*/
package jalview.bin;
-import static org.junit.Assert.*;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.gui.JvOptionPane;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
+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;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
public class CommandLineOperations
{
- @BeforeClass
- public static void setUpBeforeClass() throws Exception
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- @AfterClass
- public static void tearDownAfterClass() throws Exception
- {
- }
+ 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<String> successfulCMDs = new ArrayList<>();
/***
* from
{
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
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;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
}
- private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
- int timeout) throws InterruptedException, IOException
+ 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 "
+ (withAwt ? "-Djava.awt.headless=true" : "")
- + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("###############Jalview CMD: " + _cmd + cmd);
- Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
- BufferedReader outputReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getInputStream()));
-
- BufferedReader errorReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getErrorStream()));
- Worker worker = new Worker(ls2_proc);
- worker.start();
- worker.join(timeout);
- System.out.println("Output: ");
+ + " -classpath " + classpath + " 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");
+ e.printStackTrace();
+ }
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @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 = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
- while ((ln = outputReader.readLine()) != null)
+ while ((ln = worker.getOutputReader().readLine()) != null)
{
System.out.println(ln);
+ successfulCMDs.add(ln);
}
+ }
- System.out.println("Error: ");
- while ((ln = errorReader.readLine()) != null)
+ @BeforeTest(alwaysRun = true)
+ public void setUpForCommandLineInputOperations() throws IOException
+ {
+ String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
+ Worker worker = getJalviewDesktopRunner(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.exit == null)
+ {
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
}
- return worker;
}
- @Test
- public void testHeadlessModeEPS() throws Exception
+ @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
+ public void testAllInputOperations(String expectedString,
+ String failureMsg)
{
- String[] headlessArgs = new String[]
- { "nodisplay", "headless", "nogui" };
- for (String _harg : headlessArgs)
+ 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 = getJalviewDesktopRunner(withAWT, cmd, timeout);
+ assertNotNull(worker);
+ String msg = "Didn't create an output" + type + " file.[" + harg + "]";
+ assertTrue(file.exists());
+ FileAssert.assertFile(file, msg);
+ FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+ if (worker != null && worker.exit == null)
{
- boolean _switch = false, withAwt = false;
- do
- {
- if (_switch)
+ 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 "
+ + SETUP_TIMEOUT + "ms). ["
+ + harg + "]");
+ }
+ new File(fileName).delete();
+ }
+
+ @DataProvider(name = "allInputOperationsData")
+ 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" },
{
- withAwt = true;
- }
- _switch = true;
- String jalview_input = "examples/uniref50.fa";
- String jalview_output = "test_uniref50_out.eps";
- String cmd = "" + _harg + " -open " + jalview_input + " -eps "
- + jalview_output;
- String harg = _harg
- + (withAwt ? "-Djava.awt.headless=true"
- : " NO AWT.HEADLESS");
- System.out.println("Testing with Headless argument: '" + harg
- + "'\n");
- Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
- assertTrue("Didn't create an output EPS file.[" + harg + "]",
- new File("test_uniref50_out.eps").exists());
- assertTrue("Didn't create an EPS file with any content[" + harg
- + "]", new File("test_uniref50_out.eps").length() > 4096);
- if (worker.exit == null)
+ "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" },
{
- worker.interrupt();
- Thread.currentThread().interrupt();
- worker.process.destroy();
- fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["
- + harg + "]");
- }
- } while (!withAwt);
- }
+ "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()
+ {
+ 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 }, };
}
- // @Test
- // public void testJalview2XMLDataset() throws Exception
- // {
- // String jalview_input = "examples/uniref50.fa";
- // String jalview_output = "test_uniref50_out.eps";
- // String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output;
- // //String harg = _harg+(withAwt ?
- // "-Djava.awt.headless=true":" NO AWT.HEADLESS");
- // System.out.println("Testing with Headless argument: '"+harg+"'\n");
- // Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000);
- // assertTrue("Didn't create an output EPS file.["+harg+"]", new
- // File("test_uniref50_out.eps").exists());
- // assertTrue("Didn't create an EPS file with any content["+harg+"]", new
- // File("test_uniref50_out.eps").length()>4096);
- // if (worker.exit == null){
- // worker.interrupt();
- // Thread.currentThread().interrupt();
- // worker.process.destroy();
- // fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]");
- // }
- // }
}
git://source.jalview.org / jalview.git / blobdiff