X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=a5067bee5269d4ea18382b21523a7767199d417d;hb=fc5c76dd3312c6ac928f0057249d13a65ef97b85;hp=70f60790b9ff0b0c9b13bf208317058e2802489e;hpb=e9c752522f4b0b9ef072e7c1f198f9ec59de957d;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index 70f6079..a5067be 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -20,22 +20,59 @@ */ package jalview.bin; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; + +import jalview.gui.JvOptionPane; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.IdentifyFile; + import java.io.BufferedReader; import java.io.File; import java.io.IOException; import java.io.InputStreamReader; +import java.nio.file.Path; +import java.nio.file.Paths; 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.ModuleRef; +import io.github.classgraph.ScanResult; + public class CommandLineOperations { - private ArrayList successfulCMDs = new ArrayList(); + @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 successfulCMDs = new ArrayList<>(); /*** * from @@ -48,8 +85,11 @@ public class CommandLineOperations private static class Worker extends Thread { private final Process process; + private BufferedReader outputReader; + private BufferedReader errorReader; + private Integer exit; private Worker(Process process) @@ -57,6 +97,7 @@ public class CommandLineOperations this.process = process; } + @Override public void run() { try @@ -89,19 +130,61 @@ public class CommandLineOperations } } - private Worker jalviewDesktopRunner(boolean withAwt, String cmd, + 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) { - String _cmd = "java " + // 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" : "") - + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview "; - System.out.println("CMD [" + cmd + "]"); + + " -classpath " + classpath + + (modules.length() > 2 ? "--add-modules=\"" + modules + "\"" + : "") + + " jalview.bin.Jalview "; Process ls2_proc = null; Worker worker = null; try { ls2_proc = Runtime.getRuntime().exec(_cmd + cmd); - } catch (IOException e1) + } catch (Throwable e1) { e1.printStackTrace(); } @@ -109,7 +192,6 @@ public class CommandLineOperations { BufferedReader outputReader = new BufferedReader( new InputStreamReader(ls2_proc.getInputStream())); - BufferedReader errorReader = new BufferedReader( new InputStreamReader(ls2_proc.getErrorStream())); worker = new Worker(ls2_proc); @@ -119,7 +201,7 @@ public class CommandLineOperations worker.join(timeout); } catch (InterruptedException e) { - // e.printStackTrace(); + System.err.println("Thread interrupted"); } worker.setOutputReader(outputReader); worker.setErrorReader(errorReader); @@ -127,41 +209,58 @@ public class CommandLineOperations return worker; } - @BeforeTest + @Test(groups = { "Functional" }) + 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(); + } + } + + @BeforeTest(alwaysRun = true) public void initialize() { new CommandLineOperations(); } - - @BeforeTest + @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 uniref50_test_features -annotations uniref50_test_annot -tree uniref50_test_tree"; - Worker worker = jalviewDesktopRunner(true, cmds, 9000); + 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 + @BeforeTest(alwaysRun = true) public void setUpForCommandLineInputOperations() throws IOException { String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats"; - Worker worker = jalviewDesktopRunner(false, cmds, 9000); + 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) + if (++count > 25) { break; } @@ -174,115 +273,147 @@ public class CommandLineOperations } } - @Test(groups = - { "Functional" }, dataProvider = "allInputOpearationsData") + @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData") public void testAllInputOperations(String expectedString, String failureMsg) { Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg); } - @Test(groups = - { "Functional" }, dataProvider = "headlessModeOutputOperationsData") + @Test( + groups = + { "Functional", "testben" }, + dataProvider = "headlessModeOutputOperationsData") public void testHeadlessModeOutputOperations(String harg, String type, String fileName, boolean withAWT, int expectedMinFileSize, - int timeout) + int timeout, String fileFormatType) { 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); + 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 (fileFormatType!=null && fileFormatType.length()>0) + { + FileFormatI format = FileFormats.getInstance() + .forName(fileFormatType); + if (format!=null) + { + try + { + FileFormatI exportedType = new IdentifyFile() + .identify(file.getAbsolutePath(), DataSourceType.FILE); + assertEquals(exportedType, format, + "Exported file type was wrong"); + } catch (FileFormatException e) + { + Assert.fail("Couldn't identify file " + file + + " as an alignment format", e); + } + } + } 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 9000ms). [" - + harg + "]"); + Assert.fail("Jalview did not exit after " + type + + " generation (try running test again to verify - timeout at " + + timeout + "ms). [" + harg + "]"); } - new File(fileName).delete(); + file.delete(); } - - @DataProvider(name = "allInputOpearationsData") + @DataProvider(name = "allInputOperationsData") public Object[][] getHeadlessModeInputParams() { - return new Object[][] - { + return new Object[][] { // headless mode input operations { "CMD [-color zappo] executed successfully!", "Failed command : -color zappo" }, - { "CMD [-props FILE] executed successfully!", + { "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!", + { "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 uniref50_test_features] executed successfully!", - "Failed command : -features uniref50_test_features" }, - { "CMD [-annotations uniref50_test_annot] executed successfully!", - "Failed command : -annotations uniref50_test_annot" }, - { "CMD [-tree uniref50_test_tree] executed successfully!", - "Failed command : -tree uniref50_test_tree" }, + { "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" } - }; - + "Failed command : -noquestionnaire" } }; } - + @DataProvider(name = "headlessModeOutputOperationsData") public static Object[][] getHeadlessModeOutputParams() { - return new Object[][] - { - { "nodisplay -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 3000 }, + // 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[][] { { "nodisplay -open examples/uniref50.fa", + " -eps", workingDir + "test_uniref50_out.eps", true, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "nodisplay -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", false, 4096, 3000 }, + workingDir + "test_uniref50_out.eps", false, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "nogui -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 3000 }, + workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, + TEST_TIMEOUT, null }, { "nogui -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", false, 4096, 3000 }, + workingDir + "test_uniref50_out.eps", false, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -eps", - "test_uniref50_out.eps", true, 4096, 3000 }, + workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, + TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -svg", - "test_uniref50_out.svg", false, 4096, 3000 }, + workingDir + "test_uniref50_out.svg", false, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -png", - "test_uniref50_out.png", true, 4096, 3000 }, + workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG, + TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -html", - "test_uniref50_out.html", true, 4096, 3000 }, + workingDir + "test_uniref50_out.html", true, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -fasta", - "test_uniref50_out.mfa", true, 2096, 3000 }, + workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.Fasta.toString() }, { "headless -open examples/uniref50.fa", " -clustal", - "test_uniref50_out.aln", true, 2096, 3000 }, + workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.Clustal.toString() }, { "headless -open examples/uniref50.fa", " -msf", - "test_uniref50_out.msf", true, 2096, 3000 }, + workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.MSF.toString() }, { "headless -open examples/uniref50.fa", " -pileup", - "test_uniref50_out.aln", true, 2096, 3000 }, + workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.Pileup.toString() }, { "headless -open examples/uniref50.fa", " -pir", - "test_uniref50_out.pir", true, 2096, 3000 }, + workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.PIR.toString() }, { "headless -open examples/uniref50.fa", " -pfam", - "test_uniref50_out.pfam", true, 2096, 3000 }, + workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.Pfam.toString() }, { "headless -open examples/uniref50.fa", " -blc", - "test_uniref50_out.blc", true, 2096, 3000 }, + workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.BLC.toString() }, { "headless -open examples/uniref50.fa", " -jalview", - "test_uniref50_out.jvp", true, 2096, 3000 }, - }; + workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, + TEST_TIMEOUT, FileFormat.Jalview.toString() }, }; } }