/*
* 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 jalview.gui.JvOptionPane;
import jalview.util.Worker;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class CommandLineOperations
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
// full test run than on
// individual tests
private static final int SETUP_TIMEOUT = 9000;
private static final int MINFILESIZE_SMALL = 2096;
private static final int MINFILESIZE_BIG = 4096;
private ArrayList successfulCMDs = new ArrayList<>();
@BeforeTest(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
@BeforeTest(alwaysRun = true)
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
+ "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
+ "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
Worker worker = Worker.jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
{
System.out.println(ln);
successfulCMDs.add(ln);
}
}
@BeforeTest(alwaysRun = true)
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
Worker worker = Worker.jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
String ln = null;
int count = 0;
while ((ln = worker.getErrorReader().readLine()) != null)
{
System.out.println(ln);
successfulCMDs.add(ln);
if (++count > 5)
{
break;
}
}
if (worker != null && worker.getExitValue() == null)
{
worker.destroyProcess();
}
}
@Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
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);
Worker worker = Worker.jalviewDesktopRunner(withAWT, cmd, timeout);
FileAssert.assertFile(file, "Didn't create an output" + type
+ " file.[" + harg + "]");
FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
if (worker != null && worker.getExitValue() == null)
{
worker.destroyProcess();
Assert.fail("Jalview did not exit after "
+ type
+ " generation (try running test again to verify - timeout at "
+ SETUP_TIMEOUT + "ms). ["
+ harg + "]");
}
new File(fileName).delete();
}
@DataProvider(name = "allInputOpearationsData")
public Object[][] getHeadlessModeInputParams()
{
return new Object[][] {
// headless mode input operations
{ "CMD [-color zappo] executed successfully!",
"Failed command : -color zappo" },
{ "CMD [-props FILE] 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 [-dasserver nickname=www.test.com] executed successfully!",
"Failed command : -dasserver nickname=www.test.com" },
{
"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 nickname=www.test.com" } };
}
@DataProvider(name = "headlessModeOutputOperationsData")
public static Object[][] getHeadlessModeOutputParams()
{
return new Object[][] {
{ "nodisplay -open examples/uniref50.fa", " -eps",
"test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nodisplay -open examples/uniref50.fa", " -eps",
"test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
"test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
"test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -eps",
"test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -svg",
"test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -png",
"test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
"test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -fasta",
"test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -clustal",
"test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -msf",
"test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pileup",
"test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pir",
"test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pfam",
"test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -blc",
"test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -jalview",
"test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
}
}