/*
* 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.read;
import java.util.HashMap;
import java.util.Map;
import org.joda.time.DateTime;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.ExitStatus;
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 OwnedRecordAnnotator extends AbstractRecordAnnotator implements Tasklet {
private Logger logger = LoggerFactory.getLogger(OwnedRecordAnnotator.class);
private String subtribe;
private String tribe;
private String subfamily;
private String family;
private String annotatedObjType;
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;
}
public void setAnnotatedObjType(String annotatedObjType) {
this.annotatedObjType = annotatedObjType;
}
@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 if (family != null) {
subsetRank = "family";
subsetValue = family;
}
String queryString = null;
Map<String, Object> queryParameters = new HashMap<String, Object>();
if (subsetValue != null) {
queryString = "insert into Annotation (annotatedObjId, annotatedObjType, jobId, dateTime, authority_id, type, code, recordType) select o.id, :annotatedObjType, :jobId, now(), :authorityId, 'Warn', 'Absent', :annotatedObjType from #annotatedObjType o join taxon t on (o.taxon_id = t.id) left join taxon a on (t.acceptedNameUsage_id = a.id) where o.authority_id = :authorityId and (t.#subsetRank = :subsetValue or a.#subsetRank = :subsetValue)";
queryString = queryString.replaceAll("#subsetRank", subsetRank);
queryParameters.put("subsetValue", subsetValue);
} else {
queryString = "insert into Annotation (annotatedObjId, annotatedObjType, jobId, dateTime, authority_id, type, code, recordType) select o.id, :annotatedObjType, :jobId, now(), :authorityId, 'Warn', 'Absent', :annotatedObjType from #annotatedObjType o where o.authority_id = :authorityId";
}
queryString = queryString.replaceAll("#annotatedObjType", annotatedObjType);
queryParameters.put("annotatedObjType", annotatedObjType);
logger.debug(queryString);
int numberUpdated = annotate(queryString, queryParameters);
logger.debug(numberUpdated + " Annotation records inserted");
return RepeatStatus.FINISHED;
}
}