Revision 37c7b75c
Added by Andreas Müller over 2 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/AlgaTerraActivator.java | ||
|---|---|---|
| 225 | 225 |
// //needed ?? |
| 226 | 226 |
// tree.getRoot().addChild(Feature.IMAGE()); |
| 227 | 227 |
|
| 228 |
app.getFeatureTreeService().saveOrUpdate(tree);
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|
| 228 |
app.getTermTreeService().saveOrUpdate(tree);
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|
| 229 | 229 |
} |
| 230 | 230 |
|
| 231 | 231 |
|
| ... | ... | |
| 269 | 269 |
addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl); |
| 270 | 270 |
addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth); |
| 271 | 271 |
addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity); |
| 272 |
app.getFeatureTreeService().saveOrUpdate(specimenTree);
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| 272 |
app.getTermTreeService().saveOrUpdate(specimenTree);
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|
| 273 | 273 |
} |
| 274 | 274 |
|
| 275 | 275 |
private TermNode<Feature> makeNitrogenNode(TermNode<Feature> root, ITermService termService) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/CampanulaceaeActivator.java | ||
|---|---|---|
| 177 | 177 |
//make feature tree |
| 178 | 178 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| 179 | 179 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 1); |
| 180 |
app.getFeatureTreeService().saveOrUpdate(tree);
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| 180 |
app.getTermTreeService().saveOrUpdate(tree);
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|
| 181 | 181 |
} |
| 182 | 182 |
|
| 183 | 183 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/EuroMedActivator.java | ||
|---|---|---|
| 414 | 414 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 415 | 415 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 1); |
| 416 | 416 |
tree.getRoot().addChild(Feature.COMMON_NAME(), 2); |
| 417 |
app.getFeatureTreeService().saveOrUpdate(tree);
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|
| 417 |
app.getTermTreeService().saveOrUpdate(tree);
|
|
| 418 | 418 |
|
| 419 | 419 |
app.commitTransaction(tx); |
| 420 | 420 |
} catch (Exception e) {
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| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/IldisActivator.java | ||
|---|---|---|
| 160 | 160 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| 161 | 161 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 162 | 162 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 2); |
| 163 |
app.getFeatureTreeService().saveOrUpdate(tree);
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|
| 163 |
app.getTermTreeService().saveOrUpdate(tree);
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|
| 164 | 164 |
} |
| 165 | 165 |
|
| 166 | 166 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTMooseActivator.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
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| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
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| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 27 | 27 |
|
| 28 | 28 |
/** |
| 29 | 29 |
* TODO add the following to a wiki page: |
| 30 |
* 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
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|
| 30 |
* 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 |
|
| 31 | 31 |
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names. |
| 32 |
*
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| 33 |
*
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* |
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* |
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| 34 | 34 |
* @author a.mueller |
| 35 | 35 |
* |
| 36 | 36 |
*/ |
| ... | ... | |
| 40 | 40 |
//database validation status (create, update, validate ...) |
| 41 | 41 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE_DROP; |
| 42 | 42 |
static final Source berlinModelSource = BerlinModelSources.MT_MOOSE(); |
| 43 |
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| 43 |
|
|
| 44 | 44 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 45 | 45 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_moose_dev(); |
| 46 | 46 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_moose_production(); |
| 47 | 47 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_moose(); |
| 48 | 48 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test(); |
| 49 |
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| 49 |
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| 50 | 50 |
static final UUID classificationUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d");
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| 51 | 51 |
static final UUID sourceRefUuid = UUID.fromString("601d8a00-cffe-4509-af93-b15b543ccf8d");
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| 52 |
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| 52 |
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| 53 | 53 |
// static final UUID featureTreeUuid = UUID.fromString("4c5b5bbe-6fef-4607-96b2-1b0104eac19e");
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| 54 |
// static final Object[] featureKeyList = new Integer[]{7,201,202,203,204,205,206,207};
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| 55 |
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| 56 |
static final boolean includeFlatClassifications = true;
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// static final Object[] featureKeyList = new Integer[]{7,201,202,203,204,205,206,207};
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| 55 |
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static final boolean includeFlatClassifications = true; |
|
| 57 | 57 |
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| 58 |
static final String relPTaxonIdQuery = "SELECT * FROM RelPTaxon r " +
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| 58 |
static final String relPTaxonIdQuery = "SELECT * FROM RelPTaxon r " + |
|
| 59 | 59 |
" WHERE NOT (r.PTRefFk1 <> r.PTRefFk2 AND r.RelQualifierFk = 1)"; |
| 60 |
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| 60 |
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| 61 | 61 |
//check - import |
| 62 | 62 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 63 | 63 |
|
| 64 | 64 |
|
| 65 | 65 |
//NomenclaturalCode |
| 66 | 66 |
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP; |
| 67 |
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| 67 |
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| 68 | 68 |
static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR; |
| 69 | 69 |
|
| 70 | 70 |
// ****************** ALL ***************************************** |
| 71 |
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| 71 |
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| 72 | 72 |
//authors |
| 73 | 73 |
static final boolean doAuthors = true; |
| 74 | 74 |
//references |
| ... | ... | |
| 77 | 77 |
static final boolean doTaxonNames = true; |
| 78 | 78 |
static final boolean doRelNames = true; |
| 79 | 79 |
static final boolean doNameStatus = true; |
| 80 |
static final boolean doTypes = true;
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| 80 |
static final boolean doTypes = true; |
|
| 81 | 81 |
static final boolean doNameFacts = false; //no name facts exist |
| 82 |
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| 82 |
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| 83 | 83 |
//taxa |
| 84 | 84 |
static final boolean doTaxa = true; |
| 85 | 85 |
static final boolean doRelTaxa = true; |
| ... | ... | |
| 88 | 88 |
static final boolean doCommonNames = false; //no common names exist |
| 89 | 89 |
|
| 90 | 90 |
// ************************ NONE **************************************** // |
| 91 |
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| 91 |
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| 92 | 92 |
// //authors |
| 93 | 93 |
// static final boolean doAuthors = false; |
| 94 | 94 |
// //references |
| ... | ... | |
| 99 | 99 |
// static final boolean doNameStatus = false; |
| 100 | 100 |
// static final boolean doTypes = false; |
| 101 | 101 |
// static final boolean doNameFacts = false; |
| 102 |
//
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| 102 |
// |
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| 103 | 103 |
// //taxa |
| 104 | 104 |
// static final boolean doTaxa = false; |
| 105 | 105 |
// static final boolean doRelTaxa = false; |
| 106 | 106 |
// static final boolean doFacts = false; |
| 107 | 107 |
// static final boolean doOccurences = false; |
| 108 | 108 |
// static final boolean doCommonNames = false; |
| 109 |
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| 111 | 111 |
public void invoke(String[] args){
|
| 112 | 112 |
System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");
|
| 113 | 113 |
logger.debug("Start");
|
| 114 | 114 |
//make BerlinModel Source |
| 115 | 115 |
Source source = berlinModelSource; |
| 116 | 116 |
ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination; |
| 117 |
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| 117 |
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| 118 | 118 |
BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination); |
| 119 |
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| 119 |
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| 120 | 120 |
config.setClassificationUuid(classificationUuid); |
| 121 | 121 |
// bmImportConfigurator.setSourceSecId(sourceSecId); |
| 122 | 122 |
config.setNomenclaturalCode(nomenclaturalCode); |
| ... | ... | |
| 130 | 130 |
config.setDoNameStatus(doNameStatus); |
| 131 | 131 |
config.setDoTypes(doTypes); |
| 132 | 132 |
config.setDoNameFacts(doNameFacts); |
| 133 |
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| 133 |
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| 134 | 134 |
config.setDoTaxa(doTaxa); |
| 135 | 135 |
config.setDoRelTaxa(doRelTaxa); |
| 136 | 136 |
config.setDoFacts(doFacts); |
| ... | ... | |
| 138 | 138 |
config.setDoCommonNames(doCommonNames); |
| 139 | 139 |
config.setSourceRefUuid(sourceRefUuid); |
| 140 | 140 |
config.setRelTaxaIdQuery(relPTaxonIdQuery); |
| 141 |
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| 141 |
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| 142 | 142 |
config.setDbSchemaValidation(hbm2dll); |
| 143 | 143 |
|
| 144 | 144 |
config.setCheck(check); |
| 145 |
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| 145 |
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| 146 | 146 |
// invoke import |
| 147 | 147 |
CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
| 148 | 148 |
bmImport.invoke(config); |
| 149 | 149 |
|
| 150 | 150 |
// if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ) ){
|
| 151 | 151 |
// ICdmRepository app = bmImport.getCdmAppController(); |
| 152 |
//
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| 152 |
// |
|
| 153 | 153 |
// //make feature tree |
| 154 | 154 |
// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| 155 | 155 |
// FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
| 156 |
// tree.getRoot().addChild(distributionNode, 0);
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| 157 |
// app.getFeatureTreeService().saveOrUpdate(tree);
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| 156 |
// tree.getRoot().addChild(distributionNode, 0); |
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// app.getTermTreeService().saveOrUpdate(tree);
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| 158 | 158 |
// } |
| 159 |
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| 161 | 161 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| 162 | 162 |
} |
| 163 |
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| 165 | 165 |
/** |
| 166 | 166 |
* @param args |
| 167 | 167 |
*/ |
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/MTStandardlisteActivator.java | ||
|---|---|---|
| 155 | 155 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| 156 | 156 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 157 | 157 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 2); |
| 158 |
app.getFeatureTreeService().saveOrUpdate(tree);
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| 158 |
app.getTermTreeService().saveOrUpdate(tree);
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| 159 | 159 |
} |
| 160 | 160 |
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| 161 | 161 |
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| app-import/src/main/java/eu/etaxonomy/cdm/app/cuba/CubaActivator.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.app.cuba; |
| 11 | 11 |
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| 12 |
import eu.etaxonomy.cdm.common.URI; |
|
| 13 | 12 |
import java.util.UUID; |
| 14 | 13 |
|
| 15 | 14 |
import org.apache.log4j.Logger; |
| ... | ... | |
| 18 | 17 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 19 | 18 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 20 | 19 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 20 |
import eu.etaxonomy.cdm.common.URI; |
|
| 21 | 21 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 22 | 22 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 23 | 23 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| ... | ... | |
| 211 | 211 |
|
| 212 | 212 |
if (doVocabularies){
|
| 213 | 213 |
TermTree<Feature> tree = makeFeatureNodes(myImport.getCdmAppController().getTermService()); |
| 214 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
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| 214 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
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| 215 | 215 |
this.doVocabularies = false; |
| 216 | 216 |
} |
| 217 | 217 |
System.out.println("End import from ("+ source.toString() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusActivator.java | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.app.cyprus; |
| 11 | 11 |
|
| 12 |
import eu.etaxonomy.cdm.common.URI; |
|
| 13 | 12 |
import java.net.URISyntaxException; |
| 14 | 13 |
import java.util.UUID; |
| 15 | 14 |
|
| ... | ... | |
| 18 | 17 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
| 19 | 18 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 20 | 19 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 20 |
import eu.etaxonomy.cdm.common.URI; |
|
| 21 | 21 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 22 | 22 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 23 | 23 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| ... | ... | |
| 88 | 88 |
myImport.invoke(config); |
| 89 | 89 |
if (doTaxa){
|
| 90 | 90 |
TermTree<Feature> tree = makeFeatureNodes(myImport.getCdmAppController().getTermService()); |
| 91 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
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| 91 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
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| 92 | 92 |
} |
| 93 | 93 |
|
| 94 | 94 |
System.out.println("End import from ("+ source.toString() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/globis/GlobisActivator.java | ||
|---|---|---|
| 140 | 140 |
// //make feature tree |
| 141 | 141 |
// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, ermsImportConfigurator.getFeatureMap(), featureKeyList); |
| 142 | 142 |
// app = ermsImport.getCdmAppController(); |
| 143 |
// app.getFeatureTreeService().saveOrUpdate(tree);
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|
| 143 |
// app.getTermTreeService().saveOrUpdate(tree);
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|
| 144 | 144 |
} |
| 145 | 145 |
System.out.println("End import from ("+ source.getDatabase() + ")...");
|
| 146 | 146 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/EuroMedActivatorVibrant.java | ||
|---|---|---|
| 236 | 236 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| 237 | 237 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 238 | 238 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 2); |
| 239 |
app.getFeatureTreeService().saveOrUpdate(tree);
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| 239 |
app.getTermTreeService().saveOrUpdate(tree);
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|
| 240 | 240 |
} |
| 241 | 241 |
|
| 242 | 242 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/vibrant/EuroMedVibrantActivator.java | ||
|---|---|---|
| 236 | 236 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| 237 | 237 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 238 | 238 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 2); |
| 239 |
app.getFeatureTreeService().saveOrUpdate(tree);
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|
| 239 |
app.getTermTreeService().saveOrUpdate(tree);
|
|
| 240 | 240 |
} |
| 241 | 241 |
|
| 242 | 242 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/CichorieaeActivator.java | ||
|---|---|---|
| 10 | 10 |
package eu.etaxonomy.cdm.app.wp6.cichorieae; |
| 11 | 11 |
|
| 12 | 12 |
import java.io.File; |
| 13 |
import eu.etaxonomy.cdm.common.URI; |
|
| 14 | 13 |
import java.net.URISyntaxException; |
| 15 | 14 |
import java.util.UUID; |
| 16 | 15 |
|
| ... | ... | |
| 21 | 20 |
import eu.etaxonomy.cdm.app.berlinModelImport.TreeCreator; |
| 22 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 23 | 22 |
import eu.etaxonomy.cdm.app.images.ImageImportConfigurator; |
| 23 |
import eu.etaxonomy.cdm.common.URI; |
|
| 24 | 24 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 25 | 25 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 26 | 26 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
| ... | ... | |
| 225 | 225 |
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList); |
| 226 | 226 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 227 | 227 |
tree.getRoot().addChild(Feature.DISTRIBUTION(), 2); |
| 228 |
app.getFeatureTreeService().saveOrUpdate(tree);
|
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| 228 |
app.getTermTreeService().saveOrUpdate(tree);
|
|
| 229 | 229 |
} |
| 230 | 230 |
|
| 231 | 231 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/cichorieae/TaraxacumActivator.java | ||
|---|---|---|
| 184 | 184 |
// FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
| 185 | 185 |
// FeatureNode featureNode = tree.getRoot(); |
| 186 | 186 |
// tree.getRoot().addChild(distributionNode, featureNode.getChildCount() + 1); |
| 187 |
// app.getFeatureTreeService().saveOrUpdate(tree);
|
|
| 187 |
// app.getTermTreeService().saveOrUpdate(tree);
|
|
| 188 | 188 |
mergeIntoCichorieae(app); |
| 189 | 189 |
app.commitTransaction(tx); |
| 190 | 190 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraActivator.java | ||
|---|---|---|
| 199 | 199 |
tree.getRoot().addChild(Feature.IMAGE()); |
| 200 | 200 |
// add distribution |
| 201 | 201 |
tree.getRoot().addChild(Feature.DISTRIBUTION()); |
| 202 |
app.getFeatureTreeService().saveOrUpdate(tree);
|
|
| 202 |
app.getTermTreeService().saveOrUpdate(tree);
|
|
| 203 | 203 |
} |
| 204 | 204 |
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
| 205 | 205 |
return success; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaeActivator.java | ||
|---|---|---|
| 123 | 123 |
ICdmRepository app = tcsImport.getCdmAppController(); |
| 124 | 124 |
|
| 125 | 125 |
TermTree<Feature> tree = getFeatureTree(); |
| 126 |
app.getFeatureTreeService().saveOrUpdate(tree);
|
|
| 126 |
app.getTermTreeService().saveOrUpdate(tree);
|
|
| 127 | 127 |
System.out.println("End import from TCS ("+ source.toString() + ")...");
|
| 128 | 128 |
|
| 129 | 129 |
return success; |
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaePostImportUpdater.java | ||
|---|---|---|
| 17 | 17 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 18 |
|
| 19 | 19 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 20 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
|
| 20 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 21 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 22 | 23 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 51 | 52 |
try{
|
| 52 | 53 |
int count = 0; |
| 53 | 54 |
UUID featureTreeUuid = PalmaeActivator.featureTreeUuid; |
| 54 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 55 |
ICdmRepository cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 55 | 56 |
|
| 56 | 57 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 57 | 58 |
|
| 58 | 59 |
@SuppressWarnings("unchecked")
|
| 59 |
TermTree<Feature> tree = cdmApp.getFeatureTreeService().find(featureTreeUuid);
|
|
| 60 |
TermTree<Feature> tree = cdmApp.getTermTreeService().find(featureTreeUuid);
|
|
| 60 | 61 |
TermNode<Feature> root = tree.getRoot(); |
| 61 | 62 |
|
| 62 | 63 |
List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null); |
| ... | ... | |
| 91 | 92 |
public boolean updateNameUsage(ICdmDataSource dataSource) {
|
| 92 | 93 |
try{
|
| 93 | 94 |
boolean result = true; |
| 94 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 95 |
ICdmRepository cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
|
|
| 95 | 96 |
|
| 96 | 97 |
TransactionStatus tx = cdmApp.startTransaction(); |
| 97 | 98 |
|
| ... | ... | |
| 131 | 132 |
//add citation feature to feature tree |
| 132 | 133 |
UUID featureTreeUuid = PalmaeActivator.featureTreeUuid; |
| 133 | 134 |
@SuppressWarnings("unchecked")
|
| 134 |
TermTree<Feature> tree = cdmApp.getFeatureTreeService().find(featureTreeUuid);
|
|
| 135 |
TermTree<Feature> tree = cdmApp.getTermTreeService().find(featureTreeUuid);
|
|
| 135 | 136 |
TermNode<Feature> root = tree.getRoot(); |
| 136 | 137 |
List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null); |
| 137 | 138 |
count = 0; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraFactEcologyImport.java | ||
|---|---|---|
| 22 | 22 |
import org.springframework.stereotype.Component; |
| 23 | 23 |
|
| 24 | 24 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 25 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeCacheStrategy; |
|
| 26 | 25 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException; |
| 27 | 26 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 28 | 27 |
import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator; |
| ... | ... | |
| 45 | 44 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 46 | 45 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 47 | 46 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 47 |
import eu.etaxonomy.cdm.strategy.cache.occurrence.DerivedUnitDefaultCacheStrategy; |
|
| 48 | 48 |
|
| 49 | 49 |
|
| 50 | 50 |
/** |
| ... | ... | |
| 138 | 138 |
|
| 139 | 139 |
this.doIdCreatedUpdatedNotes(state, identifiedSpecimen, rs, factId, getDerivedUnitNameSpace()); |
| 140 | 140 |
|
| 141 |
identifiedSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());
|
|
| 141 |
identifiedSpecimen.setCacheStrategy(DerivedUnitDefaultCacheStrategy.NewInstance());
|
|
| 142 | 142 |
taxaToSave.add(taxon); |
| 143 | 143 |
} |
| 144 | 144 |
}else{
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelFactsImport.java | ||
|---|---|---|
| 11 | 11 |
|
| 12 | 12 |
import java.io.File; |
| 13 | 13 |
import java.io.IOException; |
| 14 |
import eu.etaxonomy.cdm.common.URI; |
|
| 15 | 14 |
import java.net.URISyntaxException; |
| 16 | 15 |
import java.sql.ResultSet; |
| 17 | 16 |
import java.sql.SQLException; |
| ... | ... | |
| 31 | 30 |
|
| 32 | 31 |
import au.com.bytecode.opencsv.CSVReader; |
| 33 | 32 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 33 |
import eu.etaxonomy.cdm.common.URI; |
|
| 34 | 34 |
import eu.etaxonomy.cdm.common.UTF8; |
| 35 | 35 |
import eu.etaxonomy.cdm.common.media.CdmImageInfo; |
| 36 | 36 |
import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException; |
| ... | ... | |
| 179 | 179 |
if (createFeatureTree){
|
| 180 | 180 |
featureTree.getRoot().addChild(Feature.DISTRIBUTION(),2); |
| 181 | 181 |
featureTree.getRoot().addChild(Feature.NOTES(), featureTree.getRoot().getChildCount()-1); |
| 182 |
getFeatureTreeService().save(featureTree);
|
|
| 182 |
getTermTreeService().save(featureTree);
|
|
| 183 | 183 |
} |
| 184 | 184 |
return result; |
| 185 | 185 |
} catch (SQLException e) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaTermImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.greece; |
| 10 | 10 |
|
| 11 |
import eu.etaxonomy.cdm.common.URI; |
|
| 12 | 11 |
import java.text.ParseException; |
| 13 | 12 |
import java.util.UUID; |
| 14 | 13 |
|
| ... | ... | |
| 17 | 16 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 17 |
|
| 19 | 18 |
import eu.etaxonomy.cdm.api.service.ITermService; |
| 19 |
import eu.etaxonomy.cdm.common.URI; |
|
| 20 | 20 |
import eu.etaxonomy.cdm.ext.geo.GeoServiceArea; |
| 21 | 21 |
import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.CdmImportBase; |
| ... | ... | |
| 431 | 431 |
if (hasFeatureTree ){
|
| 432 | 432 |
return; |
| 433 | 433 |
} |
| 434 |
if (getFeatureTreeService().find(state.getConfig().getUuidFeatureTree()) != null){
|
|
| 434 |
if (getTermTreeService().find(state.getConfig().getUuidFeatureTree()) != null){
|
|
| 435 | 435 |
hasFeatureTree = true; |
| 436 | 436 |
return; |
| 437 | 437 |
} |
| ... | ... | |
| 477 | 477 |
newFeature = (Feature)service.find(Feature.NOTES().getUuid()); |
| 478 | 478 |
root.addChild(newFeature); |
| 479 | 479 |
|
| 480 |
getFeatureTreeService().saveOrUpdate(result);
|
|
| 480 |
getTermTreeService().saveOrUpdate(result);
|
|
| 481 | 481 |
hasFeatureTree = true; |
| 482 |
|
|
| 483 | 482 |
} |
| 484 | 483 |
|
| 485 |
|
|
| 486 | 484 |
private State addState(SimpleExcelTaxonImportState<FloraHellenicaImportConfigurator> state, |
| 487 | 485 |
String abbrev, String stateLabel, String description, UUID uuid, OrderedTermVocabulary<State> voc) {
|
| 488 | 486 |
State newState = State.NewInstance( |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/in/BfnXmlImportFeature.java | ||
|---|---|---|
| 148 | 148 |
} |
| 149 | 149 |
|
| 150 | 150 |
private void createFeatureTree(List<Feature> featureList) {
|
| 151 |
TermTree<Feature> featureTree = TermTree.NewInstance(featureList); |
|
| 151 |
TermTree<Feature> featureTree = TermTree.NewFeatureInstance(featureList);
|
|
| 152 | 152 |
String featureTreeName = "RedListFeatureTree"; |
| 153 | 153 |
featureTree.setTitleCache(featureTreeName, true); |
| 154 |
getFeatureTreeService().save(featureTree);
|
|
| 154 |
getTermTreeService().save(featureTree);
|
|
| 155 | 155 |
} |
| 156 | 156 |
|
| 157 | 157 |
private void makeFeature(IVocabularyService vocabularyService, |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaChecklistActivator.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| 9 |
|
|
| 10 | 9 |
package eu.etaxonomy.cdm.app.eflora; |
| 11 | 10 |
|
| 12 | 11 |
import java.util.UUID; |
| 13 | 12 |
|
| 14 | 13 |
import org.apache.log4j.Logger; |
| 15 | 14 |
|
| 16 |
import eu.etaxonomy.cdm.app.eflora.CdmDestinations; |
|
| 17 |
import eu.etaxonomy.cdm.app.eflora.CdmImportSources; |
|
| 18 | 15 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 19 | 16 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 20 | 17 |
import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
| 21 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 22 | 18 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
| 19 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 23 | 20 |
import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.CentralAfricaChecklistImportConfigurator; |
| 24 | 21 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 25 | 22 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
| 27 | 24 |
/** |
| 28 | 25 |
* @author a.mueller |
| 29 | 26 |
* @since 20.06.2008 |
| 30 |
* @version 1.0 |
|
| 31 | 27 |
*/ |
| 32 | 28 |
public class CentralAfricaChecklistActivator {
|
| 33 | 29 |
@SuppressWarnings("unused")
|
| 34 | 30 |
private static final Logger logger = Logger.getLogger(CentralAfricaChecklistActivator.class); |
| 35 |
|
|
| 31 |
|
|
| 36 | 32 |
//database validation status (create, update, validate ...) |
| 37 | 33 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
| 38 | 34 |
static final Source mySource = CdmImportSources.AFRICA_CHECKLIST_ACCESS(); |
| 39 |
|
|
| 35 |
|
|
| 40 | 36 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
| 41 | 37 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
| 42 | 38 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
| 43 | 39 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 44 | 40 |
|
| 45 | 41 |
int recordsPerTransaction = 1000; |
| 46 |
|
|
| 42 |
|
|
| 47 | 43 |
//feature tree uuid |
| 48 | 44 |
public static final UUID featureTreeUuid = UUID.fromString("ebe558b5-d04d-41d5-83d9-b61c56e6e34a");
|
| 49 |
|
|
| 45 |
|
|
| 50 | 46 |
public static final String sourceReference = "Flora of Central Africa - Checklist"; |
| 51 |
|
|
| 47 |
|
|
| 52 | 48 |
private UUID uuidGenevaReference = UUID.fromString("cf3fd13d-6cad-430c-ab70-7ea841b7159f");
|
| 53 |
|
|
| 49 |
|
|
| 54 | 50 |
private String genevaReferenceTitle = "Geneva Database"; |
| 55 |
|
|
| 51 |
|
|
| 56 | 52 |
//classification |
| 57 | 53 |
public static final UUID classificationUuid = UUID.fromString("ce1d035a-79a9-4a3a-95bf-26641ecb4fbe");
|
| 58 |
|
|
| 54 |
|
|
| 59 | 55 |
//check - import |
| 60 | 56 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| 61 |
|
|
| 57 |
|
|
| 62 | 58 |
//taxa |
| 63 | 59 |
static final boolean doTaxa = true; |
| 64 | 60 |
|
| 65 | 61 |
private void doImport(ICdmDataSource cdmDestination){
|
| 66 |
|
|
| 62 |
|
|
| 67 | 63 |
//make Source |
| 68 | 64 |
Source source = mySource; |
| 69 |
|
|
| 65 |
|
|
| 70 | 66 |
CentralAfricaChecklistImportConfigurator config= CentralAfricaChecklistImportConfigurator.NewInstance(source, cdmDestination); |
| 71 | 67 |
config.setClassificationUuid(classificationUuid); |
| 72 | 68 |
config.setDoTaxa(doTaxa); |
| ... | ... | |
| 75 | 71 |
config.setRecordsPerTransaction(recordsPerTransaction); |
| 76 | 72 |
config.setGenevaReferenceTitle(genevaReferenceTitle); |
| 77 | 73 |
config.setUuidGenevaReference(uuidGenevaReference); |
| 78 |
|
|
| 74 |
|
|
| 79 | 75 |
CdmDefaultImport<CentralAfricaChecklistImportConfigurator> myImport = new CdmDefaultImport<CentralAfricaChecklistImportConfigurator>(); |
| 80 | 76 |
|
| 81 | 77 |
System.out.println("Start import from ("+ source.toString() + ") ...");
|
| 82 | 78 |
config.setSourceReference(getSourceReference(sourceReference)); |
| 83 | 79 |
myImport.invoke(config); |
| 84 | 80 |
System.out.println("End import from ("+ source.toString() + ")...");
|
| 85 |
|
|
| 86 | 81 |
|
| 87 |
|
|
| 88 | 82 |
// FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 89 |
// myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 90 |
|
|
| 83 |
// myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 84 |
|
|
| 91 | 85 |
} |
| 92 |
|
|
| 86 |
|
|
| 93 | 87 |
private Reference getSourceReference(String string) {
|
| 94 | 88 |
Reference result = ReferenceFactory.newGeneric(); |
| 95 |
result.setTitleCache(string); |
|
| 89 |
result.setTitleCache(string, true);
|
|
| 96 | 90 |
return result; |
| 97 | 91 |
} |
| 98 | 92 |
|
| 99 | 93 |
// private FeatureTree makeFeatureNode(ITermService service){
|
| 100 | 94 |
// FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
| 101 |
//
|
|
| 95 |
// |
|
| 102 | 96 |
// FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
| 103 | 97 |
// result.setTitleCache("Flora Malesiana Presentation Feature Tree");
|
| 104 | 98 |
// FeatureNode root = result.getRoot(); |
| 105 | 99 |
// FeatureNode newNode; |
| 106 |
//
|
|
| 100 |
// |
|
| 107 | 101 |
// newNode = FeatureNode.NewInstance(Feature.CITATION()); |
| 108 | 102 |
// root.addChild(newNode); |
| 109 |
//
|
|
| 103 |
// |
|
| 110 | 104 |
// newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
| 111 | 105 |
// root.addChild(newNode); |
| 112 |
//
|
|
| 106 |
// |
|
| 113 | 107 |
// return result; |
| 114 | 108 |
// } |
| 115 |
|
|
| 116 |
|
|
| 117 | 109 |
|
| 118 |
/** |
|
| 119 |
* @param args |
|
| 120 |
*/ |
|
| 121 | 110 |
public static void main(String[] args) {
|
| 122 | 111 |
CentralAfricaChecklistActivator me = new CentralAfricaChecklistActivator(); |
| 123 | 112 |
me.doImport(cdmDestination); |
| 124 | 113 |
} |
| 125 |
|
|
| 126 |
} |
|
| 114 |
} |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java | ||
|---|---|---|
| 133 | 133 |
|
| 134 | 134 |
if (doFeatureTree){
|
| 135 | 135 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 136 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 136 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 137 | 137 |
} |
| 138 | 138 |
|
| 139 | 139 |
//check keys |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaFernsActivator.java | ||
|---|---|---|
| 20 | 20 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
| 21 | 21 |
import eu.etaxonomy.cdm.io.common.Source; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportConfigurator; |
| 23 |
import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer; |
|
| 24 | 23 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 25 | 24 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 26 | 25 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
| 94 | 93 |
System.out.println("End import from ("+ source.toString() + ")...");
|
| 95 | 94 |
// } |
| 96 | 95 |
|
| 97 |
|
|
| 98 |
|
|
| 99 | 96 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 100 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 97 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 101 | 98 |
|
| 102 | 99 |
//check keys |
| 103 | 100 |
// if (doPrintKeys){
|
| 104 | 101 |
// TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
| 105 |
// List<FeatureTree> keys = myImport.getCdmAppController().getFeatureTreeService().list(PolytomousKey.class, null, null, null, null);
|
|
| 102 |
// List<FeatureTree> keys = myImport.getCdmAppController().getTermTreeService().list(PolytomousKey.class, null, null, null, null);
|
|
| 106 | 103 |
// for(FeatureTree key : keys){
|
| 107 | 104 |
// ((PolytomousKey)key).print(System.out); |
| 108 | 105 |
// System.out.println(); |
| ... | ... | |
| 119 | 116 |
} |
| 120 | 117 |
|
| 121 | 118 |
private TermTree<Feature> makeFeatureNode(ITermService service){
|
| 122 |
FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
|
| 123 | 119 |
|
| 124 | 120 |
TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid); |
| 125 | 121 |
result.setTitleCache("Flora Malesiana Presentation Feature Tree", true);
|
| ... | ... | |
| 131 | 127 |
return result; |
| 132 | 128 |
} |
| 133 | 129 |
|
| 134 |
|
|
| 135 |
|
|
| 136 |
/** |
|
| 137 |
* @param args |
|
| 138 |
*/ |
|
| 139 | 130 |
public static void main(String[] args) {
|
| 140 | 131 |
CentralAfricaFernsActivator me = new CentralAfricaFernsActivator(); |
| 141 | 132 |
me.doImport(cdmDestination); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraGuianasActivator.java | ||
|---|---|---|
| 183 | 183 |
executeVolume(fotg30, includeFotg30 ^ inverseInclude); |
| 184 | 184 |
|
| 185 | 185 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 186 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 186 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 187 | 187 |
|
| 188 | 188 |
//check keys |
| 189 | 189 |
if (doPrintKeys){
|
| ... | ... | |
| 200 | 200 |
|
| 201 | 201 |
private Reference getSourceReference(String string) {
|
| 202 | 202 |
Reference result = ReferenceFactory.newGeneric(); |
| 203 |
result.setTitleCache(string); |
|
| 203 |
result.setTitleCache(string, true);
|
|
| 204 | 204 |
return result; |
| 205 | 205 |
} |
| 206 | 206 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator.java | ||
|---|---|---|
| 363 | 363 |
// makeGeoService(); |
| 364 | 364 |
|
| 365 | 365 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 366 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 366 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 367 | 367 |
|
| 368 | 368 |
//check keys |
| 369 | 369 |
if (doPrintKeys){
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaActivator_OLD.java | ||
|---|---|---|
| 123 | 123 |
} |
| 124 | 124 |
|
| 125 | 125 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 126 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 126 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 127 | 127 |
|
| 128 | 128 |
//check keys |
| 129 | 129 |
if (doPrintKeys){
|
| ... | ... | |
| 140 | 140 |
|
| 141 | 141 |
private Reference getSourceReference(String string) {
|
| 142 | 142 |
Reference result = ReferenceFactory.newGeneric(); |
| 143 |
result.setTitleCache(string); |
|
| 143 |
result.setTitleCache(string, true);
|
|
| 144 | 144 |
return result; |
| 145 | 145 |
} |
| 146 | 146 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloreGabonActivator.java | ||
|---|---|---|
| 310 | 310 |
//Vol45 |
| 311 | 311 |
executeVolume(fdg45, includeFdg45 ^ inverseInclude); |
| 312 | 312 |
|
| 313 |
|
|
| 314 |
|
|
| 315 | 313 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 316 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 314 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 317 | 315 |
|
| 318 | 316 |
makeAutomatedFeatureTree(myImport.getCdmAppController(), config.getState(), |
| 319 | 317 |
featureTreeUuid, featureTreeTitle); |
| 320 | 318 |
|
| 321 |
|
|
| 322 | 319 |
//check keys |
| 323 | 320 |
if (doPrintKeys){
|
| 324 | 321 |
TransactionStatus tx = myImport.getCdmAppController().startTransaction(); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/NepenthesActivator.java | ||
|---|---|---|
| 138 | 138 |
// makeGeoService(); |
| 139 | 139 |
|
| 140 | 140 |
TermTree<Feature> tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
| 141 |
myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
|
|
| 141 |
myImport.getCdmAppController().getTermTreeService().saveOrUpdate(tree);
|
|
| 142 | 142 |
|
| 143 | 143 |
//check keys |
| 144 | 144 |
if (doPrintKeys){
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/testUpdate/EricaceaeTestUpdateActivator.java | ||
|---|---|---|
| 32 | 32 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 33 | 33 |
import eu.etaxonomy.cdm.model.term.TermNode; |
| 34 | 34 |
import eu.etaxonomy.cdm.model.term.TermTree; |
| 35 |
import eu.etaxonomy.cdm.model.term.TermType; |
|
| 35 | 36 |
|
| 36 | 37 |
/** |
| 37 | 38 |
* @author a.mueller |
| ... | ... | |
| 103 | 104 |
app = myImport.getCdmAppController(); |
| 104 | 105 |
|
| 105 | 106 |
TransactionStatus tx = app.startTransaction(); |
| 106 |
List<TermTree<Feature>> featureTrees = app.getFeatureTreeService().list(null, null, null, null, null);
|
|
| 107 |
List<TermTree> featureTrees = app.getTermTreeService().list(TermType.Feature, null, null, null, null);
|
|
| 107 | 108 |
for (TermTree<Feature> tree :featureTrees){
|
| 108 | 109 |
if (tree.getClass().getSimpleName().equalsIgnoreCase("FeatureTree")){
|
| 109 | 110 |
moveChild(app, tree); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraImportState.java | ||
|---|---|---|
| 67 | 67 |
this.featureNodesToSave = featureNodesToSave; |
| 68 | 68 |
} |
| 69 | 69 |
|
| 70 |
public Set<TermNode<Feature>> getFeatureNodesToSave() {
|
|
| 71 |
return featureNodesToSave; |
|
| 70 |
public Set<TermNode> getFeatureNodesToSave() {
|
|
| 71 |
return (Set)featureNodesToSave;
|
|
| 72 | 72 |
} |
| 73 | 73 |
|
| 74 | 74 |
public Set<PolytomousKeyNode> getPolytomousKeyNodesToSave() {
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/EfloraTaxonImport.java | ||
|---|---|---|
| 184 | 184 |
//invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap); |
| 185 | 185 |
logger.info(i + " taxa handled. Saving ..."); |
| 186 | 186 |
getTaxonService().saveOrUpdate(taxaToSave); |
| 187 |
getFeatureTreeService().saveOrUpdateFeatureNodesAll((Set)state.getFeatureNodesToSave());
|
|
| 187 |
getTermNodeService().saveOrUpdate(state.getFeatureNodesToSave());
|
|
| 188 | 188 |
state.getFeatureNodesToSave().clear(); |
| 189 | 189 |
commitTransaction(tx); |
| 190 | 190 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/IndexFungorumImportActivator.java | ||
|---|---|---|
| 79 | 79 |
// //make feature tree |
| 80 | 80 |
// FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, ermsImportConfigurator.getFeatureMap(), featureKeyList); |
| 81 | 81 |
// app = ermsImport.getCdmAppController(); |
| 82 |
// app.getFeatureTreeService().saveOrUpdate(tree);
|
|
| 82 |
// app.getTermTreeService().saveOrUpdate(tree);
|
|
| 83 | 83 |
} |
| 84 | 84 |
System.out.println("End import from ("+ source.getDatabase() + ")...");
|
| 85 | 85 |
} |
Also available in: Unified diff
cleanup and remove usage of feature tree service