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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.plantglossary;
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import java.io.File;
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import java.net.URI;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.csv.in.CsvImportBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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*
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* @author pplitzner
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* @since Dec 7, 2018
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*
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*/
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@Component
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public class PlantGlossaryStateImport extends CsvImportBase<PlantGlossaryCsvImportConfigurator, PlantGlossaryCsvImportState, File>{
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private static final long serialVersionUID = -5600766240192189822L;
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private static Logger logger = Logger.getLogger(PlantGlossaryStateImport.class);
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final String HEADER_LABEL = "dcterms:identifier";
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final String HEADER_DEFINITION = "definition";
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final String HEADER_CATEGORY = "vann:termGroup";
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final String HEADER_NOTES = "skos:example";
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final String SOURCE_HEADER = "sourceDataset";
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final String HEADER_URI = "term_URI";
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@Override
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protected void handleSingleLine(PlantGlossaryCsvImportState importState) {
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Map<String, String> currentRecord = importState.getCurrentRecord();
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String termLabel = currentRecord.get(HEADER_LABEL);
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//check if already present
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if(importState.isTermPresent(termLabel, getTermService())){
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return;
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}
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State stateTerm = State.NewInstance(currentRecord.get(HEADER_DEFINITION), termLabel, null);
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stateTerm.setIdInVocabulary(termLabel);
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stateTerm.setUri(URI.create(currentRecord.get(HEADER_URI)));
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if(CdmUtils.isNotBlank(currentRecord.get(HEADER_NOTES))){
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stateTerm.addAnnotation(Annotation.NewInstance(currentRecord.get(HEADER_NOTES), AnnotationType.EDITORIAL(), Language.ENGLISH()));
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}
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String vocName = currentRecord.get(HEADER_CATEGORY);
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// TODO how should we handle multiple possible categories?
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// for now we just take the first one
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if(vocName.contains(",")){
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vocName = vocName.split(",")[0];
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}
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TermVocabulary vocabulary = importState.checkVocabularies(vocName, getVocabularyService());
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if(vocabulary==null){
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logger.error("No vocabulary found for term: "+stateTerm+" with vocName: "+vocName);
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return;
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}
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vocabulary.addTerm(stateTerm);
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IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, importState.getCitation().getTitle(), null, importState.getCitation(), null);
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source.setIdInSource(termLabel);
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stateTerm.addSource(source);
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getVocabularyService().saveOrUpdate(vocabulary);
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getTermService().saveOrUpdate(stateTerm);
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}
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}
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