*/
package jalview.bin;
-import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.IdentifyFile;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
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 io.github.classgraph.ClassGraph;
import io.github.classgraph.ModuleRef;
import io.github.classgraph.ScanResult;
+import jalview.gui.JvOptionPane;
public class CommandLineOperations
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed
- // on
- // full test run than on
- // individual tests
+ // 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 = 9000;
+ private static final int SETUP_TIMEOUT = 9500;
private static final int MINFILESIZE_SMALL = 2096;
* @author jimp
*
*/
- private static class Worker extends Thread
+ public static class Worker extends Thread
{
private final Process process;
return classpath;
}
- private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+ public static 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
+ + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+ + classpath
+ (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
: "")
+ " jalview.bin.Jalview ";
new InputStreamReader(ls2_proc.getInputStream()));
BufferedReader errorReader = new BufferedReader(
new InputStreamReader(ls2_proc.getErrorStream()));
- worker = new Worker(ls2_proc);
+ worker = new CommandLineOperations.Worker(ls2_proc);
worker.start();
try
{
}
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(alwaysRun = true)
public void setUpForHeadlessCommandLineInputOperations()
throws IOException
{
- String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo "
+ 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(ln);
+ System.out.println("STDOUT: " + ln);
successfulCMDs.add(ln);
}
while ((ln = worker.getErrorReader().readLine()) != null)
{
- System.err.println(ln);
+ System.err.println("STDERR: " + ln);
+ successfulCMDs.add(ln);
}
}
- @BeforeTest(alwaysRun = true)
+ @BeforeClass(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)
+ 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()
{
- System.out.println(ln);
- successfulCMDs.add(ln);
- if (++count > 25)
+ @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)
{
- break;
}
}
+ runner.interrupt();
if (worker != null && worker.exit == null)
{
worker.interrupt();
@Test(
groups =
- { "Functional", "testben" },
+ { "Functional" },
dataProvider = "headlessModeOutputOperationsData")
public void testHeadlessModeOutputOperations(String harg, String type,
String fileName, boolean withAWT, int expectedMinFileSize,
- int timeout, String fileFormatType)
+ int timeout)
{
String cmd = harg + type + " " + fileName;
// System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
assertTrue(file.exists(), msg);
FileAssert.assertFile(file, msg);
FileAssert.assertMinLength(file, expectedMinFileSize);
- if (fileFormatType!=null && fileFormatType.length()>0)
- {
- String format = FileFormats.getInstance().forName(fileFormatType).getName();
- if (format!=null)
- {
- try
- {
- FileFormatI exportedType = new IdentifyFile()
- .identify(file.getAbsolutePath(), DataSourceType.FILE);
- assertEquals(exportedType, format,
- "Exported file type was wrong");
- } catch (FileFormatException e)
- {
- Assert.fail("Couldn't identify file " + file
- + " as an alignment format", e);
- }
- }
- }
if (worker != null && worker.exit == null)
{
worker.interrupt();
{
return new Object[][] {
// headless mode input operations
- { "CMD [-color zappo] executed successfully!",
- "Failed command : -color zappo" },
- { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!",
+ { "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" },
// 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, null },
+ 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, null },
+ 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, null },
+ TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- workingDir + "test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT, null },
+ 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, null },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -svg",
- workingDir + "test_uniref50_out.svg", false,
- MINFILESIZE_BIG, TEST_TIMEOUT, null },
+ 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, null },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
- workingDir + "test_uniref50_out.html", true,
- MINFILESIZE_BIG, TEST_TIMEOUT, null },
+ 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, FileFormat.Fasta.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -clustal",
workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.Clustal.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -msf",
workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.MSF.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pileup",
workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.Pileup.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pir",
workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.PIR.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pfam",
workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.Pfam.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -blc",
workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.BLC.toString() },
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -jalview",
workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
- TEST_TIMEOUT, FileFormat.Jalview.toString() }, };
+ TEST_TIMEOUT },
+ //
+ };
}
}
git://source.jalview.org / jalview.git / blobdiff