+ 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 "
+ + timeout + "ms). [" + harg + "]");
+ }
+ file.delete();
+ }
+
+ @DataProvider(name = "allInputOperationsData")
+ public Object[][] getHeadlessModeInputParams()
+ {
+ return new Object[][] {
+ // headless mode input operations
+ { "CMD [-color zappo] executed successfully!",
+ "Failed command : -color zappo" },
+ { "CMD [-props test/jalview/bin/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!",
+ "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 [-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" } };
+ }
+
+ @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", workingDir + "test_uniref50_out.eps", true,
+ MINFILESIZE_BIG, TEST_TIMEOUT, null },