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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.bin

File CommandLineOperations.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

22
86
17
2
393
315
35
0.41
5.06
8.5
2.06

Classes

Class Line # Actions
CommandLineOperations 47 78 28
0.819819882%
CommandLineOperations.Worker 78 8 7
1.0100%
 

Contributing tests

No tests hitting this source file were found.

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.bin;
22   
23    import static org.testng.Assert.assertNotNull;
24    import static org.testng.Assert.assertTrue;
25   
26    import jalview.gui.JvOptionPane;
27   
28    import java.io.BufferedReader;
29    import java.io.File;
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;
35   
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;
42   
43    import io.github.classgraph.ClassGraph;
44    import io.github.classgraph.ModuleRef;
45    import io.github.classgraph.ScanResult;
46   
 
47    public class CommandLineOperations
48    {
49   
 
50  1 toggle @BeforeClass(alwaysRun = true)
51    public void setUpJvOptionPane()
52    {
53  1 JvOptionPane.setInteractiveMode(false);
54  1 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55    }
56   
57    private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
58    // on
59    // full test run than on
60    // individual tests
61   
62    private static final int SETUP_TIMEOUT = 9000;
63   
64    private static final int MINFILESIZE_SMALL = 2096;
65   
66    private static final int MINFILESIZE_BIG = 4096;
67   
68    private ArrayList<String> successfulCMDs = new ArrayList<>();
69   
70    /***
71    * from
72    * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
73    * -using-javas-runtime-exec
74    *
75    * @author jimp
76    *
77    */
 
78    private static class Worker extends Thread
79    {
80    private final Process process;
81   
82    private BufferedReader outputReader;
83   
84    private BufferedReader errorReader;
85   
86    private Integer exit;
87   
 
88  18 toggle private Worker(Process process)
89    {
90  18 this.process = process;
91    }
92   
 
93  18 toggle @Override
94    public void run()
95    {
96  18 try
97    {
98  18 exit = process.waitFor();
99    } catch (InterruptedException ignore)
100    {
101  1 return;
102    }
103    }
104   
 
105  16 toggle public BufferedReader getOutputReader()
106    {
107  16 return outputReader;
108    }
109   
 
110  18 toggle public void setOutputReader(BufferedReader outputReader)
111    {
112  18 this.outputReader = outputReader;
113    }
114   
 
115  37 toggle public BufferedReader getErrorReader()
116    {
117  37 return errorReader;
118    }
119   
 
120  18 toggle public void setErrorReader(BufferedReader errorReader)
121    {
122  18 this.errorReader = errorReader;
123    }
124    }
125   
126    private static ClassGraph scanner = null;
127   
128    private static String classpath = null;
129   
130    private static String modules = null;
131   
132    private static String java_exe = null;
133   
 
134  18 toggle public synchronized static String getClassPath()
135    {
136  18 if (scanner == null)
137    {
138  1 scanner = new ClassGraph();
139  1 ScanResult scan = scanner.scan();
140  1 classpath = scan.getClasspath();
141  1 modules = "";
142  1 for (ModuleRef mr : scan.getModules())
143    {
144  0 modules.concat(mr.getName());
145    }
146  1 java_exe = System.getProperty("java.home") + File.separator + "bin"
147    + File.separator + "java";
148   
149    }
150  18 while (classpath == null)
151    {
152  0 try
153    {
154  0 Thread.sleep(10);
155    } catch (InterruptedException x)
156    {
157   
158    }
159    }
160  18 return classpath;
161    }
162   
 
163  18 toggle private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
164    int timeout)
165    {
166    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
167    // not expanded by the shell
168  18 String classpath = getClassPath();
169  18 String _cmd = java_exe + " "
170  18 + (withAwt ? "-Djava.awt.headless=true" : "")
171    + " -classpath " + classpath
172  18 + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
173    : "")
174    + " jalview.bin.Jalview ";
175  18 Process ls2_proc = null;
176  18 Worker worker = null;
177  18 try
178    {
179  18 ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
180    } catch (Throwable e1)
181    {
182  0 e1.printStackTrace();
183    }
184  18 if (ls2_proc != null)
185    {
186  18 BufferedReader outputReader = new BufferedReader(
187    new InputStreamReader(ls2_proc.getInputStream()));
188  18 BufferedReader errorReader = new BufferedReader(
189    new InputStreamReader(ls2_proc.getErrorStream()));
190  18 worker = new Worker(ls2_proc);
191  18 worker.start();
192  18 try
193    {
194  18 worker.join(timeout);
195    } catch (InterruptedException e)
196    {
197  1 System.err.println("Thread interrupted");
198    }
199  18 worker.setOutputReader(outputReader);
200  18 worker.setErrorReader(errorReader);
201    }
202  18 return worker;
203    }
204   
 
205  1 toggle @Test(groups = { "Functional" })
206    public void reportCurrentWorkingDirectory()
207    {
208  1 try
209    {
210  1 Path currentRelativePath = Paths.get("");
211  1 String s = currentRelativePath.toAbsolutePath().toString();
212  1 System.out.println("Test CWD is " + s);
213    } catch (Exception q)
214    {
215  0 q.printStackTrace();
216    }
217    }
218   
 
219  1 toggle @BeforeTest(alwaysRun = true)
220    public void initialize()
221    {
222  1 new CommandLineOperations();
223    }
224   
 
225  1 toggle @BeforeTest(alwaysRun = true)
226    public void setUpForHeadlessCommandLineInputOperations()
227    throws IOException
228    {
229  1 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  1 Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
233  1 String ln = null;
234  ? while ((ln = worker.getOutputReader().readLine()) != null)
235    {
236  15 System.out.println(ln);
237  15 successfulCMDs.add(ln);
238    }
239  ? while ((ln = worker.getErrorReader().readLine()) != null)
240    {
241  10 System.err.println(ln);
242    }
243    }
244   
 
245  1 toggle @BeforeTest(alwaysRun = true)
246    public void setUpForCommandLineInputOperations() throws IOException
247    {
248  1 String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
249  1 Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
250  1 String ln = null;
251  1 int count = 0;
252  ? while ((ln = worker.getErrorReader().readLine()) != null)
253    {
254  26 System.out.println(ln);
255  26 successfulCMDs.add(ln);
256  26 if (++count > 25)
257    {
258  1 break;
259    }
260    }
261  1 if (worker != null && worker.exit == null)
262    {
263  1 worker.interrupt();
264  1 Thread.currentThread().interrupt();
265  1 worker.process.destroy();
266    }
267    }
268   
 
269  11 toggle @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
270    public void testAllInputOperations(String expectedString,
271    String failureMsg)
272    {
273  11 Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
274    }
275   
 
276  16 toggle @Test(
277    groups =
278    { "Functional", "testben" },
279    dataProvider = "headlessModeOutputOperationsData")
280    public void testHeadlessModeOutputOperations(String harg, String type,
281    String fileName, boolean withAWT, int expectedMinFileSize,
282    int timeout)
283    {
284  16 String cmd = harg + type + " " + fileName;
285    // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
286  16 File file = new File(fileName);
287  16 file.deleteOnExit();
288  16 Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
289  16 assertNotNull(worker, "worker is null");
290  16 String msg = "Didn't create an output" + type + " file.[" + harg + "]";
291  16 assertTrue(file.exists(), msg);
292  16 FileAssert.assertFile(file, msg);
293  16 FileAssert.assertMinLength(file, expectedMinFileSize);
294  16 if (worker != null && worker.exit == null)
295    {
296  0 worker.interrupt();
297  0 Thread.currentThread().interrupt();
298  0 worker.process.destroy();
299  0 Assert.fail("Jalview did not exit after " + type
300    + " generation (try running test again to verify - timeout at "
301    + timeout + "ms). [" + harg + "]");
302    }
303  16 file.delete();
304    }
305   
 
306  1 toggle @DataProvider(name = "allInputOperationsData")
307    public Object[][] getHeadlessModeInputParams()
308    {
309  1 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" } };
334    }
335   
 
336  1 toggle @DataProvider(name = "headlessModeOutputOperationsData")
337    public static Object[][] getHeadlessModeOutputParams()
338    {
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
341    // since it works.
342    // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
343  1 String workingDir = "test/jalview/bin/";
344  1 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,
352    TEST_TIMEOUT },
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,
358    TEST_TIMEOUT },
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,
364    TEST_TIMEOUT },
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,
370    TEST_TIMEOUT },
371    { "headless -open examples/uniref50.fa", " -clustal",
372    workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
373    TEST_TIMEOUT },
374    { "headless -open examples/uniref50.fa", " -msf",
375    workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
376    TEST_TIMEOUT },
377    { "headless -open examples/uniref50.fa", " -pileup",
378    workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
379    TEST_TIMEOUT },
380    { "headless -open examples/uniref50.fa", " -pir",
381    workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
382    TEST_TIMEOUT },
383    { "headless -open examples/uniref50.fa", " -pfam",
384    workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
385    TEST_TIMEOUT },
386    { "headless -open examples/uniref50.fa", " -blc",
387    workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
388    TEST_TIMEOUT },
389    { "headless -open examples/uniref50.fa", " -jalview",
390    workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
391    TEST_TIMEOUT }, };
392    }
393    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.