X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=b9959dd69d864d5c018a3d38f007aa846e53f4f9;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=d829aae7ab157a977cd1e7e37830d1ca23ab15f5;hpb=7897d440305e772159ac07a504b935b9c58e118f;p=jalview.git diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java index d829aae..b9959dd 100644 --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@ -20,10 +20,17 @@ */ 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; @@ -54,12 +61,12 @@ public class CommandLineOperations JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - private static final int TEST_TIMEOUT = 12500; // 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; @@ -167,8 +174,8 @@ 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 "; @@ -226,7 +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); @@ -248,16 +255,16 @@ public class CommandLineOperations 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; - + 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; @@ -310,11 +317,11 @@ public class CommandLineOperations @Test( groups = - { "Functional" }, + { "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); @@ -326,6 +333,25 @@ 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(); @@ -345,7 +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" }, @@ -378,51 +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() }, }; } }