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Graph I/O library which can be used to load and store graphs
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/* 
 *  Copyright or © or Copr. Ecole des Mines d'Alès (2012-2014) 
 *  
 *  This software is a computer program whose purpose is to provide 
 *  several functionalities for the processing of semantic data 
 *  sources such as ontologies or text corpora.
 *  
 *  This software is governed by the CeCILL  license under French law and
 *  abiding by the rules of distribution of free software.  You can  use, 
 *  modify and/ or redistribute the software under the terms of the CeCILL
 *  license as circulated by CEA, CNRS and INRIA at the following URL
 *  "http://www.cecill.info". 
 * 
 *  As a counterpart to the access to the source code and  rights to copy,
 *  modify and redistribute granted by the license, users are provided only
 *  with a limited warranty  and the software's author,  the holder of the
 *  economic rights,  and the successive licensors  have only  limited
 *  liability. 

 *  In this respect, the user's attention is drawn to the risks associated
 *  with loading,  using,  modifying and/or developing or reproducing the
 *  software by the user in light of its specific status of free software,
 *  that may mean  that it is complicated to manipulate,  and  that  also
 *  therefore means  that it is reserved for developers  and  experienced
 *  professionals having in-depth computer knowledge. Users are therefore
 *  encouraged to load and test the software's suitability as regards their
 *  requirements in conditions enabling the security of their systems and/or 
 *  data to be ensured and,  more generally, to use and operate it in the 
 *  same conditions as regards security. 
 * 
 *  The fact that you are presently reading this means that you have had
 *  knowledge of the CeCILL license and that you accept its terms.
 */
package slib.graph.io.loader;

import java.util.Collection;

import org.openrdf.model.URI;
import org.openrdf.rio.RDFFormat;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import slib.graph.algo.utils.GraphActionExecutor;
import slib.graph.io.conf.GDataConf;
import slib.graph.io.conf.GraphConf;
import slib.graph.io.loader.annot.GraphLoader_TSVannot;
import slib.graph.io.loader.bio.gaf2.GraphLoader_GAF_2;
import slib.graph.io.loader.bio.mesh.GraphLoader_MESH_XML;
import slib.graph.io.loader.bio.obo.GraphLoader_OBO_1_2;
import slib.graph.io.loader.bio.snomedct.GraphLoaderSnomedCT_RF2;
import slib.graph.io.loader.csv.GraphLoader_CSV;
import slib.graph.io.loader.rdf.RDFLoader;
import slib.graph.io.loader.slibformat.GraphLoader_SLIB;
import slib.graph.io.loader.wordnet.GraphLoader_Wordnet;
import slib.graph.io.util.GFormat;
import slib.graph.model.graph.G;
import slib.graph.model.impl.graph.memory.GraphMemory;
import slib.graph.model.impl.repo.GraphRepositoryMemory;
import slib.graph.model.repo.URIFactory;
import slib.graph.model.impl.repo.URIFactoryMemory;
import slib.utils.ex.SLIB_Ex_Critic;
import slib.utils.ex.SLIB_Exception;

/**
 *
 * Graph Loader is a class used to facilitate graph loading.
 *
 * @author Sébastien Harispe 
 */
public class GraphLoaderGeneric {

    public static Logger logger = LoggerFactory.getLogger(GraphLoaderGeneric.class);
    /**
     * The formats currently supported by the generic loader.
     */
    public static GFormat[] supportedFormat = {
        GFormat.OBO, GFormat.GAF2, GFormat.NTRIPLES, GFormat.RDF_XML,
        GFormat.RDF_XML, GFormat.SNOMED_CT_RF2, GFormat.MESH_XML, GFormat.CSV, GFormat.TSV_ANNOT,
        GFormat.WORDNET_DATA
    };

    /**
     * Populate a given graph considering a configuration.
     *
     * @param dataConf the object defining the configuration of the data to load
     * @param g the graph to populate with the data
     * @return the graph which have been populated. The treatment is performed
     * in place, i.e. no extra graph is created and the reference to the graph
     * returned will be the same as the one passed in parameter.
     *
     * @throws SLIB_Exception if an error is encountered during loading.
     */
    public static G populate(GDataConf dataConf, G g) throws SLIB_Exception {

        logger.debug("Populate " + g.getURI() + " based on " + dataConf.getLoc());

        GraphLoader gLoader = getLoader(dataConf);

        gLoader.populate(dataConf, g);

        return g;
    }

    /**
     * Create a graph and register it.
     *
     * @param uri the URI of the graph
     * @return the created graph.
     */
    public static G createGraph(URI uri) {

        logger.debug("Create graph " + uri);

        G g = new GraphMemory(uri);
        GraphRepositoryMemory.getSingleton().registerGraph(g);
        return g;
    }

    /**
     * Build the graph considering the given configuration.
     *
     * @param graphConf the graph configuration
     * @return the graph which as been build form the configuration
     *
     * @throws SLIB_Exception
     */
    public static G load(GraphConf graphConf) throws SLIB_Exception {

        logger.info("Loading Graph " + graphConf.getUri());

        G g = createGraph(graphConf.getUri());

        return load(graphConf, g);
    }

    /**
     * Impact the given graph considering the given configuration. The graph
     * will be populated by the data and actions will be performed on it if any
     * exist.
     *
     *
     * @param graphConf the graph configuration
     * @param g the graph
     * @return the graph which as been build form the configuration
     *
     * @throws SLIB_Exception
     */
    public static G load(GraphConf graphConf, G g) throws SLIB_Exception {

        logger.info("-------------------------------------");
        logger.info(" Loading DATA");
        logger.info("-------------------------------------");
        for (GDataConf dataConf : graphConf.getData()) {
            populate(dataConf, g);
        }

        URIFactory factory = URIFactoryMemory.getSingleton();

        GraphActionExecutor.applyActions(factory, graphConf.getActions(), g);
        return g;
    }

    /**
     * Load the collection of configurations.
     *
     * @param graphConfs the collection of configurations
     *
     * @throws SLIB_Exception
     */
    public static void load(Collection graphConfs) throws SLIB_Exception {

        for (GraphConf conf : graphConfs) {
            load(conf);
        }
    }

    /**
     * Retrieve the loader associated to a specific data configuration.
     *
     * @param data the data configuration
     * @return the corresponding Graph loader if any
     *
     * @throws SLIB_Ex_Critic
     */
    private static GraphLoader getLoader(GDataConf data) throws SLIB_Ex_Critic {

        if (data.getFormat() == GFormat.OBO) {
            return new GraphLoader_OBO_1_2();
        } else if (data.getFormat() == GFormat.GAF2) {
            return new GraphLoader_GAF_2();
        } else if (data.getFormat() == GFormat.RDF_XML) {
            return new RDFLoader(RDFFormat.RDFXML);
        } else if (data.getFormat() == GFormat.NTRIPLES) {
            return new RDFLoader(RDFFormat.NTRIPLES);
        } else if (data.getFormat() == GFormat.TURTLE) {
            return new RDFLoader(RDFFormat.TURTLE);
        } else if (data.getFormat() == GFormat.CSV) {
            return new GraphLoader_CSV();
        } else if (data.getFormat() == GFormat.SNOMED_CT_RF2) {
            return new GraphLoaderSnomedCT_RF2();
        } else if (data.getFormat() == GFormat.SLIB) {
            return new GraphLoader_SLIB();
        } else if (data.getFormat() == GFormat.MESH_XML) {
            return new GraphLoader_MESH_XML();
        } else if (data.getFormat() == GFormat.TSV_ANNOT) {
            return new GraphLoader_TSVannot();
        } else if (data.getFormat() == GFormat.WORDNET_DATA) {
            return new GraphLoader_Wordnet();
        } else {
            throw new SLIB_Ex_Critic("Unknown Graph format " + data.getFormat());
        }
    }

    /**
     * Check if the generic loader support the given format.
     *
     * @param format the format
     * @return true if the format is supported.
     */
    public static boolean supportFormat(String format) {
        for (GFormat f : supportedFormat) {
            if (f.name().equalsIgnoreCase(format)) {
                return true;
            }
        }
        return false;
    }

    /**
     * Access to the set of supported format.
     *
     * @return the list of format which are supported by the generic loader.
     */
    public static GFormat[] getSupportedFormat() {
        return supportedFormat;
    }
}