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

Example 1 with JSONParser

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

the class ExampleJSONParsingTest method test_ThatJSONExamplesRun.

public void test_ThatJSONExamplesRun(String dir) {
    try {
        Logger.FILE_MODE = Logger.LogFileMode.overwrite;
        System.out.println("Test that JSON Examples run in " + dir);
        File exampleDir = new File(dir);
        String[] exampleFiles = exampleDir.list(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.endsWith(".json");
            }
        });
        List<String> failedFiles = new ArrayList<String>();
        int seed = 127;
        for (String fileName : exampleFiles) {
            Randomizer.setSeed(seed);
            // need more than one to prevent trouble with multiMCMC logs
            seed += 10;
            System.out.println("Processing " + fileName);
            JSONParser parser = new JSONParser();
            try {
                beast.core.Runnable runable = parser.parseFile(new File(dir + "/" + fileName));
                if (runable instanceof MCMC) {
                    MCMC mcmc = (MCMC) runable;
                    mcmc.setInputValue("preBurnin", 0);
                    mcmc.setInputValue("chainLength", 1000l);
                    mcmc.run();
                }
            } catch (Exception e) {
                System.out.println("ExampleJSONParsing::Failed for " + fileName + ": " + e.getMessage());
                failedFiles.add(fileName);
            }
            System.out.println("Done " + fileName);
        }
        if (failedFiles.size() > 0) {
            System.out.println("\ntest_ThatJSONExamplesRun::Failed for : " + failedFiles.toString());
        } else {
            System.out.println("SUCCESS!!!");
        }
        assertTrue(failedFiles.toString(), failedFiles.size() == 0);
    } catch (Exception e) {
        System.out.println("exception thrown ");
        System.out.println(e.getMessage());
        ;
    }
}

Example 2 with JSONParser

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

the class BeastMCMC method parseArgs.

/**
 * parse command line arguments, and load file if specified
 * @throws IOException
 * @throws JSONException
 * @throws JSONParserException
 */
public void parseArgs(String[] args) throws IOException, XMLParserException, JSONException {
    int i = 0;
    boolean resume = false;
    boolean useStrictVersions = false;
    Map<String, String> parserDefinitions = new HashMap<>();
    File beastFile = null;
    try {
        while (i < args.length) {
            int old = i;
            if (i < args.length) {
                if (args[i].equals("")) {
                    i += 1;
                } else if (args[i].equals("-batch")) {
                    Logger.FILE_MODE = Logger.LogFileMode.only_new_or_exit;
                    i += 1;
                } else if (args[i].equals("-resume")) {
                    resume = true;
                    Logger.FILE_MODE = Logger.LogFileMode.resume;
                    System.setProperty("beast.resume", "true");
                    System.setProperty("beast.debug", "false");
                    i += 1;
                } else if (args[i].equals("-overwrite")) {
                    Logger.FILE_MODE = Logger.LogFileMode.overwrite;
                    i += 1;
                } else if (args[i].equals("-seed")) {
                    if (args[i + 1].equals("random")) {
                        m_nSeed = Randomizer.getSeed();
                    } else {
                        m_nSeed = Long.parseLong(args[i + 1]);
                    }
                    i += 2;
                } else if (args[i].equals("-threads")) {
                    m_nThreads = Integer.parseInt(args[i + 1]);
                    g_exec = Executors.newFixedThreadPool(m_nThreads);
                    i += 2;
                // use BEAST environment variable to set Beast directories as colon separated list
                // } else if (args[i].equals("-beastlib")) {
                // ClassDiscovery.setJarPath(args[i + 1]);
                // i += 2;
                } else if (args[i].equals("-prefix")) {
                    System.setProperty("file.name.prefix", args[i + 1].trim());
                    i += 2;
                } else if (args[i].equals("-D")) {
                    String[] strs = args[i + 1].split(",");
                    for (String str : strs) {
                        String[] strs2 = str.split("=");
                        if (strs2.length != 2) {
                            throw new IllegalArgumentException("Argument \"" + str + "\" is not well-formed: expecting name=value pairs");
                        }
                        String name = strs2[0];
                        String value = strs2[1];
                        parserDefinitions.put(name, value);
                    }
                    i += 2;
                } else if (args[i].equals("-strictversions")) {
                    useStrictVersions = true;
                    i += 1;
                }
                if (i == old) {
                    if (i == args.length - 1) {
                        beastFile = new File(args[i]);
                        i++;
                    } else {
                        throw new IllegalArgumentException("Wrong argument");
                    }
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
        throw new IllegalArgumentException("Error parsing command line arguments: " + Arrays.toString(args) + "\nArguments ignored\n\n" + getUsage());
    }
    if (beastFile == null) {
        // Not resuming so get starting options...
        List<String> MCMCargs = new ArrayList<>();
        Version version = new BEASTVersion2();
        String titleString = "<html><center><p>Bayesian Evolutionary Analysis Sampling Trees<br>" + "Version " + version.getVersionString() + ", " + version.getDateString() + "</p></center></html>";
        javax.swing.Icon icon = IconUtils.getIcon(BeastMain.class, "images/beast.png");
        String nameString = "BEAST " + version.getVersionString();
        BeastDialog dialog = new BeastDialog(new JFrame(), titleString, icon);
        if (!dialog.showDialog(nameString, m_nSeed)) {
            return;
        }
        switch(dialog.getLogginMode()) {
            case 0:
                /* do not ovewrite */
                break;
            case 1:
                MCMCargs.add("-overwrite");
                break;
            case 2:
                MCMCargs.add("-resume");
                break;
        }
        MCMCargs.add("-seed");
        MCMCargs.add(dialog.getSeed() + "");
        if (dialog.getThreadPoolSize() > 0) {
            MCMCargs.add("-threads");
            MCMCargs.add(dialog.getThreadPoolSize() + "");
        }
        boolean useBeagle = dialog.useBeagle();
        boolean beagleShowInfo = false;
        long beagleFlags = 0;
        if (useBeagle) {
            beagleShowInfo = dialog.showBeagleInfo();
            if (dialog.preferBeagleCPU()) {
                beagleFlags |= BeagleFlag.PROCESSOR_CPU.getMask();
            }
            if (dialog.preferBeagleSSE()) {
                beagleFlags |= BeagleFlag.VECTOR_SSE.getMask();
            }
            if (dialog.preferBeagleGPU()) {
                beagleFlags |= BeagleFlag.PROCESSOR_GPU.getMask();
            }
            if (dialog.preferBeagleDouble()) {
                beagleFlags |= BeagleFlag.PRECISION_DOUBLE.getMask();
            }
            if (dialog.preferBeagleSingle()) {
                beagleFlags |= BeagleFlag.PRECISION_SINGLE.getMask();
            }
        }
        if (beagleFlags != 0) {
            System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
        }
        if (!useBeagle) {
            System.setProperty("java.only", "true");
        }
        File inputFile = dialog.getInputFile();
        if (!beagleShowInfo && inputFile == null) {
            System.err.println("No input file specified");
            System.exit(1);
        }
        MCMCargs.add(inputFile.getAbsolutePath());
        // BeastStartDialog dlg = new BeastStartDialog();
        // if (dlg.m_bOK) {
        // parseArgs(dlg.getArgs());
        // }
        parseArgs(MCMCargs.toArray(new String[0]));
        return;
    }
    Log.warning.println("File: " + beastFile.getName() + " seed: " + m_nSeed + " threads: " + m_nThreads);
    if (resume) {
        Log.info.println("Resuming from file");
    }
    if (useStrictVersions) {
        // grab "required" attribute from beast spec
        if (beastFile.getPath().toLowerCase().endsWith(".json")) {
            throw new IllegalArgumentException("The -strictversions flag is not implemented for JSON files yet (only XML files are supported).");
        } else {
            BufferedReader fin = new BufferedReader(new FileReader(beastFile));
            StringBuffer buf = new StringBuffer();
            String str = null;
            int lineCount = 0;
            while (fin.ready() && lineCount < 100) {
                str = fin.readLine();
                buf.append(str);
                buf.append(' ');
            }
            fin.close();
            str = buf.toString();
            int start = str.indexOf("required=");
            if (start < 0) {
                throw new IllegalArgumentException("Could not find a 'required' attribute in the XML. Add the required attribute, or run without the -strictversions flag");
            }
            char c = str.charAt(start + 9);
            start += 10;
            int end = str.indexOf(c, start);
            String packages = str.substring(start, end);
            PackageManager.loadExternalJars(packages);
        }
    } else {
        PackageManager.loadExternalJars();
    }
    // parse xml
    Randomizer.setSeed(m_nSeed);
    if (beastFile.getPath().toLowerCase().endsWith(".json")) {
        m_runnable = new JSONParser(parserDefinitions).parseFile(beastFile);
    } else {
        try {
            m_runnable = new XMLParser(parserDefinitions).parseFile(beastFile);
        } catch (SAXException | ParserConfigurationException e) {
            throw new IllegalArgumentException(e);
        }
    }
    m_runnable.setStateFile(beastFile.getName() + ".state", resume);
}

Example 3 with JSONParser

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

the class JSONTest method testJSONFragmentParsing.

@Test
public void testJSONFragmentParsing() throws Exception {
    JSONParser parser = new JSONParser();
    String json = "{version: \"2.5\",\n" + "\n" + "beast: [\n" + "{spec:\"beast.core.parameter.RealParameter\",\n" + " value:\"2.345\"\n" + "}\n" + "]\n" + "}\n";
    ;
    List<Object> objects = parser.parseFragment(json, true);
    assertEquals(1, objects.size());
    RealParameter p = (RealParameter) objects.get(0);
    assertEquals(2.345, p.getValue(), 1e-13);
}

Example 4 with JSONParser

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

the class JSONTest method testJSONtoXMLtoJSON.

@Test
public void testJSONtoXMLtoJSON() throws Exception {
    JSONParser parser = new JSONParser();
    BEASTObject beastObject = parser.parseFile(new File(JSON_FILE));
    JSONProducer producer = new JSONProducer();
    // .replaceAll("\\s+", " ");
    String actual = producer.toJSON(beastObject).trim();
    // .replaceAll("\\s+", " ");
    String expected = BeautiDoc.load(JSON_FILE).trim();
    assertEquals("Produced JSON differs from original", expected, actual);
}

Example 5 with JSONParser

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

the class JSONTest method testAnnotatedConstructor.

@Test
public void testAnnotatedConstructor() 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);
    JSONProducer producer = new JSONProducer();
    String json = producer.toJSON(t);
    assertEquals(3, (int) t.getParam1());
    FileWriter outfile = new FileWriter(new File("/tmp/JSONTest.json"));
    outfile.write(json);
    outfile.close();
    JSONParser parser = new JSONParser();
    BEASTInterface b = parser.parseFile(new File("/tmp/JSONTest.json"));
    assertEquals(3, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
    // test that default value for param1 comes through
    String json2 = "{version: \"2.5\",\n" + "namespace: \"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\",\n" + "\n" + "beast: [\n" + "\n" + "\n" + "        {id: \"JSONTest\",\n" + "         spec: \"test.beast.util.AnnotatedRunnableTestClass\",\n" + "         taxon: [\n" + "                 {id: \"first one\" },\n" + "                 {id: \"second one\" }\n" + "          ]\n" + "        }\n" + "]\n" + "}";
    outfile = new FileWriter(new File("/tmp/JSONTest2.json"));
    outfile.write(json2);
    outfile.close();
    parser = new JSONParser();
    b = parser.parseFile(new File("/tmp/JSONTest2.json"));
    assertEquals(10, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
    // test that array of doubles comes through in second constructor
    String json3 = "{version: \"2.5\",\n" + "namespace: \"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\",\n" + "\n" + "beast: [\n" + "\n" + "\n" + "        {id: \"JSONTest\",\n" + "         spec: \"test.beast.util.AnnotatedRunnableTestClass\",\n" + "         array: [1.0, 2.0, 3.0]\n" + "        }\n" + "]\n" + "}";
    outfile = new FileWriter(new File("/tmp/JSONTest3.json"));
    outfile.write(json3);
    outfile.close();
    parser = new JSONParser();
    b = parser.parseFile(new File("/tmp/JSONTest3.json"));
    assertEquals(3, ((AnnotatedRunnableTestClass) b).getArray().size());
}