app-import/src/main/java/eu/etaxonomy/cdm/io/PalmaeProtologueImport.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;
  11
  12 import java.net.URI;
  13 import java.net.URISyntaxException;
  14 import java.util.ArrayList;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.app.images.AbstractImageImporter;
  23 import eu.etaxonomy.cdm.app.images.ImageImportConfigurator;
  24 import eu.etaxonomy.cdm.app.images.ImageImportState;
  25 import eu.etaxonomy.cdm.common.ExcelUtils;
  26 import eu.etaxonomy.cdm.model.description.Feature;
  27 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  28 import eu.etaxonomy.cdm.model.description.TextData;
  29 import eu.etaxonomy.cdm.model.media.Media;
  30 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  31 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  32 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  33
  34 /**
  35  * @author n.hoffmann
  36  * @created 19.11.2008
  37  * @version 1.0
  38  */
  39 @Component
  40 public class PalmaeProtologueImport extends AbstractImageImporter {
  41         private static final Logger logger = Logger.getLogger(PalmaeProtologueImport.class);
  42
  43         public static final String SPECIES = "Species";
  44         public static final String TAXONID = "Taxon ID";
  45         public static final String LINK_PROTO = "Link proto";
  46
  47         /* (non-Javadoc)
  48          * @see eu.etaxonomy.cdm.app.images.AbstractImageImporter#invokeImageImport(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  49          */
  50         @Override
  51         protected void invokeImageImport(ImageImportState state) {
  52
  53                 ArrayList<HashMap<String, String>> contents;
  54                 try {
  55                         contents = ExcelUtils.parseXLS(state.getConfig().getSource());
  56                 } catch (/*FileNotFound*/Exception e) {
  57                         logger.error("FileNotFound: " + state.getConfig().getSource().toString());
  58                         state.setUnsuccessfull();
  59                         return;
  60                 }
  61
  62                 Set<TaxonNameBase> taxonNameStore = new HashSet<TaxonNameBase>();
  63
  64                 int count = 0;
  65
  66                 for (HashMap<String, String> row : contents){
  67                         count++;
  68
  69                         TaxonNameBase taxonNameBase = null;
  70                         String species = null;
  71                         String taxonId = null;
  72                         String linkProto = null;
  73                         try{
  74                                 species = row.get(PalmaeProtologueImport.SPECIES).trim();
  75                                 taxonId = row.get(PalmaeProtologueImport.TAXONID);
  76                                 linkProto= row.get(PalmaeProtologueImport.LINK_PROTO).trim();
  77                                 taxonNameBase = (TaxonNameBase)getCommonService().getSourcedObjectByIdInSource(TaxonNameBase.class, "palm_tn_" + taxonId.replace(".0", ""), "TaxonName");
  78                         }catch (Exception e){
  79                                 logger.error("The row has errors: rowNumber: " +count + ", content: "  + row, e);
  80                         }
  81
  82
  83
  84                         if(taxonNameBase == null){
  85                                 logger.warn("no taxon with this name found: " + species + ", idInSource: " + taxonId);
  86                         }else{
  87
  88                                 URI uri;
  89                                 try {
  90                                         uri = new URI(linkProto);
  91                                         MediaRepresentationPart representationPart = MediaRepresentationPart.NewInstance(uri, 0);
  92                                         MediaRepresentation representation = MediaRepresentation.NewInstance("text/html", null);
  93                                         representation.addRepresentationPart(representationPart);
  94
  95                                         Media media = Media.NewInstance();
  96                                         media.addRepresentation(representation);
  97
  98                                         TaxonNameDescription description = TaxonNameDescription.NewInstance();
  99                                         TextData protolog = TextData.NewInstance(Feature.PROTOLOGUE());
 100                                         protolog.addMedia(media);
 101                                         description.addElement(protolog);
 102                                         taxonNameBase.addDescription(description);
 103                                 } catch (URISyntaxException e) {
 104                                         String message= "URISyntaxException when trying to convert: " + linkProto;
 105                                         logger.error(message);
 106                                         e.printStackTrace();
 107                                 }
 108
 109                                 taxonNameStore.add(taxonNameBase);
 110                                 if(count % 50 == 0){
 111                                         logger.info(count + " protologues processed.");
 112                                 }
 113                         }
 114                 }
 115
 116
 117                 getNameService().save(taxonNameStore);
 118                 logger.info(count + " protologues imported to CDM store.");
 119
 120                 return;
 121         }
 122
 123 }