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package eu.etaxonomy.cdm.io.xper;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmIoBase;
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import eu.etaxonomy.cdm.io.common.IoStateBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.WorkingSet;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import fr_jussieu_snv_lis.XPApp;
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import fr_jussieu_snv_lis.Xper;
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import fr_jussieu_snv_lis.IO.IExternalAdapter;
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import fr_jussieu_snv_lis.base.Individual;
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import fr_jussieu_snv_lis.base.Mode;
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import fr_jussieu_snv_lis.base.Variable;
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import fr_jussieu_snv_lis.utils.Utils;
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@Component
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public class CdmXperAdapter extends CdmIoBase implements IExternalAdapter{
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private static final Logger logger = Logger.getLogger(CdmXperAdapter.class);
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private CdmXperAdapter adapter = this;
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// private CdmApplicationController cdmApplicationController;
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private CdmXperBaseControler baseController;
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private UUID uuidWorkingSet;
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// private WorkingSet workingSet;
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//TODO preliminary
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//CONFIGURATION
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private boolean isLazyModes = false;
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private boolean isLazyIndMatrix = true;
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private boolean useSecInTaxonName = false;
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public CdmXperAdapter(){
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BaseCdm base = new BaseCdm();
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CdmXperBaseControler baseController = new CdmXperBaseControler(base, this);
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setBaseController(baseController);
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}
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public boolean startXper(UUID uuidWorkingSet){
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this.uuidWorkingSet = uuidWorkingSet;
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Thread t = new Thread() {
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public void run() {
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new Xper(adapter);
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}
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};
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System.out.println("xper2 start");
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t.start();
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// while(!XPApp.xperReady){
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// //TODO
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// }
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// System.out.println("xper2 started :::");
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return true;
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}
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//************************* GETTER /SETTER **********************/
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public void setBaseController(CdmXperBaseControler baseController) {
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this.baseController = baseController;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.IO.IExternalAdapter#getBaseController()
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*/
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public CdmXperBaseControler getBaseController() {
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return baseController;
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}
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public WorkingSet getWorkingSet() {
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// if (this.workingSet == null){
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WorkingSet workingSet = getWorkingSetService().find(uuidWorkingSet);
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// }
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return workingSet;
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}
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public WorkingSet getLanguage() {
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// if (this.workingSet == null){
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WorkingSet workingSet = getWorkingSetService().find(uuidWorkingSet);
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// }
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return workingSet;
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}
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//*********************** METHODS **********************/
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public void load(){
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loadFeatures();
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loadTaxa();
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}
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// Load the featureTree with the UUID
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public void loadFeatures() {
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logger.warn("load features start");
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TransactionStatus tx = startTransaction();
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FeatureTree featureTree = getWorkingSet().getDescriptiveSystem();
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getFeatureTreeService().saveOrUpdate(featureTree);
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if (featureTree != null) {
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loadFeatureNode(featureTree.getRoot(), -1);
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}else{
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logger.warn("No feature tree available");
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}
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commitTransaction(tx);
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logger.warn("load features end :::");
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}
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/**
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* Recursive methode to load FeatureNode and all its children
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*
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* @param featureNode
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* @param indiceParent
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*/
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public void loadFeatureNode(FeatureNode featureNode, int indiceParent){
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List<FeatureNode> featureList = featureNode.getChildren();
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adaptFeatureListToVariableList(indiceParent, featureList);
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}
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/**
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* @param indiceParent
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* @param featureList
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*/
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public void adaptFeatureListToVariableList(int indiceParent, List<FeatureNode> featureList) {
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// List<Variable> result = new ArrayList<Variable>(featureList.size());
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for(FeatureNode child : featureList){
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boolean alreadyExist = false;
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Variable variable = adaptFeatureNodeToVariable(child);
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//?? TODO
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List<Variable> vars = XPApp.getCurrentBase().getVariables();
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for(Variable var : vars){
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if(var.getName().equals(variable.getName()))
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alreadyExist = true;
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}
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if(!alreadyExist && (child.getFeature().isSupportsCategoricalData() || child.getFeature().isSupportsQuantitativeData())){
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XPApp.getCurrentBase().addVariable(variable);
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// result.add(variable);
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if(child.getFeature().isSupportsCategoricalData()){
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// Add states to the feature
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if (! isLazyModes){
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addModesToVariable(child, variable);
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}
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}
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if(indiceParent != -1 && XPApp.getCurrentBase().getVariableAt(indiceParent) != null){
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// if(indiceParent != -1 && result.get(indiceParent) != null){
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variable.addMother((XPApp.getCurrentBase().getVariableAt(indiceParent -1)));
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// variable.addMother(result.get(indiceParent -1 ));
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}
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adaptFeatureListToVariableList(variable.getIndexInt(), child.getChildren());
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}else{
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adaptFeatureListToVariableList(indiceParent, child.getChildren());
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}
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}
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return;
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}
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/**
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* @param child
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* @param variable
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*/
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private void addModesToVariable(FeatureNode child, Variable variable) {
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Set<TermVocabulary<State>> termVocabularySet = child.getFeature().getSupportedCategoricalEnumerations();
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for(TermVocabulary<State> termVocabulary : termVocabularySet){
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for(State state : termVocabulary.getTerms()){
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Mode mode = adaptStateToMode(state);
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variable.addMode(mode);
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}
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}
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}
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/**
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* @param child
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* @return
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*/
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private Variable adaptFeatureNodeToVariable(FeatureNode child) {
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Variable variable = new Variable(child.getFeature().getLabel());
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variable.setUuid(child.getFeature().getUuid());
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if (child.getFeature().isSupportsQuantitativeData()){
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// Specify the character type (numerical)
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variable.setType(Utils.numType);
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}else if (child.getFeature().isSupportsCategoricalData()){
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variable.setType(Utils.catType);
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}
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return variable;
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}
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// ******************** STATE - MODE ***********************************/
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private Mode adaptStateToMode(State state) {
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Mode result = new Mode(state.getLabel());
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result.setUuid(state.getUuid());
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return result;
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}
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public State adaptModeToState(Mode mode) {
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State state = State.NewInstance(mode.getDescription(), mode.getName(), null);
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mode.setUuid(state.getUuid());
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return state;
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}
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// ******************** TAXON - INDIVIDUAL ***********************************/
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/**
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* @param taxonBase
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* @return
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*/
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public Individual adaptTaxonToIndividual(TaxonBase taxonBase) {
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String name = useSecInTaxonName? taxonBase.getTitleCache() : taxonBase.getName().getTitleCache();
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Individual individual = new Individual(name);
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individual.setUuid(taxonBase.getUuid());
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return individual;
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}
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// ******************************** ******************************************/
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// // OLD
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// // Load all the taxa and 1 description
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// public void loadTaxaAndDescription() {
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// logger.warn("load taxa start");
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// //fill all variables with empty lists
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//
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//
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// TransactionStatus tx = startTransaction();
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//
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// getWorkingSet().getDescriptions();
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//
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// logger.warn("load taxa from CDM");
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// List<TaxonBase> taxonList = getTaxonService().list(Taxon.class , null, null, null, null);
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//
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// for(TaxonBase taxonBase : taxonList){
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// if (XPApp.getCurrentBase() != null) {
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//
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// // Add a image to the taxon
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// BaseObjectResource bor = new BaseObjectResource(new XPResource("http://www.cheloniophilie.com/Images/Photos/Chelonia-mydas/tortue-marine.JPG"));
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// individual.addResource(bor);
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//
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// // Add an empty description
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//
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// loadDescription(individual, taxonBase);
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//
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// }
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// }
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// commitTransaction(tx);
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// logger.warn("load taxa end :::");
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// }
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/**
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* Load taxa and convert to individuals.
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* Loads the
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* - uuid
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* - name
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* - varModMatrix,
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* - varNumValuesMatrix
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* - varComment (TODO)
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* - varUnknown (TODO)
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*/
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public void loadTaxa(){
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//categorical data
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logger.warn("load categorical data");
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Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> categoricalData = getCategoricalData();
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handleCategoricalData(categoricalData);
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logger.warn("load categorical data :::");
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//quantitative data
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logger.warn("load quantitative data");
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Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> quantitativeData = getQuantitativeData();
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handleQuantitativeData(quantitativeData);
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logger.warn("load quantitative data :::");
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//TODO
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//descriptions with no data
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//TODO varComment
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//TODO varUnknown
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//TODO Resources
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// TODO private String index;
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// TODO private String description;
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}
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/**
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* @return
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*/
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private Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> getCategoricalData() {
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Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> data = getWorkingSetService().getTaxonFeatureDescriptionElementMap(
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CategoricalData.class, uuidWorkingSet, null);
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return data;
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}
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private Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> getQuantitativeData() {
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Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> data = getWorkingSetService().getTaxonFeatureDescriptionElementMap(
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QuantitativeData.class, uuidWorkingSet, null);
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return data;
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}
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private void handleCategoricalData(Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> categoricalData) {
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for (UuidAndTitleCache taxon : categoricalData.keySet()){
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Map<UUID, Set<CategoricalData>> variableMap = categoricalData.get(taxon);
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Individual individual = getIndividualByUuidAndTitleCache(taxon);
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handleCategoricalData(variableMap, individual);
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}
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}
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private void handleQuantitativeData(Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> quantitativeData) {
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for (UuidAndTitleCache taxon : quantitativeData.keySet()){
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Map<UUID, Set<QuantitativeData>> variableMap = quantitativeData.get(taxon);
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Individual individual = getIndividualByUuidAndTitleCache(taxon);
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handleQuantitativeData(variableMap, individual);
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}
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}
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private void handleCategoricalData(Map<UUID, Set<CategoricalData>> variableMap, Individual individual) {
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for (UUID featureUuid : variableMap.keySet()){
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Variable variable = baseController.findVariableByUuid(featureUuid);
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if (variable != null){
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for (CategoricalData categorical : variableMap.get(featureUuid)) {
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// create a list of xper Mode corresponding
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List<Mode> modesList = variable.getModes();
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List<StateData> stateDataList = categorical.getStates();
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for (StateData stateData : stateDataList) {
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for (Mode mode : modesList) {
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if (stateData.getState().getUuid().equals(mode.getUuid())) {
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// Add state to the Description
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individual.addModeMatrix(variable, mode);
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}
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}
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}
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}
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}else{
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logger.warn("Variable not found for uuid " + featureUuid.toString());
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}
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}
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}
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387
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private void handleQuantitativeData(Map<UUID, Set<QuantitativeData>> variableMap, Individual individual) {
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for (UUID featureUuid : variableMap.keySet()){
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Variable variable = baseController.findVariableByUuid(featureUuid);
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if (variable != null){
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for (QuantitativeData qdCDM : variableMap.get(featureUuid)){
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fr_jussieu_snv_lis.base.QuantitativeData qdXper = adaptQdCdm2QdXper(qdCDM);
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individual.addNumMatrix(variable, qdXper);
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}
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}else{
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logger.warn("Variable not found for uuid " + featureUuid.toString());
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}
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}
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}
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/**
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* @param qdCDM
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* @return
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*/
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private fr_jussieu_snv_lis.base.QuantitativeData adaptQdCdm2QdXper(
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QuantitativeData qdCDM) {
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fr_jussieu_snv_lis.base.QuantitativeData qdXper = new fr_jussieu_snv_lis.base.QuantitativeData();
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if (qdCDM.getMax() != null){
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qdXper.setMax(new Double(qdCDM.getMax()));
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}
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if (qdCDM.getMin() != null){
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qdXper.setMin(new Double(qdCDM.getMin()));
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}
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if (qdCDM.getTypicalLowerBoundary() != null){
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qdXper.setUmethLower(new Double(qdCDM
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.getTypicalLowerBoundary()));
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}
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if (qdCDM.getTypicalUpperBoundary() != null){
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qdXper.setUmethUpper(new Double(qdCDM
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.getTypicalUpperBoundary()));
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}
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if (qdCDM.getAverage() != null){
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qdXper.setMean(new Double(qdCDM.getAverage()));
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}
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if (qdCDM.getStandardDeviation() != null){
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qdXper.setSd(new Double(qdCDM.getStandardDeviation()));
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}
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if (qdCDM.getSampleSize() != null){
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qdXper.setNSample(new Integer(Math.round(qdCDM.getSampleSize())));
|
432
|
}
|
433
|
return qdXper;
|
434
|
}
|
435
|
|
436
|
|
437
|
private Individual getIndividualByUuidAndTitleCache(UuidAndTitleCache taxon) {
|
438
|
Individual result = this.getBaseController().findIndividualByName(taxon.getTitleCache());
|
439
|
if (result == null){
|
440
|
result= new Individual(taxon.getTitleCache());
|
441
|
result.setUuid(taxon.getUuid());
|
442
|
this.getBaseController().addIndividual(result);
|
443
|
}
|
444
|
return result;
|
445
|
}
|
446
|
|
447
|
|
448
|
// // Create a workingSet if not exist
|
449
|
// public void createWorkingSet(){
|
450
|
//
|
451
|
// if(getWorkingSetService().list(WorkingSet.class, null, null, null, null).size() <= 0){
|
452
|
// WorkingSet ws = WorkingSet.NewInstance();
|
453
|
//
|
454
|
// UUID featureTreeUUID = UUID.fromString("47eda782-89c7-4c69-9295-e4052ebe16c6");
|
455
|
// List<String> featureTreeInit = Arrays.asList(new String[]{"root.children.feature.representations"});
|
456
|
//
|
457
|
// FeatureTree featureTree = getFeatureTreeService().load(featureTreeUUID, featureTreeInit);
|
458
|
// ws.setDescriptiveSystem(featureTree);
|
459
|
//
|
460
|
// List<TaxonBase> taxonList = getTaxonService().list(Taxon.class , null, null, null, null);
|
461
|
// for(TaxonBase taxonBase : taxonList){
|
462
|
// Pager<TaxonDescription> taxonDescriptionPager = getDescriptionService().getTaxonDescriptions((Taxon)taxonBase, null, null, null, 0, Arrays.asList(new String[]{"elements.states", "elements.feature"} ));
|
463
|
// List<TaxonDescription> taxonDescriptionList = taxonDescriptionPager.getRecords();
|
464
|
// TaxonDescription taxonDescription = taxonDescriptionList.get(0);
|
465
|
// ws.addDescription(taxonDescription);
|
466
|
// System.out.println(taxonDescription.getUuid());
|
467
|
// }
|
468
|
//
|
469
|
// getWorkingSetService().save(ws);
|
470
|
// }
|
471
|
// }
|
472
|
|
473
|
// ************************************ SAVE *************************************/
|
474
|
|
475
|
@Override
|
476
|
public void save() {
|
477
|
List<Variable> vars = XPApp.getCurrentBase().getVariables();
|
478
|
saveFeatureTree(vars);
|
479
|
saveFeatures(vars);
|
480
|
}
|
481
|
|
482
|
|
483
|
private void saveFeatureTree(List<Variable> vars) {
|
484
|
logger.warn("Save feature tree not yet implemented");
|
485
|
}
|
486
|
|
487
|
/**
|
488
|
* @param vars
|
489
|
*/
|
490
|
private void saveFeatures(List<Variable> vars) {
|
491
|
TransactionStatus tx = startTransaction();
|
492
|
for (Variable variable : vars){
|
493
|
Feature feature = getFeature(variable);
|
494
|
if (variable.isNumType()){
|
495
|
saveNumericalFeature(variable, feature);
|
496
|
}else if (Utils.catType.equals(variable.getType())){
|
497
|
saveCategoricalFeature(variable, feature);
|
498
|
}else{
|
499
|
logger.warn("variable type undefined");
|
500
|
}
|
501
|
}
|
502
|
commitTransaction(tx);
|
503
|
}
|
504
|
|
505
|
|
506
|
/**
|
507
|
* @param variable
|
508
|
* @return
|
509
|
*/
|
510
|
public Feature getFeature(Variable variable) {
|
511
|
UUID uuid = variable.getUuid();
|
512
|
ITermService termService = getTermService();
|
513
|
DefinedTermBase<?> term = termService.find(uuid);
|
514
|
Feature feature = CdmBase.deproxy(term, Feature.class);
|
515
|
return feature;
|
516
|
}
|
517
|
|
518
|
private void saveCategoricalFeature(Variable variable, Feature feature) {
|
519
|
ITermService termService = getTermService();
|
520
|
IVocabularyService vocService = getVocabularyService();
|
521
|
if (feature == null){
|
522
|
saveNewFeature(variable, termService, vocService);
|
523
|
}else{
|
524
|
if (isChanged(feature, variable)){
|
525
|
feature.setLabel(variable.getName());
|
526
|
termService.save(feature);
|
527
|
}else{
|
528
|
logger.info("No change for variable: " + variable.getName());
|
529
|
}
|
530
|
|
531
|
HashMap<UUID, State> allStates = getAllSupportedStates(feature);
|
532
|
for (Mode mode : variable.getModes()){
|
533
|
State state = allStates.get(mode.getUuid());
|
534
|
if (state == null){
|
535
|
saveNewState(mode, feature);
|
536
|
}else{
|
537
|
allStates.remove(state.getUuid());
|
538
|
if (modeHasChanged(mode, state)){
|
539
|
String stateDescription = null;
|
540
|
String stateLabel = mode.getName();
|
541
|
String stateAbbrev = null;
|
542
|
Language lang = Language.DEFAULT();
|
543
|
Representation rep = state.getRepresentation(lang);
|
544
|
rep.setLabel(stateLabel);
|
545
|
termService.saveOrUpdate(state);
|
546
|
// State state = State.NewInstance(stateDescription, stateLabel, stateAbbrev);
|
547
|
// termService.save(state);
|
548
|
// voc.addTerm(state);
|
549
|
// vocService.save(voc);
|
550
|
}
|
551
|
}
|
552
|
}
|
553
|
for (State state : allStates.values()){
|
554
|
logger.warn("There is a state to delete: " + feature.getLabel() + "-" + state.getLabel());
|
555
|
for (TermVocabulary<State> voc :feature.getSupportedCategoricalEnumerations()){
|
556
|
voc.removeTerm(state);
|
557
|
}
|
558
|
}
|
559
|
}
|
560
|
}
|
561
|
|
562
|
|
563
|
private boolean modeHasChanged(Mode mode, State state) {
|
564
|
if (CdmUtils.nullSafeEqual(mode.getName(), state.getLabel())){
|
565
|
return false;
|
566
|
}else{
|
567
|
return true;
|
568
|
}
|
569
|
}
|
570
|
|
571
|
|
572
|
public void saveNewState(Mode mode, Feature feature) {
|
573
|
TransactionStatus ta = startTransaction();
|
574
|
ITermService termService = getTermService();
|
575
|
IVocabularyService vocService = getVocabularyService();
|
576
|
|
577
|
termService.saveOrUpdate(feature);
|
578
|
int numberOfVocs = feature.getSupportedCategoricalEnumerations().size();
|
579
|
|
580
|
TermVocabulary<State> voc;
|
581
|
if (numberOfVocs <= 0){
|
582
|
//new voc
|
583
|
String vocLabel = "Vocabulary for feature " + feature.getLabel();
|
584
|
String vocDescription = vocLabel + ". Automatically created by Xper.";
|
585
|
String vocAbbrev = null;
|
586
|
String termSourceUri = null;
|
587
|
voc = TermVocabulary.NewInstance(vocDescription, vocLabel, vocAbbrev, termSourceUri);
|
588
|
}else if (numberOfVocs == 1){
|
589
|
voc = feature.getSupportedCategoricalEnumerations().iterator().next();
|
590
|
}else{
|
591
|
//numberOfVocs > 1
|
592
|
//FIXME preliminary
|
593
|
logger.warn("Multiple supported vocabularies not yet correctly implemented");
|
594
|
voc = feature.getSupportedCategoricalEnumerations().iterator().next();
|
595
|
}
|
596
|
saveNewModeToVoc(termService, vocService, voc, mode);
|
597
|
commitTransaction(ta);
|
598
|
}
|
599
|
|
600
|
|
601
|
/**
|
602
|
* @param variable
|
603
|
* @param termService
|
604
|
* @param vocService
|
605
|
*/
|
606
|
private void saveNewFeature(Variable variable, ITermService termService,
|
607
|
IVocabularyService vocService) {
|
608
|
Feature feature;
|
609
|
//new feature
|
610
|
String description = null;
|
611
|
String label = variable.getName();
|
612
|
String labelAbbrev = null;
|
613
|
feature = Feature.NewInstance(description, label, labelAbbrev);
|
614
|
variable.setUuid(feature.getUuid());
|
615
|
termService.save(feature);
|
616
|
//new voc
|
617
|
String vocDescription = null;
|
618
|
String vocLabel = "Vocabulary for feature " + label;
|
619
|
String vocAbbrev = null;
|
620
|
String termSourceUri = null;
|
621
|
TermVocabulary<State> voc = TermVocabulary.NewInstance(vocDescription, vocLabel, vocAbbrev, termSourceUri);
|
622
|
for (Mode mode:variable.getModes()){
|
623
|
saveNewModeToVoc(termService, vocService, voc, mode);
|
624
|
}
|
625
|
feature.addSupportedCategoricalEnumeration(voc);
|
626
|
termService.saveOrUpdate(feature);
|
627
|
}
|
628
|
|
629
|
|
630
|
/**
|
631
|
* @param termService
|
632
|
* @param vocService
|
633
|
* @param voc
|
634
|
* @param mode
|
635
|
*/
|
636
|
private void saveNewModeToVoc(ITermService termService, IVocabularyService vocService, TermVocabulary<State> voc, Mode mode) {
|
637
|
State state = adaptModeToState(mode);
|
638
|
termService.save(state);
|
639
|
voc.addTerm(state);
|
640
|
vocService.saveOrUpdate(voc);
|
641
|
}
|
642
|
|
643
|
|
644
|
|
645
|
private HashMap<UUID, State> getAllSupportedStates(Feature feature) {
|
646
|
HashMap<UUID, State> result = new HashMap<UUID,State>();
|
647
|
Set<TermVocabulary<State>> vocs = feature.getSupportedCategoricalEnumerations();
|
648
|
for (TermVocabulary<State> voc : vocs){
|
649
|
for (State state : voc.getTerms()){
|
650
|
result.put(state.getUuid(), state);
|
651
|
}
|
652
|
}
|
653
|
return result;
|
654
|
}
|
655
|
|
656
|
|
657
|
private boolean isChanged(Feature feature, Variable variable) {
|
658
|
//preliminary
|
659
|
return ! variable.getName().equals(feature.getLabel());
|
660
|
}
|
661
|
|
662
|
|
663
|
|
664
|
private void saveNumericalFeature(Variable variable, Feature feature) {
|
665
|
// IVocabularyService vocService = getVocabularyService();
|
666
|
String variableUnit = variable.getUnit();
|
667
|
Set<MeasurementUnit> units = feature.getRecommendedMeasurementUnits();
|
668
|
//preliminary
|
669
|
if (StringUtils.isBlank(variableUnit) ){
|
670
|
//unit is empty
|
671
|
if (!units.isEmpty()){
|
672
|
feature.getRecommendedMeasurementUnits().clear();
|
673
|
}
|
674
|
}else{
|
675
|
// unit is not empty
|
676
|
boolean unitExists = false;
|
677
|
for (MeasurementUnit measurementUnit: units){
|
678
|
//TODO ??
|
679
|
String labelOfUnit = measurementUnit.getLabel();
|
680
|
if (variableUnit.equals(labelOfUnit)){
|
681
|
unitExists = true;
|
682
|
break;
|
683
|
}
|
684
|
}
|
685
|
if (! unitExists){
|
686
|
units.clear();
|
687
|
MeasurementUnit existingUnit = findExistingUnit(variableUnit);
|
688
|
if (existingUnit == null){
|
689
|
String unitDescription = null;
|
690
|
String unitLabel = variableUnit;
|
691
|
String labelAbbrev = null;
|
692
|
MeasurementUnit newUnit = MeasurementUnit.NewInstance(unitDescription, unitLabel, labelAbbrev);
|
693
|
getTermService().save(newUnit);
|
694
|
UUID defaultMeasurmentUnitVocabularyUuid = UUID.fromString("3b82c375-66bb-4636-be74-dc9cd087292a");
|
695
|
TermVocabulary voc = getVocabularyService().find(defaultMeasurmentUnitVocabularyUuid);
|
696
|
if (voc == null){
|
697
|
logger.warn("Could not find MeasurementService vocabulary");
|
698
|
}else{
|
699
|
voc.addTerm(newUnit);
|
700
|
getVocabularyService().saveOrUpdate(voc);
|
701
|
}
|
702
|
existingUnit = newUnit;
|
703
|
}
|
704
|
feature.addRecommendedMeasurementUnit(existingUnit);
|
705
|
}
|
706
|
}
|
707
|
}
|
708
|
|
709
|
|
710
|
private MeasurementUnit findExistingUnit(String variableUnit) {
|
711
|
Pager<MeasurementUnit> existingUnits = getTermService().findByRepresentationText(variableUnit, MeasurementUnit.class, null, null);
|
712
|
for (MeasurementUnit exUnit : existingUnits.getRecords()){
|
713
|
if (variableUnit.equals(exUnit.getLabel())){
|
714
|
return exUnit;
|
715
|
}
|
716
|
}
|
717
|
return null;
|
718
|
}
|
719
|
|
720
|
|
721
|
// ************************** Override ********************************/
|
722
|
|
723
|
@Override
|
724
|
protected boolean doInvoke(IoStateBase state) {
|
725
|
//not needed
|
726
|
return false;
|
727
|
}
|
728
|
|
729
|
@Override
|
730
|
protected boolean doCheck(IoStateBase state) {
|
731
|
//not needed
|
732
|
return false;
|
733
|
}
|
734
|
|
735
|
@Override
|
736
|
protected boolean isIgnore(IoStateBase state) {
|
737
|
//not needed
|
738
|
return false;
|
739
|
}
|
740
|
|
741
|
@Override
|
742
|
public String toString() {
|
743
|
String ws = uuidWorkingSet == null ?"-" : uuidWorkingSet.toString();
|
744
|
return "CdmXperAdapter (" + ws + ")";
|
745
|
}
|
746
|
|
747
|
public void controlModeIndVar(boolean selected, Variable v, Individual i, Mode m) {
|
748
|
// (boolean selected, Variable v, Individual i, Mode m);
|
749
|
TransactionStatus txStatus = startTransaction();
|
750
|
Taxon taxon = (Taxon)getTaxonService().find(i.getUuid());
|
751
|
Feature feature = (Feature)getTermService().find(v.getUuid());
|
752
|
Set<Feature> features = new HashSet<Feature>();
|
753
|
features.add(feature);
|
754
|
List<CategoricalData> catData = getDescriptionService().getDescriptionElementsForTaxon(taxon, features, CategoricalData.class, null, null, null);
|
755
|
if (catData.size()>1){
|
756
|
logger.warn("There is more than one categorical data for the same taxon and the same feature");
|
757
|
}
|
758
|
if (selected && catData.size() == 0 ){
|
759
|
CategoricalData data = CategoricalData.NewInstance();
|
760
|
data.setFeature(feature);
|
761
|
TaxonDescription desc = taxon.getDescriptions().iterator().next();
|
762
|
desc.addElement(data);
|
763
|
addModeToCategoricalData(m, data);
|
764
|
getDescriptionService().saveDescriptionElement(data);
|
765
|
}else{
|
766
|
for (CategoricalData data: catData){
|
767
|
State tmpState = adaptModeToState(m);
|
768
|
StateData existingState = null;
|
769
|
//test data exists
|
770
|
for (StateData sd : data.getStates()){
|
771
|
if (tmpState.equals(sd.getState())){
|
772
|
existingState = sd;
|
773
|
break;
|
774
|
}
|
775
|
}
|
776
|
if (selected && existingState == null){
|
777
|
//selected
|
778
|
addModeToCategoricalData(m, data);
|
779
|
}else if (!selected && existingState != null){
|
780
|
//unselected
|
781
|
data.getStates().remove(existingState);
|
782
|
}
|
783
|
getDescriptionService().saveDescriptionElement(data);
|
784
|
}
|
785
|
}
|
786
|
commitTransaction(txStatus);
|
787
|
|
788
|
}
|
789
|
|
790
|
/**
|
791
|
* @param m
|
792
|
* @param data
|
793
|
*/
|
794
|
private void addModeToCategoricalData(Mode m, CategoricalData data) {
|
795
|
StateData sd = StateData.NewInstance();
|
796
|
State state = (State)getTermService().find(m.getUuid());
|
797
|
sd.setState(state);
|
798
|
data.getStates().add(sd);
|
799
|
}
|
800
|
|
801
|
|
802
|
|
803
|
|
804
|
}
|