app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaExcludedTaxonImport.java

   1 /**
   2 * Copyright (C) 2016 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.greece;
  10
  11 import java.util.Arrays;
  12 import java.util.HashMap;
  13 import java.util.List;
  14 import java.util.Set;
  15
  16 import org.apache.log4j.Logger;
  17 import org.springframework.stereotype.Component;
  18
  19 import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
  20 import eu.etaxonomy.cdm.model.agent.Person;
  21 import eu.etaxonomy.cdm.model.common.TimePeriod;
  22 import eu.etaxonomy.cdm.model.name.IBotanicalName;
  23 import eu.etaxonomy.cdm.model.name.INonViralName;
  24 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  25 import eu.etaxonomy.cdm.model.name.Rank;
  26 import eu.etaxonomy.cdm.model.name.TaxonName;
  27 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
  28 import eu.etaxonomy.cdm.model.reference.Reference;
  29 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  30 import eu.etaxonomy.cdm.model.taxon.Classification;
  31 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  32 import eu.etaxonomy.cdm.model.taxon.Taxon;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  34 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  35
  36 /**
  37  * @author a.mueller
  38  * @since 14.12.2016
  39  *
  40  */
  41
  42 @Component
  43 public class FloraHellenicaExcludedTaxonImport<CONFIG extends FloraHellenicaImportConfigurator>
  44             extends FloraHellenicaImportBase<CONFIG>{
  45
  46
  47     private static final long serialVersionUID = 2629253144140992196L;
  48     private static final Logger logger = Logger.getLogger(FloraHellenicaExcludedTaxonImport.class);
  49
  50     private static final String TAXON = "Taxon";
  51     private static final String UNIQUE_ID = "Unique ID";
  52     private static final String FAMILY = "Family";
  53
  54     private  static List<String> expectedKeys= Arrays.asList(new String[]{
  55             UNIQUE_ID,FAMILY,TAXON
  56     });
  57
  58     private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
  59     private TaxonNode excludedFamilyNode;
  60
  61     @Override
  62     protected String getWorksheetName() {
  63         return "excluded taxa";
  64     }
  65
  66     boolean isFirst = true;
  67     /**
  68      * {@inheritDoc}
  69      */
  70     @Override
  71     protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
  72
  73         String line = state.getCurrentLine() + ": ";
  74         HashMap<String, String> record = state.getOriginalRecord();
  75
  76         Set<String> keys = record.keySet();
  77         for (String key: keys) {
  78             if (! expectedKeys.contains(key)){
  79                 logger.warn(line + "Unexpected Key: " + key);
  80             }
  81         }
  82         if (isFirst){
  83             System.out.println("Start excluded taxa");
  84             isFirst = false;
  85         }
  86
  87         String noStr = getValue(record, UNIQUE_ID);
  88         TaxonNode taxonNode = makeTaxon(state, line, record, noStr);
  89         if (taxonNode != null){
  90             state.putTaxon(noStr, taxonNode.getTaxon());
  91         }
  92     }
  93
  94
  95     /**
  96      * @param state
  97      * @param line
  98      * @param record
  99      * @param noStr
 100      * @return
 101      */
 102     private TaxonNode makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line,
 103             HashMap<String, String> record,
 104             String noStr) {
 105
 106         TaxonNode familyTaxonNode = getFamilyTaxon(record, state);
 107         familyTaxonNode = getTaxonNodeService().find(familyTaxonNode.getUuid());
 108         if (familyTaxonNode == null){
 109             logger.warn(line + "Family not created, can't add excluded taxon: " + record.get(FAMILY));
 110             return null;
 111         }
 112
 113         String taxonStr = getValue(record, TAXON);
 114         Reference sec = getSecReference(state);
 115         if (taxonStr.endsWith(" sec. Hayek 1929")){
 116             sec = makeHayek1929();
 117             taxonStr = taxonStr.substring(0, taxonStr.length() - " sec. Hayek 1929".length()).trim();
 118         }
 119         boolean isSensuStrictu = false;
 120         if (taxonStr.endsWith("s.str.")){
 121             isSensuStrictu = true;
 122             taxonStr = taxonStr.substring(0, taxonStr.length() - "s.str.".length() ).trim();
 123         }
 124         INonViralName name = parser.parseFullName(taxonStr, NomenclaturalCode.ICNAFP, null);
 125         name = replaceNameAuthorsAndReferences(state, name);
 126         if (name.isProtectedTitleCache()){
 127             logger.warn(line + "Name could not be parsed: " + taxonStr);
 128         }
 129
 130         Taxon taxon = Taxon.NewInstance(name, sec);
 131         if (isSensuStrictu){
 132             taxon.setAppendedPhrase("s.str.");
 133         }
 134         taxon.addImportSource(noStr, getWorksheetName(), getSourceCitation(state), null);
 135         TaxonNode excludedNode = familyTaxonNode.addChildTaxon(taxon, getSecReference(state), null);
 136         excludedNode.setExcluded(true);
 137         getTaxonNodeService().saveOrUpdate(excludedNode);
 138         return excludedNode;
 139     }
 140
 141
 142
 143    /**
 144      * @return
 145      */
 146     private Reference makeHayek1929() {
 147         Reference ref = ReferenceFactory.newGeneric();
 148         Person hayek = Person.NewInstance();
 149         hayek.setLastname("Hayek");
 150         ref.setAuthorship(hayek);
 151         ref.setDatePublished(TimePeriod.NewInstance(1929));
 152         return ref;
 153     }
 154
 155
 156 /**
 157      * @param record
 158      * @param state
 159      * @return
 160      */
 161     private TaxonNode getFamilyTaxon(HashMap<String, String> record,
 162             SimpleExcelTaxonImportState<CONFIG> state) {
 163
 164         String familyStr = getValue(record, FAMILY);
 165         if (familyStr == null){
 166             return null;
 167         }
 168         familyStr = familyStr.trim();
 169
 170 //        Taxon family = state.getHigherTaxon(familyStr);
 171         Taxon family = this.getHigherTaxon(record, state, FAMILY);
 172         TaxonNode familyNode;
 173         if (family != null){
 174             familyNode = family.getTaxonNodes().iterator().next();
 175         }else{
 176             IBotanicalName name = makeFamilyName(state, familyStr);
 177             name = replaceNameAuthorsAndReferences(state, name);
 178
 179             Reference sec = getSecReference(state);
 180             family = Taxon.NewInstance(name, sec);
 181
 182             ITaxonTreeNode groupNode = getExcludedFamilyTaxon(state);
 183             familyNode = groupNode.addChildTaxon(family, sec, null);
 184             state.putHigherTaxon(familyStr, family);
 185             getTaxonNodeService().saveOrUpdate(familyNode);
 186 //            logger.warn(state.getCurrentLine() +": " + "Family not found for excluded taxon");
 187         }
 188         return familyNode;
 189     }
 190
 191
 192     private ITaxonTreeNode getExcludedFamilyTaxon(
 193             SimpleExcelTaxonImportState<CONFIG> state) {
 194
 195         if (excludedFamilyNode != null){
 196             return this.excludedFamilyNode;
 197         }
 198         Classification classification = getClassificationService().load(state.getConfig().getClassificationUuid());
 199         TaxonNode plantae = classification.getChildNodes().iterator().next();
 200
 201         TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.SUPERFAMILY());
 202         name.setTitleCache("Excluded", true);
 203         Taxon taxon = Taxon.NewInstance(name, getSecReference(state));
 204         excludedFamilyNode = plantae.addChildTaxon(taxon, getSourceCitation(state), null);
 205         excludedFamilyNode.setExcluded(true);
 206         getTaxonNodeService().saveOrUpdate(excludedFamilyNode);
 207         return excludedFamilyNode;
 208     }
 209
 210 }