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/**
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* Copyright (C) 2007 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;
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import eu.etaxonomy.cdm.common.URI;
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import java.net.URISyntaxException;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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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.app.images.AbstractImageImporter;
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import eu.etaxonomy.cdm.app.images.ImageImportState;
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import eu.etaxonomy.cdm.common.ExcelUtils;
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import eu.etaxonomy.cdm.model.media.ExternalLinkType;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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/**
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* @author n.hoffmann
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* @since 19.11.2008
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*/
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@Component
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public class PalmaeProtologueImport extends AbstractImageImporter {
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private static final long serialVersionUID = -7178567387220714414L;
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private static final Logger logger = Logger.getLogger(PalmaeProtologueImport.class);
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public static final String SPECIES = "Species";
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public static final String TAXONID = "Taxon ID";
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public static final String LINK_PROTO = "Link proto";
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@Override
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protected void invokeImageImport(ImageImportState state) {
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List<Map<String, String>> contents;
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try {
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contents = ExcelUtils.parseXLS(state.getConfig().getSource());
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} catch (/*FileNotFound*/Exception e) {
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logger.error("FileNotFound: " + state.getConfig().getSource().toString());
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state.setUnsuccessfull();
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return;
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}
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Set<TaxonName> taxonNameStore = new HashSet<>();
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int count = 0;
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for (Map<String, String> row : contents){
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count++;
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TaxonName taxonName = null;
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String species = null;
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String taxonId = null;
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String linkProto = null;
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try{
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species = row.get(PalmaeProtologueImport.SPECIES).trim();
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taxonId = row.get(PalmaeProtologueImport.TAXONID);
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linkProto= row.get(PalmaeProtologueImport.LINK_PROTO).trim();
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taxonName = getCommonService().getSourcedObjectByIdInSource(TaxonName.class, "palm_tn_" + taxonId.replace(".0", ""), "TaxonName");
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}catch (Exception e){
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logger.error("The row has errors: rowNumber: " +count + ", content: " + row, e);
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}
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if(taxonName == null){
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logger.warn("no taxon with this name found: " + species + ", idInSource: " + taxonId);
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}else{
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try {
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URI uri = new URI(linkProto);
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taxonName.addProtologue(uri, null, ExternalLinkType.WebSite);
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} catch (URISyntaxException e) {
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String message= "URISyntaxException when trying to convert: " + linkProto;
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logger.error(message);
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e.printStackTrace();
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}
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taxonNameStore.add(taxonName);
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if(count % 50 == 0){
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logger.info(count + " protologues processed.");
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}
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}
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}
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getNameService().save(taxonNameStore);
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logger.info(count + " protologues imported to CDM store.");
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return;
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}
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}
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