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
.wp6
.cichorieae
;
14 import java
.net
.URISyntaxException
;
15 import java
.util
.UUID
;
17 import org
.apache
.log4j
.Logger
;
19 import eu
.etaxonomy
.cdm
.api
.application
.ICdmRepository
;
20 import eu
.etaxonomy
.cdm
.app
.berlinModelImport
.BerlinModelSources
;
21 import eu
.etaxonomy
.cdm
.app
.berlinModelImport
.TreeCreator
;
22 import eu
.etaxonomy
.cdm
.app
.common
.CdmDestinations
;
23 import eu
.etaxonomy
.cdm
.app
.images
.ImageImportConfigurator
;
24 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
25 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
26 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelImportConfigurator
;
27 import eu
.etaxonomy
.cdm
.io
.common
.CdmDefaultImport
;
28 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
;
29 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.CHECK
;
30 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.DO_REFERENCES
;
31 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.EDITOR
;
32 import eu
.etaxonomy
.cdm
.io
.common
.ImportResult
;
33 import eu
.etaxonomy
.cdm
.io
.common
.Source
;
34 import eu
.etaxonomy
.cdm
.io
.wp6
.CichorieaeImageImport
;
35 import eu
.etaxonomy
.cdm
.model
.common
.ISourceable
;
36 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
37 import eu
.etaxonomy
.cdm
.model
.description
.FeatureNode
;
38 import eu
.etaxonomy
.cdm
.model
.description
.FeatureTree
;
39 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalCode
;
40 import eu
.etaxonomy
.cdm
.model
.name
.TaxonName
;
44 * TODO add the following to a wiki page:
45 * 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
46 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
52 public class CichorieaeActivator
{
53 private static final Logger logger
= Logger
.getLogger(CichorieaeActivator
.class);
55 //database validation status (create, update, validate ...)
56 static DbSchemaValidation hbm2dll
= DbSchemaValidation
.CREATE
;
57 static final Source berlinModelSource
= BerlinModelSources
.EDIT_CICHORIEAE();
58 static final ICdmDataSource cdmDestination
= CdmDestinations
.cdm_test_local_mysql_test();
60 static final UUID secUuid
= UUID
.fromString("6924c75d-e0d0-4a6d-afb7-3dd8c71195ca");
61 static final UUID classificationUuid
= UUID
.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");
62 // static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9");
63 static final int sourceSecId
= 7800000;
65 static final UUID featureTreeUuid
= UUID
.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");
66 static final Object
[] featureKeyList
= new Integer
[]{1, 43, 31, 4, 12, 98, 41};
68 /* --------- MEDIA recources ------------ */
69 static final boolean stopOnMediaErrors
= false;
70 static final String protologueUrlString
= "http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/";
72 //static final File protologuePath = new File("/Volumes/protolog/protolog/");
74 public static final String imageFolderString
= "//media/editwp6/photos";
75 static final File protologuePath
= new File("//media/editwp6/protolog");
76 // public static final File imageFolder = new File("/media/photos");
77 // static final File protologuePath = new File("/media/protolog");
78 /* -------------------------------------- */
80 // set to zero for unlimited nameFacts
81 static final int maximumNumberOfNameFacts
= 0;
82 static final int recordsPerTransaction
= 2000;
84 //should the other imports run as well?
85 static final boolean includeTaraxacum
= true;
86 static final boolean includeImages
= false;
90 static final CHECK check
= CHECK
.CHECK_AND_IMPORT
;
93 static final EDITOR editor
= EDITOR
.EDITOR_AS_EDITOR
;
96 static final NomenclaturalCode nomenclaturalCode
= NomenclaturalCode
.ICNAFP
;
99 static final boolean ignoreNull
= true;
101 static boolean useClassification
= true;
104 // **************** ALL *********************
106 static final boolean doUser
= true;
108 static final boolean doAuthors
= true;
110 static final DO_REFERENCES doReferences
= DO_REFERENCES
.ALL
;
112 static final boolean doTaxonNames
= true;
113 static final boolean doRelNames
= true;
114 static final boolean doNameStatus
= true;
115 static final boolean doTypes
= true;
116 static final boolean doNameFacts
= true;
119 static final boolean doTaxa
= true;
120 static final boolean doRelTaxa
= true;
121 static final boolean doFacts
= false;
122 static final boolean doOccurences
= false;
123 static final boolean doCommonNames
= true;
126 static final boolean doMarker
= false;
129 // **************** SELECTED *********************
131 // static final boolean doUser = false;
133 // static final boolean doAuthors = false;
135 // static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
137 // static final boolean doTaxonNames = false;
138 // static final boolean doRelNames = false;
139 // static final boolean doNameStatus = false;
140 // static final boolean doTypes = false;
141 // static final boolean doNameFacts = false;
144 // static final boolean doTaxa = false;
145 // static final boolean doRelTaxa = false;
146 // static final boolean doCommonNames = false;
147 // static final boolean doFacts = false;
148 // static final boolean doOccurences = false;
151 // static final boolean doMarker = false;
154 private ImportResult
doInvoke(ICdmDataSource destination
){
155 ImportResult success
= new ImportResult();
156 Source source
= berlinModelSource
;
158 BerlinModelImportConfigurator bmImportConfigurator
= BerlinModelImportConfigurator
.NewInstance(source
, destination
);
160 bmImportConfigurator
.setClassificationUuid(classificationUuid
);
161 bmImportConfigurator
.setSourceSecId(sourceSecId
);
163 bmImportConfigurator
.setNomenclaturalCode(nomenclaturalCode
);
165 bmImportConfigurator
.setIgnoreNull(ignoreNull
);
166 bmImportConfigurator
.setDoAuthors(doAuthors
);
167 bmImportConfigurator
.setDoReferences(doReferences
);
168 bmImportConfigurator
.setDoTaxonNames(doTaxonNames
);
169 bmImportConfigurator
.setDoRelNames(doRelNames
);
170 bmImportConfigurator
.setDoNameStatus(doNameStatus
);
171 bmImportConfigurator
.setDoTypes(doTypes
);
172 bmImportConfigurator
.setDoNameFacts(doNameFacts
);
173 bmImportConfigurator
.setUseClassification(useClassification
);
175 bmImportConfigurator
.setDoTaxa(doTaxa
);
176 bmImportConfigurator
.setDoRelTaxa(doRelTaxa
);
177 bmImportConfigurator
.setDoFacts(doFacts
);
178 bmImportConfigurator
.setDoOccurrence(doOccurences
);
179 bmImportConfigurator
.setDoCommonNames(doCommonNames
);
181 bmImportConfigurator
.setDoMarker(doMarker
);
182 bmImportConfigurator
.setDoUser(doUser
);
183 bmImportConfigurator
.setEditor(editor
);
184 bmImportConfigurator
.setDbSchemaValidation(hbm2dll
);
185 bmImportConfigurator
.setRecordsPerTransaction(recordsPerTransaction
);
188 // protologueResourceLocations
189 if ( protologuePath
.exists() && protologuePath
.isDirectory()){
190 bmImportConfigurator
.setMediaUrl(protologueUrlString
);
191 bmImportConfigurator
.setMediaPath(protologuePath
);
193 if(stopOnMediaErrors
){
194 logger
.error("Could not configure protologue ResourceLocations -> will quit.");
197 logger
.error("Could not configure protologue ResourceLocations");
200 File imageFolder
= new File(imageFolderString
);
201 // also check the image source folder
202 if ( !imageFolder
.exists() || !imageFolder
.isDirectory()){
203 if(stopOnMediaErrors
){
204 logger
.error("Could not configure imageFolder -> will quit.");
207 logger
.error("Could not configure imageFolder");
210 // maximum number of name facts to import
211 bmImportConfigurator
.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts
);
214 bmImportConfigurator
.setCheck(check
);
215 bmImportConfigurator
.setEditor(editor
);
218 CdmDefaultImport
<BerlinModelImportConfigurator
> bmImport
= new CdmDefaultImport
<BerlinModelImportConfigurator
>();
219 success
= bmImport
.invoke(bmImportConfigurator
);
221 if (doFacts
&& (bmImportConfigurator
.getCheck().equals(CHECK
.CHECK_AND_IMPORT
) || bmImportConfigurator
.getCheck().equals(CHECK
.IMPORT_WITHOUT_CHECK
) ) ){
222 ICdmRepository app
= bmImport
.getCdmAppController();
223 ISourceable obj
= app
.getCommonService().getSourcedObjectByIdInSource(TaxonName
.class, "1000027", null);
227 FeatureTree tree
= TreeCreator
.flatTree(featureTreeUuid
, bmImportConfigurator
.getFeatureMap(), featureKeyList
);
228 FeatureNode imageNode
= FeatureNode
.NewInstance(Feature
.IMAGE());
229 tree
.getRoot().addChild(imageNode
);
230 FeatureNode distributionNode
= FeatureNode
.NewInstance(Feature
.DISTRIBUTION());
231 tree
.getRoot().addChild(distributionNode
, 2);
232 app
.getFeatureTreeService().saveOrUpdate(tree
);
235 System
.out
.println("End import from BerlinModel ("+ source
.getDatabase() + ")...");
239 if (includeTaraxacum
) {
240 System
.out
.println("Start Taraxacum import from BerlinModel ...");
241 TaraxacumActivator taraxacumActivator
= new TaraxacumActivator();
242 ImportResult successTaraxacum
= taraxacumActivator
.doImport(destination
, DbSchemaValidation
.UPDATE
);
243 success
.merge(successTaraxacum
);
244 logger
.warn("Taraxacum import still needs to be tested");
245 System
.out
.println("End Taraxacum import from BerlinModel ...");
247 } catch (Exception e
) {
248 success
.addException(e
);
249 logger
.error("Exception occurred during Taraxacum import.");
256 System
.out
.println("Start importing images ...");
257 CdmDefaultImport
<IImportConfigurator
> imageImporter
= new CdmDefaultImport
<IImportConfigurator
>();
258 URI imageFolderCichorieae
;
260 imageFolderCichorieae
= new URI(CichorieaeActivator
.imageFolderString
);
261 ImageImportConfigurator imageConfigurator
= ImageImportConfigurator
.NewInstance(
262 imageFolderCichorieae
, destination
, CichorieaeImageImport
.class);
263 imageConfigurator
.setSecUuid(secUuid
);
264 imageConfigurator
.setClassificationUuid(classificationUuid
);
265 ImportResult resultImageImport
= imageImporter
.invoke(imageConfigurator
);
266 success
.merge(resultImageImport
);
267 } catch (URISyntaxException e
) {
270 System
.out
.println("End importing images ...");
272 logger
.warn("!!!! NOTE: RefDetail notes and RelPTaxon notes are not imported automatically. Please check for these notes and import them manually.");
281 public static void main(String
[] args
) {
282 ICdmDataSource destination
= CdmDestinations
.chooseDestination(args
) != null ? CdmDestinations
.chooseDestination(args
) : cdmDestination
;
284 System
.out
.println("Start import from BerlinModel("+ berlinModelSource
.getDatabase() + ") to " + destination
.getDatabase() + " ...");
285 CichorieaeActivator me
= new CichorieaeActivator();
286 me
.doInvoke(destination
);