package util;

import java.io.BufferedReader;

import java.io.BufferedWriter;

import java.io.File;

import java.io.FileReader;

import java.io.FileWriter;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Collections;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

/**

 * This class provides disease mapping between DCN and OMIM disease

 * @author zhengc

 *

 */

public class DCNOMIMUMLSIDmap {

    public static Map<String, List<String>> dcnidnamemap = new HashMap<>();

    public static Map<String, String> dcnnameidmap = new HashMap<>();

    public static Map<String, List<String>> omimidnamemap = new HashMap<>();

    public static Map<String, String> omimnameidmap = new HashMap<>();

    private static Map<String, List<String>> DCN_OMIM = new HashMap<>();

    /**

     * Initiates and creates a DCNOMIMUMLSIDmap object

     * @param DCN_disease DCN disease name

     * @param OMIM_dispattern OMIM disease name pattern that equals DCN disease name

     */

    public DCNOMIMUMLSIDmap(String DCN_disease, String OMIM_dispattern) {

        String DCN_id = dcnnameidmap.get(DCN_disease);

        List<String> OMIM_ids = new ArrayList<>();

        for (String dis : omimnameidmap.keySet()) {

            if (dis.contains(OMIM_dispattern)) {

                OMIM_ids.add(omimnameidmap.get(dis));

            }   

        }

        Collections.sort(OMIM_ids);

        DCN_OMIM.put(DCN_id, OMIM_ids);

    }

    /**

     * Creates a DCN name_UMLS mapping

     * @param mapfile a name_UMLS mapping file

     * @throws IOException

     */

    public static void createDCNIdNameMap(String mapfile) throws IOException {

        BufferedReader br = new BufferedReader(new FileReader(mapfile));

        String line = null;

        while((line = br.readLine()) != null){

            String[] parts = line.split("\\|");

            String name = parts[0].toLowerCase();

            String id = parts[1];

            if (!dcnnameidmap.containsKey(name)) {

                dcnnameidmap.put(name, id);

            }

            if (!dcnidnamemap.containsKey(id)) {

                List<String> names = new ArrayList<>();

                names.add(name);

                dcnidnamemap.put(id, names);

            } else {

                dcnidnamemap.get(id).add(name);

            }

        }

        br.close();

    } 

    /**

     * Creates a OMIM name_UMLS mapping

     * @param mapfile a name_UMLS mapping file

     * @throws IOException

     */

    public static void createOMIMIdNameMap(String mapfile) throws IOException {

        BufferedReader br = new BufferedReader(new FileReader(mapfile));

        String line = null;

        while((line = br.readLine()) != null){

            String[] parts = line.split("\\|");

            String name = parts[0].toLowerCase();

            String id = parts[1];

            if (!omimnameidmap.containsKey(name)) {

                omimnameidmap.put(name, id);

            }

            if (!omimidnamemap.containsKey(id)) {

                List<String> names = new ArrayList<>();

                names.add(name);

                omimidnamemap.put(id, names);

            } else {

                omimidnamemap.get(id).add(name);

            }

        }

        br.close();

    } 

    /**

     * Get DCN_OMIM mapping

     * @return DCN_OMIM mapping

     */

    public Map<String, List<String>> getDCNOMIMUMLSIDmap() {

        return DCN_OMIM;

    }

    public static void main(String[] args) throws IOException {

        String dcnmapfile = "/Users/zhengc/workspace/FARES_final/data/FARES/map/term_umls_id_diso";

        String omimmapfile = "/Users/zhengc/workspace/FARES_final/data/OMIM/map/OMIM_umls_id_diso";

        createDCNIdNameMap(dcnmapfile);

        createOMIMIdNameMap(omimmapfile);

        String DCN_dis = "dementia";

        String OMIM_pat = "alzheimer";

        DCNOMIMUMLSIDmap domim = new DCNOMIMUMLSIDmap(DCN_dis, OMIM_pat);

        Map<String, List<String>> dcn_omim = domim.getDCNOMIMUMLSIDmap();

        System.out.println(DCN_dis + ": " + dcnnameidmap.get(DCN_dis));

        String DCN_dis_id = dcnnameidmap.get(DCN_dis);

        List<String> OMIM_ids = dcn_omim.get(DCN_dis_id);

        for (String id : OMIM_ids) {

            List<String> names = omimidnamemap.get(id);

            for (String name : names) {

                System.out.println(name + ": " + id);

            }

        }

    }

}