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• Anno4j.java

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package com.github.anno4j;

import com.github.anno4j.annotations.Evaluator;
import com.github.anno4j.annotations.Partial;
import com.github.anno4j.model.impl.ResourceObject;
import com.github.anno4j.querying.QueryService;
import com.github.anno4j.querying.evaluation.LDPathEvaluatorConfiguration;
import com.github.anno4j.querying.extension.QueryEvaluator;
import com.github.anno4j.querying.extension.TestEvaluator;
import org.apache.commons.lang3.ClassUtils;
import org.apache.http.annotation.NotThreadSafe;
import org.apache.marmotta.ldpath.api.functions.SelectorFunction;
import org.apache.marmotta.ldpath.api.functions.TestFunction;
import org.apache.marmotta.ldpath.api.selectors.NodeSelector;
import org.apache.marmotta.ldpath.api.tests.NodeTest;
import org.openrdf.idGenerator.IDGenerator;
import org.openrdf.idGenerator.IDGeneratorAnno4jURN;
import org.openrdf.model.Resource;
import org.openrdf.model.URI;
import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryException;
import org.openrdf.repository.config.RepositoryConfigException;
import org.openrdf.repository.object.ObjectConnection;
import org.openrdf.repository.object.ObjectRepository;
import org.openrdf.repository.object.config.ObjectRepositoryConfig;
import org.openrdf.repository.object.config.ObjectRepositoryFactory;
import org.openrdf.repository.sail.SailRepository;
import org.openrdf.sail.memory.MemoryStore;
import org.reflections.Reflections;
import org.reflections.scanners.SubTypesScanner;
import org.reflections.scanners.TypeAnnotationsScanner;
import org.reflections.util.ClasspathHelper;
import org.reflections.util.ConfigurationBuilder;
import org.reflections.util.FilterBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.net.URL;
import java.util.*;


/**
 * Read and write API for W3C Web Annotation Data Model (http://www.w3.org/TR/annotation-model/) and W3C Open Annotation Data Model (http://www.openannotation.org/spec/core/).
 * 

 * 

Anno4j can be configured by using the specific setter-methodes (e.g. setIdGenerator, setRepository). A default configuration (in-memory SPARQL endpoint) will be used if no configuration is set.
 * 

 * 

 Anno4j methods are not thread-safe. Use Anno4j transactions in threaded environment.
 */
@NotThreadSafe
public class Anno4j implements TransactionCommands {

    /**
     * Logger of this class.
     */
    private final Logger logger = LoggerFactory.getLogger(Anno4j.class);
    private final URI defaultContext;
    private IDGenerator idGenerator;

    /**
     * Configured openrdf/sesame repository for connecting a local/remote SPARQL endpoint.
     */
    private Repository repository;

    /**
     * Wrapper of the repository field for alibaba, will be updated if a new repository is set.
     */
    private ObjectRepository objectRepository;

    /**
     * Wrapper to store the evaluators for the different LDPath components
     */
    private LDPathEvaluatorConfiguration evaluatorConfiguration = new LDPathEvaluatorConfiguration();

    /**
     * Stores alls partial implementations of the defined interfaces, such as the ResourceObject or the
     * Annotation interface.
     */
    private Set> partialClasses;


    public Anno4j() throws RepositoryException, RepositoryConfigException {
        this(new SailRepository(new MemoryStore()));
    }

    public Anno4j(URI defaultContext) throws RepositoryException, RepositoryConfigException {
        this(new SailRepository(new MemoryStore()), defaultContext);
    }

    public Anno4j(IDGenerator idGenerator) throws RepositoryException, RepositoryConfigException {
        this(new SailRepository(new MemoryStore()), idGenerator, null);
    }

    public Anno4j(IDGenerator idGenerator, URI defaultContext) throws RepositoryException, RepositoryConfigException {
        this(new SailRepository(new MemoryStore()), idGenerator, defaultContext);
    }

    public Anno4j(Repository repository) throws RepositoryException, RepositoryConfigException {
        this(repository, new IDGeneratorAnno4jURN(), null);
    }

    public Anno4j(Repository repository, IDGenerator idGenerator) throws RepositoryException, RepositoryConfigException {
        this(repository, idGenerator, null);
    }

    public Anno4j(Repository repository, URI defaultContext) throws RepositoryException, RepositoryConfigException {
        this(repository, new IDGeneratorAnno4jURN(), defaultContext);
    }

    public Anno4j(Repository repository, IDGenerator idGenerator, URI defaultContext) throws RepositoryConfigException, RepositoryException {
        this.idGenerator = idGenerator;
        this.defaultContext = defaultContext;

        Set classpath = new HashSet<>();
        classpath.addAll(ClasspathHelper.forClassLoader());
        classpath.addAll(ClasspathHelper.forJavaClassPath());
        classpath.addAll(ClasspathHelper.forManifest());
        classpath.addAll(ClasspathHelper.forPackage(""));

        Reflections annotatedClasses = new Reflections(new ConfigurationBuilder()
                .setUrls(classpath)
                .useParallelExecutor()
                .filterInputsBy(FilterBuilder.parsePackages("-java, -javax, -sun, -com.sun"))
                .setScanners(new SubTypesScanner(), new TypeAnnotationsScanner()));

        // Bugfix: Searching for Reflections creates a lot ot Threads, that are not closed at the end by themselves,
        // so we close them manually.
        annotatedClasses.getConfiguration().getExecutorService().shutdown();

        // find classes with @Partial annotation
        this.partialClasses = annotatedClasses.getTypesAnnotatedWith(Partial.class, true);

        scanForEvaluators(annotatedClasses);

        if(!repository.isInitialized()) {
            repository.initialize();
        }

        this.setRepository(repository);
    }
    
    private void scanForEvaluators(Reflections annotatedClasses) {
        Set> defaultEvaluatorAnnotations = annotatedClasses.getTypesAnnotatedWith(Evaluator.class, true);

        Map, Class> testFunctionEvaluators = new HashMap<>();
        Map, Class> defaultEvaluators = new HashMap<>();
        Map, Class> testEvaluators = new HashMap<>();
        Map, Class> functionEvaluators = new HashMap<>();

        for (Class clazz : defaultEvaluatorAnnotations) {
            Evaluator evaluator = (Evaluator) clazz.getAnnotation(Evaluator.class);

            Class[] functionClasses = evaluator.value();

            for(Class functionClass : functionClasses) {
                if (ClassUtils.isAssignable(functionClass, TestFunction.class)) {
                    logger.debug("Found evaluator {} for TestFunction {}", clazz.getCanonicalName(), functionClass.getCanonicalName());
                    testFunctionEvaluators.put((Class) functionClass, clazz);
                } else if (ClassUtils.isAssignable(functionClass, NodeTest.class)) {
                    logger.debug("Found evaluator {} for NodeTest {}", clazz.getCanonicalName(), functionClass.getCanonicalName());
                    testEvaluators.put((Class) functionClass, clazz);
                } else if (ClassUtils.isAssignable(functionClass, SelectorFunction.class)) {
                    logger.debug("Found evaluator {} for NodeFunction {}", clazz.getCanonicalName(), functionClass.getCanonicalName());
                    functionEvaluators.put((Class) functionClass, clazz);
                } else {
                    logger.debug("Found evaluator {} for NodeSelector {}", clazz.getCanonicalName(), functionClass.getCanonicalName());
                    defaultEvaluators.put((Class) functionClass, clazz);
                }
            }
        }

        evaluatorConfiguration.setDefaultEvaluators(defaultEvaluators);
        evaluatorConfiguration.setTestEvaluators(testEvaluators);
        evaluatorConfiguration.setTestFunctionEvaluators(testFunctionEvaluators);
        evaluatorConfiguration.setFunctionEvaluators(functionEvaluators);
    }

    private ObjectConnection createObjectConnection(URI context) throws RepositoryException {
        ObjectConnection connection = objectRepository.getConnection();

        if(context != null) {
            connection.setReadContexts(context);
            connection.setInsertContext(context);
            connection.setRemoveContexts(context);
        } else if (defaultContext != null) {
            connection.setReadContexts(defaultContext);
            connection.setInsertContext(defaultContext);
            connection.setRemoveContexts(defaultContext);
        }

       return connection;
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public void persist(ResourceObject resource) throws RepositoryException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }

        transaction.persist(resource);
    }

    /**
     * Writes the resource object to the configured SPARQL endpoint with a corresponding INSERT query.
     * @param resource resource object to write to the SPARQL endpoint
     * @param context Graph context to query
     * @throws RepositoryException
     */
    public void persist(ResourceObject resource, URI context) throws RepositoryException {
        Transaction transaction = createTransaction();
        transaction.setAllContexts(context);
        transaction.persist(resource);
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public  T findByID(Class type, String id) throws RepositoryException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }

        return transaction.findByID(type, id);
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public  T findByID(Class type, URI id) throws RepositoryException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }
        return transaction.findByID(type, id);
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public void clearContext(URI context) throws RepositoryException {
        Transaction transaction = createTransaction();
        transaction.clearContext(context);
        transaction.close();
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public void clearContext(String context) throws RepositoryException {
        Transaction transaction = createTransaction();
        transaction.clearContext(context);
        transaction.close();
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public  List findAll(Class type) throws RepositoryException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }

        return transaction.findAll(type);
    }

    public  List findAll(Class type, URI context) throws RepositoryException {
        Transaction transaction = createTransaction();
        transaction.setAllContexts(context);

        return transaction.findAll(type);
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public  T createObject(Class clazz) throws RepositoryException, IllegalAccessException, InstantiationException {
        return createObject(clazz, null);
    }

    @Override
    public  T createObject(Class clazz, Resource id) throws RepositoryException, IllegalAccessException, InstantiationException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }

        return transaction.createObject(clazz, id);
    }

    /**
     * Creates a instance of the given class.
     * @param clazz Class of the instance to create. Can be an annotated interface.
     * @param context The graph context where the triples are inserted into. can be null for default graph.
     * @return A instance of the given class.
     */
    public  T createObject(Class clazz, URI context) throws RepositoryException, IllegalAccessException, InstantiationException {
        return createObject(clazz, context, null);
    }

    public  T createObject(Class clazz, URI context, Resource id) throws RepositoryException, IllegalAccessException, InstantiationException {
        Transaction transaction = createTransaction();
        transaction.setAllContexts(context);

        return transaction.createObject(clazz, id);
    }

    /**
     * {@inheritDoc }
     */
    @Override
    public QueryService createQueryService() throws RepositoryException {
        Transaction transaction = createTransaction();

        if(defaultContext != null) {
            transaction.setAllContexts(defaultContext);
        }

        return transaction.createQueryService();
    }

    /**
     * Create query service
     *
     * @param context context to query
     * @return query service object for specified type
     */
    public QueryService createQueryService(URI context) throws RepositoryException {
        Transaction transaction = createTransaction();
        transaction.setAllContexts(context);
        return transaction.createQueryService();
    }

    /**
     * Getter for the configured Repository instance (Connector for local/remote SPARQL repository).
     *
     * @return configured Repository instance
     */
    public Repository getRepository() {
        return repository;
    }

    /**
     * Configures the Repository (Connector for local/remote SPARQL repository) to use in Anno4j.
     *
     * @param repository Repository to use in Anno4j.
     * @throws RepositoryException
     * @throws RepositoryConfigException
     */
    public void setRepository(Repository repository) throws RepositoryException, RepositoryConfigException {
        this.repository = repository;
        // update alibaba wrapper

        ObjectRepositoryFactory factory = new ObjectRepositoryFactory();
        ObjectRepositoryConfig config = factory.getConfig();

        if(partialClasses != null) {
            for(Class clazz : this.partialClasses){
                config.addBehaviour(clazz);
            }
        }

        this.objectRepository = new ObjectRepositoryFactory().createRepository(config, repository);
        this.objectRepository.setIdGenerator(idGenerator);
    }

    /**
     * Getter for configured ObjectRepository (openrdf/alibaba wrapper for the internal Repository).
     *
     * @return configured ObjectRepository.
     */
    public ObjectRepository getObjectRepository() {
        return objectRepository;
    }

    public IDGenerator getIdGenerator() {
        return idGenerator;
    }

    public void setIdGenerator(IDGenerator idGenerator) {
        this.idGenerator = idGenerator;
        this.objectRepository.setIdGenerator(idGenerator);
    }

    public URI getDefaultContext() {
        return defaultContext;
    }

    public Transaction createTransaction() throws RepositoryException {
        return new Transaction(objectRepository, evaluatorConfiguration);
    }
}