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/**
 * Copyright CSIRO Australian e-Health Research Centre (http://aehrc.com).
 * All rights reserved. Use is subject to license terms and conditions.
 */
package au.csiro.ontology.importer.rf2;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import au.csiro.ontology.importer.ImportException;
import au.csiro.ontology.snomed.refset.rf2.IModuleDependencyRefset;
import au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRefset;
import au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow;
import au.csiro.ontology.snomed.refset.rf2.ValidationException;

/**
 * Imports RF2 reference sets.
 *
 * @author Alejandro Metke
 *
 */
public class RefsetImporter {

    // Logger
    private final static Logger log = LoggerFactory.getLogger(RefsetImporter.class);

    /**
     * Imports a module dependency reference set from a {@link Set} of
     * {@link InputStream}s. This method closes the {@link InputStream}s after
     * loading the reference sets.
     *
     * @param refsetFiles The input streams.
     * @return
     * @throws ImportException
     */
    public static IModuleDependencyRefset importModuleDependencyRefset(
            Set refsetFiles) throws ImportException {

        Set members = new HashSet();
        for(InputStream refsetFile : refsetFiles) {
            BufferedReader br = null;
            try {
                br = new BufferedReader(new InputStreamReader(refsetFile));
                String line = br.readLine();

                String[] cols = line.split("[\t]");
                assert(cols.length >= 6);

                // Test if it is a module dependency refset
                if (cols.length == 8
                        && cols[6].equals("sourceEffectiveTime")
                        && cols[7].equals("targetEffectiveTime")) {

                    while (null != (line = br.readLine())) {
                        cols = line.split("[\t]");
                        boolean active = cols[2].equals("1");
                        ModuleDependencyRow m =
                                new ModuleDependencyRow(cols[0],
                                        cols[1], active , cols[3], cols[4],
                                        cols[5], cols[6], cols[7]);
                        members.add(m);
                    }
                } else {
                    throw new ImportException("Malformed module dependency reference set with " + cols.length + " columns "+Arrays.asList(cols));
                }
            } catch (IOException e) {
                log.error("Problem reading refset file "+refsetFile, e);
                throw new ImportException("Problem reading refset file ", e);
            } finally {
                if(br != null) {
                    try { br.close(); } catch(Exception e) {}
                }
            }
        }

        try {
            return new ModuleDependencyRefset(members, !Boolean.getBoolean("mdrs.ignoreErrors"));
        } catch (ValidationException e) {
            throw new ImportException("Can not continue import with invalid MDRS", e);
        }
    }

}