+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.bin;
-import static org.junit.Assert.*;
+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.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+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
- 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 = 4500; // 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
+ * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+ * -using-javas-runtime-exec
+ *
+ * @author jimp
+ *
+ */
+ private static class Worker extends Thread
{
+ 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
+ {
+ exit = process.waitFor();
+ } catch (InterruptedException ignore)
+ {
+ 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;
+ }
}
-/***
- * 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 {
- private final Process process;
- private Integer exit;
- private Worker(Process process) {
- this.process = process;
- }
- public void run() {
- try {
- exit = process.waitFor();
- } catch (InterruptedException ignore) {
- return;
+
+ private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout)
+ {
+ String cp_sep = ":";
+ if (System.getProperty("os.name").indexOf("Windows") >= 0)
+ {
+ cp_sep = ";";
+ }
+ String _cmd = "java "
+ + (withAwt ? "-Djava.awt.headless=true" : "")
+ + " -classpath \"./lib/*" + cp_sep
+ + "./classes\" jalview.bin.Jalview ";
+ System.out.println("CMD [" + cmd + "]");
+ Process ls2_proc = null;
+ Worker worker = null;
+ try
+ {
+ ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+ } catch (IOException 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)
+ {
+ // e.printStackTrace();
+ }
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
}
+ return worker;
}
-}
- @Test
- public void testHeadlessModeEPS() throws Exception
+
+ @BeforeTest(alwaysRun = true)
+ public void initialize()
{
- String jalview_input = "examples/uniref50.fa";
- String jalview_output = "test_uniref50_out.eps";
- String cmd = "java -Djava.awt.headless=true -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview -nodisplay -open "+ jalview_input + " -eps " + jalview_output;
-
- System.out.println("###############Jalview CMD: " + cmd);
- Process ls2_proc = Runtime.getRuntime().exec(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(9000);
- System.out.println("Output: ");
- String ln=null;
- while ((ln=outputReader.readLine())!=null) {
+ 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 = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+ String ln = 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 = 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;
+ }
}
- assertTrue("Didn't create an output EPS file.", new File("test_uniref50_out.eps").exists());
- assertTrue("Didn't create an EPS file with any content", new File("test_uniref50_out.eps").length()>4096);
- if (worker.exit == null){
+ if (worker != null && worker.exit == null)
+ {
worker.interrupt();
Thread.currentThread().interrupt();
- ls2_proc.destroy();
- fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms).");
-}
+ worker.process.destroy();
+ }
+ }
+
+ @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 = 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.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 "
+ + 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 }, };
+ }
}
git://source.jalview.org / jalview.git / blobdiff