/*
* This is eMonocot, a global online biodiversity information resource.
*
* Copyright © 2011–2015 The Board of Trustees of the Royal Botanic Gardens, Kew and The University of Oxford
*
* eMonocot is free software: you can redistribute it and/or modify it under the terms of the
* GNU Affero General Public License as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* eMonocot is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* The complete text of the GNU Affero General Public License is in the source repository as the file
* ‘COPYING’. It is also available from <http://www.gnu.org/licenses/>.
*/
package org.emonocot.job.dwc.taxon;
import java.util.HashMap;
import java.util.Map;
import org.emonocot.job.dwc.read.AbstractRecordAnnotator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
/**
*
* @author ben
*
*/
public class CheckingRecordAnnotator extends AbstractRecordAnnotator implements Tasklet {
Logger logger = LoggerFactory.getLogger(CheckingRecordAnnotator.class);
private String subtribe;
private String tribe;
private String subfamily;
private String family;
public void setSubtribe(String subtribe) {
this.subtribe = subtribe;
}
public void setTribe(String tribe) {
this.tribe = tribe;
}
public void setSubfamily(String subfamily) {
this.subfamily = subfamily;
}
public void setFamily(String family) {
this.family = family;
}
@Override
public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception {
String subsetRank = null;
String subsetValue = null;
if(subtribe != null) {
subsetRank = "subtribe";
subsetValue = subtribe;
} else if(tribe != null) {
subsetRank = "tribe";
subsetValue = tribe;
} else if(subfamily != null) {
subsetRank = "subfamily";
subsetValue = subfamily;
} else {
subsetRank = "family";
subsetValue = family;
}
String queryString = "insert into Annotation (annotatedObjId, annotatedObjType, jobId, dateTime, authority_id, type, code, recordType) select t.id, 'Taxon', :jobId, now(), :authorityId, 'Warn', 'Absent', 'Taxon' from Taxon t left join Taxon a on (t.acceptedNameUsage_id = a.id) where (t.#subsetRank = :subsetValue or a.#subsetRank = :subsetValue)";
queryString = queryString.replaceAll("#subsetRank", subsetRank);
Map<String, Object> queryParameters = new HashMap<String,Object>();
queryParameters.put("subsetValue", subsetValue);
logger.debug(queryString);
int numberOfRecords = annotate(queryString, queryParameters);
logger.debug(numberOfRecords + " records inserted");
return RepeatStatus.FINISHED;
}
}