2 * Copyright (C) 2007 EDIT
3 * European Distributed Institute of Taxonomy
4 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.cdm
.io
.faunaEuropaea
;
12 import java
.sql
.ResultSet
;
13 import java
.sql
.SQLException
;
14 import java
.util
.HashMap
;
17 import org
.apache
.log4j
.Logger
;
18 import org
.springframework
.stereotype
.Component
;
20 import eu
.etaxonomy
.cdm
.common
.ResultWrapper
;
21 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
22 import eu
.etaxonomy
.cdm
.model
.description
.PresenceAbsenceTermBase
;
23 import eu
.etaxonomy
.cdm
.model
.description
.PresenceTerm
;
24 import eu
.etaxonomy
.cdm
.model
.location
.NamedArea
;
25 import eu
.etaxonomy
.cdm
.model
.location
.TdwgArea
;
26 import eu
.etaxonomy
.cdm
.model
.name
.HybridRelationshipType
;
27 import eu
.etaxonomy
.cdm
.model
.name
.Rank
;
28 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignationStatus
;
29 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationshipType
;
30 import eu
.etaxonomy
.cdm
.strategy
.exceptions
.UnknownCdmTypeException
;
33 * @author a.babadshanjan
38 public final class FaunaEuropaeaTransformer
{
39 private static final Logger logger
= Logger
.getLogger(FaunaEuropaeaTransformer
.class);
42 public static final int Q_NO_RESTRICTION
= -1;
45 public static final int T_STATUS_ACCEPTED
= 1;
46 public static final int T_STATUS_NOT_ACCEPTED
= 0;
49 public static final int A_AUCT
= 1;
52 public static final int P_PARENTHESIS
= 1;
55 public static final int R_KINGDOM
= 1;
56 public static final int R_SUBKINGDOM
= 2;
57 public static final int R_SUPERPHYLUM
= 3;
58 public static final int R_PHYLUM
= 4;
59 public static final int R_SUBPHYLUM
= 5;
60 public static final int R_INFRAPHYLUM
= 6;
61 public static final int R_CLASS
= 7;
62 public static final int R_SUBCLASS
= 8;
63 public static final int R_INFRACLASS
= 9;
64 public static final int R_SUPERORDER
= 10;
65 public static final int R_ORDER
= 11;
66 public static final int R_SUBORDER
= 12;
67 public static final int R_INFRAORDER
= 13;
68 public static final int R_SUPERFAMILY
= 14;
69 public static final int R_FAMILY
= 15;
70 public static final int R_SUBFAMILY
= 16;
71 public static final int R_TRIBE
= 17;
72 public static final int R_SUBTRIBE
= 18;
73 public static final int R_GENUS
= 19;
74 public static final int R_SUBGENUS
= 20;
75 public static final int R_SPECIES
= 21;
76 public static final int R_SUBSPECIES
= 22;
78 private static Map
<String
, String
> tdwgAreas
= null;
80 public static PresenceAbsenceTermBase
<?
> occStatus2PresenceAbsence (int occStatusId
) throws UnknownCdmTypeException
{
83 case 110: return PresenceTerm
.CULTIVATED_REPORTED_IN_ERROR();
84 case 120: return PresenceTerm
.CULTIVATED();
85 case 210: return PresenceTerm
.INTRODUCED_REPORTED_IN_ERROR();
86 case 220: return PresenceTerm
.INTRODUCED_PRESENCE_QUESTIONABLE();
87 case 230: return PresenceTerm
.INTRODUCED_FORMERLY_INTRODUCED();
88 case 240: return PresenceTerm
.INTRODUCED_DOUBTFULLY_INTRODUCED();
89 case 250: return PresenceTerm
.INTRODUCED();
90 case 260: return PresenceTerm
.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
91 case 270: return PresenceTerm
.INTRODUCED_ADVENTITIOUS();
92 case 280: return PresenceTerm
.INTRODUCED_NATURALIZED();
93 case 310: return PresenceTerm
.NATIVE_REPORTED_IN_ERROR();
94 case 320: return PresenceTerm
.NATIVE_PRESENCE_QUESTIONABLE();
95 case 330: return PresenceTerm
.NATIVE_FORMERLY_NATIVE();
96 case 340: return PresenceTerm
.NATIVE_DOUBTFULLY_NATIVE();
97 case 350: return PresenceTerm
.NATIVE();
99 logger
.warn("endemic for EM can not be transformed in legal status");
101 return PresenceTerm
.PRESENT();
104 throw new UnknownCdmTypeException("Unknown occurrence status (id=" + Integer
.valueOf(occStatusId
).toString() + ")");
110 public static Rank
rankId2Rank (ResultSet rs
, boolean useUnknown
) throws UnknownCdmTypeException
{
113 int rankId
= rs
.getInt("rnk_id");
114 int parentRankId
= rs
.getInt("rnk_rnk_id");
115 String rankName
= rs
.getString("rnk_name");
116 String rankLatinName
= rs
.getString("rnk_latinname");
117 int rankCategory
= rs
.getInt("rnk_category");
119 if (logger
.isDebugEnabled()) {
120 logger
.debug(rankId
+ ", " + parentRankId
+ ", " + rankName
+ ", " + rankCategory
);
124 result
= Rank
.getRankByNameOrAbbreviation(rankName
);
125 } catch (UnknownCdmTypeException e1
) {
129 case R_KINGDOM
: return Rank
.KINGDOM();
130 case R_SUBKINGDOM
: return Rank
.SUBKINGDOM();
131 case R_SUPERPHYLUM
: return Rank
.SUPERPHYLUM();
132 case R_PHYLUM
: return Rank
.PHYLUM();
133 case R_SUBPHYLUM
: return Rank
.SUBPHYLUM();
134 case R_INFRAPHYLUM
: return Rank
.INFRAPHYLUM();
135 case R_CLASS
: return Rank
.CLASS();
136 case R_SUBCLASS
: return Rank
.SUBCLASS();
137 case R_INFRACLASS
: return Rank
.INFRACLASS();
138 case R_SUPERORDER
: return Rank
.SUPERORDER();
139 case R_ORDER
: return Rank
.ORDER();
140 case R_SUBORDER
: return Rank
.SUBORDER();
141 case R_INFRAORDER
: return Rank
.INFRAORDER();
142 case R_SUPERFAMILY
: return Rank
.SUPERFAMILY();
143 case R_FAMILY
: return Rank
.FAMILY();
144 case R_SUBFAMILY
: return Rank
.SUBFAMILY();
145 case R_TRIBE
: return Rank
.TRIBE();
146 case R_SUBTRIBE
: return Rank
.SUBTRIBE();
147 case R_GENUS
: return Rank
.GENUS();
148 case R_SUBGENUS
: return Rank
.SUBGENUS();
149 case R_SPECIES
: return Rank
.SPECIES();
150 case R_SUBSPECIES
: return Rank
.SUBSPECIES();
154 logger
.error("Rank unknown. Created UNKNOWN_RANK");
155 return Rank
.UNKNOWN_RANK();
157 throw new UnknownCdmTypeException("Unknown Rank id" + Integer
.valueOf(rankId
).toString());
162 } catch (SQLException e
) {
164 logger
.warn("Exception occurred. Created UNKNOWN_RANK instead");
165 return Rank
.UNKNOWN_RANK();
170 public static NamedArea
areaId2TdwgArea (ResultSet rs
) throws UnknownCdmTypeException
{
172 NamedArea tdwgArea
= null;
175 int areaId
= rs
.getInt("ara_id");
176 String areaName
= rs
.getString("ara_name");
177 String areaCode
= rs
.getString("ara_code");
178 int extraLimital
= rs
.getInt("ara_extralimital");
180 //TODO: Verify mappings with comments. Are those the best matches?
182 if (areaCode
.equals("AD")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SPA-AN");
183 else if (areaCode
.equals("AFR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa
184 else if (areaCode
.equals("AL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ALB-OO");
185 else if (areaCode
.equals("AT")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("AUT-AU");
186 else if (areaCode
.equals("AUS")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("50"); // Australian region - Australia
187 else if (areaCode
.equals("BA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("YUG-BH");
188 else if (areaCode
.equals("BE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BGM-BE");
189 else if (areaCode
.equals("BG")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BUL-OO");
190 else if (areaCode
.equals("BY")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLR-OO");
191 else if (areaCode
.equals("CH")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SWI-OO");
192 else if (areaCode
.equals("CY")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("CYP-OO");
193 else if (areaCode
.equals("CZ")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("CZE-CZ");
194 else if (areaCode
.equals("DE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("GER-OO");
195 else if (areaCode
.equals("DK-DEN")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("DEN-OO");
196 else if (areaCode
.equals("DK-FOR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("FOR-OO");
197 else if (areaCode
.equals("EE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLT-ES");
198 else if (areaCode
.equals("EPA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("Palaearctic");
199 else if (areaCode
.equals("ES-BAL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLT-ES");
200 else if (areaCode
.equals("ES-CNY")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("CNY-OO");
201 else if (areaCode
.equals("ES-SPA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SPA-SP");
202 else if (areaCode
.equals("FI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("FIN-OO");
203 else if (areaCode
.equals("FR-COR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("COR-OO");
204 else if (areaCode
.equals("FR-FRA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("FRA-FR");
205 else if (areaCode
.equals("GB-CI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("FRA-CI");
206 else if (areaCode
.equals("GB-GI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SPA-GI");
207 else if (areaCode
.equals("GB-GRB")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("GRB-OO");
208 else if (areaCode
.equals("GB-NI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("IRE-NI");
209 else if (areaCode
.equals("GR-AEG")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is.
210 else if (areaCode
.equals("GR-CYC")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece
211 else if (areaCode
.equals("GR-DOD")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is.
212 else if (areaCode
.equals("GR-GRC")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("GRC-OO");
213 else if (areaCode
.equals("GR-KRI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("KRI-OO");
214 else if (areaCode
.equals("HR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("YUG-CR");
215 else if (areaCode
.equals("HU")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("HUN-OO");
216 else if (areaCode
.equals("IE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("IRE-IR");
217 else if (areaCode
.equals("IS")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ICE-OO");
218 else if (areaCode
.equals("IT-ITA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ITA-IT");
219 else if (areaCode
.equals("IT-SAR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SAR-OO");
220 else if (areaCode
.equals("IT-SI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SIC-SI");
221 else if (areaCode
.equals("LI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("AUT-LI");
222 else if (areaCode
.equals("LT")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLT-LI");
223 else if (areaCode
.equals("LU")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BGM-LU");
224 else if (areaCode
.equals("LV")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLT-LA");
225 else if (areaCode
.equals("MC")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("FRA-MO");
226 else if (areaCode
.equals("MD")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("UKR-MO");
227 else if (areaCode
.equals("MK")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("YUG-MA");
228 else if (areaCode
.equals("MT")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SIC-MA");
229 else if (areaCode
.equals("NAF")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("20"); // North Africa - Northern Africa
230 else if (areaCode
.equals("NEA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("7"); // Nearctic region - Northern America
231 else if (areaCode
.equals("NEO")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("8"); // Neotropical region - Southern America
232 else if (areaCode
.equals("NL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("NET-OO");
233 else if (areaCode
.equals("NO-NOR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("NOR-OO");
234 else if (areaCode
.equals("NO-SVA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SVA-OO");
235 else if (areaCode
.equals("NRE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("34"); // Near East - Western Asia
236 else if (areaCode
.equals("ORR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("35"); // Oriental region - Arabian Peninsula
237 else if (areaCode
.equals("PL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("POL-OO");
238 else if (areaCode
.equals("PT-AZO")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("AZO-OO");
239 else if (areaCode
.equals("PT-MDR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("MDR-OO");
240 else if (areaCode
.equals("PT-POR")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("POR-OO");
241 else if (areaCode
.equals("PT-SEL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SEL-OO");
242 else if (areaCode
.equals("RO")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ROM-OO");
243 else if (areaCode
.equals("RU-FJL")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("WSB-OO");
244 else if (areaCode
.equals("RU-KGD")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("BLT-KA");
245 else if (areaCode
.equals("RU-NOZ")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("WSB-OO");
246 else if (areaCode
.equals("RU-RUC")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("RUC-OO");
247 else if (areaCode
.equals("RU-RUE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("RUE-OO");
248 else if (areaCode
.equals("RU-RUN")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("RUN-OO");
249 else if (areaCode
.equals("RU-RUS")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("RUS-OO");
250 else if (areaCode
.equals("RU-RUW")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("RUW-OO");
251 else if (areaCode
.equals("SE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("SWE-OO");
252 else if (areaCode
.equals("SI")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("YUG-SL");
253 else if (areaCode
.equals("SK")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("CZE-SK");
254 else if (areaCode
.equals("SM")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ITA-SM");
255 else if (areaCode
.equals("TR-TUE")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("TUE-OO");
256 else if (areaCode
.equals("UA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("UKR-UK");
257 else if (areaCode
.equals("VA")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("ITA-VC");
258 else if (areaCode
.equals("YU")) tdwgArea
= TdwgArea
.getAreaByTdwgAbbreviation("YUG");
260 throw new UnknownCdmTypeException("Unknown Area " + areaCode
);
263 if (logger
.isDebugEnabled()) {
264 logger
.debug(areaId
+ ", " + areaName
+ ", " + areaCode
+ ", " + extraLimital
);
267 } catch (SQLException e
) {
269 logger
.warn("Exception occurred. Area could not be mapped.");