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
.app
.vibrant
;
12 import java
.lang
.reflect
.Method
;
13 import java
.sql
.ResultSet
;
14 import java
.util
.UUID
;
16 import org
.apache
.log4j
.Logger
;
18 import eu
.etaxonomy
.cdm
.app
.berlinModelImport
.BerlinModelSources
;
19 import eu
.etaxonomy
.cdm
.app
.common
.CdmDestinations
;
20 import eu
.etaxonomy
.cdm
.database
.DatabaseTypeEnum
;
21 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
22 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
23 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelImportConfigurator
;
24 import eu
.etaxonomy
.cdm
.io
.common
.CdmDefaultImport
;
25 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.CHECK
;
26 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.DO_REFERENCES
;
27 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.EDITOR
;
28 import eu
.etaxonomy
.cdm
.io
.common
.Source
;
29 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
30 import eu
.etaxonomy
.cdm
.model
.common
.ExtensionType
;
31 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalCode
;
32 import eu
.etaxonomy
.cdm
.model
.name
.NonViralName
;
33 import eu
.etaxonomy
.cdm
.model
.name
.Rank
;
34 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
38 * TODO add the following to a wiki page:
39 * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
40 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
46 public class IopiActivator
{
47 private static final Logger logger
= Logger
.getLogger(IopiActivator
.class);
49 //database validation status (create, update, validate ...)
50 static DbSchemaValidation hbm2dll
= DbSchemaValidation
.CREATE
;
51 static final Source berlinModelSource
= BerlinModelSources
.iopi();
53 // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
54 static final ICdmDataSource cdmDestination
= cdm_test_local_iopi();
56 static final boolean useSingleClassification
= true;
57 static final Integer sourceSecId
= 1892; //7000000;
58 static final UUID classificationUuid
= null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
60 static final UUID sourceRefUuid
= UUID
.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
62 // set to zero for unlimited nameFacts
63 static final int maximumNumberOfNameFacts
= 0;
65 static final int partitionSize
= 1500;
68 static final CHECK check
= CHECK
.CHECK_AND_IMPORT
;
71 static final EDITOR editor
= EDITOR
.EDITOR_AS_EDITOR
;
74 static final NomenclaturalCode nomenclaturalCode
= NomenclaturalCode
.ICNAFP
;
77 static final boolean ignoreNull
= true;
79 static boolean useClassification
= true;
83 static String taxonTable
= "v_cdm_exp_taxaAll";
84 static String classificationQuery
= " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId
;
85 static String relPTaxonIdQuery
= " SELECT r.RelPTaxonId " +
86 " FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
87 static String nameIdTable
= " v_cdm_exp_namesAll ";
88 static String referenceIdTable
= " v_cdm_exp_refAll ";
89 static String factFilter
= " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
90 static String authorTeamFilter
= null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
91 static String authorFilter
= null; // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
93 static String occurrenceFilter
= " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
94 static String occurrenceSourceFilter
= " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
95 static String commonNameFilter
= " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
99 // **************** ALL *********************
102 static final boolean doAuthors
= true;
104 static final DO_REFERENCES doReferences
= DO_REFERENCES
.ALL
;
106 static final boolean doTaxonNames
= true;
107 static final boolean doRelNames
= true;
108 static final boolean doNameStatus
= true;
111 static final boolean doTaxa
= true;
112 static final boolean doRelTaxa
= true;
113 static final boolean doFacts
= true;
118 // **************** SELECTED *********************
120 // static final boolean doUser = true;
122 // static final boolean doAuthors = false;
124 // static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
126 // static final boolean doTaxonNames = false;
127 // static final boolean doRelNames = false;
128 // static final boolean doNameStatus = false;
129 // static final boolean doTypes = false;
130 // static final boolean doNameFacts = false;
133 // static final boolean doTaxa = false;
134 // static final boolean doRelTaxa = false;
135 // static final boolean doFacts = false;
138 // static final boolean doMarker = false;
141 //******** ALWAYS IGNORE *****************************
143 static final boolean doUser
= false;
144 static final boolean doOccurences
= false;
145 static final boolean doCommonNames
= false;
146 static final boolean doTypes
= false;
147 static final boolean doNameFacts
= false;
148 static final boolean doMarker
= false;
151 public void importIopi (Source source
, ICdmDataSource destination
, DbSchemaValidation hbm2dll
){
152 System
.out
.println("Start import from BerlinModel("+ berlinModelSource
.getDatabase() + ") to " + cdmDestination
.getDatabase() + " ...");
153 //make BerlinModel Source
155 BerlinModelImportConfigurator config
= BerlinModelImportConfigurator
.NewInstance(source
, destination
);
157 config
.setClassificationUuid(classificationUuid
);
158 config
.setSourceSecId(sourceSecId
);
160 config
.setNomenclaturalCode(nomenclaturalCode
);
163 Method makeUrlMethod
= this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase
.class, ResultSet
.class);
164 config
.setMakeUrlForTaxon(makeUrlMethod
);
165 } catch (Exception e
) {
170 config
.setIgnoreNull(ignoreNull
);
171 config
.setDoAuthors(doAuthors
);
172 config
.setDoReferences(doReferences
);
173 config
.setDoTaxonNames(doTaxonNames
);
174 config
.setDoRelNames(doRelNames
);
175 config
.setDoNameStatus(doNameStatus
);
176 config
.setDoTypes(doTypes
);
177 config
.setDoNameFacts(doNameFacts
);
178 config
.setUseClassification(useClassification
);
179 config
.setSourceRefUuid(sourceRefUuid
);
181 config
.setDoTaxa(doTaxa
);
182 config
.setDoRelTaxa(doRelTaxa
);
183 config
.setDoFacts(doFacts
);
184 config
.setDoOccurrence(doOccurences
);
185 config
.setDoCommonNames(doCommonNames
);
187 config
.setDoMarker(doMarker
);
188 config
.setDoUser(doUser
);
189 config
.setEditor(editor
);
190 config
.setDbSchemaValidation(hbm2dll
);
192 // maximum number of name facts to import
193 config
.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts
);
195 config
.setUseSingleClassification(useSingleClassification
);
197 config
.setCheck(check
);
198 config
.setEditor(editor
);
199 config
.setRecordsPerTransaction(partitionSize
);
202 config
.setTaxonTable(taxonTable
);
203 config
.setClassificationQuery(classificationQuery
);
204 config
.setRelTaxaIdQuery(relPTaxonIdQuery
);
205 config
.setNameIdTable(nameIdTable
);
206 config
.setReferenceIdTable(referenceIdTable
);
207 config
.setAuthorTeamFilter(authorTeamFilter
);
208 config
.setAuthorFilter(authorFilter
);
209 config
.setFactFilter(factFilter
);
210 config
.setCommonNameFilter(commonNameFilter
);
211 config
.setOccurrenceFilter(occurrenceFilter
);
212 config
.setOccurrenceSourceFilter(occurrenceSourceFilter
);
213 config
.setUseSingleClassification(useSingleClassification
);
218 CdmDefaultImport
<BerlinModelImportConfigurator
> bmImport
= new CdmDefaultImport
<BerlinModelImportConfigurator
>();
219 bmImport
.invoke(config
);
221 System
.out
.println("End import from BerlinModel ("+ source
.getDatabase() + ")...");
228 public static void main(String
[] args
) {
229 IopiActivator importActivator
= new IopiActivator();
230 Source source
= berlinModelSource
;
231 ICdmDataSource cdmRepository
= CdmDestinations
.chooseDestination(args
) != null ? CdmDestinations
.chooseDestination(args
) : cdmDestination
;
233 importActivator
.importIopi(source
, cdmRepository
, hbm2dll
);
237 public static ICdmDataSource
cdm_test_local_iopi(){
238 DatabaseTypeEnum dbType
= DatabaseTypeEnum
.MySQL
;
239 String cdmServer
= "127.0.0.1";
240 String cdmDB
= "iopi";
241 String cdmUserName
= "root";
242 return CdmDestinations
.makeDestination(dbType
, cdmServer
, cdmDB
, -1, cdmUserName
, null);
246 //for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)
247 private static final String URLbase
= "http://rbg-web2.rbge.org.uk/cgi-bin/nph-readbtree.pl/feout?FAMILY_XREF=%s&GENUS_XREF=%s&SPECIES_XREF=%s&TAXON_NAME_XREF=%s&RANK=%s";
248 public static Method
makeUrlForTaxon(TaxonBase
<?
> taxon
, ResultSet rs
){
249 Method result
= null;
250 ExtensionType urlExtensionType
= ExtensionType
.URL();
255 String taxonName
= "";
258 NonViralName
<?
> name
= CdmBase
.deproxy(taxon
.getName(), NonViralName
.class);
259 Rank rank
= name
.getRank();
260 rankStr
= transformFeRanks(rank
);
263 if (rank
.equals(Rank
.FAMILY())){
264 family
= name
.getGenusOrUninomial();
265 taxonName
= name
.getGenusOrUninomial();
266 }else if (rank
.isHigher(Rank
.GENUS())){
267 taxonName
= name
.getGenusOrUninomial();
268 }else if (rank
.isGenus()){
269 genus
= name
.getGenusOrUninomial();
271 }else if (rank
.isInfraGeneric()){
272 genus
= name
.getGenusOrUninomial();
273 taxonName
= name
.getInfraGenericEpithet();
274 }else if (rank
.isSpecies()){
275 genus
= name
.getGenusOrUninomial();
276 species
= name
.getSpecificEpithet();
278 }else if (rank
.isInfraSpecific()){
279 genus
= name
.getGenusOrUninomial();
280 species
= name
.getSpecificEpithet();
281 taxonName
= name
.getInfraSpecificEpithet();
285 String url
= String
.format(URLbase
,family
, genus
, species
, taxonName
, rankStr
);
286 taxon
.addExtension(url
, urlExtensionType
);
291 private static String
transformFeRanks(Rank rank
){
292 if (rank
.equals(Rank
.SPECIESAGGREGATE())){ return "agg.";
293 }else if (rank
.equals(Rank
.CLASS())){ return "Class";
294 }else if (rank
.equals(Rank
.DIVISION())){ return "Division";
295 }else if (rank
.equals(Rank
.FAMILY())){ return "family";
296 }else if (rank
.equals(Rank
.FORM())){ return "forma";
297 }else if (rank
.equals(Rank
.GENUS())){ return "genus";
298 }else if (rank
.equals(Rank
.GREX())){ return "grex";
299 }else if (rank
.equals(Rank
.SPECIESGROUP())){ return "group";
300 }else if (rank
.equals(Rank
.ORDER())){ return "Order";
301 // }else if (rank.equals(Rank.PROL())){ return "proles";
302 //-- }else if (rank.equals(Rank.RACE())){ return "race";
303 }else if (rank
.equals(Rank
.SECTION_BOTANY())){ return "Sect.";
304 }else if (rank
.equals(Rank
.SERIES())){ return "Ser.";
305 }else if (rank
.equals(Rank
.SPECIES())){ return "species";
306 }else if (rank
.equals(Rank
.SUBCLASS())){ return "Subclass";
307 }else if (rank
.equals(Rank
.SUBDIVISION())){ return "Subdivision";
308 }else if (rank
.equals(Rank
.SUBFORM())){ return "Subf.";
309 }else if (rank
.equals(Rank
.SUBGENUS())){ return "Subgen.";
310 }else if (rank
.equals(Rank
.SUBORDER())){ return "Suborder";
311 }else if (rank
.equals(Rank
.SUBSECTION_BOTANY())){ return "Subsect.";
312 }else if (rank
.equals(Rank
.SUBSERIES())){ return "Subser.";
313 }else if (rank
.equals(Rank
.SUBSPECIES())){ return "subsp";
314 }else if (rank
.equals(Rank
.SUBVARIETY())){ return "subvar.";
315 }else if (rank
.equals(Rank
.SUPERORDER())){ return "Superorder";
316 }else if (rank
.equals(Rank
.TRIBE())){ return "Tribe";
317 }else if (rank
.equals(Rank
.VARIETY())){ return "var.";
319 logger
.debug("Rank not found: " + rank
.getTitleCache());