| 1 |
91904a96
|
Andreas Müller
|
/**
|
| 2 |
|
|
* Copyright (C) 2009 EDIT
|
| 3 |
7d882578
|
Andreas Müller
|
* European Distributed Institute of Taxonomy
|
| 4 |
91904a96
|
Andreas Müller
|
* http://www.e-taxonomy.eu
|
| 5 |
7d882578
|
Andreas Müller
|
*
|
| 6 |
91904a96
|
Andreas Müller
|
* 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.wp6;
|
| 11 |
|
|
|
| 12 |
|
|
import java.util.ArrayList;
|
| 13 |
|
|
import java.util.HashMap;
|
| 14 |
|
|
import java.util.List;
|
| 15 |
|
|
import java.util.Map;
|
| 16 |
|
|
import java.util.regex.Matcher;
|
| 17 |
|
|
import java.util.regex.Pattern;
|
| 18 |
|
|
|
| 19 |
|
|
import org.apache.commons.lang.StringUtils;
|
| 20 |
|
|
import org.apache.log4j.Logger;
|
| 21 |
|
|
|
| 22 |
7d882578
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
| 23 |
91904a96
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
| 24 |
|
|
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
|
| 25 |
|
|
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
|
| 26 |
|
|
|
| 27 |
|
|
/**
|
| 28 |
|
|
* @author a.babadshanjan
|
| 29 |
|
|
* @created 13.01.2009
|
| 30 |
|
|
* @version 1.0
|
| 31 |
|
|
*/
|
| 32 |
|
|
public class CommonNameRow {
|
| 33 |
|
|
private static final Logger logger = Logger.getLogger(CommonNameRow.class);
|
| 34 |
|
|
|
| 35 |
|
|
|
| 36 |
|
|
private String species;
|
| 37 |
|
|
private String reference;
|
| 38 |
|
|
private String area;
|
| 39 |
218a4795
|
Andreas Müller
|
private String nameUsedInSource;
|
| 40 |
7d882578
|
Andreas Müller
|
|
| 41 |
91904a96
|
Andreas Müller
|
private Map<String, List<String>> commonNames = new HashMap<String, List<String>>();
|
| 42 |
7d882578
|
Andreas Müller
|
|
| 43 |
|
|
|
| 44 |
91904a96
|
Andreas Müller
|
public CommonNameRow() {
|
| 45 |
|
|
this.species = "";
|
| 46 |
|
|
this.reference = "";
|
| 47 |
|
|
this.area = "";
|
| 48 |
|
|
commonNames = new HashMap<String, List<String>>();
|
| 49 |
|
|
}
|
| 50 |
7d882578
|
Andreas Müller
|
|
| 51 |
|
|
// **************************** GETTER / SETTER *********************************/
|
| 52 |
|
|
|
| 53 |
91904a96
|
Andreas Müller
|
public void setCommonNames(String commonNamesString){
|
| 54 |
218a4795
|
Andreas Müller
|
commonNamesString = makeNameUsedInSource(commonNamesString);
|
| 55 |
91904a96
|
Andreas Müller
|
String[] split = commonNamesString.split(";");
|
| 56 |
|
|
for (String oneLanguage : split){
|
| 57 |
|
|
oneLanguage = oneLanguage.trim();
|
| 58 |
34b56211
|
Andreas Müller
|
String reLangPattern = "\\((\\*|[a-z]{2,3}|.{2,},\\sno\\sISO-Code)\\)$";
|
| 59 |
91904a96
|
Andreas Müller
|
String pattern = ".+" + reLangPattern;
|
| 60 |
|
|
if (! oneLanguage.matches(pattern)){
|
| 61 |
|
|
logger.warn("Common name does not match: " + oneLanguage);
|
| 62 |
|
|
}else{
|
| 63 |
|
|
Pattern langPattern = Pattern.compile(reLangPattern);
|
| 64 |
|
|
Matcher matcher = langPattern.matcher(oneLanguage);
|
| 65 |
|
|
if (matcher.find()){
|
| 66 |
|
|
String lang = matcher.group().substring(1);
|
| 67 |
|
|
lang = lang.substring(0, lang.length()-1);
|
| 68 |
|
|
String names = "";
|
| 69 |
|
|
try {
|
| 70 |
|
|
names = oneLanguage.substring(0,matcher.start()-1);
|
| 71 |
|
|
} catch (Exception e) {
|
| 72 |
|
|
e.printStackTrace();
|
| 73 |
|
|
}
|
| 74 |
|
|
String[] splitNames = names.split(",");
|
| 75 |
|
|
List<String> nameList = new ArrayList<String>();
|
| 76 |
|
|
for (String singleName : splitNames){
|
| 77 |
|
|
if (StringUtils.isNotBlank(singleName)){
|
| 78 |
|
|
nameList.add(singleName.trim());
|
| 79 |
|
|
}
|
| 80 |
|
|
}
|
| 81 |
|
|
if (!nameList.isEmpty()){
|
| 82 |
|
|
this.commonNames.put(lang, nameList);
|
| 83 |
|
|
}
|
| 84 |
|
|
}else{
|
| 85 |
|
|
logger.warn("Common name does not match: " + oneLanguage);
|
| 86 |
|
|
}
|
| 87 |
|
|
}
|
| 88 |
|
|
}
|
| 89 |
|
|
}
|
| 90 |
7d882578
|
Andreas Müller
|
|
| 91 |
218a4795
|
Andreas Müller
|
private String makeNameUsedInSource(String commonNamesString) {
|
| 92 |
|
|
String[] split = commonNamesString.split(":");
|
| 93 |
|
|
if (split.length > 1){
|
| 94 |
001bef66
|
Andreas Müller
|
logger.debug("NameUsedInSource: " + split[0]);
|
| 95 |
218a4795
|
Andreas Müller
|
this.nameUsedInSource = split[0].trim();
|
| 96 |
|
|
if (split.length > 2){
|
| 97 |
|
|
logger.warn("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX:" + commonNamesString);
|
| 98 |
|
|
}
|
| 99 |
|
|
return split[1].trim();
|
| 100 |
|
|
}else{
|
| 101 |
|
|
return split[0].trim();
|
| 102 |
|
|
}
|
| 103 |
|
|
}
|
| 104 |
|
|
|
| 105 |
91904a96
|
Andreas Müller
|
public Map<String, List<String>> getCommonNames() {
|
| 106 |
|
|
return commonNames;
|
| 107 |
|
|
}
|
| 108 |
7d882578
|
Andreas Müller
|
|
| 109 |
91904a96
|
Andreas Müller
|
public void parseSpecies(String species){
|
| 110 |
7d882578
|
Andreas Müller
|
INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();
|
| 111 |
|
|
IBotanicalName name = (IBotanicalName)parser.parseFullName(species, NomenclaturalCode.ICNAFP, null);
|
| 112 |
91904a96
|
Andreas Müller
|
if (name.isProtectedTitleCache()){
|
| 113 |
|
|
logger.warn("Name could not be parsed: " + species);
|
| 114 |
|
|
}
|
| 115 |
c273c734
|
Andreas Müller
|
this.species = species;
|
| 116 |
91904a96
|
Andreas Müller
|
}
|
| 117 |
|
|
|
| 118 |
|
|
public String getSpecies() {
|
| 119 |
|
|
return species;
|
| 120 |
|
|
}
|
| 121 |
7d882578
|
Andreas Müller
|
|
| 122 |
91904a96
|
Andreas Müller
|
public void setSpecies(String species) {
|
| 123 |
|
|
this.species = species;
|
| 124 |
|
|
}
|
| 125 |
|
|
|
| 126 |
|
|
public void setReference(String reference) {
|
| 127 |
|
|
reference = reference.replace(".", "");
|
| 128 |
|
|
if (! reference.matches("\\d{7}")){
|
| 129 |
|
|
logger.warn("Unexpected reference");
|
| 130 |
|
|
}
|
| 131 |
218a4795
|
Andreas Müller
|
this.reference = reference.substring(0,6);
|
| 132 |
91904a96
|
Andreas Müller
|
}
|
| 133 |
|
|
|
| 134 |
|
|
public String getReference() {
|
| 135 |
|
|
return reference;
|
| 136 |
|
|
}
|
| 137 |
|
|
|
| 138 |
|
|
public void setArea(String area) {
|
| 139 |
|
|
this.area = area;
|
| 140 |
|
|
}
|
| 141 |
7d882578
|
Andreas Müller
|
|
| 142 |
91904a96
|
Andreas Müller
|
public String getArea() {
|
| 143 |
|
|
return area;
|
| 144 |
|
|
}
|
| 145 |
|
|
|
| 146 |
218a4795
|
Andreas Müller
|
public void setNameUsedInSource(String nameUsedInSource) {
|
| 147 |
|
|
this.nameUsedInSource = nameUsedInSource;
|
| 148 |
|
|
}
|
| 149 |
|
|
|
| 150 |
|
|
public String getNameUsedInSource() {
|
| 151 |
|
|
return nameUsedInSource;
|
| 152 |
|
|
}
|
| 153 |
|
|
|
| 154 |
91904a96
|
Andreas Müller
|
|
| 155 |
7d882578
|
Andreas Müller
|
|
| 156 |
91904a96
|
Andreas Müller
|
}
|