org.ala.hbase.SensitiveStatusLoader.java Source code

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Here is the source code for org.ala.hbase.SensitiveStatusLoader.java

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/***************************************************************************
 * Copyright (C) 2010 Atlas of Living Australia
 * All Rights Reserved.
 *
 * The contents of this file are subject to the Mozilla Public
 * License Version 1.1 (the "License"); you may not use this file
 * except in compliance with the License. You may obtain a copy of
 * the License at http://www.mozilla.org/MPL/
 *
 * Software distributed under the License is distributed on an "AS
 * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
 * implied. See the License for the specific language governing
 * rights and limitations under the License.
 ***************************************************************************/
package org.ala.hbase;

import java.io.FileReader;
import java.io.IOException;

import javax.inject.Inject;

import org.ala.dao.InfoSourceDAO;
import org.ala.dao.TaxonConceptDao;
import org.ala.model.InfoSource;
import org.ala.model.SensitiveStatus;
import org.ala.util.SpringUtils;
import org.apache.log4j.Logger;
import org.springframework.context.ApplicationContext;
import org.springframework.stereotype.Component;

import au.com.bytecode.opencsv.CSVReader;

/**
 * A temporary loader that adds sensitivity status values to taxa.
 *
 * To create dump file :
 * select ss.scientific_name, IFNULL(ss.family,''), IFNULL(ss.common_name,''),ssz.sensitivity_zone, ssz.authority_name,ssz.sensitivity_category,
case authority_name  when 'Birds Australia' then 'http://www.birdsaustralia.com.au/'
when 'DERM' then 'http://www.derm.qld.gov.au' when 'NSW DECCW' then 'http://www.environment.nsw.gov.au' when 'NT DNRETA' then 'http://www.nt.gov.au/nreta'
when 'Tasmania' then 'http://www.dpiw.tas.gov.au' when 'Vic DSE' then 'http://www.dse.vic.gov.au' else '' end
From sensitive_species ss join sensitive_species_zones ssz on ss.scientific_name = ssz.scientific_name where ssz.authority_name <> 'AQIS'
into outfile '/data/bie-staging/sds/SensitiveSpecies.csv'
 * 
 * This should eventually be replaced with a class that relies on SDS
 * webservices.
 * 
 * @author Dave Martin
 */
@Component("sensitiveStatusLoader")
public class SensitiveStatusLoader {

    protected static Logger logger = Logger.getLogger(SensitiveStatusLoader.class);

    private static final String DEFAULT_INPUT_FILE_NAME = "/data/bie-staging/sds/SensitiveSpecies.csv";
    @Inject
    protected TaxonConceptDao taxonConceptDao;
    @Inject
    protected InfoSourceDAO infoSourceDao;

    /**
     * Usage: inputFileName
     * 
     * @param args
     */
    public static void main(String[] args) {
        System.out.println("Starting Sensitive data process.....");
        ApplicationContext context = SpringUtils.getContext();
        SensitiveStatusLoader l = context.getBean(SensitiveStatusLoader.class);
        try {
            System.out.println("Starting load process.....");
            String fileName = DEFAULT_INPUT_FILE_NAME;

            if (args.length == 1) {
                fileName = args[0];
            }

            l.load(fileName);
            System.out.println("load process finished.....");
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
        System.exit(0);
    }

    /**
     * data load process
     */
    private void load(String fileName) {
        int ctr = 0;
        String[] nextLine = null;
        CSVReader reader = null;
        int lineNo = 1;
        try {
            reader = new CSVReader(new FileReader(fileName), ',');
            //first data line
            nextLine = reader.readNext();

            while (nextLine != null && nextLine.length == 7) {
                //a single line contains multiple status

                //retrieve taxon concept
                String guid = taxonConceptDao.findLsidByName(nextLine[0], null);
                if (guid != null) {
                    //retrieve the infosource to be used
                    SensitiveStatus ss = new SensitiveStatus();
                    //TODO should the categories be mapped to a vocabulary?
                    ss.setSensitivityCategory(nextLine[5]);
                    ss.setSensitivityZone(nextLine[3]);
                    InfoSource infosource = infoSourceDao.getByUri(nextLine[6].trim());
                    if (infosource != null) {
                        ss.setInfoSourceId(Integer.toString(infosource.getId()));
                        ss.setInfoSourceName(infosource.getName());
                        ss.setInfoSourceURL(infosource.getWebsiteUrl());
                    }
                    taxonConceptDao.addSensitiveStatus(guid, ss);
                    ctr++;
                }
                lineNo++;
                nextLine = reader.readNext();
            }
        } catch (Exception e) {
            logger.error("Line number: " + lineNo, e);
            e.printStackTrace();
        } finally {
            System.out.println("*** Total Records Updated: " + ctr);
            if (reader != null) {
                try {
                    reader.close();
                } catch (IOException e) {
                    logger.error(e);
                }
            }
        }
    }
}