cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/identifier/IdentifierImport.java

   1 /**
   2 * Copyright (C) 2017 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.identifier;
  10
  11 import java.io.File;
  12 import java.io.IOException;
  13 import java.io.InputStreamReader;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Set;
  17 import java.util.UUID;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import au.com.bytecode.opencsv.CSVReader;
  24 import eu.etaxonomy.cdm.io.common.SimpleImport;
  25 import eu.etaxonomy.cdm.model.common.CdmBase;
  26 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  27 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  28 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  29 import eu.etaxonomy.cdm.model.common.Identifier;
  30 import eu.etaxonomy.cdm.model.common.TermType;
  31
  32 /**
  33  * Imports identifiers for a certain {@link IdentifiableEntity} class from a csv
  34  * file. The class and the identifier type are defined in the configurator.
  35  *
  36  * The csv file has to follow the following format:
  37  * <BR><BR>
  38  * 1. field: uuid of the {@link IdentifiableEntity} of class defined in configurator<BR>
  39  * 2. The value of the identifier (of type defined in configurator)<BR>
  40  *
  41  * NOTE: This import was first written for #6542
  42  * NOTE 2: TODO It was observed that the last line was not imported.
  43  *
  44  * @author a.mueller
  45  * @date 25.03.2017
  46  */
  47 @Component
  48 public class IdentifierImport
  49         extends SimpleImport<IdentifierImportConfigurator, File>{
  50
  51     private static final long serialVersionUID = 5797541146159665997L;
  52     private static Logger logger = Logger.getLogger(IdentifierImport.class);
  53
  54     /**
  55      * {@inheritDoc}
  56      */
  57     @Override
  58     protected void doInvoke(IdentifierImportConfigurator config) {
  59         try {
  60             InputStreamReader inputReader = config.getSource();
  61             CSVReader csvReader = new CSVReader(inputReader, ';');
  62             List<String[]> lines = csvReader.readAll();
  63             if (lines.isEmpty()){
  64                 logger.info("Import file is empty");
  65                 csvReader.close();
  66                 return;
  67             }
  68
  69             @SuppressWarnings("rawtypes")
  70             Set<IdentifiableEntity> entitiesToSave = new HashSet<>();
  71
  72             UUID identifierTypeUuid = config.getIdentifierTypeUuid();
  73
  74             DefinedTermBase<?> identifierType = getTermService().find(identifierTypeUuid);
  75             if (identifierType == null || identifierType.getTermType() != TermType.IdentifierType){
  76                 logger.warn("IdentifierType not recognized. Skip import");
  77                 csvReader.close();
  78                 return;
  79             }
  80             DefinedTerm idType = CdmBase.deproxy(identifierType, DefinedTerm.class);
  81
  82             int i = 0;
  83             for (String[] strs : lines){
  84                 IdentifiableEntity<?> entity = handleSingleLine(config, strs, idType, i);
  85                 if (entity != null){
  86                     entitiesToSave.add(entity);
  87                 }
  88                 i++;
  89             }
  90             csvReader.close();
  91
  92             //not needed as the objects update automatically during transactions in handleSingleLine()
  93 //            getCommonService().saveOrUpdate(entitiesToSave);
  94
  95         } catch (IOException e) {
  96             throw new RuntimeException(e);
  97         }
  98     }
  99
 100     /**
 101      * @param config configurator
 102      * @param strs text array for given line
 103      * @param i line counter
 104      * @return
 105      */
 106     private IdentifiableEntity<?> handleSingleLine(IdentifierImportConfigurator config, String[] strs,
 107             DefinedTerm idType, int i) {
 108
 109         //no data
 110         if (strs.length < 1){
 111             String message = String.format(
 112                     "No data available in line %d. Skipped", i);
 113             logger.warn(message);
 114             return null;
 115         }
 116
 117         //entity uuid
 118         String uuidStr = strs[0];
 119         UUID uuid;
 120         try {
 121             uuid = UUID.fromString(uuidStr);
 122         } catch (Exception e) {
 123             String message = String.format(
 124                     "Entity identifier not recognized as UUID in line %d. Skipped", i);
 125             logger.warn(message);
 126             return null;
 127         }
 128
 129         TransactionStatus tx = this.startTransaction();
 130         IdentifiableEntity<?> entity = getEntityFromRepository(config, uuid);
 131         if (entity == null){
 132             String message = String.format(
 133                     "Entity for uuid %s could not be found in line %d. Skipped", uuid.toString(), i);
 134             logger.warn(message);
 135             return null;
 136         }
 137
 138         //identifier value
 139         if (strs.length < 2){
 140             String message = String.format(
 141                     "Record in line %d has no identifier value information. Skipped", i);
 142             logger.warn(message);
 143             return null;
 144         }
 145         //skip column 1, it is for default language label, but not used during import
 146         String value = null;
 147         if (isNotBlank(strs[1])){
 148             value = strs[1];
 149         }
 150
 151         Identifier<?> identifier = Identifier.NewInstance(value, idType);
 152         entity.addIdentifier(identifier);
 153
 154         this.commitTransaction(tx);
 155         return entity;
 156     }
 157
 158     private IdentifiableEntity<?> getEntityFromRepository(IdentifierImportConfigurator config, UUID uuid) {
 159         IdentifiableEntity<?> result = getCommonService().find(config.getCdmClass(), uuid);
 160         return result;
 161     }
 162 }