package gov.nih.nlm.nls.metamap;

import com.sun.deploy.util.StringUtils;
import org.json.JSONArray;
import org.json.JSONObject;

import java.sql.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Created by Christine on 7/24/2017.
 */
public class AbstractProcessor {
    // JDBC driver name and database URL
    static final String JDBC_DRIVER = "com.mysql.jdbc.Driver";
    static final String DB_URL = "jdbc:mysql://trec2017.ckdnt5fqmiqn.ap-northeast-2.rds.amazonaws.com:3306/trec2017";

    //  Database credentials
    static final String USER = "trec2017";
    static final String PASS = "kaistknowtrec2017";

    static String serverhost = MetaMapApi.DEFAULT_SERVER_HOST;
    static int serverport = MetaMapApi.DEFAULT_SERVER_PORT; 	// default port
    static int timeout = -1; // use default timeout

    static MetaMapApi api = new MetaMapApiImpl(serverhost,serverport);

    static Connection conn = null;
    static Statement stmt = null;

    static List<String> semanticFilter = Arrays.asList("aapp","acab","amas","antb","bacs","bdsu",
            "bdsy","biof","blor","bpoc","celf","celc","cell","chem","chvf","chvs","clna",
            "clnd","comd","diap","drdd","dsyn","enzy","genf","gngm","hops","horm","imft",
            "lbpr","irda","lbtr","inch","lipd","mbrt","medd","menp","mobd","moft","mosq",
            "neop","nnon","nsba","orch","ortf","patf","phsu","phsf","sbst","sosy","topp",
            "virs","strd","tisu","vita","fndg"
    );

    public static void main(String args[]) throws Exception { //Receives file directory as argument

        //STEP 2: Register JDBC driver
        Class.forName("com.mysql.jdbc.Driver");

        //STEP 3: Open a connection
        System.out.println("Connecting to a selected database...");
        conn = DriverManager.getConnection(DB_URL, USER, PASS);
        System.out.println("Connected database successfully...");

        api.setOptions("-Q 0");
        api.setOptions("--prune 30");

        ArrayList<String> years = new ArrayList<String>(
                Arrays.asList("2010","2011","2012","2013","2014","2015","2016","2017")); //todo: go back to 2009 later

        for(int i=0;i<years.size();i++){
            System.out.println("YEAR :"+years.get(i));
            dbOperations(conn,years.get(i));
        }

        api.disconnect();
    }

    public static void updateTables(Connection conn,ArrayList<String> params1) throws Exception{ //params1 is for clinical_trials_mapped, params2 is for clinical_trials
        // create the java mysql update preparedstatement

        String table_name = "extra_abstracts";
        String id = params1.get(0);
        String mesh_main_topics = params1.get(1);
        String other_topics = params1.get(2);

        String query1 =  "update trec2017.extra_abstracts set mesh_main_topic = ?, other_topic = ? where id = ?;";//updating entries for clinical_trials_mapped

        PreparedStatement preparedStmt1 = conn.prepareStatement(query1);
        preparedStmt1.setString(1, mesh_main_topics);
        preparedStmt1.setString(2, other_topics);
        preparedStmt1.setString(3, id);

        preparedStmt1.executeUpdate();

    }

    public static void dbOperations(Connection con,String year)
            throws SQLException {

        Statement stmt = null;
        String query1 =
                "select * from trec2017.extra_abstracts where year="+year; //retrieving rows

        try {
            stmt = con.createStatement();
            ResultSet rs = stmt.executeQuery(query1);
            while (rs.next()) {

                ArrayList<String> params1 = new ArrayList<String>();

                String id= rs.getString("id");
                System.out.println(id);

                String title = rs.getString("title");
                String abs = rs.getString("abstract");

                //String diseaseCuis = processCondition(title,patient_condition);
                String mesh_main_topics = getCuis(title);
                System.out.println("Mesh Main Topics "+mesh_main_topics);

                String other_topics = getCuis(abs);

                params1.add(id);
                params1.add(mesh_main_topics);
                params1.add(other_topics);
                updateTables(con,params1);
            }

        } catch (SQLException e ) {
            e.printStackTrace();
        } catch (Exception e){
            e.printStackTrace();
        }
//        finally {
        //          if (stmt != null) { stmt.close(); }
        //    }
    }

    public static String getCuis(String title) throws Exception{ //Get the CUI of any disease mentioned in the title and condition
        ArrayList<String> cuis = new ArrayList<String>();

        List<Result> resultList = api.processCitationsFromString(title);

        for(Result result: resultList){
            for (Utterance utterance: result.getUtteranceList()) {
                for (PCM pcm: utterance.getPCMList()) {
                    for (Mapping map : pcm.getMappingList()) {
                        for (Ev mapEv : map.getEvList()) {
                            String cui = mapEv.getConceptId();
                            List<String> semanticTypes = mapEv.getSemanticTypes();
                            int negation = mapEv.getNegationStatus();
                            for(int sem=0; sem<semanticTypes.size();sem++){
                                if(semanticFilter.contains(semanticTypes.get(sem))&&!cuis.contains(cui)&&negation!=1){
                                    cuis.add(cui);
                                }
                            }
                        }
                    }
                }
            }
        }

        return StringUtils.join(cuis,",");

    }

}