app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoEfloraRefArticlesImport.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
  10 package eu.etaxonomy.cdm.io.mexico;
  11
  12 import java.sql.ResultSet;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.Map;
  16 import java.util.Set;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20
  21 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  22 import eu.etaxonomy.cdm.model.common.CdmBase;
  23 import eu.etaxonomy.cdm.model.reference.IJournal;
  24 import eu.etaxonomy.cdm.model.reference.Reference;
  25 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  26
  27 /**
  28  * @author a.mueller
  29  * @since 08.02.2022
  30  */
  31 @Component
  32 public class MexicoEfloraRefArticlesImport extends MexicoEfloraReferenceImportBase {
  33
  34     private static final long serialVersionUID = -1186364983750790695L;
  35
  36     private static final Logger logger = Logger.getLogger(MexicoEfloraRefArticlesImport.class);
  37
  38         private static final String pluralString = "Articles";
  39         private static final String dbTableName = "RefArticles";
  40         private static final Map<String,IJournal> journalMap = new HashMap<>();
  41
  42         public MexicoEfloraRefArticlesImport(){
  43                 super(dbTableName, pluralString);
  44         }
  45
  46         @Override
  47         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {
  48
  49             boolean success = true ;
  50                 Set<Reference> refsToSave = new HashSet<>();
  51
  52                 ResultSet rs = partitioner.getResultSet();
  53                 try{
  54                         while (rs.next()){
  55
  56                         //      if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
  57
  58                                 //create TaxonName element
  59                                 int refId = rs.getInt("CONABIO-BIB-ID");
  60                                 String type = rs.getString("PubType");
  61                                 String authorStr = rs.getString("Author");
  62                                 String yearStr = rs.getString("Year");
  63                                 String articleTitleStr = rs.getString("ArticleTitle");
  64                 String journalTitleStr = rs.getString("JournalTitle");
  65                 String concat = rs.getString("Concatenation");
  66                 //TODO _minor V and P in articles
  67                 String vStr = rs.getString("V");
  68                 String pStr = rs.getString("P");
  69                 String urlStr = rs.getString("URL");
  70                 String doiStr = rs.getString("DOI");
  71                 String issnStr = rs.getString("ISSN");
  72
  73                 try {
  74                     Reference ref = ReferenceFactory.newArticle();
  75                     //type
  76                     if (!"A".equals(type)) {
  77                         logger.warn(refId + ": Type not 'A'");
  78                     }
  79
  80                     //author
  81                     handleAuthorStr(state, authorStr, ref, refId);
  82
  83                     //year
  84                     handleYearStr(state, yearStr, ref, refId);
  85
  86                     //articleTitle
  87                     handleTitleStr(state, articleTitleStr, ref, refId);
  88
  89                     //journalTitle
  90                     if (isNotBlank(journalTitleStr)) {
  91
  92                         IJournal journal = journalMap.get(journalTitleStr);
  93                         if (journal == null) {
  94                             journal = ReferenceFactory.newJournal();
  95                             journal.setTitle(journalTitleStr);
  96                             journalMap.put(journalTitleStr, journal);
  97                         }
  98
  99                         ref.setInJournal(journal);
 100                     }else {
 101                         logger.warn(refId + ": No journal title");
 102                     }
 103
 104                     //concat
 105                     if (isNotBlank(concat)) {
 106                         String[] split = concat.split(":");
 107                         String volume = split[0];
 108                         ref.setVolume(volume);
 109                         if (split.length > 1) {
 110                             String pages = split[1];
 111                             ref.setPages(pages);
 112                         }
 113                     }else {
 114                         logger.info(refId + ": No volume");
 115                     }
 116
 117                     //url
 118                     handleUrlStr(state, urlStr, ref, refId);
 119
 120                     //doi
 121                     handleDoiStr(state, doiStr, ref, refId);
 122
 123                     //issn
 124                     if (isNotBlank(issnStr) && !"NA".equals(issnStr)) {
 125                         if (issnStr.startsWith("ISSN:")) {
 126                             issnStr = issnStr.replace("ISSN:", "").trim();
 127                         }else if (issnStr.startsWith("ISSN ")) {
 128                             issnStr = issnStr.replace("ISSN ", "").trim();
 129                         }
 130                         ref.getInJournal().setIssn(issnStr);
 131                     }
 132
 133                     //register id and make import source
 134                     handleId(state, refId, ref);
 135
 136                                         partitioner.startDoSave();
 137                                         refsToSave.add(ref);
 138                                 } catch (Exception e) {
 139                                         logger.warn("An exception (" +e.getMessage()+") occurred when creating reference with id " + refId + ". Reference could not be saved.");
 140                                         success = false;
 141                                 }
 142                         }
 143                 } catch (Exception e) {
 144                         logger.error("SQLException:" +  e);
 145                         return false;
 146                 }
 147
 148                 getReferenceService().save(refsToSave);
 149                 return success;
 150         }
 151
 152
 153     @Override
 154         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, MexicoEfloraImportState state) {
 155
 156                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 157                 return result;
 158         }
 159
 160         @Override
 161         protected String getTableName() {
 162                 return dbTableName;
 163         }
 164
 165         @Override
 166         public String getPluralString() {
 167                 return pluralString;
 168         }
 169
 170 }