*/
package jalview.bin;
+import jalview.gui.JvOptionPane;
+import jalview.ws.utils.Worker;
+
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.ScanResult;
+
public class CommandLineOperations
{
- private ArrayList<String> successfulCMDs = new ArrayList<String>();
-
- /***
- * 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
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
{
- private final Process process;
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
- private BufferedReader outputReader;
+ private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on
+ // full test run than on
+ // individual tests
- private BufferedReader errorReader;
+ private static final int SETUP_TIMEOUT = 9000;
- private Integer exit;
+ private static final int MINFILESIZE_SMALL = 2096;
- private Worker(Process process)
- {
- this.process = process;
- }
+ private static final int MINFILESIZE_BIG = 4096;
- public void run()
- {
- try
- {
- exit = process.waitFor();
- } catch (InterruptedException ignore)
- {
- return;
- }
- }
+ private ArrayList<String> successfulCMDs = new ArrayList<>();
- public BufferedReader getOutputReader()
- {
- return outputReader;
- }
- public void setOutputReader(BufferedReader outputReader)
- {
- this.outputReader = outputReader;
- }
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
- public BufferedReader getErrorReader()
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
{
- return errorReader;
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
}
-
- public void setErrorReader(BufferedReader errorReader)
+ while (classpath == null)
{
- this.errorReader = errorReader;
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
}
+ return classpath;
}
-
private Worker jalviewDesktopRunner(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("CMD [" + cmd + "]");
+ + " -classpath " + classpath + " jalview.bin.Jalview ";
Process ls2_proc = null;
Worker worker = null;
try
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 = jalviewDesktopRunner(true, cmds, 9000);
+ Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
String ln = null;
while ((ln = worker.getOutputReader().readLine()) != null)
{
public void setUpForCommandLineInputOperations() throws IOException
{
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
- Worker worker = jalviewDesktopRunner(false, cmds, 9000);
+ Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
String ln = null;
int count = 0;
while ((ln = worker.getErrorReader().readLine()) != null)
break;
}
}
- if (worker != null && worker.exit == null)
+ if (worker != null && worker.getExitValue() == null)
{
- worker.interrupt();
- Thread.currentThread().interrupt();
- worker.process.destroy();
+ worker.destroyProcess();
+
}
}
FileAssert.assertFile(file, "Didn't create an output" + type
+ " file.[" + harg + "]");
FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
- if (worker != null && worker.exit == null)
+ if (worker != null && worker.getExitValue() == null)
{
- worker.interrupt();
- Thread.currentThread().interrupt();
- worker.process.destroy();
+ worker.destroyProcess();
Assert.fail("Jalview did not exit after "
+ type
- + " generation (try running test again to verify - timeout at 9000ms). ["
+ + " generation (try running test again to verify - timeout at "
+ + SETUP_TIMEOUT + "ms). ["
+ harg + "]");
}
new File(fileName).delete();
{
return new Object[][] {
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096, 4000 },
+ "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096, 4000 },
+ "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096, 4000 },
+ "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096, 4000 },
+ "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096, 4000 },
+ "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", false, 4096, 3000 },
+ "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", true, 4096, 3000 },
+ "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", true, 4096, 3000 },
+ "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", true, 2096, 3000 },
+ "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", true, 2096, 3000 },
+ "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", true, 2096, 3000 },
+ "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", true, 2096, 3000 },
+ "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", true, 2096, 3000 },
+ "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", true, 2096, 3000 },
+ "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", true, 2096, 3000 },
+ "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", true, 2096, 3000 }, };
+ "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
}
}
git://source.jalview.org / jalview.git / blobdiff