org.ihtsdo.otf.refset.service.upload.ImportRF2Service.java Source code

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Here is the source code for org.ihtsdo.otf.refset.service.upload.ImportRF2Service.java

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/**
* Copyright 2014 IHTSDO
* 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.ihtsdo.otf.refset.service.upload;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.UUID;

import org.apache.commons.lang3.StringUtils;
import org.ihtsdo.otf.refset.exception.EntityNotFoundException;
import org.ihtsdo.otf.refset.exception.RefsetServiceException;
import org.joda.time.format.DateTimeFormat;
import org.joda.time.format.DateTimeFormatter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;

/**
 *
 */
@Service
public class ImportRF2Service implements ImportService {

    private static final Logger LOGGER = LoggerFactory.getLogger(ImportRF2Service.class);
    private static final DateTimeFormatter fmt = DateTimeFormat.forPattern("yyyyMMdd");

    private RefsetProcessor srp;

    /**
     * @param srp the srp to set
     */
    @Autowired
    public void setSrp(RefsetProcessor srp) {
        this.srp = srp;
    }

    /* (non-Javadoc)
     * @see org.ihtsdo.otf.refset.service.upload.ImportService#importFile(org.springframework.web.multipart.MultipartFile, java.lang.String)
     */
    @Override
    public Map<String, String> importFile(InputStream is, String refsetId, String user)
            throws RefsetServiceException, EntityNotFoundException {

        if (is == null || StringUtils.isBlank(refsetId)) {

            throw new IllegalArgumentException("Mandatory data ie file or refsetId is missing in request");
        }

        BufferedReader reader = null;
        try {

            reader = new BufferedReader(new InputStreamReader(is));

            String line;

            int row = 0;

            List<Rf2Record> rf2RLst = new ArrayList<Rf2Record>();

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

                row++;

                if (StringUtils.isEmpty(line) || row == 1) {

                    LOGGER.debug("Line {} is empty skipping", line);
                    continue;

                }

                String[] columns = StringUtils.splitByWholeSeparator(line, "\t");

                if (columns != null & columns.length == 6) {

                    Rf2Record rf2r = new Rf2Record();

                    rf2r.setId(columns[0]);//Per Robert preserve uuid. No need to generate refset tool uuid instead of using RF2 file.
                    rf2r.setEffectiveTime(fmt.parseDateTime(columns[1]));
                    rf2r.setActive(columns[2]);
                    rf2r.setModuleId(columns[3]);
                    rf2r.setRefsetId(columns[4]);
                    rf2r.setReferencedComponentId(columns[5]);
                    rf2r.setCreatedBy(user);
                    rf2r.setModifiedBy(user);
                    rf2RLst.add(rf2r);

                } else {

                    throw new RefsetServiceException("Insufficient data, no further processing is possible");

                }

            }

            return srp.process(rf2RLst, refsetId, user);

        } catch (IOException e) {

            throw new RefsetServiceException(e);

        } finally {

            try {

                reader.close();

            } catch (IOException e) {

                LOGGER.info("Could not close IO resources");
            }
        }
    }

}