X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=b9959dd69d864d5c018a3d38f007aa846e53f4f9;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=98e4eb54297ca74f2197b2e938ee834870bf3296;hpb=05efc2ac3c6427a4dabce842ebbd6f2ae17f49b9;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index 98e4eb5..b9959dd 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -20,12 +20,24 @@ */ 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; @@ -49,12 +61,12 @@ 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 + private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed + // on + // full test run than on + // individual tests - private static final int SETUP_TIMEOUT = 9000; + private static final int SETUP_TIMEOUT = 9500; private static final int MINFILESIZE_SMALL = 2096; @@ -124,6 +136,8 @@ public class CommandLineOperations private static String modules = null; + private static String java_exe = null; + public synchronized static String getClassPath() { if (scanner == null) @@ -136,6 +150,9 @@ public class CommandLineOperations { modules.concat(mr.getName()); } + java_exe = System.getProperty("java.home") + File.separator + "bin" + + File.separator + "java"; + } while (classpath == null) { @@ -156,8 +173,9 @@ public class CommandLineOperations // 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 + String _cmd = java_exe + " " + + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath " + + classpath + (modules.length() > 2 ? "--add-modules=\"" + modules + "\"" : "") + " jalview.bin.Jalview "; @@ -191,6 +209,20 @@ public class CommandLineOperations return worker; } + @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() { @@ -201,7 +233,7 @@ public class CommandLineOperations 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); @@ -221,18 +253,53 @@ public class CommandLineOperations 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 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 count = 0; + try + { + while ((ln = worker.getErrorReader().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) { - break; } } + runner.interrupt(); if (worker != null && worker.exit == null) { worker.interrupt(); @@ -254,7 +321,7 @@ public class CommandLineOperations 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); @@ -262,11 +329,29 @@ public class CommandLineOperations file.deleteOnExit(); Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout); assertNotNull(worker, "worker is null"); - String msg = "Didn't create an output" + type + " file at '" - + file.getAbsolutePath() + "'.[" + harg + "]"; + 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(); @@ -286,7 +371,7 @@ public class CommandLineOperations // headless mode input operations { "CMD [-color zappo] executed successfully!", "Failed command : -color zappo" }, - { "CMD [-props test/jalview/io/testProps.jvprops] executed successfully!", + { "CMD [-props test/jalview/bin/testProps.jvprops] executed successfully!", "Failed command : -props File" }, { "CMD [-sortbytree] executed successfully!", "Failed command : -sortbytree" }, @@ -319,51 +404,51 @@ public class CommandLineOperations String workingDir = "test/jalview/bin/"; return new Object[][] { { "nodisplay -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", true, - MINFILESIZE_BIG, TEST_TIMEOUT }, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "nodisplay -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", false, - MINFILESIZE_BIG, TEST_TIMEOUT }, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "nogui -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, - TEST_TIMEOUT }, + TEST_TIMEOUT, null }, { "nogui -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", false, - MINFILESIZE_BIG, TEST_TIMEOUT }, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, - TEST_TIMEOUT }, + TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -svg", workingDir + "test_uniref50_out.svg", false, - MINFILESIZE_BIG, TEST_TIMEOUT }, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -png", workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG, - TEST_TIMEOUT }, + TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -html", workingDir + "test_uniref50_out.html", true, - MINFILESIZE_BIG, TEST_TIMEOUT }, + MINFILESIZE_BIG, TEST_TIMEOUT, null }, { "headless -open examples/uniref50.fa", " -fasta", workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.Fasta.toString() }, { "headless -open examples/uniref50.fa", " -clustal", workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.Clustal.toString() }, { "headless -open examples/uniref50.fa", " -msf", workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.MSF.toString() }, { "headless -open examples/uniref50.fa", " -pileup", workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.Pileup.toString() }, { "headless -open examples/uniref50.fa", " -pir", workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.PIR.toString() }, { "headless -open examples/uniref50.fa", " -pfam", workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.Pfam.toString() }, { "headless -open examples/uniref50.fa", " -blc", workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, + TEST_TIMEOUT, FileFormat.BLC.toString() }, { "headless -open examples/uniref50.fa", " -jalview", workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, - TEST_TIMEOUT }, }; + TEST_TIMEOUT, FileFormat.Jalview.toString() }, }; } }