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.assertEquals;
24 import static org.testng.Assert.assertNotNull;
25 import static org.testng.Assert.assertTrue;
27 import jalview.gui.JvOptionPane;
28 import jalview.io.DataSourceType;
29 import jalview.io.FileFormat;
30 import jalview.io.FileFormatException;
31 import jalview.io.FileFormatI;
32 import jalview.io.FileFormats;
33 import jalview.io.IdentifyFile;
35 import java.io.BufferedReader;
37 import java.io.IOException;
38 import java.io.InputStreamReader;
39 import java.nio.file.Path;
40 import java.nio.file.Paths;
41 import java.util.ArrayList;
43 import org.testng.Assert;
44 import org.testng.FileAssert;
45 import org.testng.annotations.BeforeClass;
46 import org.testng.annotations.BeforeTest;
47 import org.testng.annotations.DataProvider;
48 import org.testng.annotations.Test;
50 import io.github.classgraph.ClassGraph;
51 import io.github.classgraph.ModuleRef;
52 import io.github.classgraph.ScanResult;
54 public class CommandLineOperations
57 @BeforeClass(alwaysRun = true)
58 public void setUpJvOptionPane()
60 JvOptionPane.setInteractiveMode(false);
61 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64 private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed
66 // full test run than on
69 private static final int SETUP_TIMEOUT = 9500;
71 private static final int MINFILESIZE_SMALL = 2096;
73 private static final int MINFILESIZE_BIG = 4096;
75 private ArrayList<String> successfulCMDs = new ArrayList<>();
79 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
80 * -using-javas-runtime-exec
85 private static class Worker extends Thread
87 private final Process process;
89 private BufferedReader outputReader;
91 private BufferedReader errorReader;
95 private Worker(Process process)
97 this.process = process;
105 exit = process.waitFor();
106 } catch (InterruptedException ignore)
112 public BufferedReader getOutputReader()
117 public void setOutputReader(BufferedReader outputReader)
119 this.outputReader = outputReader;
122 public BufferedReader getErrorReader()
127 public void setErrorReader(BufferedReader errorReader)
129 this.errorReader = errorReader;
133 private static ClassGraph scanner = null;
135 private static String classpath = null;
137 private static String modules = null;
139 private static String java_exe = null;
141 public synchronized static String getClassPath()
145 scanner = new ClassGraph();
146 ScanResult scan = scanner.scan();
147 classpath = scan.getClasspath();
149 for (ModuleRef mr : scan.getModules())
151 modules.concat(mr.getName());
153 java_exe = System.getProperty("java.home") + File.separator + "bin"
154 + File.separator + "java";
157 while (classpath == null)
162 } catch (InterruptedException x)
170 private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
173 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
174 // not expanded by the shell
175 String classpath = getClassPath();
176 String _cmd = java_exe + " "
177 + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
179 + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
181 + " jalview.bin.Jalview ";
182 Process ls2_proc = null;
183 Worker worker = null;
186 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
187 } catch (Throwable e1)
189 e1.printStackTrace();
191 if (ls2_proc != null)
193 BufferedReader outputReader = new BufferedReader(
194 new InputStreamReader(ls2_proc.getInputStream()));
195 BufferedReader errorReader = new BufferedReader(
196 new InputStreamReader(ls2_proc.getErrorStream()));
197 worker = new Worker(ls2_proc);
201 worker.join(timeout);
202 } catch (InterruptedException e)
204 System.err.println("Thread interrupted");
206 worker.setOutputReader(outputReader);
207 worker.setErrorReader(errorReader);
212 @Test(groups = { "Functional" })
213 public void reportCurrentWorkingDirectory()
217 Path currentRelativePath = Paths.get("");
218 String s = currentRelativePath.toAbsolutePath().toString();
219 System.out.println("Test CWD is " + s);
220 } catch (Exception q)
226 @BeforeTest(alwaysRun = true)
227 public void initialize()
229 new CommandLineOperations();
232 @BeforeTest(alwaysRun = true)
233 public void setUpForHeadlessCommandLineInputOperations()
236 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
237 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
238 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
239 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
241 while ((ln = worker.getOutputReader().readLine()) != null)
243 System.out.println(ln);
244 successfulCMDs.add(ln);
246 while ((ln = worker.getErrorReader().readLine()) != null)
248 System.err.println(ln);
252 @BeforeTest(alwaysRun = true)
253 public void setUpForCommandLineInputOperations() throws IOException
255 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
256 final Worker worker = getJalviewDesktopRunner(false, cmds,
259 // number of lines expected on STDERR when Jalview starts up normally
260 // may need to adjust this if Jalview is excessively noisy ?
261 final int STDERR_SETUPLINES = 50;
263 // thread monitors stderr - bails after SETUP_TIMEOUT or when
264 // STDERR_SETUPLINES have been read
265 Thread runner = new Thread(new Runnable()
274 while ((ln = worker.getErrorReader().readLine()) != null)
276 System.out.println(ln);
277 successfulCMDs.add(ln);
278 if (++count > STDERR_SETUPLINES)
283 } catch (Exception e)
286 "Unexpected Exception reading stderr from the Jalview process");
291 long t = System.currentTimeMillis() + SETUP_TIMEOUT;
293 while (!runner.isInterrupted() && System.currentTimeMillis() < t)
298 } catch (InterruptedException e)
303 if (worker != null && worker.exit == null)
306 Thread.currentThread().interrupt();
307 worker.process.destroy();
311 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
312 public void testAllInputOperations(String expectedString,
315 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
320 { "Functional", "testben" },
321 dataProvider = "headlessModeOutputOperationsData")
322 public void testHeadlessModeOutputOperations(String harg, String type,
323 String fileName, boolean withAWT, int expectedMinFileSize,
324 int timeout, String fileFormatType)
326 String cmd = harg + type + " " + fileName;
327 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
328 File file = new File(fileName);
330 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
331 assertNotNull(worker, "worker is null");
332 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
333 assertTrue(file.exists(), msg);
334 FileAssert.assertFile(file, msg);
335 FileAssert.assertMinLength(file, expectedMinFileSize);
336 if (fileFormatType!=null && fileFormatType.length()>0)
338 FileFormatI format = FileFormats.getInstance()
339 .forName(fileFormatType);
344 FileFormatI exportedType = new IdentifyFile()
345 .identify(file.getAbsolutePath(), DataSourceType.FILE);
346 assertEquals(exportedType, format,
347 "Exported file type was wrong");
348 } catch (FileFormatException e)
350 Assert.fail("Couldn't identify file " + file
351 + " as an alignment format", e);
355 if (worker != null && worker.exit == null)
358 Thread.currentThread().interrupt();
359 worker.process.destroy();
360 Assert.fail("Jalview did not exit after " + type
361 + " generation (try running test again to verify - timeout at "
362 + timeout + "ms). [" + harg + "]");
367 @DataProvider(name = "allInputOperationsData")
368 public Object[][] getHeadlessModeInputParams()
370 return new Object[][] {
371 // headless mode input operations
372 { "CMD [-color zappo] executed successfully!",
373 "Failed command : -color zappo" },
374 { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
375 "Failed command : -props File" },
376 { "CMD [-sortbytree] executed successfully!",
377 "Failed command : -sortbytree" },
378 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
379 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
380 { "CMD [-open examples/uniref50.fa] executed successfully!",
381 "Failed command : -open examples/uniref50.fa" },
382 { "CMD [-nosortbytree] executed successfully!",
383 "Failed command : -nosortbytree" },
384 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
385 "Failed command : -features examples/testdata/plantfdx.features" },
386 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
387 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
388 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
389 "Failed command : -tree examples/testdata/uniref50_test_tree" },
390 // non headless mode input operations
391 { "CMD [-nousagestats] executed successfully!",
392 "Failed command : -nousagestats" },
393 { "CMD [-noquestionnaire] executed successfully!",
394 "Failed command : -noquestionnaire" } };
397 @DataProvider(name = "headlessModeOutputOperationsData")
398 public static Object[][] getHeadlessModeOutputParams()
400 // JBPNote: I'm not clear why need to specify full path for output file
401 // when running tests on build server, but we will keep this patch for now
403 // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
404 String workingDir = "test/jalview/bin/";
405 return new Object[][] { { "nodisplay -open examples/uniref50.fa",
406 " -eps", workingDir + "test_uniref50_out.eps", true,
407 MINFILESIZE_BIG, TEST_TIMEOUT, null },
408 { "nodisplay -open examples/uniref50.fa", " -eps",
409 workingDir + "test_uniref50_out.eps", false,
410 MINFILESIZE_BIG, TEST_TIMEOUT, null },
411 { "nogui -open examples/uniref50.fa", " -eps",
412 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
413 TEST_TIMEOUT, null },
414 { "nogui -open examples/uniref50.fa", " -eps",
415 workingDir + "test_uniref50_out.eps", false,
416 MINFILESIZE_BIG, TEST_TIMEOUT, null },
417 { "headless -open examples/uniref50.fa", " -eps",
418 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
419 TEST_TIMEOUT, null },
420 { "headless -open examples/uniref50.fa", " -svg",
421 workingDir + "test_uniref50_out.svg", false,
422 MINFILESIZE_BIG, TEST_TIMEOUT, null },
423 { "headless -open examples/uniref50.fa", " -png",
424 workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
425 TEST_TIMEOUT, null },
426 { "headless -open examples/uniref50.fa", " -html",
427 workingDir + "test_uniref50_out.html", true,
428 MINFILESIZE_BIG, TEST_TIMEOUT, null },
429 { "headless -open examples/uniref50.fa", " -fasta",
430 workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
431 TEST_TIMEOUT, FileFormat.Fasta.toString() },
432 { "headless -open examples/uniref50.fa", " -clustal",
433 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
434 TEST_TIMEOUT, FileFormat.Clustal.toString() },
435 { "headless -open examples/uniref50.fa", " -msf",
436 workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
437 TEST_TIMEOUT, FileFormat.MSF.toString() },
438 { "headless -open examples/uniref50.fa", " -pileup",
439 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
440 TEST_TIMEOUT, FileFormat.Pileup.toString() },
441 { "headless -open examples/uniref50.fa", " -pir",
442 workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
443 TEST_TIMEOUT, FileFormat.PIR.toString() },
444 { "headless -open examples/uniref50.fa", " -pfam",
445 workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
446 TEST_TIMEOUT, FileFormat.Pfam.toString() },
447 { "headless -open examples/uniref50.fa", " -blc",
448 workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
449 TEST_TIMEOUT, FileFormat.BLC.toString() },
450 { "headless -open examples/uniref50.fa", " -jalview",
451 workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
452 TEST_TIMEOUT, FileFormat.Jalview.toString() }, };