+++ /dev/null
-/*
- * 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.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 io.github.classgraph.ClassGraph;
-import io.github.classgraph.ScanResult;
-
-public class CommandLineOperations
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- 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
- * 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;
- }
- }
-
- 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 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" : "")
- + " -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");
- }
- 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 test/jalview/io/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);
- successfulCMDs.add(ln);
- }
- while ((ln = worker.getErrorReader().readLine()) != null)
- {
- System.err.println(ln);
- }
- }
-
- @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();
- }
- }
-
- @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)
- {
- 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 "
- + SETUP_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/io/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()
- {
- return new Object[][] {
- { "nodisplay -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
- { "nodisplay -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
- { "nogui -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
- { "nogui -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -eps",
- "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -svg",
- "test/jalview/bin/test_uniref50_out.svg", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -png",
- "test/jalview/bin/test_uniref50_out.png", true, MINFILESIZE_BIG,
- TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -html",
- "test/jalview/bin/test_uniref50_out.html", true,
- MINFILESIZE_BIG, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -fasta",
- "test/jalview/bin/test_uniref50_out.mfa", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -clustal",
- "test/jalview/bin/test_uniref50_out.aln", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -msf",
- "test/jalview/bin/test_uniref50_out.msf", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -pileup",
- "test/jalview/bin/test_uniref50_out.aln", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -pir",
- "test/jalview/bin/test_uniref50_out.pir", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -pfam",
- "test/jalview/bin/test_uniref50_out.pfam", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -blc",
- "test/jalview/bin/test_uniref50_out.blc", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT },
- { "headless -open examples/uniref50.fa", " -jalview",
- "test/jalview/bin/test_uniref50_out.jvp", true,
- MINFILESIZE_SMALL, TEST_TIMEOUT }, };
- }
-}
git://source.jalview.org / jalview.git / blobdiff