Revision 7e45cf97
Added by Andreas Müller over 11 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/AlgaTerraActivator.java | ||
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import org.apache.log4j.Logger; |
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import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration; |
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import eu.etaxonomy.cdm.api.service.ITermService; |
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import eu.etaxonomy.cdm.app.common.CdmDestinations; |
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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportConfigurator; |
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import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportTransformer; |
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import eu.etaxonomy.cdm.io.algaterra.AlgaTerraSpecimenImportBase; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
| ... | ... | |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
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static final Source berlinModelSource = BerlinModelSources.AlgaTerra(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview(); |
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static final UUID treeUuid = UUID.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");
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| ... | ... | |
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static final UUID featureTreeUuid = UUID.fromString("a970168a-36fd-4c7c-931e-87214a965c14");
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static final Object[] featureKeyList = new Integer[]{7,201,202,203,204,205,206,207};
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static final UUID specimenFeatureTreeUuid = UUID.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");
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//check - import |
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
| ... | ... | |
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// ****************** ALL ***************************************** |
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// //authors |
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// static final boolean doAuthors = true; |
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// //references |
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// static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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// //names |
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// static final boolean doTaxonNames = true; |
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// static final boolean doRelNames = true; |
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// static final boolean doNameStatus = true; |
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// static final boolean doTypes = true; |
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// |
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// //taxa |
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// static final boolean doTaxa = true; |
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// static final boolean doRelTaxa = true; |
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// static final boolean doFacts = true; |
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// |
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// //alga terra specific |
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// static final boolean ecoFacts = true; |
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// static final boolean doFactEcology = true; |
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// static final boolean doImages = true; |
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// ************************ NONE **************************************** // |
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//authors |
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static final boolean doAuthors = true;
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static final boolean doAuthors = false;
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//references |
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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//names |
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static final boolean doTaxonNames = true; |
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static final boolean doRelNames = true; |
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static final boolean doNameStatus = true; |
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static final boolean doTypes = true; |
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static final boolean doTaxonNames = false; |
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static final boolean doRelNames = false; |
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static final boolean doNameStatus = false; |
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static final boolean doTypes = false; |
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static final boolean doNameFacts = false; |
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//taxa |
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static final boolean doTaxa = true; |
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static final boolean doRelTaxa = true;
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static final boolean doRelTaxa = false;
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static final boolean doFacts = true; |
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//alga terra specific
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//alga terra specific
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static final boolean ecoFacts = true; |
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static final boolean doFactEcology = true;
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static final boolean doFactEcology = false;
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static final boolean doImages = true; |
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// ************************ NONE **************************************** // |
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// //authors |
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// static final boolean doAuthors = false; |
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// //references |
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// static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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// //names |
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// static final boolean doTaxonNames = false; |
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// static final boolean doRelNames = false; |
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// static final boolean doNameStatus = false; |
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// static final boolean doTypes = false; |
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// static final boolean doNameFacts = false; |
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// |
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// //taxa |
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// static final boolean doTaxa = true; |
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// static final boolean doRelTaxa = true; |
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// static final boolean doFacts = false; |
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// |
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// //alga terra specific |
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// static final boolean ecoFacts = false; |
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// static final boolean doFactEcology = false; |
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// static final boolean doImages = false; |
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public void invoke(String[] args){
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ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
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//make feature tree |
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE()); |
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tree.getRoot().addChild(imageNode);
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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tree.getRoot().addChild(distributionNode, 2);
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app.getFeatureTreeService().saveOrUpdate(tree); |
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makeTaxonFeatureTree(config, app);
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//make specimen feature tree
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//TODO more specimen specific
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makeSpecimenFeatureTree(config, app);
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} |
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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} |
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/** |
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* @param config |
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* @param app |
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*/ |
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private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
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tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);
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FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT()); |
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tree.getRoot().addChild(node); |
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node = FeatureNode.NewInstance(Feature.OBSERVATION()); |
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tree.getRoot().addChild(node); |
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node = FeatureNode.NewInstance(Feature.SPECIMEN()); |
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tree.getRoot().addChild(node); |
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node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION()); |
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tree.getRoot().addChild(node); |
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//needed ?? |
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION()); |
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tree.getRoot().addChild(distributionNode, 2); |
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//needed ?? |
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE()); |
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tree.getRoot().addChild(imageNode); |
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app.getFeatureTreeService().saveOrUpdate(tree); |
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} |
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/** |
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* @param config |
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* @param app |
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* @param tree |
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*/ |
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private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {
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ITermService termService = app.getTermService(); |
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FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid); |
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// FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList); |
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specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);
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FeatureNode root = specimenTree.getRoot(); |
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE()); |
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root.addChild(imageNode); |
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addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate); |
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FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT()); |
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root.addChild(node); |
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addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation); |
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addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm); |
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addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData); |
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addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica); |
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FeatureNode nitrogenNode = makeNitrogenNode(root, termService); |
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addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate); |
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addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite); |
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addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth); |
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addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity); |
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app.getFeatureTreeService().saveOrUpdate(specimenTree); |
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} |
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private FeatureNode makeNitrogenNode(FeatureNode root, ITermService termService) {
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Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");
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termService.save(nFeature); |
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FeatureNode nNode = FeatureNode.NewInstance(nFeature); |
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root.addChild(nNode); |
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return nNode; |
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} |
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// private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){
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// FeatureNode lastChild = null; |
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// for (UUID featureUuid : featureUuidList){
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// addFeatureNodeByUuid(root, termService, featureUuid); |
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// } |
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// |
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// return lastChild; |
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// } |
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/** |
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* @param root |
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* @param termService |
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* @param featureUuid |
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*/ |
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private void addFeatureNodeByUuid(FeatureNode root, ITermService termService, UUID featureUuid) {
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Feature feature = (Feature)termService.find(featureUuid); |
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if (feature != null){
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FeatureNode child = FeatureNode.NewInstance(feature); |
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root.addChild(child); |
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} |
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} |
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/** |
Also available in: Unified diff
Latest AlgaTerra Import developments