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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.common;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IOriginalSource;
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import eu.etaxonomy.cdm.model.common.ISourceable;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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/**
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* @author a.mueller
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* @created 01.07.2008
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* @version 1.0
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*/
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public abstract class CdmImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmIoBase<STATE> implements ICdmImport<CONFIG, STATE>{
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private static Logger logger = Logger.getLogger(CdmImportBase.class);
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protected TaxonomicTree makeTree(STATE state, ReferenceBase ref){
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String treeName = "TaxonTree (Import)";
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if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){
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treeName = ref.getTitleCache();
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}
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TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);
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tree.setReference(ref);
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// use defined uuid for first tree
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CONFIG config = (CONFIG)state.getConfig();
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if (state.countTrees() < 1 ){
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tree.setUuid(config.getTaxonomicTreeUuid());
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}
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getTaxonTreeService().save(tree);
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state.putTree(ref, tree);
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return tree;
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}
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/**
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* Alternative memory saving method variant of
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* {@link #makeTree(STATE state, ReferenceBase ref)} which stores only the
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* UUID instead of the full tree in the <code>ImportStateBase</code> by
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* using <code>state.putTreeUuid(ref, tree);</code>
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*
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* @param state
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* @param ref
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* @return
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*/
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protected TaxonomicTree makeTreeMemSave(STATE state, ReferenceBase ref){
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String treeName = "TaxonTree (Import)";
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if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){
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treeName = ref.getTitleCache();
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}
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TaxonomicTree tree = TaxonomicTree.NewInstance(treeName);
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tree.setReference(ref);
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// use defined uuid for first tree
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CONFIG config = (CONFIG)state.getConfig();
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if (state.countTrees() < 1 ){
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tree.setUuid(config.getTaxonomicTreeUuid());
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}
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getTaxonTreeService().save(tree);
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state.putTreeUuid(ref, tree);
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return tree;
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}
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protected ExtensionType getExtensionType(STATE state, UUID uuid, String label, String text, String labelAbbrev){
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ExtensionType extensionType = state.getExtensionType(uuid);
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if (extensionType == null){
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extensionType = (ExtensionType)getTermService().find(uuid);
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if (extensionType == null){
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extensionType = ExtensionType.NewInstance(text, label, labelAbbrev);
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extensionType.setUuid(uuid);
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extensionType.setVocabulary(ExtensionType.DOI().getVocabulary());
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getTermService().save(extensionType);
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}
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state.putExtensionType(extensionType);
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}
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return extensionType;
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}
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protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev){
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MarkerType markerType = state.getMarkerType(uuid);
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if (markerType == null){
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markerType = (MarkerType)getTermService().find(uuid);
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if (markerType == null){
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markerType = MarkerType.NewInstance(label, text, labelAbbrev);
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markerType.setUuid(uuid);
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markerType.setVocabulary(MarkerType.COMPLETE().getVocabulary());
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getTermService().save(markerType);
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}
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state.putMarkerType(markerType);
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}
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return markerType;
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}
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protected AnnotationType getAnnotationType(STATE state, UUID uuid, String label, String text, String labelAbbrev){
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AnnotationType annotationType = state.getAnnotationType(uuid);
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if (annotationType == null){
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annotationType = (AnnotationType)getTermService().find(uuid);
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if (annotationType == null){
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annotationType = AnnotationType.NewInstance(label, text, labelAbbrev);
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annotationType.setUuid(uuid);
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annotationType.setVocabulary(AnnotationType.EDITORIAL().getVocabulary());
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getTermService().save(annotationType);
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}
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state.putAnnotationType(annotationType);
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}
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return annotationType;
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}
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/**
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* Returns a named area for a given uuid by first . If the named area does not
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* @param state
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* @param uuid
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* @param label
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* @param text
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* @param labelAbbrev
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* @param areaType
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* @param level
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* @return
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*/
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protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level){
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NamedArea namedArea = state.getNamedArea(uuid);
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if (namedArea == null){
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namedArea = (NamedArea)getTermService().find(uuid);
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if (namedArea == null){
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namedArea = NamedArea.NewInstance(text, label, labelAbbrev);
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namedArea.setType(areaType);
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namedArea.setLevel(level);
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namedArea.setUuid(uuid);
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getTermService().save(namedArea);
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}
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state.putNamedArea(namedArea);
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}
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return namedArea;
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}
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/**
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* Adds an orginal source to a sourceable objects (implemented for Identifiable entity and description element.
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* If cdmBase is not sourceable nothing happens.
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* TODO Move to DbImportBase once this exists.
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* TODO also implemented in DbImportObjectCreationMapper (reduce redundance)
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* @param rs
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* @param cdmBase
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* @param dbIdAttribute
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* @param namespace
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* @param citation
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* @throws SQLException
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*/
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public void addOriginalSource(ResultSet rs, CdmBase cdmBase, String dbIdAttribute, String namespace, ReferenceBase citation) throws SQLException {
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if (cdmBase instanceof ISourceable ){
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IOriginalSource source;
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ISourceable sourceable = (ISourceable)cdmBase;
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Object id = rs.getObject(dbIdAttribute);
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String strId = String.valueOf(id);
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String microCitation = null;
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if (cdmBase instanceof IdentifiableEntity){
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source = IdentifiableSource.NewInstance(strId, namespace, citation, microCitation);
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}else if (cdmBase instanceof DescriptionElementBase){
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source = DescriptionElementSource.NewInstance(strId, namespace, citation, microCitation);
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}else{
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logger.warn("ISourceable not beeing identifiable entities or description element base are not yet supported. CdmBase is of type " + cdmBase.getClass().getName() + ". Original source not added.");
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return;
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}
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sourceable.addSource(source);
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}
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}
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}
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