<commit_before>package cz.cuni.mff.odcleanstore.crbatch;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;

import org.simpleframework.xml.core.PersistenceException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;

import cz.cuni.mff.odcleanstore.configuration.ConflictResolutionConfig;
import cz.cuni.mff.odcleanstore.conflictresolution.AggregationSpec;
import cz.cuni.mff.odcleanstore.conflictresolution.CRQuad;
import cz.cuni.mff.odcleanstore.conflictresolution.ConflictResolver;
import cz.cuni.mff.odcleanstore.conflictresolution.ConflictResolverFactory;
import cz.cuni.mff.odcleanstore.conflictresolution.NamedGraphMetadataMap;
import cz.cuni.mff.odcleanstore.conflictresolution.exceptions.ConflictResolutionException;
import cz.cuni.mff.odcleanstore.crbatch.config.Config;
import cz.cuni.mff.odcleanstore.crbatch.config.ConfigReader;
import cz.cuni.mff.odcleanstore.crbatch.config.Output;
import cz.cuni.mff.odcleanstore.crbatch.config.QueryConfig;
import cz.cuni.mff.odcleanstore.crbatch.exceptions.CRBatchException;
import cz.cuni.mff.odcleanstore.crbatch.exceptions.InvalidInputException;
import cz.cuni.mff.odcleanstore.crbatch.io.CloseableRDFWriter;
import cz.cuni.mff.odcleanstore.crbatch.io.IncrementalN3Writer;
import cz.cuni.mff.odcleanstore.crbatch.io.IncrementalRdfXmlWriter;
import cz.cuni.mff.odcleanstore.crbatch.loaders.NamedGraphLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.QuadLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.SameAsLinkLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.TripleSubjectsLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.TripleSubjectsLoader.SubjectsIterator;
import cz.cuni.mff.odcleanstore.crbatch.urimapping.AlternativeURINavigator;
import cz.cuni.mff.odcleanstore.crbatch.urimapping.URIMappingIterable;
import cz.cuni.mff.odcleanstore.shared.ODCSUtils;
import cz.cuni.mff.odcleanstore.vocabulary.ODCSInternal;
import de.fuberlin.wiwiss.ng4j.Quad;

/**
 * The main entry point of the application.
 * @author <NAME>
 */
public final class Application {
    private static final Logger LOG = LoggerFactory.getLogger(Application.class);

    private static String getUsage() {
        return "Usage:\n java -jar odcs-cr-batch-<version>.jar <config file>.xml";
    }

    /**
     * Main application entry point.
     * @param args command line arguments
     */
    public static void main(String[] args) {
        if (args == null || args.length < 1) {
            System.err.println(getUsage());
            return;
        }
        File configFile = new File(args[0]);
        if (!configFile.isFile() || !configFile.canRead()) {
            System.err.println("Cannot read the given config file.\n");
            System.err.println(getUsage());
            return;
        }

        Config config = null;
        try {
            config = ConfigReader.parseConfigXml(configFile);
        } catch (InvalidInputException e) {
            System.err.println("Error in config file:");
            System.err.println("  " + e.getMessage());
            if (e.getCause() instanceof PersistenceException) {
                System.err.println("  " + e.getCause().getMessage());
            }
            return;
        }

        // TODO: check valid input (incl. validity of prefixes)
        
        long startTime = System.currentTimeMillis();
        try {
            executeCRBatch(config);
        } catch (CRBatchException e) {
            System.err.println("Error:");
            System.err.println("  " + e.getMessage());
            if (e.getCause() != null) {
                System.err.println("  " + e.getCause().getMessage());
            }
            return;
        } catch (ConflictResolutionException e) {
            System.err.println("Conflict resolution error:");
            System.err.println("  " + e.getMessage());
            return;
        } catch (IOException e) {
            System.err.println("Error when writing results:");
            System.err.println("  " + e.getMessage());
            return;
        }

        System.out.println("----------------------------");
        System.out.printf("CR-batch executed in {} s\n",
                (System.currentTimeMillis() - startTime) / (double) ODCSUtils.MILLISECONDS);
    }

    /**
     * Performs the actual CR-batch task.
     * @param config global configuration
     * @throws CRBatchException general batch error
     * @throws IOException I/O error when writing results
     * @throws ConflictResolutionException conflict resolution error
     */
    private static void executeCRBatch(Config config) throws CRBatchException, IOException, ConflictResolutionException {
        ConnectionFactory connectionFactory = new ConnectionFactory(config);

        // Load source named graphs metadata<commit_msg>improved output<commit_after>package cz.cuni.mff.odcleanstore.crbatch;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;

import org.simpleframework.xml.core.PersistenceException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.hp.hpl.jena.graph.Node;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;

import cz.cuni.mff.odcleanstore.configuration.ConflictResolutionConfig;
import cz.cuni.mff.odcleanstore.conflictresolution.AggregationSpec;
import cz.cuni.mff.odcleanstore.conflictresolution.CRQuad;
import cz.cuni.mff.odcleanstore.conflictresolution.ConflictResolver;
import cz.cuni.mff.odcleanstore.conflictresolution.ConflictResolverFactory;
import cz.cuni.mff.odcleanstore.conflictresolution.NamedGraphMetadataMap;
import cz.cuni.mff.odcleanstore.conflictresolution.exceptions.ConflictResolutionException;
import cz.cuni.mff.odcleanstore.crbatch.config.Config;
import cz.cuni.mff.odcleanstore.crbatch.config.ConfigReader;
import cz.cuni.mff.odcleanstore.crbatch.config.Output;
import cz.cuni.mff.odcleanstore.crbatch.config.QueryConfig;
import cz.cuni.mff.odcleanstore.crbatch.exceptions.CRBatchException;
import cz.cuni.mff.odcleanstore.crbatch.exceptions.InvalidInputException;
import cz.cuni.mff.odcleanstore.crbatch.io.CloseableRDFWriter;
import cz.cuni.mff.odcleanstore.crbatch.io.IncrementalN3Writer;
import cz.cuni.mff.odcleanstore.crbatch.io.IncrementalRdfXmlWriter;
import cz.cuni.mff.odcleanstore.crbatch.loaders.NamedGraphLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.QuadLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.SameAsLinkLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.TripleSubjectsLoader;
import cz.cuni.mff.odcleanstore.crbatch.loaders.TripleSubjectsLoader.SubjectsIterator;
import cz.cuni.mff.odcleanstore.crbatch.urimapping.AlternativeURINavigator;
import cz.cuni.mff.odcleanstore.crbatch.urimapping.URIMappingIterable;
import cz.cuni.mff.odcleanstore.shared.ODCSUtils;
import cz.cuni.mff.odcleanstore.vocabulary.ODCSInternal;
import de.fuberlin.wiwiss.ng4j.Quad;

/**
 * The main entry point of the application.
 * @author <NAME>
 */
public final class Application {
    private static final Logger LOG = LoggerFactory.getLogger(Application.class);

    private static String getUsage() {
        return "Usage:\n java -jar odcs-cr-batch-<version>.jar <config file>.xml";
    }

    /**
     * Main application entry point.
     * @param args command line arguments
     */
    public static void main(String[] args) {
        if (args == null || args.length < 1) {
            System.err.println(getUsage());
            return;
        }
        File configFile = new File(args[0]);
        if (!configFile.isFile() || !configFile.canRead()) {
            System.err.println("Cannot read the given config file.\n");
            System.err.println(getUsage());
            return;
        }

        Config config = null;
        try {
            config = ConfigReader.parseConfigXml(configFile);
        } catch (InvalidInputException e) {
            System.err.println("Error in config file:");
            System.err.println("  " + e.getMessage());
            if (e.getCause() instanceof PersistenceException) {
                System.err.println("  " + e.getCause().getMessage());
            }
            return;
        }

        // TODO: check valid input (incl. validity of prefixes)
        
        long startTime = System.currentTimeMillis();
        System.out.println("Starting conflict resolution batch, this may take a while... \n");
        
        try {
            executeCRBatch(config);
        } catch (CRBatchException e) {
            System.err.println("Error:");
            System.err.println("  " + e.getMessage());
            if (e.getCause() != null) {
                System.err.println("  " + e.getCause().getMessage());
            }
            return;
        } catch (ConflictResolutionException e) {
            System.err.println("Conflict resolution error:");
            System.err.println("  " + e.getMessage());
            return;
        } catch (IOException e) {
            System.err.println("Error when writing results:");
            System.err.println("  " + e.getMessage());
            return;
        }

        System.out.println("----------------------------");
        System.out.printf("CR-batch executed in %.3f s\n",
                (System.currentTimeMillis() - startTime) / (double) ODCSUtils.MILLISECONDS);
    }

    /**
     * Performs the actual CR-batch task.
     * @param config global configuration
     * @throws CRBatchException general batch error
     * @throws IOException I/O error when writing results
     * @throws ConflictResolutionException conflict resolution error
     */
    private static void executeCRBatch(Config config) throws CRBatchException, IOException, ConflictResolutionException {
        ConnectionFactory connectionFactory = new ConnectionFactory(config);

        // Load source named graphs metadata
{'fraction_non_alphanumeric': 0.11634137007271336, 'fraction_numerical': 0.0012437810945273632, 'mean_word_length': 3.1414421553090333, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 4}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6201830', 'n_tokens_mistral': 3143, 'n_tokens_neox': 3100, 'n_words': 557}