X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=3ac86567ec24e6329b0ac3bc10bc11c34239b82c;hb=3e84d5cd04e35a03ae504fa3249069c41c989fbe;hp=1c3714abf5ea4887a4dcde4e168b95007e3278c0;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index 1c3714a..3ac8656 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,29 +20,45 @@ */ 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; + +import io.github.classgraph.ClassGraph; +import io.github.classgraph.ScanResult; 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 = 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 successfulCMDs = new ArrayList<>(); /*** * from @@ -56,6 +72,10 @@ public class CommandLineOperations { private final Process process; + private BufferedReader outputReader; + + private BufferedReader errorReader; + private Integer exit; private Worker(Process process) @@ -63,6 +83,7 @@ public class CommandLineOperations this.process = process; } + @Override public void run() { try @@ -73,98 +94,245 @@ public class CommandLineOperations 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 jalviewDesktopRunner(boolean withAwt, String cmd, - int timeout) throws InterruptedException, IOException + 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("###############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: "); + + " -classpath " + classpath + " jalview.bin.Jalview "; + 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; + } + + @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 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 = outputReader.readLine()) != 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; + } } - return worker; + if (worker != null && worker.exit == null) + { + worker.interrupt(); + Thread.currentThread().interrupt(); + worker.process.destroy(); + } + } + + @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData") + public void testAllInputOperations(String expectedString, + String failureMsg) + { + Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg); } - @Test - public void testHeadlessModeEPS() throws Exception + @Test( + groups = { "Functional" }, + dataProvider = "headlessModeOutputOperationsData") + public void testHeadlessModeOutputOperations(String harg, String type, + String fileName, boolean withAWT, int expectedMinFileSize, + int timeout) { - String[] headlessArgs = new String[] - { "nodisplay", "headless", "nogui" }; - for (String _harg : headlessArgs) + 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) { - boolean _switch = false, withAwt = false; - do - { - if (_switch) + 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" }, { - withAwt = true; - } - _switch = true; - String jalview_input = "examples/uniref50.fa"; - String jalview_output = "test_uniref50_out.eps"; - String cmd = "" + _harg + " -open " + jalview_input + " -eps " - + jalview_output; - String harg = _harg - + (withAwt ? "-Djava.awt.headless=true" - : " NO AWT.HEADLESS"); - System.out.println("Testing with Headless argument: '" + harg - + "'\n"); - Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); - assertTrue("Didn't create an output EPS file.[" + harg + "]", - new File("test_uniref50_out.eps").exists()); - assertTrue("Didn't create an EPS file with any content[" + harg - + "]", new File("test_uniref50_out.eps").length() > 4096); - if (worker.exit == null) + "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" }, { - worker.interrupt(); - Thread.currentThread().interrupt(); - worker.process.destroy(); - fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). [" - + harg + "]"); - } - } while (!withAwt); - } + "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 }, }; } - // @Test - // public void testJalview2XMLDataset() throws Exception - // { - // String jalview_input = "examples/uniref50.fa"; - // String jalview_output = "test_uniref50_out.eps"; - // String cmd = ""+" -open "+ jalview_input + " -eps " + jalview_output; - // //String harg = _harg+(withAwt ? - // "-Djava.awt.headless=true":" NO AWT.HEADLESS"); - // System.out.println("Testing with Headless argument: '"+harg+"'\n"); - // Worker worker = jalviewDesktopRunner(withAwt, cmd, 9000); - // assertTrue("Didn't create an output EPS file.["+harg+"]", new - // File("test_uniref50_out.eps").exists()); - // assertTrue("Didn't create an EPS file with any content["+harg+"]", new - // File("test_uniref50_out.eps").length()>4096); - // if (worker.exit == null){ - // worker.interrupt(); - // Thread.currentThread().interrupt(); - // worker.process.destroy(); - // fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms). ["+harg+"]"); - // } - // } }