Main.java

package fr.emse.gitlab.saref;

import static fr.emse.gitlab.saref.CMDConfigurations.ARG_DIRECTORY;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_DIRECTORY_DEFAULT;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_HELP;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_IGNORE_EXAMPLES;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_IGNORE_GIT;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_IGNORE_TERMS;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_INCLUDE_MASTER;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_NO_SITE;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_REMOTE_ONLY;
import static fr.emse.gitlab.saref.CMDConfigurations.ARG_VERBOSE;

import java.awt.Desktop;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.StringWriter;
import java.net.URI;
import java.net.URISyntaxException;
import java.nio.charset.StandardCharsets;
import java.nio.file.FileSystem;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.PathMatcher;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.jena.atlas.io.IndentedWriter;
import org.apache.jena.atlas.web.TypedInputStream;
import org.apache.jena.graph.NodeFactory;
import org.apache.jena.query.Dataset;
import org.apache.jena.query.ReadWrite;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.sparql.core.Var;
import org.apache.jena.sparql.engine.binding.Binding;
import org.apache.jena.sparql.engine.binding.BindingHashMap;
import org.apache.jena.sparql.util.Context;
import org.apache.jena.tdb.TDBFactory;
import org.apache.jena.vocabulary.RDF;
import org.apache.log4j.Layout;
import org.apache.log4j.PatternLayout;
import org.eclipse.jgit.api.Git;
import org.eclipse.jgit.api.errors.CheckoutConflictException;
import org.eclipse.jgit.api.errors.GitAPIException;
import org.eclipse.jgit.api.errors.InvalidRefNameException;
import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
import org.eclipse.jgit.api.errors.RefNotFoundException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import fr.emse.ci.sparqlext.SPARQLExt;
import fr.emse.ci.sparqlext.engine.PlanFactory;
import fr.emse.ci.sparqlext.engine.RootPlan;
import fr.emse.ci.sparqlext.stream.LocationMapperAccept;
import fr.emse.ci.sparqlext.stream.LocatorFileAccept;
import fr.emse.ci.sparqlext.stream.LookUpRequest;
import fr.emse.ci.sparqlext.stream.SPARQLExtStreamManager;
import fr.emse.ci.sparqlext.utils.ContextUtils;
import fr.emse.ci.sparqlext.utils.VarUtils;
import fr.emse.gitlab.saref.entities.git.Repositories;
import fr.emse.gitlab.saref.entities.git.Repository;
import fr.emse.gitlab.saref.entities.git.Version;
import fr.emse.gitlab.saref.entities.tests.TestSuites;
import fr.emse.gitlab.saref.jobs.CheckConfig;
import fr.emse.gitlab.saref.jobs.CheckOWLProfile;
import fr.emse.gitlab.saref.jobs.CheckRepositoryStructure;
import fr.emse.gitlab.saref.jobs.CheckoutJob;
import fr.emse.gitlab.saref.jobs.GeneratePortal;
import fr.emse.gitlab.saref.jobs.ReadExamples;
import fr.emse.gitlab.saref.jobs.ReadOntology;
import fr.emse.gitlab.saref.jobs.ReadRepositories;
import fr.emse.gitlab.saref.utils.TestSuitesAppender;
import fr.emse.gitlab.saref.vocabs.EX;

public class Main {

	static final Logger LOG = LoggerFactory.getLogger(Constants.LOGGER_BASE + ".Main");
	public final static String BASE_DOC = Constants.BASE + "documentation/";
	public static final PathMatcher ttlMatcher = FileSystems.getDefault().getPathMatcher("glob:**/*.ttl");

	private static TestSuites testSuites = new TestSuites("SAREF pipeline");
	private static final Map<String, String> testSuiteNames = new HashMap<>();

	private static File directory;
	private static File target;
	private static SPARQLExtStreamManager streamManager;
	private static boolean openBrowser = true;

	private static Dataset dataset;
	private static Var VAR_TEST_SUITES = VarUtils.allocVar("testsuites");

	static boolean remoteOnly;
	static boolean ignoreGit;
	static boolean includeMaster;
	static boolean generateSite;
	static boolean ignoreTerms;
	static boolean ignoreExamples;
	static boolean verbose;

	public static void main(String[] args) throws IOException, InterruptedException, URISyntaxException, JAXBException,
			ParseException, RefAlreadyExistsException, RefNotFoundException, InvalidRefNameException,
			CheckoutConflictException, GitAPIException {

		CommandLine cl = CMDConfigurations.parseArguments(args);
		if (cl.getOptions().length == 0 || cl.hasOption(ARG_HELP)) {
			CMDConfigurations.displayHelp();
			return;
		}

		String dirName = cl.getOptionValue(ARG_DIRECTORY, ARG_DIRECTORY_DEFAULT);
		directory = new File(dirName).getCanonicalFile();
		if (!directory.isDirectory()) {
			LOG.error("The directory does not exist " + directory);
			System.exit(-1);
		}

		remoteOnly = cl.hasOption(ARG_REMOTE_ONLY);
		ignoreGit = cl.hasOption(ARG_IGNORE_GIT);
		includeMaster = cl.hasOption(ARG_INCLUDE_MASTER);
		generateSite = !cl.hasOption(ARG_NO_SITE);
		ignoreExamples = cl.hasOption(ARG_IGNORE_EXAMPLES);
		ignoreTerms = cl.hasOption(ARG_IGNORE_TERMS);
		verbose = cl.hasOption(ARG_VERBOSE);

		setLogAppenders();
		prepareDirectory();
		streamManager = initializeStreamManager();
		dataset = createFreshDataset();
		LOG.info("Starting pipeline in " + directory);

		Repositories repositories;
		try {
			repositories = new ReadRepositories("Fetching required repositories").readRepositories(directory,
					remoteOnly, ignoreGit, includeMaster);
		} catch (Exception ex) {
			reportAndExit(-1);
			return;
		}

		if (repositories.getDefaultRepository() != null) {
			Repository repository = repositories.getDefaultRepository();
			boolean checkExamples = !ignoreExamples;
			testRepository(repository, checkExamples);
		}
		for (Repository repository : repositories.getNamedRepositories()) {
			boolean checkExamples = !ignoreExamples && remoteOnly;
			testRepository(repository, checkExamples);
		}

		checkOWLProfile();
		new CheckConfig().doJob(dataset, ignoreExamples);

		if (generateSite) {
			new GeneratePortal("Generate static files for the portal", streamManager).doJob(dataset, directory, verbose,
					ignoreExamples, ignoreTerms);
		}

		if (repositories.getDefaultRepository() != null && !ignoreGit) {
			Repository repository = repositories.getDefaultRepository();
			resetCheckout(repository);
		}
		for (Repository repository : repositories.getNamedRepositories()) {
			resetCheckout(repository);
		}

		testSuites.clean();

		reportAndExit((int) -Math.signum(testSuites.getErrors() + testSuites.getFailures()));
	}

	private static void setLogAppenders() throws IOException {
		File logFile = new File(directory, Constants.LOG_FILE_NAME);
		Layout layout = new PatternLayout("%d{mm:ss,SSS} %t %-5p %c:%L - %m%n");
		org.apache.log4j.Logger rootLogger = org.apache.log4j.Logger.getRootLogger();
		rootLogger.addAppender(new org.apache.log4j.RollingFileAppender(layout, logFile.getAbsolutePath(), false));

		org.apache.log4j.Logger loggerBase = org.apache.log4j.Logger.getLogger(Constants.LOGGER_BASE);
		TestSuitesAppender appender = new TestSuitesAppender(testSuites);
		loggerBase.addAppender(appender);
	}

	private static void prepareDirectory() throws IOException {
		target = new File(directory, Constants.TARGET_DIR);
		File site = new File(directory, Constants.SITE_DIR);
		FileUtils.forceMkdir(target);
		if (generateSite) {
			try (Git git = Git.cloneRepository().setURI(Constants.SAREF_PORTAL_STATIC_GIT).setDirectory(site).call()) {
				LOG.info(String.format("Cloning site repository %s", Constants.SAREF_PORTAL_STATIC_GIT));
			} catch (Exception ex) {
				try (Git git = Git.open(site)) {
					git.pull().call();
					LOG.info(String.format("Pulling site repository %s", Constants.SAREF_PORTAL_STATIC_GIT));
				} catch (Exception e) {
					throw new IOException(String.format("Failed to clone or pull site repository %s", Constants.SAREF_PORTAL_STATIC_GIT), e);
				}
			}
		}
	}

	private static Dataset createFreshDataset() throws IOException {
		File datasetDir = new File(directory, Constants.DATASET_DIR);
		FileUtils.forceMkdir(datasetDir);
		dataset = TDBFactory.createDataset(datasetDir.getAbsolutePath());
		dataset.begin(ReadWrite.WRITE);
		dataset.getDefaultModel().removeAll();
		List<String> toRemove = new ArrayList<>();
		Iterator<String> it = dataset.listNames();
		while (it.hasNext()) {
			toRemove.add(it.next());
		}
		for (String name : toRemove) {
			dataset.removeNamedModel(name);
		}
		dataset.addNamedModel(Constants.CONFIG, ModelFactory.createDefaultModel());
		dataset.commit();
		return dataset;
	}

	private static void testRepository(Repository repository, boolean checkExamples) {
		for (Version version : repository.getVersions()) {
			try {
				String versionTestSuiteName = version.toString() + " - testing repository structure";
				new CheckoutJob(versionTestSuiteName).checkoutVersion(version);
				new CheckRepositoryStructure(versionTestSuiteName).check(version);
			} catch (SAREFPipelineException ex) {
				LOG.error("Error while testing repository structure " + version, ex);
				continue;
			}

			try {
				String ontologyTestSuiteName = version.toString() + " - testing ontology file";
				testSuiteNames.put(version.getUri(), ontologyTestSuiteName);
				new ReadOntology(ontologyTestSuiteName).doJob(dataset, version);
			} catch (SAREFPipelineException ex) {
				LOG.error(version.toString() + " Found errors for " + version.toString()
						+ ". This version and all the examples will be ignored.", ex);
				continue;
			}

			if (!checkExamples) {
				continue;
			}
			File examplesDir = new File(version.getRepository().getDirectory(), "examples");
			try {
				for (Iterator<Path> it = Files.walk(examplesDir.toPath()).filter(p -> {
					return ttlMatcher.matches(p);
				}).iterator();it.hasNext();) {
					Path p = it.next();
					Path rel = examplesDir.toPath().relativize(p);
					String iri = version.getResource().getURI() + "example/"
							+ rel.toString().substring(0, rel.toString().length() - 4);
					String exampleTestSuiteName = version.toString() + " testing example " + rel;
					testSuiteNames.put(iri, exampleTestSuiteName);
					File exampleFile = p.toFile();
					try {
						new ReadExamples(exampleTestSuiteName).doJob(dataset, version, iri, exampleFile);
					} catch (SAREFPipelineException ex) {
						LOG.error(version.toString() + " Found errors for example  " + rel
								+ ". This example will be ignored.");
					}
				}
			} catch (Exception ex) {
				LOG.error(version.toString() + " Error while walking through the examples. They will be ignored.", ex);
				continue;
			}
		}
	}

	private static void checkOWLProfile() {
		dataset.begin(ReadWrite.READ);
		Model config = dataset.getNamedModel(Constants.CONFIG);
		for (ResIterator it = config.listResourcesWithProperty(RDF.type, EX.OntologyVersion); it.hasNext();) {
			String ontology = it.next().getURI();
			String testSuiteName = testSuiteNames.get(ontology);
			try {
				new CheckOWLProfile(testSuiteName).doJob(dataset, ontology);
			} catch (SAREFPipelineException ex) {
				LOG.warn("Found errors for ontology " + ontology, ex);
			}
		}
		for (ResIterator it = config.listResourcesWithProperty(RDF.type, EX.Example); it.hasNext();) {
			String ontology = it.next().getURI();
			String testSuiteName = testSuiteNames.get(ontology);
			try {
				new CheckOWLProfile(testSuiteName).doJob(dataset, ontology);
			} catch (SAREFPipelineException ex) {
				LOG.warn("Found errors for example " + ontology, ex);
			}
		}
		dataset.end();
	}

	private static SPARQLExtStreamManager initializeStreamManager() throws IOException, URISyntaxException {
		SPARQLExtStreamManager sm = SPARQLExtStreamManager.makeStreamManager();
		LocationMapperAccept mapper = new LocationMapperAccept();

		// set mapper for saref-pipeline src/documentation directory
		URI uri = Main.class.getClassLoader().getResource("documentation").toURI();
		boolean isJar = uri.getScheme().equals("jar");
		Path dirPath;
		if (isJar) {
			FileSystem fileSystem = FileSystems.newFileSystem(uri, Collections.<String, Object>emptyMap());
			dirPath = fileSystem.getPath("/documentation");
		} else {
			dirPath = Paths.get(uri);
		}
		walk(dirPath, isJar, mapper);
		
		// override with local files in documentation directory
		dirPath = Paths.get(new File(directory, "documentation").toURI());
		walk(dirPath, false, mapper);
		
		sm.setLocationMapper(mapper);
		return sm;
	}
	
	private static void walk(Path dirPath, boolean isJar, LocationMapperAccept mapper) throws IOException {
		Files.walk(dirPath).forEach((p) -> {
			String relativePath = dirPath.relativize(p).toString().replace("\\", "/");
			String fileurl = BASE_DOC + relativePath;
			if(isJar) {
				mapper.addAltEntry(fileurl, p.toString().substring(1));
			} else {
				mapper.addAltEntry(fileurl, p.toString());
			}
		});
	}


	private static void resetCheckout(Repository repository) {
		try (Git git = Git.open(repository.getDirectory())) {
			String currentBranch = repository.getCurrentBranch();
			if (currentBranch != null) {
				git.checkout().setName(currentBranch).call();
			}
		} catch (IOException | GitAPIException ex) {
			LOG.warn("Error while reseting repository " + repository, ex);
		}
	}

	private static void reportAndExit(int code) {
		try {
			File report = new File(target, "report_output.xml");
			JAXBContext jaxbContext = JAXBContext.newInstance(TestSuites.class);

			Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
			jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
			jaxbMarshaller.marshal(testSuites, report);
			final StringWriter sw = new StringWriter();
			jaxbMarshaller.marshal(testSuites, sw);

			if (generateSite) {
				// generate the report.html
				File reportHTML = new File(directory, Constants.SITE_DIR + File.separator + "report.html");
				try (IndentedWriter writer = new IndentedWriter(new FileOutputStream(reportHTML));) {
					Context context = ContextUtils.build(writer).setBase(Constants.BASE).setDebugTemplate(verbose)
							.setStreamManager(streamManager).build();
					BindingHashMap binding = new BindingHashMap();
					binding.add(VAR_TEST_SUITES, NodeFactory.createLiteral(sw.toString()));
					List<Binding> bindings = new ArrayList<>();
					bindings.add(binding);
					String query = IOUtils.toString(
							streamManager
									.open(new LookUpRequest("documentation/report/main.rqg", SPARQLExt.MEDIA_TYPE)),
							StandardCharsets.UTF_8);
					RootPlan reportPlan = PlanFactory.create(query, BASE_DOC);
					reportPlan.execTemplateStream(bindings, context);
				}

				if (openBrowser) {
					if (Desktop.isDesktopSupported() && Desktop.getDesktop().isSupported(Desktop.Action.BROWSE)) {
						Desktop.getDesktop().browse(reportHTML.toURI());
					} else {
						System.out.println("\n\n\nURL to the SAREF pipeline report:\n" + reportHTML.toURI());
					}
				}
			}
		} catch (JAXBException | IOException ex) {
			LOG.error("Exception:", ex);
			ex.printStackTrace();
		}

		System.exit(code);
	}

}