org.gbif.occurrence.parsing.xml.HigherTaxonParser.java Source code

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Here is the source code for org.gbif.occurrence.parsing.xml.HigherTaxonParser.java

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/*
 * Copyright 2011 Global Biodiversity Information Facility (GBIF)
 *
 * Licensed under the Apache License, Version 2.0 (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.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.gbif.occurrence.parsing.xml;

import org.gbif.occurrence.constants.TaxonRankEnum;
import org.gbif.occurrence.model.Taxon;

import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;

import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class HigherTaxonParser {

    private static final Logger LOG = LoggerFactory.getLogger(HigherTaxonParser.class);

    private Properties taxonRankMapping = new Properties();
    private final String taxonRankMappingFilename = "/taxonRankMapping.properties";

    public HigherTaxonParser() {
        init();
    }

    private void init() {
        // load taxonRank mappings
        try {
            InputStream is = getClass().getResourceAsStream(taxonRankMappingFilename);
            taxonRankMapping.load(is);
        } catch (IOException e) {
            LOG.error("Unable to load taxonRankMapping - parsing higher taxons will fail", e);
        }
    }

    /**
     * Given a raw taxon rank and name, finds the matching Linnean rank (if any) and builds a Taxon
     * object with the rank and name.
     */
    public Taxon parseTaxon(String rawTaxonRank, String taxonName) {
        Taxon taxon = null;
        String processedTaxonRank = StringUtils.trimToNull(rawTaxonRank);
        if (processedTaxonRank != null && !StringUtils.equals(processedTaxonRank, "null")) {
            processedTaxonRank = processedTaxonRank.replaceAll(" ", "").toUpperCase();
            String rawRank = taxonRankMapping.getProperty(processedTaxonRank);
            if (rawRank == null) {
                LOG.info("Could not process taxon ranking of [{}], skipping.", processedTaxonRank);
            } else {
                int rank = Integer.valueOf(rawRank.trim());
                LOG.debug("ProcessedTaxonRank [{}] gives numeric rank [{}]", processedTaxonRank, rank);
                switch (rank) {
                case 1000:
                    taxon = new Taxon(TaxonRankEnum.KINGDOM, taxonName);
                    break;
                case 2000:
                    taxon = new Taxon(TaxonRankEnum.PHYLUM, taxonName);
                    break;
                case 3000:
                    taxon = new Taxon(TaxonRankEnum.CLASS, taxonName);
                    break;
                case 4000:
                    taxon = new Taxon(TaxonRankEnum.ORDER, taxonName);
                    break;
                case 5000:
                    taxon = new Taxon(TaxonRankEnum.FAMILY, taxonName);
                    break;
                }
            }
        }

        return taxon;
    }
}