/* * 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.description; import java.util.HashMap; import java.util.HashSet; import java.util.Map; import java.util.Set; import org.emonocot.api.DescriptionService; import org.emonocot.api.ReferenceService; import org.emonocot.job.dwc.exception.RequiredFieldException; import org.emonocot.job.dwc.read.OwnedEntityProcessor; import org.emonocot.model.Annotation; import org.emonocot.model.Description; import org.emonocot.model.Reference; 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.beans.factory.annotation.Autowired; /** * * @author ben * */ public class Processor extends OwnedEntityProcessor<Description, DescriptionService> { private Map<String, Reference> boundReferences = new HashMap<String, Reference>(); private Logger logger = LoggerFactory.getLogger(Processor.class); private ReferenceService referenceService; @Autowired public void setReferenceService(ReferenceService referenceService) { this.referenceService = referenceService; } @Autowired public void setDescriptionService(DescriptionService service) { super.service = service; } @Override protected void doValidate(Description t) { if (t.getType() == null) { throw new RequiredFieldException("Description " + t + " at line " + getLineNumber() + " has no Feature set", RecordType.Description, getStepExecution().getReadCount()); } if (t.getDescription() == null || t.getDescription().length() == 0) { throw new RequiredFieldException("Description " + t + " at line " + getLineNumber() + " has no Content set", RecordType.Description, getStepExecution().getReadCount()); } } @Override protected void doUpdate(Description persisted, Description t) { persisted.setAudience(t.getAudience()); persisted.setContributor(t.getContributor()); persisted.setCreator(t.getCreator()); persisted.setDescription(t.getDescription()); persisted.setLanguage(t.getLanguage()); persisted.setSource(t.getSource()); persisted.setType(t.getType()); persisted.getReferences().clear(); for(Reference r : t.getReferences()) { resolveReference(persisted,r.getIdentifier()); } } @Override protected void doCreate(Description t) { Set<Reference> references = new HashSet<Reference>(); references.addAll(t.getReferences()); t.getReferences().clear(); for(Reference r : references) { resolveReference(t,r.getIdentifier()); } } @Override protected RecordType getRecordType() { return RecordType.Description; } @Override public void afterChunk() { super.afterChunk(); logger.info("After Chunk"); } /** * * @param object * Set the text content object * @param value * the source of the reference to resolve */ private void resolveReference(Description object, String value) { if (value == null || value.trim().length() == 0) { // there is not citation identifier return; } else { if (boundReferences.containsKey(value)) { object.getReferences().add(boundReferences.get(value)); } else { Reference r = referenceService.find(value); if (r == null) { r = new Reference(); r.setIdentifier(value); Annotation annotation = super.createAnnotation(r, RecordType.Reference, AnnotationCode.Create, AnnotationType.Info); r.getAnnotations().add(annotation); r.setAuthority(getSource()); } boundReferences.put(value, r); object.getReferences().add(r); } } } @Override public void beforeChunk() { super.beforeChunk(); logger.info("Before Chunk"); boundReferences = new HashMap<String, Reference>(); } }