X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=3855dc70192cea743d9320a9919ab24fd3786a29;hb=aabbea350930b8c2904e4f1544f0d786e7d59792;hp=c7b1d53c9c5225939abfcba19d738c5281a33dcf;hpb=fe89eb16394e69db5448f386de6402850286418b;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index c7b1d53..3855dc7 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -23,23 +23,24 @@ 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.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; +import jalview.gui.JvOptionPane; public class CommandLineOperations { @@ -51,11 +52,10 @@ public class CommandLineOperations JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - private static final int TEST_TIMEOUT = 9000; // Note longer timeout needed on - // full test run than on - // individual tests + // Note longer timeout needed on full test run than on individual tests + private static final int TEST_TIMEOUT = 15000; - private static final int SETUP_TIMEOUT = 9000; + private static final int SETUP_TIMEOUT = 9500; private static final int MINFILESIZE_SMALL = 2096; @@ -71,7 +71,7 @@ public class CommandLineOperations * @author jimp * */ - private static class Worker extends Thread + public static class Worker extends Thread { private final Process process; @@ -123,6 +123,10 @@ public class CommandLineOperations private static String classpath = null; + private static String modules = null; + + private static String java_exe = null; + public synchronized static String getClassPath() { if (scanner == null) @@ -130,6 +134,14 @@ public class CommandLineOperations 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) { @@ -144,15 +156,18 @@ public class CommandLineOperations return classpath; } - private Worker getJalviewDesktopRunner(boolean withAwt, String cmd, + public static 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 "; + String _cmd = java_exe + " " + + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath " + + classpath + + (modules.length() > 2 ? "--add-modules=\"" + modules + "\"" + : "") + + " jalview.bin.Jalview "; Process ls2_proc = null; Worker worker = null; try @@ -168,7 +183,7 @@ public class CommandLineOperations new InputStreamReader(ls2_proc.getInputStream())); BufferedReader errorReader = new BufferedReader( new InputStreamReader(ls2_proc.getErrorStream())); - worker = new Worker(ls2_proc); + worker = new CommandLineOperations.Worker(ls2_proc); worker.start(); try { @@ -183,48 +198,109 @@ public class CommandLineOperations return worker; } - @BeforeTest(alwaysRun = true) + @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(); + } + } + + @BeforeClass(alwaysRun = true) public void initialize() { new CommandLineOperations(); } - @BeforeTest(alwaysRun = true) + @BeforeClass(alwaysRun = true) public void setUpForHeadlessCommandLineInputOperations() throws IOException { - String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo " + String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/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); + System.out.println("STDOUT: " + ln); successfulCMDs.add(ln); } while ((ln = worker.getErrorReader().readLine()) != null) { - System.err.println(ln); + System.err.println("STDERR: " + ln); + successfulCMDs.add(ln); } } - @BeforeTest(alwaysRun = true) + @BeforeClass(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) + 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 STDOUT_SETUPLINES = 50; + 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() { - System.out.println(ln); - successfulCMDs.add(ln); - if (++count > 5) + @Override + public void run() + { + String ln = null; + int stdoutcount = 0; + int stderrcount = 0; + try + { + while ((ln = worker.getOutputReader().readLine()) != null) + { + System.out.println(ln); + successfulCMDs.add(ln); + if (++stdoutcount > STDOUT_SETUPLINES) + { + break; + } + } + while ((ln = worker.getErrorReader().readLine()) != null) + { + System.err.println(ln); + successfulCMDs.add(ln); + if (++stderrcount > 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) { - break; } } + runner.interrupt(); if (worker != null && worker.exit == null) { worker.interrupt(); @@ -241,7 +317,8 @@ public class CommandLineOperations } @Test( - groups = { "Functional" }, + groups = + { "Functional" }, dataProvider = "headlessModeOutputOperationsData") public void testHeadlessModeOutputOperations(String harg, String type, String fileName, boolean withAWT, int expectedMinFileSize, @@ -262,11 +339,9 @@ public class CommandLineOperations worker.interrupt(); Thread.currentThread().interrupt(); worker.process.destroy(); - Assert.fail("Jalview did not exit after " - + type + Assert.fail("Jalview did not exit after " + type + " generation (try running test again to verify - timeout at " - + SETUP_TIMEOUT + "ms). [" - + harg + "]"); + + timeout + "ms). [" + harg + "]"); } file.delete(); } @@ -276,9 +351,9 @@ public class CommandLineOperations { 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!", + { "CMD [-colour zappo] executed successfully!", + "Failed command : -colour zappo" }, + { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!", "Failed command : -props File" }, { "CMD [-sortbytree] executed successfully!", "Failed command : -sortbytree" }, @@ -304,54 +379,62 @@ public class CommandLineOperations @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[][] { + // { "nodisplay -open examples/uniref50.fa", " -eps", - "test/jalview/bin/test_uniref50_out.eps", true, MINFILESIZE_BIG, + workingDir + "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 }, + workingDir + "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, + workingDir + "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 }, + workingDir + "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, + workingDir + "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 }, + workingDir + "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, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, + workingDir + "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 }, }; + workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, + TEST_TIMEOUT }, + // + }; } }