X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=3bfd4f39d6d931c8e58eb1f0ed63cf810951d8ae;hb=efba321f20b819819c0b1cd9c9133d9d1a2ab314;hp=a5067bee5269d4ea18382b21523a7767199d417d;hpb=fc5c76dd3312c6ac928f0057249d13a65ef97b85;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index a5067be..3bfd4f3 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -20,18 +20,9 @@ */ 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; @@ -50,6 +41,7 @@ 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 { @@ -61,12 +53,12 @@ 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; @@ -174,8 +166,8 @@ public class CommandLineOperations // not expanded by the shell String classpath = getClassPath(); String _cmd = java_exe + " " - + (withAwt ? "-Djava.awt.headless=true" : "") - + " -classpath " + classpath + + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath " + + classpath + (modules.length() > 2 ? "--add-modules=\"" + modules + "\"" : "") + " jalview.bin.Jalview "; @@ -233,7 +225,7 @@ 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); @@ -253,18 +245,53 @@ 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 = 30; + + // 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 > 25) + @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(); @@ -282,11 +309,11 @@ public class CommandLineOperations @Test( groups = - { "Functional", "testben" }, + { "Functional" }, dataProvider = "headlessModeOutputOperationsData") public void testHeadlessModeOutputOperations(String harg, String type, String fileName, boolean withAWT, int expectedMinFileSize, - int timeout, String fileFormatType) + int timeout) { String cmd = harg + type + " " + fileName; // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd); @@ -298,25 +325,6 @@ public class CommandLineOperations 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(); @@ -336,7 +344,7 @@ 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" }, @@ -369,51 +377,51 @@ 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, null }, + MINFILESIZE_BIG, TEST_TIMEOUT }, { "nodisplay -open examples/uniref50.fa", " -eps", - workingDir + "test_uniref50_out.eps", false, - MINFILESIZE_BIG, TEST_TIMEOUT, null }, + workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, { "nogui -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, - TEST_TIMEOUT, null }, + TEST_TIMEOUT }, { "nogui -open examples/uniref50.fa", " -eps", - workingDir + "test_uniref50_out.eps", false, - MINFILESIZE_BIG, TEST_TIMEOUT, null }, + workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -eps", workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG, - TEST_TIMEOUT, null }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -svg", - workingDir + "test_uniref50_out.svg", false, - MINFILESIZE_BIG, TEST_TIMEOUT, null }, + workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -png", workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG, - TEST_TIMEOUT, null }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -html", - workingDir + "test_uniref50_out.html", true, - MINFILESIZE_BIG, TEST_TIMEOUT, null }, + workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -fasta", workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.Fasta.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -clustal", workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.Clustal.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -msf", workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.MSF.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pileup", workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.Pileup.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pir", workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.PIR.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -pfam", workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.Pfam.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -blc", workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.BLC.toString() }, + TEST_TIMEOUT }, { "headless -open examples/uniref50.fa", " -jalview", workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, - TEST_TIMEOUT, FileFormat.Jalview.toString() }, }; + TEST_TIMEOUT }, }; } }