app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraReferenceImportBase.java

   1 /**
   2 * Copyright (C) 2007 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.mexico;
  10
  11 import java.net.URISyntaxException;
  12
  13 import org.apache.log4j.Logger;
  14 import org.springframework.stereotype.Component;
  15
  16 import eu.etaxonomy.cdm.common.DOI;
  17 import eu.etaxonomy.cdm.common.URI;
  18 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  19 import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
  20 import eu.etaxonomy.cdm.model.reference.Reference;
  21 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  22 import eu.etaxonomy.cdm.strategy.parser.BibliographicAuthorParser;
  23 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
  24
  25 /**
  26  * @author a.mueller
  27  * @since 08.02.2022
  28  */
  29 @Component
  30 public abstract class MexicoEfloraReferenceImportBase  extends MexicoEfloraImportBase {
  31
  32     public static final String NAMESPACE = "References";
  33
  34     private static final long serialVersionUID = -5161951752826380728L;
  35     private static final Logger logger = Logger.getLogger(MexicoEfloraReferenceImportBase.class);
  36
  37     public MexicoEfloraReferenceImportBase(String dbTableName, String pluralString){
  38                 super(dbTableName, pluralString);
  39         }
  40
  41         @Override
  42         protected String getIdQuery(MexicoEfloraImportState state) {
  43                 String sql = " SELECT 'CONABIO-BIB-ID' "
  44                         + " FROM " + getTableName()
  45                         + " ORDER BY 'CONABIO-BIB-ID' ";
  46                 return sql;
  47         }
  48
  49         @Override
  50         protected String getRecordQuery(MexicoEfloraImportConfigurator config) {
  51                 String sqlSelect = " SELECT * ";
  52                 String sqlFrom = " FROM " + getTableName();
  53                 String sqlWhere = " WHERE ( 'CONABIO-BIB-ID' IN (" + ID_LIST_TOKEN + ") )";
  54
  55                 String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;
  56                 return strRecordQuery;
  57         }
  58
  59     @Override
  60         protected boolean doCheck(MexicoEfloraImportState state){
  61             return true;
  62         }
  63
  64         protected void handleAuthorStr(MexicoEfloraImportState state, String authorStr, Reference ref, int refId) {
  65
  66         //author
  67         if (isNotBlank(authorStr)) {
  68             TeamOrPersonBase<?> author = BibliographicAuthorParser
  69                     .Instance().parse(authorStr);
  70             //TODO is parsed really ok?
  71             state.getDeduplicationHelper().getExistingAgent(author, true);
  72             ref.setAuthorship(author);
  73         }else {
  74             logger.warn(refId + ": No author");
  75         }
  76         }
  77
  78     protected void handleYearStr(@SuppressWarnings("unused") MexicoEfloraImportState state,
  79             String yearStr, Reference ref, int refId) {
  80         //year
  81         if (isNotBlank(yearStr)) {
  82             VerbatimTimePeriod tp = TimePeriodParser.parseStringVerbatim(yearStr);
  83             ref.setDatePublished(tp);
  84         }else {
  85             logger.warn(refId + ": No year");
  86             }
  87     }
  88
  89     protected void handleTitleStr(@SuppressWarnings("unused") MexicoEfloraImportState state,
  90             String titleStr, Reference ref, int refId) {
  91
  92         //articleTitle
  93         if (isNotBlank(titleStr)) {
  94             ref.setTitle(titleStr);
  95         }else {
  96 //            logger.warn(refId + ": No title");
  97         }
  98     }
  99
 100     protected void handleUrlStr(@SuppressWarnings("unused") MexicoEfloraImportState state,
 101             String urlStr, Reference ref, int refId) {
 102
 103         //url
 104         if (isNotBlank(urlStr)) {
 105             try {
 106                 URI uri = new URI(urlStr);
 107                 //for now we handle the uri in the URI field also for non-websites
 108                 //will be moved to external link by model update script in future
 109                 ref.setUri(uri);
 110             } catch (URISyntaxException e) {
 111                 logger.warn(refId + ": URL could not be parsed: " + urlStr);
 112             }
 113         }
 114     }
 115
 116     protected void handleDoiStr(@SuppressWarnings("unused") MexicoEfloraImportState state,
 117             String doiStr, Reference ref, int refId) {
 118
 119         //doi
 120         if (isNotBlank(doiStr)) {
 121             DOI doi;
 122             try {
 123                 doi = DOI.fromString(doiStr);
 124                 ref.setDoi(doi);
 125             } catch (Exception e) {
 126                 logger.warn(refId + ": Doi could not be parsed: " + doiStr);
 127             }
 128         }
 129     }
 130
 131     protected void handleId(MexicoEfloraImportState state, int refId, Reference ref) {
 132         state.getReferenceUuidMap().put(refId, ref.getUuid());
 133 //        state.getRefDetailMap().put(refId, detail);
 134
 135         //TODO not needed anymore once "related objects" are adapted everywhere
 136         Reference sourceRef = getSourceReference(state.getConfig().getSourceReference());
 137         ref.addImportSource(String.valueOf(refId), MexicoEfloraReferenceImportBase.NAMESPACE,
 138                 sourceRef, null);
 139
 140         //.. identifier
 141         DefinedTerm conabioIdentifier = getIdentiferType(state, MexicoConabioTransformer.uuidConabioReferenceIdIdentifierType,
 142                 "CONABIO Reference Identifier", "CONABIO Reference Identifier", "CONABIO", null);
 143         ref.addIdentifier(String.valueOf(refId), conabioIdentifier);
 144     }
 145
 146         @Override
 147         protected boolean isIgnore(MexicoEfloraImportState state){
 148                 return ! state.getConfig().isDoReferences();
 149         }
 150 }