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 public synchronized static String getClassPath()
136 scanner = new ClassGraph();
137 ScanResult scan = scanner.scan();
138 classpath = scan.getClasspath();
140 for (ModuleRef mr : scan.getModules())
142 modules.concat(mr.getName());
145 while (classpath == null)
150 } catch (InterruptedException x)
158 private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
161 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
162 // not expanded by the shell
163 String classpath = getClassPath();
164 String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
165 + " -classpath " + classpath
166 + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
168 + " jalview.bin.Jalview ";
169 Process ls2_proc = null;
170 Worker worker = null;
173 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
174 } catch (Throwable e1)
176 e1.printStackTrace();
178 if (ls2_proc != null)
180 BufferedReader outputReader = new BufferedReader(
181 new InputStreamReader(ls2_proc.getInputStream()));
182 BufferedReader errorReader = new BufferedReader(
183 new InputStreamReader(ls2_proc.getErrorStream()));
184 worker = new Worker(ls2_proc);
188 worker.join(timeout);
189 } catch (InterruptedException e)
191 System.err.println("Thread interrupted");
193 worker.setOutputReader(outputReader);
194 worker.setErrorReader(errorReader);
198 @Test(alwaysRun=true)
199 public void reportCurrentWorkingDirectory()
202 Path currentRelativePath = Paths.get("");
203 String s = currentRelativePath.toAbsolutePath().toString();
204 System.out.println("Test CWD is "+s);
205 } catch (Exception q) {
209 @BeforeTest(alwaysRun = true)
210 public void initialize()
212 new CommandLineOperations();
215 @BeforeTest(alwaysRun = true)
216 public void setUpForHeadlessCommandLineInputOperations()
219 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
220 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
221 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
222 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
224 while ((ln = worker.getOutputReader().readLine()) != null)
226 System.out.println(ln);
227 successfulCMDs.add(ln);
229 while ((ln = worker.getErrorReader().readLine()) != null)
231 System.err.println(ln);
235 @BeforeTest(alwaysRun = true)
236 public void setUpForCommandLineInputOperations() throws IOException
238 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
239 Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
242 while ((ln = worker.getErrorReader().readLine()) != null)
244 System.out.println(ln);
245 successfulCMDs.add(ln);
251 if (worker != null && worker.exit == null)
254 Thread.currentThread().interrupt();
255 worker.process.destroy();
259 @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
260 public void testAllInputOperations(String expectedString,
263 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
268 { "Functional", "testben" },
269 dataProvider = "headlessModeOutputOperationsData")
270 public void testHeadlessModeOutputOperations(String harg, String type,
271 String fileName, boolean withAWT, int expectedMinFileSize,
274 String cmd = harg + type + " " + fileName;
275 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
276 File file = new File(fileName);
278 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
279 assertNotNull(worker, "worker is null");
280 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
281 assertTrue(file.exists(), msg);
282 FileAssert.assertFile(file, msg);
283 FileAssert.assertMinLength(file, expectedMinFileSize);
284 if (worker != null && worker.exit == null)
287 Thread.currentThread().interrupt();
288 worker.process.destroy();
289 Assert.fail("Jalview did not exit after " + type
290 + " generation (try running test again to verify - timeout at "
291 + timeout + "ms). [" + harg + "]");
296 @DataProvider(name = "allInputOperationsData")
297 public Object[][] getHeadlessModeInputParams()
299 return new Object[][] {
300 // headless mode input operations
301 { "CMD [-color zappo] executed successfully!",
302 "Failed command : -color zappo" },
303 { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
304 "Failed command : -props File" },
305 { "CMD [-sortbytree] executed successfully!",
306 "Failed command : -sortbytree" },
307 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
308 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
309 { "CMD [-open examples/uniref50.fa] executed successfully!",
310 "Failed command : -open examples/uniref50.fa" },
311 { "CMD [-nosortbytree] executed successfully!",
312 "Failed command : -nosortbytree" },
313 { "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
314 "Failed command : -features examples/testdata/plantfdx.features" },
315 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
316 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
317 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
318 "Failed command : -tree examples/testdata/uniref50_test_tree" },
319 // non headless mode input operations
320 { "CMD [-nousagestats] executed successfully!",
321 "Failed command : -nousagestats" },
322 { "CMD [-noquestionnaire] executed successfully!",
323 "Failed command : -noquestionnaire" } };
326 @DataProvider(name = "headlessModeOutputOperationsData")
327 public static Object[][] getHeadlessModeOutputParams()
329 // JBPNote: I'm not clear why need to specify full path for output file
330 // when running tests on build server, but we will keep this patch for now
332 // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
333 String workingDir = "test/jalview/bin/";
334 return new Object[][] { { "nodisplay -open examples/uniref50.fa",
335 " -eps", workingDir + "test_uniref50_out.eps", true,
336 MINFILESIZE_BIG, TEST_TIMEOUT },
337 { "nodisplay -open examples/uniref50.fa", " -eps",
338 workingDir + "test_uniref50_out.eps", false,
339 MINFILESIZE_BIG, TEST_TIMEOUT },
340 { "nogui -open examples/uniref50.fa", " -eps",
341 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
343 { "nogui -open examples/uniref50.fa", " -eps",
344 workingDir + "test_uniref50_out.eps", false,
345 MINFILESIZE_BIG, TEST_TIMEOUT },
346 { "headless -open examples/uniref50.fa", " -eps",
347 workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
349 { "headless -open examples/uniref50.fa", " -svg",
350 workingDir + "test_uniref50_out.svg", false,
351 MINFILESIZE_BIG, TEST_TIMEOUT },
352 { "headless -open examples/uniref50.fa", " -png",
353 workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
355 { "headless -open examples/uniref50.fa", " -html",
356 workingDir + "test_uniref50_out.html", true,
357 MINFILESIZE_BIG, TEST_TIMEOUT },
358 { "headless -open examples/uniref50.fa", " -fasta",
359 workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
361 { "headless -open examples/uniref50.fa", " -clustal",
362 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
364 { "headless -open examples/uniref50.fa", " -msf",
365 workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
367 { "headless -open examples/uniref50.fa", " -pileup",
368 workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
370 { "headless -open examples/uniref50.fa", " -pir",
371 workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
373 { "headless -open examples/uniref50.fa", " -pfam",
374 workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
376 { "headless -open examples/uniref50.fa", " -blc",
377 workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
379 { "headless -open examples/uniref50.fa", " -jalview",
380 workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,