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 java.io.BufferedReader;
28 import java.io.IOException;
29 import java.io.InputStreamReader;
30 import java.nio.file.Path;
31 import java.nio.file.Paths;
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.ModuleRef;
43 import io.github.classgraph.ScanResult;
44 import jalview.gui.JvOptionPane;
46 public class CommandLineOperations
49 @BeforeClass(alwaysRun = true)
50 public void setUpJvOptionPane()
52 JvOptionPane.setInteractiveMode(false);
53 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
56 private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed
58 // full test run than on
61 private static final int SETUP_TIMEOUT = 9500;
63 private static final int MINFILESIZE_SMALL = 2096;
65 private static final int MINFILESIZE_BIG = 4096;
67 private ArrayList<String> successfulCMDs = new ArrayList<>();
71 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
72 * -using-javas-runtime-exec
77 private static class Worker extends Thread
79 private final Process process;
81 private BufferedReader outputReader;
83 private BufferedReader errorReader;
87 private Worker(Process process)
89 this.process = process;
97 exit = process.waitFor();
98 } catch (InterruptedException ignore)
104 public BufferedReader getOutputReader()
109 public void setOutputReader(BufferedReader outputReader)
111 this.outputReader = outputReader;
114 public BufferedReader getErrorReader()
119 public void setErrorReader(BufferedReader errorReader)
121 this.errorReader = errorReader;
125 private static ClassGraph scanner = null;
127 private static String classpath = null;
129 private static String modules = null;
131 private static String java_exe = null;
133 public synchronized static String getClassPath()
137 scanner = new ClassGraph();
138 ScanResult scan = scanner.scan();
139 classpath = scan.getClasspath();
141 for (ModuleRef mr : scan.getModules())
143 modules.concat(mr.getName());
145 java_exe = System.getProperty("java.home") + File.separator + "bin"
146 + File.separator + "java";
149 while (classpath == null)
154 } catch (InterruptedException x)
162 private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
165 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
166 // not expanded by the shell
167 String classpath = getClassPath();
168 String _cmd = java_exe + " "
169 + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
171 + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
173 + " jalview.bin.Jalview ";
174 Process ls2_proc = null;
175 Worker worker = null;
178 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
179 } catch (Throwable e1)
181 e1.printStackTrace();
183 if (ls2_proc != null)
185 BufferedReader outputReader = new BufferedReader(
186 new InputStreamReader(ls2_proc.getInputStream()));
187 BufferedReader errorReader = new BufferedReader(
188 new InputStreamReader(ls2_proc.getErrorStream()));
189 worker = new Worker(ls2_proc);
193 worker.join(timeout);
194 } catch (InterruptedException e)
196 System.err.println("Thread interrupted");
198 worker.setOutputReader(outputReader);
199 worker.setErrorReader(errorReader);
204 @Test(groups = { "Functional" })
205 public void reportCurrentWorkingDirectory()
209 Path currentRelativePath = Paths.get("");
210 String s = currentRelativePath.toAbsolutePath().toString();
211 System.out.println("Test CWD is " + s);
212 } catch (Exception q)
218 @BeforeTest(alwaysRun = true)
219 public void initialize()
221 new CommandLineOperations();
224 @BeforeTest(alwaysRun = true)
225 public void setUpForHeadlessCommandLineInputOperations()
228 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
229 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
230 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
231 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
233 while ((ln = worker.getOutputReader().readLine()) != null)
235 System.out.println(ln);
236 successfulCMDs.add(ln);
238 while ((ln = worker.getErrorReader().readLine()) != null)
240 System.err.println(ln);
244 @BeforeTest(alwaysRun = true)
245 public void setUpForCommandLineInputOperations() throws IOException
247 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
248 final Worker worker = getJalviewDesktopRunner(false, cmds,
251 // number of lines expected on STDERR when Jalview starts up normally
252 // may need to adjust this if Jalview is excessively noisy ?
253 final int STDERR_SETUPLINES = 50;
255 // thread monitors stderr - bails after SETUP_TIMEOUT or when
256 // STDERR_SETUPLINES have been read
257 Thread runner = new Thread(new Runnable()
266 while ((ln = worker.getErrorReader().readLine()) != null)
268 System.out.println(ln);
269 successfulCMDs.add(ln);
270 if (++count > STDERR_SETUPLINES)
275 } catch (Exception e)
278 "Unexpected Exception reading stderr from the Jalview process");
283 long t = System.currentTimeMillis() + SETUP_TIMEOUT;
285 while (!runner.isInterrupted() && System.currentTimeMillis() < t)
290 } catch (InterruptedException e)
295 if (worker != null && worker.exit == null)
298 Thread.currentThread().interrupt();
299 worker.process.destroy();
303 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
304 public void testAllInputOperations(String expectedString,
307 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
313 dataProvider = "headlessModeOutputOperationsData")
314 public void testHeadlessModeOutputOperations(String harg, String type,
315 String fileName, boolean withAWT, int expectedMinFileSize,
318 String cmd = harg + type + " " + fileName;
319 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
320 File file = new File(fileName);
322 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
323 assertNotNull(worker, "worker is null");
324 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
325 assertTrue(file.exists(), msg);
326 FileAssert.assertFile(file, msg);
327 FileAssert.assertMinLength(file, expectedMinFileSize);
328 if (worker != null && worker.exit == null)
331 Thread.currentThread().interrupt();
332 worker.process.destroy();
333 Assert.fail("Jalview did not exit after " + type
334 + " generation (try running test again to verify - timeout at "
335 + timeout + "ms). [" + harg + "]");
340 @DataProvider(name = "allInputOperationsData")
341 public Object[][] getHeadlessModeInputParams()
343 return new Object[][] {
344 // headless mode input operations
345 { "CMD [-color zappo] executed successfully!",
346 "Failed command : -color zappo" },
347 { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
348 "Failed command : -props File" },
349 { "CMD [-sortbytree] executed successfully!",
350 "Failed command : -sortbytree" },
351 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
352 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
353 { "CMD [-open examples/uniref50.fa] executed successfully!",
354 "Failed command : -open examples/uniref50.fa" },
355 { "CMD [-nosortbytree] executed successfully!",
356 "Failed command : -nosortbytree" },
357 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
358 "Failed command : -features examples/testdata/plantfdx.features" },
359 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
360 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
361 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
362 "Failed command : -tree examples/testdata/uniref50_test_tree" },
363 // non headless mode input operations
364 { "CMD [-nousagestats] executed successfully!",
365 "Failed command : -nousagestats" },
366 { "CMD [-noquestionnaire] executed successfully!",
367 "Failed command : -noquestionnaire" } };
370 @DataProvider(name = "headlessModeOutputOperationsData")
371 public static Object[][] getHeadlessModeOutputParams()
373 // JBPNote: I'm not clear why need to specify full path for output file
374 // when running tests on build server, but we will keep this patch for now
376 // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
377 String workingDir = "test/jalview/bin/";
378 return new Object[][] { { "nodisplay -open examples/uniref50.fa",
379 " -eps", workingDir + "test_uniref50_out.eps", true,
380 MINFILESIZE_BIG, TEST_TIMEOUT },
381 { "nodisplay -open examples/uniref50.fa", " -eps",
382 workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
384 { "nogui -open examples/uniref50.fa", " -eps",
385 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
387 { "nogui -open examples/uniref50.fa", " -eps",
388 workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
390 { "headless -open examples/uniref50.fa", " -eps",
391 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
393 { "headless -open examples/uniref50.fa", " -svg",
394 workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
396 { "headless -open examples/uniref50.fa", " -png",
397 workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
399 { "headless -open examples/uniref50.fa", " -html",
400 workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
402 { "headless -open examples/uniref50.fa", " -fasta",
403 workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
405 { "headless -open examples/uniref50.fa", " -clustal",
406 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
408 { "headless -open examples/uniref50.fa", " -msf",
409 workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
411 { "headless -open examples/uniref50.fa", " -pileup",
412 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
414 { "headless -open examples/uniref50.fa", " -pir",
415 workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
417 { "headless -open examples/uniref50.fa", " -pfam",
418 workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
420 { "headless -open examples/uniref50.fa", " -blc",
421 workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
423 { "headless -open examples/uniref50.fa", " -jalview",
424 workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,