "Failed command : -color zappo" },
313 { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
314 "Failed command : -props File" },
315 { "CMD [-sortbytree] executed successfully!",
316 "Failed command : -sortbytree" },
317 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
318 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
319 { "CMD [-open examples/uniref50.fa] executed successfully!",
320 "Failed command : -open examples/uniref50.fa" },
321 { "CMD [-nosortbytree] executed successfully!",
322 "Failed command : -nosortbytree" },
323 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
324 "Failed command : -features examples/testdata/plantfdx.features" },
325 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
326 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
327 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
328 "Failed command : -tree examples/testdata/uniref50_test_tree" },
329 // non headless mode input operations
330 { "CMD [-nousagestats] executed successfully!",
331 "Failed command : -nousagestats" },
332 { "CMD [-noquestionnaire] executed successfully!",
333 "Failed command : -noquestionnaire" } };
336 @DataProvider(name = "headlessModeOutputOperationsData")
337 public static Object[][] getHeadlessModeOutputParams()
339 // JBPNote: I'm not clear why need to specify full path for output file
340 // when running tests on build server, but we will keep this patch for now
342 // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
343 String workingDir = "test/jalview/bin/";
344 return new Object[][] { { "nodisplay -open examples/uniref50.fa",
345 " -eps", workingDir + "test_uniref50_out.eps", true,
346 MINFILESIZE_BIG, TEST_TIMEOUT },
347 { "nodisplay -open examples/uniref50.fa", " -eps",
348 workingDir + "test_uniref50_out.eps", false,
349 MINFILESIZE_BIG, TEST_TIMEOUT },
350 { "nogui -open examples/uniref50.fa", " -eps",
351 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
353 { "nogui -open examples/uniref50.fa", " -eps",
354 workingDir + "test_uniref50_out.eps", false,
355 MINFILESIZE_BIG, TEST_TIMEOUT },
356 { "headless -open examples/uniref50.fa", " -eps",
357 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
359 { "headless -open examples/uniref50.fa", " -svg",
360 workingDir + "test_uniref50_out.svg", false,
361 MINFILESIZE_BIG, TEST_TIMEOUT },
362 { "headless -open examples/uniref50.fa", " -png",
363 workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
365 { "headless -open examples/uniref50.fa", " -html",
366 workingDir + "test_uniref50_out.html", true,
367 MINFILESIZE_BIG, TEST_TIMEOUT },
368 { "headless -open examples/uniref50.fa", " -fasta",
369 workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
371 { "headless -open examples/uniref50.fa", " -clustal",
372 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
374 { "headless -open examples/uniref50.fa", " -msf",
375 workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
377 { "headless -open examples/uniref50.fa", " -pileup",
378 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
380 { "headless -open examples/uniref50.fa", " -pir",
381 workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
383 { "headless -open examples/uniref50.fa", " -pfam",
384 workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
386 { "headless -open examples/uniref50.fa", " -blc",
387 workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
389 { "headless -open examples/uniref50.fa", " -jalview",
390 workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,