/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import io.github.classgraph.ClassGraph;
import io.github.classgraph.ModuleRef;
import io.github.classgraph.ScanResult;
import jalview.gui.JvOptionPane;
public class CommandLineOperations
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
// Note longer timeout needed on full test run than on individual tests
private static final int TEST_TIMEOUT = 15000;
private static final int SETUP_TIMEOUT = 9500;
private static final int MINFILESIZE_SMALL = 2096;
private static final int MINFILESIZE_BIG = 4096;
private ArrayList successfulCMDs = new ArrayList<>();
/***
* from
* http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
* -using-javas-runtime-exec
*
* @author jimp
*
*/
private static class Worker extends Thread
{
private final Process process;
private BufferedReader outputReader;
private BufferedReader errorReader;
private Integer exit;
private Worker(Process process)
{
this.process = process;
}
@Override
public void run()
{
try
{
exit = process.waitFor();
} catch (InterruptedException ignore)
{
return;
}
}
public BufferedReader getOutputReader()
{
return outputReader;
}
public void setOutputReader(BufferedReader outputReader)
{
this.outputReader = outputReader;
}
public BufferedReader getErrorReader()
{
return errorReader;
}
public void setErrorReader(BufferedReader errorReader)
{
this.errorReader = errorReader;
}
}
private static ClassGraph scanner = null;
private static String classpath = null;
private static String modules = null;
private static String java_exe = null;
public synchronized static String getClassPath()
{
if (scanner == null)
{
scanner = new ClassGraph();
ScanResult scan = scanner.scan();
classpath = scan.getClasspath();
modules = "";
for (ModuleRef mr : scan.getModules())
{
modules.concat(mr.getName());
}
java_exe = System.getProperty("java.home") + File.separator + "bin"
+ File.separator + "java";
}
while (classpath == null)
{
try
{
Thread.sleep(10);
} catch (InterruptedException x)
{
}
}
return classpath;
}
private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
int timeout)
{
// Note: JAL-3065 - don't include quotes for lib/* because the arguments are
// not expanded by the shell
String classpath = getClassPath();
String _cmd = java_exe + " "
+ (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+ classpath
+ (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
: "")
+ " jalview.bin.Jalview ";
Process ls2_proc = null;
Worker worker = null;
try
{
ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
} catch (Throwable e1)
{
e1.printStackTrace();
}
if (ls2_proc != null)
{
BufferedReader outputReader = new BufferedReader(
new InputStreamReader(ls2_proc.getInputStream()));
BufferedReader errorReader = new BufferedReader(
new InputStreamReader(ls2_proc.getErrorStream()));
worker = new Worker(ls2_proc);
worker.start();
try
{
worker.join(timeout);
} catch (InterruptedException e)
{
System.err.println("Thread interrupted");
}
worker.setOutputReader(outputReader);
worker.setErrorReader(errorReader);
}
return worker;
}
@Test(groups = { "Functional" })
public void reportCurrentWorkingDirectory()
{
try
{
Path currentRelativePath = Paths.get("");
String s = currentRelativePath.toAbsolutePath().toString();
System.out.println("Test CWD is " + s);
} catch (Exception q)
{
q.printStackTrace();
}
}
@BeforeClass(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
@BeforeClass(alwaysRun = true)
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
{
System.out.println("STDOUT: " + ln);
successfulCMDs.add(ln);
}
while ((ln = worker.getErrorReader().readLine()) != null)
{
System.err.println("STDERR: " + ln);
successfulCMDs.add(ln);
}
}
@BeforeClass(alwaysRun = true)
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
final Worker worker = getJalviewDesktopRunner(false, cmds,
SETUP_TIMEOUT);
// number of lines expected on STDERR when Jalview starts up normally
// may need to adjust this if Jalview is excessively noisy ?
final int STDOUT_SETUPLINES = 50;
final int STDERR_SETUPLINES = 50;
// thread monitors stderr - bails after SETUP_TIMEOUT or when
// STDERR_SETUPLINES have been read
Thread runner = new Thread(new Runnable()
{
@Override
public void run()
{
String ln = null;
int stdoutcount = 0;
int stderrcount = 0;
try
{
while ((ln = worker.getOutputReader().readLine()) != null)
{
System.out.println(ln);
successfulCMDs.add(ln);
if (++stdoutcount > STDOUT_SETUPLINES)
{
break;
}
}
while ((ln = worker.getErrorReader().readLine()) != null)
{
System.err.println(ln);
successfulCMDs.add(ln);
if (++stderrcount > STDERR_SETUPLINES)
{
break;
}
}
} catch (Exception e)
{
System.err.println(
"Unexpected Exception reading stderr from the Jalview process");
e.printStackTrace();
}
}
});
long t = System.currentTimeMillis() + SETUP_TIMEOUT;
runner.start();
while (!runner.isInterrupted() && System.currentTimeMillis() < t)
{
try
{
Thread.sleep(500);
} catch (InterruptedException e)
{
}
}
runner.interrupt();
if (worker != null && worker.exit == null)
{
worker.interrupt();
Thread.currentThread().interrupt();
worker.process.destroy();
}
}
@Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
public void testAllInputOperations(String expectedString,
String failureMsg)
{
Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
}
@Test(
groups =
{ "Functional" },
dataProvider = "headlessModeOutputOperationsData")
public void testHeadlessModeOutputOperations(String harg, String type,
String fileName, boolean withAWT, int expectedMinFileSize,
int timeout)
{
String cmd = harg + type + " " + fileName;
// System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
File file = new File(fileName);
file.deleteOnExit();
Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
assertNotNull(worker, "worker is null");
String msg = "Didn't create an output" + type + " file.[" + harg + "]";
assertTrue(file.exists(), msg);
FileAssert.assertFile(file, msg);
FileAssert.assertMinLength(file, expectedMinFileSize);
if (worker != null && worker.exit == null)
{
worker.interrupt();
Thread.currentThread().interrupt();
worker.process.destroy();
Assert.fail("Jalview did not exit after " + type
+ " generation (try running test again to verify - timeout at "
+ timeout + "ms). [" + harg + "]");
}
file.delete();
}
@DataProvider(name = "allInputOperationsData")
public Object[][] getHeadlessModeInputParams()
{
return new Object[][] {
// headless mode input operations
{ "CMD [-colour zappo] executed successfully!",
"Failed command : -colour zappo" },
{ "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!",
"Failed command : -props File" },
{ "CMD [-sortbytree] executed successfully!",
"Failed command : -sortbytree" },
{ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
"Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
{ "CMD [-open examples/uniref50.fa] executed successfully!",
"Failed command : -open examples/uniref50.fa" },
{ "CMD [-nosortbytree] executed successfully!",
"Failed command : -nosortbytree" },
{ "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
"Failed command : -features examples/testdata/plantfdx.features" },
{ "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
"Failed command : -annotations examples/testdata/plantfdx.annotations" },
{ "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
"Failed command : -tree examples/testdata/uniref50_test_tree" },
// non headless mode input operations
{ "CMD [-nousagestats] executed successfully!",
"Failed command : -nousagestats" },
{ "CMD [-noquestionnaire] executed successfully!",
"Failed command : -noquestionnaire" } };
}
@DataProvider(name = "headlessModeOutputOperationsData")
public static Object[][] getHeadlessModeOutputParams()
{
// JBPNote: I'm not clear why need to specify full path for output file
// when running tests on build server, but we will keep this patch for now
// since it works.
// https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
String workingDir = "test/jalview/bin/";
return new Object[][] {
//
{ "nodisplay -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "nodisplay -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -svg",
workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -png",
workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -fasta",
workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -clustal",
workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -msf",
workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pileup",
workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pir",
workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pfam",
workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -blc",
workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -jalview",
workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
//
};
}
}