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 jalview.gui.JvOptionPane;
25 import java.io.BufferedReader;
27 import java.io.IOException;
28 import java.io.InputStreamReader;
29 import java.util.ArrayList;
31 import org.testng.Assert;
32 import org.testng.FileAssert;
33 import org.testng.annotations.BeforeClass;
34 import org.testng.annotations.BeforeTest;
35 import org.testng.annotations.DataProvider;
36 import org.testng.annotations.Test;
38 import io.github.classgraph.ClassGraph;
39 import io.github.classgraph.ScanResult;
41 public class CommandLineOperations
44 @BeforeClass(alwaysRun = true)
45 public void setUpJvOptionPane()
47 JvOptionPane.setInteractiveMode(false);
48 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
51 private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
53 // full test run than on
56 private static final int SETUP_TIMEOUT = 9000;
58 private static final int MINFILESIZE_SMALL = 2096;
60 private static final int MINFILESIZE_BIG = 4096;
62 private ArrayList<String> successfulCMDs = new ArrayList<>();
66 * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
67 * -using-javas-runtime-exec
72 private static class Worker extends Thread
74 private final Process process;
76 private BufferedReader outputReader;
78 private BufferedReader errorReader;
82 private Worker(Process process)
84 this.process = process;
92 exit = process.waitFor();
93 } catch (InterruptedException ignore)
99 public BufferedReader getOutputReader()
104 public void setOutputReader(BufferedReader outputReader)
106 this.outputReader = outputReader;
109 public BufferedReader getErrorReader()
114 public void setErrorReader(BufferedReader errorReader)
116 this.errorReader = errorReader;
120 private static ClassGraph scanner = null;
122 private static String classpath = null;
124 public synchronized static String getClassPath()
128 scanner = new ClassGraph();
129 ScanResult scan = scanner.scan();
130 classpath = scan.getClasspath();
132 while (classpath == null)
137 } catch (InterruptedException x)
145 private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
148 // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
149 // not expanded by the shell
150 String classpath = getClassPath();
151 String _cmd = "java " + (withAwt ? "-Djava.awt.headless=true" : "")
152 + " -classpath " + classpath + " jalview.bin.Jalview ";
153 Process ls2_proc = null;
154 Worker worker = null;
157 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
158 } catch (IOException e1)
160 e1.printStackTrace();
162 if (ls2_proc != null)
164 BufferedReader outputReader = new BufferedReader(
165 new InputStreamReader(ls2_proc.getInputStream()));
166 BufferedReader errorReader = new BufferedReader(
167 new InputStreamReader(ls2_proc.getErrorStream()));
168 worker = new Worker(ls2_proc);
172 worker.join(timeout);
173 } catch (InterruptedException e)
175 // e.printStackTrace();
177 worker.setOutputReader(outputReader);
178 worker.setErrorReader(errorReader);
183 @BeforeTest(alwaysRun = true)
184 public void initialize()
186 new CommandLineOperations();
189 @BeforeTest(alwaysRun = true)
190 public void setUpForHeadlessCommandLineInputOperations()
193 String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
194 + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
195 + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
196 Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
198 while ((ln = worker.getOutputReader().readLine()) != null)
200 System.out.println(ln);
201 successfulCMDs.add(ln);
205 @BeforeTest(alwaysRun = true)
206 public void setUpForCommandLineInputOperations() throws IOException
208 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
209 Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
212 while ((ln = worker.getErrorReader().readLine()) != null)
214 System.out.println(ln);
215 successfulCMDs.add(ln);
221 if (worker != null && worker.exit == null)
224 Thread.currentThread().interrupt();
225 worker.process.destroy();
229 @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
230 public void testAllInputOperations(String expectedString,
233 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
238 { "Functional", "testben" },
239 dataProvider = "headlessModeOutputOperationsData")
240 public void testHeadlessModeOutputOperations(String harg, String type,
241 String fileName, boolean withAWT, int expectedMinFileSize,
244 String cmd = harg + type + " " + fileName;
245 // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
246 File file = new File(fileName);
247 Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
249 FileAssert.assertFile(file,
250 "Didn't create an output" + type + " file.[" + harg + "]");
251 // System.out.println( "File '" + file.getName() + "' has size " +
253 // FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
254 FileAssert.assertMinLength(file, expectedMinFileSize);
255 if (worker != null && worker.exit == null)
258 Thread.currentThread().interrupt();
259 worker.process.destroy();
260 Assert.fail("Jalview did not exit after " + type
261 + " generation (try running test again to verify - timeout at "
262 + timeout + "ms). [" + harg + "]");
264 new File(fileName).delete();
267 @DataProvider(name = "allInputOpearationsData")
268 public Object[][] getHeadlessModeInputParams()
270 return new Object[][] {
271 // headless mode input operations
272 { "CMD [-color zappo] executed successfully!",
273 "Failed command : -color zappo" },
274 { "CMD [-props FILE] executed successfully!",
275 "Failed command : -props File" },
276 { "CMD [-sortbytree] executed successfully!",
277 "Failed command : -sortbytree" },
278 { "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
279 "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
280 { "CMD [-open examples/uniref50.fa] executed successfully!",
281 "Failed command : -open examples/uniref50.fa" },
282 { "CMD [-nosortbytree] executed successfully!",
283 "Failed command : -nosortbytree" },
285 "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
286 "Failed command : -features examples/testdata/plantfdx.features" },
287 { "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
288 "Failed command : -annotations examples/testdata/plantfdx.annotations" },
289 { "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
290 "Failed command : -tree examples/testdata/uniref50_test_tree" },
291 // non headless mode input operations
292 { "CMD [-nousagestats] executed successfully!",
293 "Failed command : -nousagestats" },
294 { "CMD [-noquestionnaire] executed successfully!",
295 "Failed command : -noquestionnaire" } };
299 @DataProvider(name = "headlessModeOutputOperationsData")
300 public static Object[][] getHeadlessModeOutputParams()
302 return new Object[][] {
303 { "nodisplay -open examples/uniref50.fa", " -eps",
304 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
305 { "nodisplay -open examples/uniref50.fa", " -eps",
306 "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
307 { "nogui -open examples/uniref50.fa", " -eps",
308 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
309 { "nogui -open examples/uniref50.fa", " -eps",
310 "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
311 { "headless -open examples/uniref50.fa", " -eps",
312 "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
313 { "headless -open examples/uniref50.fa", " -svg",
314 "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
315 { "headless -open examples/uniref50.fa", " -png",
316 "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
317 { "headless -open examples/uniref50.fa", " -html",
318 "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
319 { "headless -open examples/uniref50.fa", " -fasta",
320 "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
322 { "headless -open examples/uniref50.fa", " -clustal",
323 "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
325 { "headless -open examples/uniref50.fa", " -msf",
326 "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
328 { "headless -open examples/uniref50.fa", " -pileup",
329 "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
331 { "headless -open examples/uniref50.fa", " -pir",
332 "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
334 { "headless -open examples/uniref50.fa", " -pfam",
335 "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
337 { "headless -open examples/uniref50.fa", " -blc",
338 "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
340 { "headless -open examples/uniref50.fa", " -jalview",
341 "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,