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
.berlinModelImport
;
12 import java
.util
.UUID
;
14 import org
.apache
.log4j
.Logger
;
16 import eu
.etaxonomy
.cdm
.api
.application
.ICdmApplicationConfiguration
;
17 import eu
.etaxonomy
.cdm
.api
.service
.ITermService
;
18 import eu
.etaxonomy
.cdm
.app
.common
.CdmDestinations
;
19 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
20 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
21 import eu
.etaxonomy
.cdm
.io
.algaterra
.AlgaTerraImportConfigurator
;
22 import eu
.etaxonomy
.cdm
.io
.algaterra
.AlgaTerraImportTransformer
;
23 import eu
.etaxonomy
.cdm
.io
.algaterra
.AlgaTerraSpecimenImportBase
;
24 import eu
.etaxonomy
.cdm
.io
.berlinModel
.in
.BerlinModelImportConfigurator
;
25 import eu
.etaxonomy
.cdm
.io
.common
.CdmDefaultImport
;
26 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.CHECK
;
27 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.DO_REFERENCES
;
28 import eu
.etaxonomy
.cdm
.io
.common
.IImportConfigurator
.EDITOR
;
29 import eu
.etaxonomy
.cdm
.io
.common
.Source
;
30 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
31 import eu
.etaxonomy
.cdm
.model
.description
.FeatureNode
;
32 import eu
.etaxonomy
.cdm
.model
.description
.FeatureTree
;
33 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalCode
;
37 * TODO add the following to a wiki page:
38 * 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
39 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
45 public class AlgaTerraActivator
{
46 private static final Logger logger
= Logger
.getLogger(AlgaTerraActivator
.class);
48 //database validation status (create, update, validate ...)
49 static DbSchemaValidation hbm2dll
= DbSchemaValidation
.CREATE
;
50 static final Source berlinModelSource
= BerlinModelSources
.AlgaTerra();
51 static final ICdmDataSource cdmDestination
= CdmDestinations
.localH2();
52 // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
54 // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview();
55 // static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_production();
58 static final UUID treeUuid
= UUID
.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");
59 static final int sourceSecId
= 7331;
60 static final UUID sourceRefUuid
= UUID
.fromString("7e1a2500-93a5-40c2-ba34-0213d7822379");
62 static final UUID featureTreeUuid
= UUID
.fromString("a970168a-36fd-4c7c-931e-87214a965c14");
63 static final Object
[] featureKeyList
= new Integer
[]{7,201,203,204,206,207};
64 static final UUID specimenFeatureTreeUuid
= UUID
.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");
66 static final boolean loginAsDefaultAdmin
= true;
67 static final boolean removeRestricted
= true;
70 static final CHECK check
= CHECK
.IMPORT_WITHOUT_CHECK
;
72 private boolean ignoreNull
= true;
74 private boolean includeFlatClassifications
= true;
75 private boolean includeAllNonMisappliedRelatedClassifications
= true;
77 private EDITOR editor
= EDITOR
.EDITOR_AS_EDITOR
;
80 static final NomenclaturalCode nomenclaturalCode
= NomenclaturalCode
.ICNAFP
;
82 static String factFilter
= " factCategoryFk NOT IN (7, 201, 202, 203, 204, 205, 206, 207, 208, 1000 ) ";
85 // ****************** ALL *****************************************
88 static final boolean doAuthors
= true;
90 static final DO_REFERENCES doReferences
= DO_REFERENCES
.ALL
;
92 static final boolean doTaxonNames
= true;
93 static final boolean doRelNames
= true;
94 static final boolean doNameStatus
= true;
95 static final boolean doTypes
= true;
98 static final boolean doTaxa
= true;
99 static final boolean doRelTaxa
= true;
100 static final boolean doFacts
= true;
102 //alga terra specific
103 static final boolean ecoFacts
= true;
104 static final boolean doFactEcology
= true;
105 static final boolean doImages
= true;
106 static final boolean doDna
= true;
107 static final boolean doMorphology
= false;
109 // ************************ NONE **************************************** //
112 // static final boolean doAuthors = false;
114 // static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
116 // static final boolean doTaxonNames = false;
117 // static final boolean doRelNames = false;
118 // static final boolean doNameStatus = false;
119 // static final boolean doTypes = false;
120 // static final boolean doNameFacts = false;
123 // static final boolean doTaxa = true;
124 // static final boolean doRelTaxa = false;
125 // static final boolean doFacts = false;
127 // //alga terra specific
128 // static final boolean ecoFacts = true;
129 // static final boolean doFactEcology = false;
130 // static final boolean doImages = false;
131 // static final boolean doDna = true;
132 // static final boolean doMorphology = false;
135 public void invoke(String
[] args
){
136 System
.out
.println("Start import from BerlinModel("+ berlinModelSource
.getDatabase() + ") ...");
137 logger
.debug("Start");
138 //make BerlinModel Source
139 Source source
= berlinModelSource
;
140 ICdmDataSource destination
= CdmDestinations
.chooseDestination(args
) != null ? CdmDestinations
.chooseDestination(args
) : cdmDestination
;
142 AlgaTerraImportConfigurator config
= AlgaTerraImportConfigurator
.NewInstance(source
, destination
);
144 config
.setClassificationUuid(treeUuid
);
145 config
.setSourceSecId(sourceSecId
);
146 config
.setNomenclaturalCode(nomenclaturalCode
);
148 config
.setDoAuthors(doAuthors
);
149 config
.setDoReferences(doReferences
);
150 config
.setDoTaxonNames(doTaxonNames
);
151 config
.setDoRelNames(doRelNames
);
152 config
.setDoNameStatus(doNameStatus
);
153 config
.setDoTypes(doTypes
);
155 config
.setDoTaxa(doTaxa
);
156 config
.setDoRelTaxa(doRelTaxa
);
157 config
.setDoFacts(doFacts
);
158 config
.setDoEcoFacts(ecoFacts
);
159 config
.setDoImages(doImages
);
160 config
.setDoFactEcology(doFactEcology
);
161 config
.setDoDna(doDna
);
162 config
.setDoMorphology(doMorphology
);
164 config
.setSourceRefUuid(sourceRefUuid
);
165 config
.setIgnoreNull(ignoreNull
);
166 config
.setRemoveRestricted(removeRestricted
);
168 config
.setIncludeFlatClassifications(includeFlatClassifications
);
169 config
.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications
);
170 config
.setFactFilter(factFilter
);
172 config
.setDbSchemaValidation(hbm2dll
);
174 config
.setCheck(check
);
175 config
.setEditor(editor
);
177 if (loginAsDefaultAdmin
){
178 config
.authenticateAsDefaultAdmin();
182 CdmDefaultImport
<BerlinModelImportConfigurator
> bmImport
= new CdmDefaultImport
<BerlinModelImportConfigurator
>();
183 bmImport
.invoke(config
);
185 if (doFacts
&& (config
.getCheck().equals(CHECK
.CHECK_AND_IMPORT
) || config
.getCheck().equals(CHECK
.IMPORT_WITHOUT_CHECK
) ) ){
186 ICdmApplicationConfiguration app
= bmImport
.getCdmAppController();
189 makeTaxonFeatureTree(config
, app
);
191 //make specimen feature tree
192 //TODO more specimen specific
193 makeSpecimenFeatureTree(config
, app
);
198 System
.out
.println("End import from BerlinModel ("+ source
.getDatabase() + ")...");
206 private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config
, ICdmApplicationConfiguration app
) {
207 FeatureTree tree
= TreeCreator
.flatTree(featureTreeUuid
, config
.getFeatureMap(), featureKeyList
);
208 tree
.setTitleCache("AlgaTerra Taxon Feature Tree", true);
210 FeatureNode node
= FeatureNode
.NewInstance(Feature
.HABITAT());
211 tree
.getRoot().addChild(node
);
213 // node = FeatureNode.NewInstance(Feature.OBSERVATION());
214 // tree.getRoot().addChild(node);
216 // node = FeatureNode.NewInstance(Feature.SPECIMEN());
217 // tree.getRoot().addChild(node);
219 // node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION());
220 // tree.getRoot().addChild(node);
223 FeatureNode distributionNode
= FeatureNode
.NewInstance(Feature
.DISTRIBUTION());
224 tree
.getRoot().addChild(distributionNode
, 2);
227 // FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
228 // tree.getRoot().addChild(imageNode);
230 app
.getFeatureTreeService().saveOrUpdate(tree
);
239 private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config
, ICdmApplicationConfiguration app
) {
240 ITermService termService
= app
.getTermService();
241 FeatureTree specimenTree
= FeatureTree
.NewInstance(specimenFeatureTreeUuid
);
242 // FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);
243 specimenTree
.setTitleCache("AlgaTerra Specimen Feature Tree", true);
244 FeatureNode root
= specimenTree
.getRoot();
247 FeatureNode imageNode
= FeatureNode
.NewInstance(Feature
.IMAGE());
248 root
.addChild(imageNode
);
250 addFeatureNodeByUuid(root
, termService
, AlgaTerraSpecimenImportBase
.uuidFeatureAlgaTerraClimate
);
251 FeatureNode node
= FeatureNode
.NewInstance(Feature
.HABITAT());
253 addFeatureNodeByUuid(root
, termService
, AlgaTerraSpecimenImportBase
.uuidFeatureHabitatExplanation
);
254 addFeatureNodeByUuid(root
, termService
, AlgaTerraSpecimenImportBase
.uuidFeatureAlgaTerraLifeForm
);
256 addFeatureNodeByUuid(root
, termService
, AlgaTerraSpecimenImportBase
.uuidFeatureAdditionalData
);
257 addFeatureNodeByUuid(root
, termService
, AlgaTerraSpecimenImportBase
.uuidFeatureSpecimenCommunity
);
259 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeaturePH
);
260 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureConductivity
);
261 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureWaterTemperature
);
262 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureSilica
);
263 FeatureNode nitrogenNode
= makeNitrogenNode(root
, termService
);
264 addFeatureNodeByUuid(nitrogenNode
, termService
, AlgaTerraImportTransformer
.uuidFeatureNitrate
);
265 addFeatureNodeByUuid(nitrogenNode
, termService
, AlgaTerraImportTransformer
.uuidFeatureNitrite
);
266 addFeatureNodeByUuid(nitrogenNode
, termService
, AlgaTerraImportTransformer
.uuidFeatureAmmonium
);
267 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeaturePhosphate
);
268 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureOrthoPhosphate
);
269 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureNPRation
);
270 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureDIN
);
271 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureSRP
);
272 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureOxygenSaturation
);
273 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureCl
);
274 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureSecchiDepth
);
275 addFeatureNodeByUuid(root
, termService
, AlgaTerraImportTransformer
.uuidFeatureCommunity
);
276 app
.getFeatureTreeService().saveOrUpdate(specimenTree
);
279 private FeatureNode
makeNitrogenNode(FeatureNode root
, ITermService termService
) {
280 Feature nFeature
= Feature
.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
281 termService
.save(nFeature
);
282 FeatureNode nNode
= FeatureNode
.NewInstance(nFeature
);
283 root
.addChild(nNode
);
288 // private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
289 // FeatureNode lastChild = null;
290 // for (UUID featureUuid : featureUuidList){
291 // addFeatureNodeByUuid(root, termService, featureUuid);
303 private void addFeatureNodeByUuid(FeatureNode root
, ITermService termService
, UUID featureUuid
) {
304 Feature feature
= (Feature
)termService
.find(featureUuid
);
305 if (feature
!= null){
306 FeatureNode child
= FeatureNode
.NewInstance(feature
);
307 root
.addChild(child
);
315 public static void main(String
[] args
) {
316 AlgaTerraActivator activator
= new AlgaTerraActivator();
317 activator
.invoke(args
);