*/
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.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
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
- 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 = 13000; // Note longer timeout needed
+ // on
+ // full test run than on
+ // individual tests
+
+ private static final int SETUP_TIMEOUT = 9500;
+
+ 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 Worker jalviewDesktopRunner(boolean withAwt, String cmd,
- int timeout) throws InterruptedException, IOException
+ 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()
{
- String _cmd = "java "
- + (withAwt ? "-Djava.awt.headless=true" : "")
- + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("############ Testing 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: ");
- // String ln = null;
- // while ((ln = outputReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
- //
- // System.out.println("Error: ");
- // while ((ln = errorReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
+ 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;
}
- @BeforeTest
+ @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();
+ }
+ }
+
+ @BeforeTest(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
- @Test(dataProvider = "headlessModeOutputParams")
- public void testHeadlessModeOutputs(String harg, String type,
- String fileName, boolean withAWT, int expectedMinFileSize)
+ @BeforeTest(alwaysRun = true)
+ public void setUpForHeadlessCommandLineInputOperations()
+ throws IOException
{
- String cmd = harg + type + " " + fileName;
- // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
- File file = new File(fileName);
- Worker worker = null;
- try
+ 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)
{
- worker = jalviewDesktopRunner(withAWT, cmd, 9000);
- } catch (InterruptedException e)
- {
- e.printStackTrace();
- } catch (IOException e)
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ }
+ while ((ln = worker.getErrorReader().readLine()) != null)
{
- e.printStackTrace();
+ System.err.println(ln);
}
+ }
- FileAssert.assertFile(file, "Didn't create an output" + type
- + " file.[" + harg + "]");
- FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+ @BeforeTest(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 STDERR_SETUPLINES = 30;
+
+ // 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 count = 0;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > 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();
- Assert.fail("Jalview did not exit after "
- + type
- + " generation (try running test again to verify - timeout at 9000ms). ["
- + harg + "]");
}
- new File(fileName).delete();
}
- @DataProvider(name = "headlessModeOutputParams")
- public static Object[][] headlessModeOutput()
+ @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)
{
- return new Object[][]
+ 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 [-color zappo] executed successfully!",
+ "Failed command : -color 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",
- "test_uniref50_out.eps", true, 4096 },
- { "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", true, 4096 },
+ 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",
- "test_uniref50_out.svg", false, 4096 },
+ workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", true, 4096 },
- { "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", false, 4096 },
- { "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", true, 4096 },
+ workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", false, 4096 },
+ workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", true, 2096 },
- { "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", false, 2096 },
- { "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", true, 2096 },
+ workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", true, 2096 },
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", false, 2096 },
+ workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", true, 2096 },
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", false, 2096 },
+ workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", false, 2096 },
- { "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", true, 2096 },
+ workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", false, 2096 },
+ workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", true, 2096 },
- { "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", false, 2096 },
- };
+ workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT }, };
}
-
-
}
git://source.jalview.org / jalview.git / blobdiff