--- /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 java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
+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 CommandLineOperationsNG
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ // Note longer timeout needed on full test run than on individual tests
+ private static final int TEST_TIMEOUT = 13000;
+
+ private static final int SETUP_TIMEOUT = 9500;
+
+ private static final int MINFILESIZE_SMALL = 2096;
+
+ private static final int MINFILESIZE_BIG = 4096;
+
+ private List<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;
+
+ private static String modules = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ modules = "";
+ for (ModuleRef mr : scan.getModules())
+ {
+ modules.concat(mr.getName());
+ }
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ }
+
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout)
+ {
+ return getJalviewDesktopRunner(withAwt, cmd, timeout, true);
+ }
+
+ private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout, boolean testoutput)
+ {
+ /*
+ boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
+ String pwd = "";
+ try
+ {
+ Path currentRelativePath = Paths.get("");
+ pwd = currentRelativePath.toAbsolutePath().toString();
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ if (pwd == null || pwd.length() == 0)
+ pwd = ".";
+ String[] classpaths = new String[] { pwd + "/bin/main",
+ pwd + "/j11lib/*", pwd + "/resources", pwd + "/help" };
+ String classpath = String.join(win ? ";" : ":", classpaths);
+ getClassPath();
+ */
+ // 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
+ + ((modules != null && modules.length() > 2)
+ ? "--add-modules=\"" + modules + "\""
+ : "")
+ + " jalview.bin.Jalview ";
+ Process ls2_proc = null;
+ Worker worker = null;
+ try
+ {
+ cmd = cmd + (testoutput ? " --testoutput " : "");
+ System.out.println("Running '" + _cmd + cmd + "'");
+ 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;
+ }
+
+ @Test(groups = { "Functional", "testTask1" })
+ public void reportCurrentWorkingDirectory()
+ {
+ try
+ {
+ Path currentRelativePath = Paths.get("");
+ String s = currentRelativePath.toAbsolutePath().toString();
+ System.out.println("Test CWD is " + s);
+ } catch (Exception q)
+ {
+ q.printStackTrace();
+ }
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void initialize()
+ {
+ new CommandLineOperationsNG();
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpForHeadlessCommandLineInputOperations()
+ throws IOException
+ {
+ String cmds = "--headless " + "--open examples/uniref50.fa "
+ + "--sortbytree "
+ + "--props test/jalview/bin/testProps.jvprops "
+ + "--colour zappo "
+ + "--jabaws http://www.compbio.dundee.ac.uk/jabaws "
+ + "--features examples/testdata/plantfdx.features "
+ + "--annotations examples/testdata/plantfdx.annotations "
+ + "--tree examples/testdata/uniref50_test_tree "
+ + "--nousagestats ";
+ 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);
+ }
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpForCommandLineInputOperations() throws IOException
+ {
+ String cmds = "--open examples/uniref50.fa --noquestionnaire --nousagestats";
+ 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 STDERR_SETUPLINES = 50;
+
+ // thread monitors stderr - bails after SETUP_TIMEOUT or when
+ // STDERR_SETUPLINES have been read
+ Thread runner = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ String ln = null;
+ int count = 0;
+ try
+ {
+ while ((ln = worker.getOutputReader().readLine()) != null)
+ {
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > 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)
+ {
+ }
+ }
+ runner.interrupt();
+ if (worker != null && worker.exit == null)
+ {
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
+ }
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "allInputOperationsData")
+ public void testAllInputOperations(String expectedString,
+ String failureMsg)
+ {
+ Assert.assertTrue(successfulCMDs.contains(expectedString),
+ failureMsg + "; was expecting '" + expectedString + "'");
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ 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 '" + fileName
+ + "'. [" + cmd + "]";
+ 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 "
+ + timeout + "ms). [" + harg + "]");
+ }
+ file.delete();
+ }
+
+ @Test(
+ groups =
+ { "Functional", "testTask1" },
+ dataProvider = "headlessModeOutputToStdout")
+ public void testHeadlessModeOutputToStdout(String args,
+ String comparisonFile, int timeout)
+ {
+ String cmd = args;
+ File file = new File(comparisonFile);
+ Worker worker = getJalviewDesktopRunner(true, cmd, timeout, false);
+ int b = -1;
+ StringBuilder sb = new StringBuilder();
+ try
+ {
+ while ((b = worker.getOutputReader().read()) != -1)
+ {
+ sb.append(Character.toChars(b));
+ }
+ } catch (IOException e)
+ {
+ Assert.fail("IOException whilst trying to read from jalview process");
+ }
+
+ String comparisonContent = null;
+ try
+ {
+ comparisonContent = new String(Files.readAllBytes(file.toPath()));
+ } catch (IOException e)
+ {
+ Assert.fail("IOException whilst trying to read comparison file");
+ }
+
+ Assert.assertEquals(sb.toString(), comparisonContent,
+ "STDOUT from jalview command did not match the comparison file");
+ }
+
+ @DataProvider(name = "allInputOperationsData")
+ public Object[][] getHeadlessModeInputParams()
+ {
+ return new Object[][] {
+ // headless mode input operations
+ { "[TESTOUTPUT] arg --colour='zappo' was set",
+ "Failed setting arg --colour" },
+ { "[TESTOUTPUT] arg --props='test/jalview/bin/testProps.jvprops' was set",
+ "Failed setting arg --props" },
+ { "[TESTOUTPUT] arg --sortbytree was set",
+ "Failed setting arg --sortbytree" },
+ { "[TESTOUTPUT] arg --jabaws='http://www.compbio.dundee.ac.uk/jabaws' was set",
+ "Failed setting arg --jabaws" },
+ { "[TESTOUTPUT] arg --open='examples/uniref50.fa' was set",
+ "Failed setting arg --open" },
+ { "[TESTOUTPUT] arg --features='examples/testdata/plantfdx.features' was set",
+ "Failed setting arg --features" },
+ { "[TESTOUTPUT] arg --annotations='examples/testdata/plantfdx.annotations' was set",
+ "Failed setting arg --annotations" },
+ { "[TESTOUTPUT] arg --tree='examples/testdata/uniref50_test_tree' was set",
+ "Failed setting arg --tree" },
+ // non headless mode input operations
+ { "[TESTOUTPUT] arg --nousagestats was set",
+ "Failed setting arg --nousagestats" },
+ { "[TESTOUTPUT] arg --noquestionnaire was set",
+ "Failed setting arg --noquestionnaire" }
+ //
+ };
+ }
+
+ @DataProvider(name = "headlessModeOutputOperationsData")
+ public static Object[][] getHeadlessModeOutputParams()
+ {
+ // JBPNote: I'm not clear why need to specify full path for output file
+ // when running tests on build server, but we will keep this patch for now
+ // 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[][] {
+ //
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --image",
+ workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ { "--headless --open examples/uniref50.fa", " --output",
+ workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+ TEST_TIMEOUT },
+ //
+ };
+ }
+
+ @DataProvider(name = "headlessModeOutputToStdout")
+ public static Object[][] getHeadlessModeOutputToStdout()
+ {
+ // JBPNote: I'm not clear why need to specify full path for output file
+ // when running tests on build server, but we will keep this patch for now
+ // 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[][] {
+ //
+ { "--open=examples/uniref50.fa --output=-",
+ workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+ { "--open examples/uniref50.fa --output -",
+ workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+ { "--open examples/uniref50.fa --output=[format=blc]-",
+ workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+ { "--open examples/uniref50.fa --output - --format blc",
+ workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+ { "./examples/uniref50.fa --output=-",
+ workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+ { "./examples/uniref50.fa --output - --format blc",
+ workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+ // remember you can't use shell wildcards for filenames in a test
+ { "./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -",
+ workingDir + "/test1-3.fa", TEST_TIMEOUT },
+ // but you can use java wildcards when using an equals sign
+ { "--open=./test/jalview/bin/argparser/testfiles/test*.fa --all --output -",
+ workingDir + "/test1-3.fa", TEST_TIMEOUT },
+ //
+ };
+ }
+}
git://source.jalview.org / jalview.git / blobdiff