Examples with XMLProducer beast.util.XMLProducer used on opensource projects

Example 11 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class XMLProducerTest method testObjectWithoutID.

// test_XmlExamples
@Test
public void testObjectWithoutID() {
    BEASTInterface o = new Nucleotide();
    XMLProducer producer = new XMLProducer();
    System.out.println(producer.toXML(o));
}

Example 12 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class XMLProducerTest method test_ThatXmlExamplesProduces.

/**
 * parse all XML files in the given directory, then produce XML from it, and see if the produced XML still parses *
 */
public void test_ThatXmlExamplesProduces(String dir, List<String> exceptions) {
    try {
        Randomizer.setSeed(127);
        Logger.FILE_MODE = Logger.LogFileMode.overwrite;
        System.out.println("Test XML Examples in " + dir);
        File exampleDir = new File(dir);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".xml");
            }
        });
        List<String> failedFiles = new ArrayList<String>();
        for (String fileName : exampleFiles) {
            if (exceptions.contains(fileName)) {
                System.out.println("Skipping exception " + fileName);
            } else {
                System.out.println("Processing " + fileName);
                XMLProducer producer = new XMLProducer();
                BEASTInterface o = null;
                try {
                    o = producer.parseFile(new File(dir + "/" + fileName));
                } catch (Exception e) {
                    o = null;
                }
                if (o != null) {
                    String xml = producer.toXML(o);
                    // FileWriter outfile = new FileWriter(new File("/tmp/XMLProducerTest.xml"));
                    // outfile.write(xml);
                    // outfile.close();
                    XMLParser parser2 = new XMLParser();
                    try {
                        parser2.parseFragment(xml, false);
                    } catch (Exception e) {
                        System.out.println("test_ThatXmlExamplesProduces::Failed for " + fileName + ": " + e.getMessage());
                        failedFiles.add(fileName);
                    }
                }
                System.out.println("Done " + fileName);
            }
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatXmlExamplesProduces::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("\ntest_ThatXmlExamplesProduces::Success");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
    }
}

Example 13 with XMLProducer

use of beast.util.XMLProducer in project beast2 by CompEvol.

the class XMLTest method testAnnotatedConstructor2.

@Test
public void testAnnotatedConstructor2() throws Exception {
    List<Taxon> taxa = new ArrayList<>();
    taxa.add(new Taxon("first one"));
    taxa.add(new Taxon("second one"));
    AnnotatedRunnableTestClass t = new AnnotatedRunnableTestClass(3, taxa);
    XMLProducer producer = new XMLProducer();
    String xml = producer.toXML(t);
    assertEquals(3, (int) t.getParam1());
    FileWriter outfile = new FileWriter(new File("/tmp/XMLTest.xml"));
    outfile.write(xml);
    outfile.close();
    XMLParser parser = new XMLParser();
    BEASTInterface b = parser.parseFile(new File("/tmp/XMLTest.xml"));
    assertEquals(3, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
}