/*
* 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.HashSet;
import java.util.Map;
import org.emonocot.api.AnnotationService;
import org.emonocot.api.TaxonService;
import org.emonocot.harvest.common.AuthorityAware;
import org.emonocot.job.dwc.exception.CannotFindRecordException;
import org.emonocot.job.dwc.exception.NoIdentifierException;
import org.emonocot.job.dwc.exception.TaxonAlreadyProcessedException;
import org.emonocot.model.Annotation;
import org.emonocot.model.Reference;
import org.emonocot.model.Taxon;
import org.emonocot.model.constants.AnnotationCode;
import org.emonocot.model.constants.AnnotationType;
import org.emonocot.model.constants.RecordType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.ChunkListener;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
/**
*
* @author ben
*
*/
public class SkippingProcessor extends AuthorityAware implements ChunkListener, ItemProcessor<Taxon,Annotation> {
private Logger logger = LoggerFactory.getLogger(SkippingProcessor.class);
private TaxonService taxonService;
private AnnotationService annotationService;
private Map<String, Annotation> boundAnnotations = new HashMap<String,Annotation>();
@Autowired
public void setTaxonService(TaxonService taxonService) {
this.taxonService = taxonService;
}
@Autowired
public void setAnnotationService(AnnotationService annotationService) {
this.annotationService = annotationService;
}
/**
* @param taxon a taxon object
* @throws Exception if something goes wrong
* @return Taxon a taxon object
*/
public final Annotation process(final Taxon taxon) throws Exception {
logger.info("Processing " + taxon.getIdentifier());
if (taxon.getIdentifier() == null) {
throw new NoIdentifierException(taxon);
}
Taxon persistedTaxon = taxonService.find(taxon.getIdentifier());
if (persistedTaxon == null) {
throw new CannotFindRecordException(taxon.getIdentifier(), taxon.toString());
}
Annotation annotation = resolveAnnotation(RecordType.Taxon,persistedTaxon.getId(), getStepExecution().getJobExecutionId());
if (annotation == null) {
annotation = this.createAnnotation(persistedTaxon, RecordType.Taxon, AnnotationCode.Skipped, AnnotationType.Info);
bindAnnotation(annotation);
} else {
if (annotation.getCode().equals(AnnotationCode.Skipped)) {
throw new TaxonAlreadyProcessedException(taxon);
}
annotation.setType(AnnotationType.Info);
annotation.setCode(AnnotationCode.Skipped);
logger.info(persistedTaxon.getIdentifier() + " was skipped");
}
return annotation;
}
private Annotation resolveAnnotation(RecordType recordType, Long taxonId, Long jobExecutionId) {
String key = taxonId + ":" + jobExecutionId;
if (boundAnnotations.containsKey(key)) {
Annotation annotation = boundAnnotations.get(taxonId + ":" + jobExecutionId);
logger.info("Found annotation with identifier " + taxonId + ":" + jobExecutionId + " from cache returning annotation with id " + annotation.getIdentifier());
return annotation;
} else {
return annotationService.findAnnotation(recordType,taxonId, jobExecutionId);
}
}
private void bindAnnotation(Annotation annotation) {
boundAnnotations.put(annotation.getAnnotatedObj().getId() + ":" + getStepExecution().getJobExecutionId(), annotation);
}
@Override
public void beforeChunk() {
boundAnnotations = new HashMap<String,Annotation>();
}
@Override
public void afterChunk() {
}
}