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Revision 3dff50a1

Added by Andreas Müller about 13 years ago

ID 3dff50a13a51ce3a5eadab4a9aa2f5a2968ceacd
Parent 5d4eb7d8
Child fd3b4e55

new implementation for Xper data fetching from persistence and some further changes to Xper

     import org.apache.commons.lang.StringUtils;
     import org.apache.log4j.Logger;
     import org.hibernate.validator.util.GetConstructor;
     import eu.etaxonomy.cdm.api.application.CdmApplicationUtils;
     import eu.etaxonomy.cdm.common.CdmUtils;
     import fr_jussieu_snv_lis.base.BaseObject;
     import fr_jussieu_snv_lis.base.BaseObjectResource;
     import fr_jussieu_snv_lis.base.Group;
-...
     	public List<Individual> getIndividuals() {
     		if (cdmIndividuals == null){
     			cdmIndividuals = new ArrayList<Individual>();
     			getAdapter().loadTaxaAndDescription();
     			getAdapter().loadTaxa();
+    		}
     		return cdmIndividuals;
+    	}
-...
     	 */
     	@Override
     	public Individual getIndividualAt(int i) {
     		logger.warn("getIndividualAt Not yet implemented");
     		return null;
     		return this.cdmIndividuals.get(i);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public int getNbIndividuals() {
     		logger.warn("getNbIndividuals Not yet implemented");
     		return 0;
     		return this.cdmIndividuals.size();
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void setNbIndividuals(int n) {
     		logger.warn("setNbIndividuals Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public Set<String> getLinks() {
     		logger.warn("getLinks Not yet implemented");
     		return null;
+    	}
     	/* (non-Javadoc)
     	 * @see fr_jussieu_snv_lis.base.IBase#getLinkAt(int)
     	 */
     	@Override
     	public String getLinkAt(int i) {
     		logger.warn("getLinkAt Not yet implemented");
     		return null;
     		logger.warn("getLinks Not yet implemented. Returns empty list");
     		return new HashSet<String>();
+    	}
     	/* (non-Javadoc)

     package eu.etaxonomy.cdm.io.xper;
     import java.util.ArrayList;
     import java.util.Arrays;
     import java.util.HashMap;
     import java.util.List;
     import java.util.Map;
     import java.util.Set;
     import java.util.UUID;
     import org.apache.commons.lang.StringUtils;
     import org.apache.log4j.Logger;
     import org.springframework.stereotype.Component;
     import org.springframework.transaction.TransactionStatus;
     import eu.etaxonomy.cdm.api.application.CdmApplicationController;
     import eu.etaxonomy.cdm.api.service.ITermService;
     import eu.etaxonomy.cdm.api.service.IVocabularyService;
     import eu.etaxonomy.cdm.api.service.pager.Pager;
     import eu.etaxonomy.cdm.common.CdmUtils;
     import eu.etaxonomy.cdm.io.common.CdmIoBase;
     import eu.etaxonomy.cdm.io.common.IoStateBase;
     import eu.etaxonomy.cdm.model.common.CdmBase;
     import eu.etaxonomy.cdm.model.common.DefinedTermBase;
     import eu.etaxonomy.cdm.model.common.Language;
     import eu.etaxonomy.cdm.model.common.Representation;
     import eu.etaxonomy.cdm.model.common.TermVocabulary;
     import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
     import eu.etaxonomy.cdm.model.description.CategoricalData;
     import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
     import eu.etaxonomy.cdm.model.description.Feature;
     import eu.etaxonomy.cdm.model.description.FeatureNode;
     import eu.etaxonomy.cdm.model.description.FeatureTree;
-...
     import eu.etaxonomy.cdm.model.description.QuantitativeData;
     import eu.etaxonomy.cdm.model.description.State;
     import eu.etaxonomy.cdm.model.description.StateData;
     import eu.etaxonomy.cdm.model.description.TaxonDescription;
     import eu.etaxonomy.cdm.model.description.WorkingSet;
     import eu.etaxonomy.cdm.model.taxon.Taxon;
     import eu.etaxonomy.cdm.model.taxon.TaxonBase;
     import fr_jussieu_snv_lis.XPApp;
     import fr_jussieu_snv_lis.Xper;
     import fr_jussieu_snv_lis.IO.IExternalAdapter;
     import fr_jussieu_snv_lis.base.BaseObjectResource;
     import fr_jussieu_snv_lis.base.Individual;
     import fr_jussieu_snv_lis.base.Mode;
     import fr_jussieu_snv_lis.base.Variable;
     import fr_jussieu_snv_lis.base.XPResource;
     import fr_jussieu_snv_lis.utils.Utils;
     public class CdmXperAdapter implements IExternalAdapter{
     @Component
     public class CdmXperAdapter extends CdmIoBase implements IExternalAdapter{
     	private static final Logger logger = Logger.getLogger(CdmXperAdapter.class);
     	TransactionStatus tx;
     	private CdmXperAdapter  adapter = this;
     	private CdmApplicationController cdmApplicationController;
     //	private CdmApplicationController cdmApplicationController;
     	private CdmXperBaseControler baseController;
     	private UUID uuidWorkingSet;
     	private WorkingSet workingSet;
     //	private WorkingSet workingSet;
     	//TODO preliminary
     	//CONFIGURATION
     	private boolean isLazyModes = false;
     	private boolean isLazyIndMatrix = true;
     	private boolean useSecInTaxonName = false;
     	public CdmXperAdapter(CdmApplicationController appCtr, UUID uuidWorkingSet) {
     		this.uuidWorkingSet = uuidWorkingSet;
     		setCdmApplicationController(appCtr);
     		BaseCdm base = new BaseCdm();
     		setBaseController(new CdmXperBaseControler(base, this));
     	public CdmXperAdapter(){
     		BaseCdm base = new BaseCdm();
     		CdmXperBaseControler baseController = new CdmXperBaseControler(base, this);
     		setBaseController(baseController);
+    	}
     //************************* GETTER /SETTER **********************/
     	public void setCdmApplicationController(CdmApplicationController appCtr) {
     		this.cdmApplicationController = appCtr;
     		 tx = cdmApplicationController.startTransaction();
     	public boolean startXper(UUID uuidWorkingSet){
     		this.uuidWorkingSet = uuidWorkingSet;
     		Thread t = new Thread() {
     			public void run() {
     				new Xper(adapter);
+    			}
     		};
     		System.out.println("xper2 start");
     		t.start();
     //		while(!XPApp.xperReady){
     //			//TODO
     //		}
     //		System.out.println("xper2 started :::");
     		return true;
+    	}
     //	public CdmApplicationController getCdmApplicationController() {
     //		return cdmApplicationController;
     //	}
     //************************* GETTER /SETTER **********************/
     	public void setBaseController(CdmXperBaseControler baseController) {
     		this.baseController = baseController;
-...
+    	}
     	public WorkingSet getWorkingSet() {
     		if (this.workingSet == null){
     			this.workingSet = cdmApplicationController.getWorkingSetService().find(uuidWorkingSet);
+    		}
     //		if (this.workingSet == null){
     			WorkingSet workingSet = getWorkingSetService().find(uuidWorkingSet);
     //		}
     		return workingSet;
+    	}
     	public WorkingSet getLanguage() {
     //		if (this.workingSet == null){
     			WorkingSet workingSet = getWorkingSetService().find(uuidWorkingSet);
     //		}
     		return workingSet;
+    	}
-...
     	public void load(){
     		loadFeatures();
     		loadTaxaAndDescription();
     		loadTaxa();
+    	}
     	// Load the featureTree with the UUID
     	public void loadFeatures() {
     		logger.warn("load features start");
     		TransactionStatus tx = startTransaction();
     		FeatureTree featureTree = getWorkingSet().getDescriptiveSystem();
     		this.cdmApplicationController.getWorkingSetService().saveOrUpdate(workingSet);
     		getFeatureTreeService().saveOrUpdate(featureTree);
     //		UUID featureTreeUUID = UUID.fromString("1045f91b-6f1a-4a7d-8783-82a58a01ab25");
     ////		UUID featureTreeUUID = UUID.fromString("43ab1efd-fa15-419a-8cd6-05477e4b37bc");
     //		List<String> featureTreeInit = Arrays.asList(new String[]{"root.children.feature.representations"});
     //
     //		TransactionStatus tx = cdmApplicationController.startTransaction();
     //		FeatureTree featureTree = cdmApplicationController.getFeatureTreeService().load(featureTreeUUID, featureTreeInit);
     		if (featureTree != null) {
     			loadFeatureNode(featureTree.getRoot(), -1);
     		}else{
     			logger.warn("No feature tree available");
+    		}
     		commitTransaction(tx);
     		logger.warn("load features end :::");
+    	}
-...
     //				result.add(variable);
     				if(child.getFeature().isSupportsCategoricalData()){
     					// Add states to the character
     					Set<TermVocabulary<State>> termVocabularySet = child.getFeature().getSupportedCategoricalEnumerations();
     					for(TermVocabulary<State> termVocabulary : termVocabularySet){
     						for(State state : termVocabulary.getTerms()){
     							Mode mode = adaptStateToMode(state);
     							variable.addMode(mode);
+    						}
     					// Add states to the feature
     					if (! isLazyModes){
     						addModesToVariable(child, variable);
+    					}
     				}else if (child.getFeature().isSupportsQuantitativeData()) {
     					// Specify the character type (numerical)
     					variable.setType(Utils.numType);
+    				}
     				if(indiceParent != -1 && XPApp.getCurrentBase().getVariableAt(indiceParent) != null){
-...
     		return;
+    	}
     	/**
     	 * @param child
     	 * @param variable
     	 */
     	private void addModesToVariable(FeatureNode child, Variable variable) {
     		Set<TermVocabulary<State>> termVocabularySet = child.getFeature().getSupportedCategoricalEnumerations();
     		for(TermVocabulary<State> termVocabulary : termVocabularySet){
     			for(State state : termVocabulary.getTerms()){
     				Mode mode = adaptStateToMode(state);
     				variable.addMode(mode);
+    			}
+    		}
+    	}
     	/**
     	 * @param child
     	 * @return
-...
     	private Variable adaptFeatureNodeToVariable(FeatureNode child) {
     		Variable variable = new Variable(child.getFeature().getLabel());
     		variable.setUuid(child.getFeature().getUuid());
     		if (child.getFeature().isSupportsQuantitativeData()){
     			// Specify the character type (numerical)
     			variable.setType(Utils.numType);
     		}else if (child.getFeature().isSupportsCategoricalData()){
     			variable.setType(Utils.catType);
+    		}
     		return variable;
+    	}
-...
     		return state;
+    	}
     // ******************** TAXON - INDIVIDUAL ***********************************/
     	/**
     	 * @param taxonBase
     	 * @return
     	 */
     	public Individual adaptTaxonToIndividual(TaxonBase taxonBase) {
     		String name = useSecInTaxonName? taxonBase.getTitleCache() : taxonBase.getName().getTitleCache();
     		Individual individual = new Individual(name);
     		individual.setUuid(taxonBase.getUuid());
     		return individual;
+    	}
     // ******************************** ******************************************/
     //    // OLD
     //	// Load all the taxa and 1 description
     //	public void loadTaxaAndDescription() {
     //		logger.warn("load taxa start");
     //		//fill all variables with empty lists
     //
     //
     //		TransactionStatus tx = startTransaction();
     //
     //		getWorkingSet().getDescriptions();
     //
     //		logger.warn("load taxa from CDM");
     //		List<TaxonBase> taxonList = getTaxonService().list(Taxon.class , null, null, null, null);
     //
     //		for(TaxonBase taxonBase : taxonList){
     //			if (XPApp.getCurrentBase() != null) {
     //
     //				// Add a image to the taxon
     //				BaseObjectResource bor = new BaseObjectResource(new XPResource("http://www.cheloniophilie.com/Images/Photos/Chelonia-mydas/tortue-marine.JPG"));
     //                individual.addResource(bor);
     //
     //				// Add an empty description
     //
     //                loadDescription(individual, taxonBase);
     //
     //			}
     //		}
     //		commitTransaction(tx);
     //		logger.warn("load taxa end :::");
     //	}
     	// Load all the taxa and 1 description
     	public void loadTaxaAndDescription() {
     		TransactionStatus tx = startTransaction();
     		List<TaxonBase> taxonList = cdmApplicationController.getTaxonService().list(Taxon.class , null, null, null, null);
     		for(TaxonBase taxonBase : taxonList){
     			if (XPApp.getCurrentBase() != null) {
     				Individual individual = new Individual(taxonBase.getName().toString());
     				individual.setUuid(taxonBase.getUuid());
     				// Add a image to the taxon
     				BaseObjectResource bor = new BaseObjectResource(new XPResource("http://www.cheloniophilie.com/Images/Photos/Chelonia-mydas/tortue-marine.JPG"));
                     individual.addResource(bor);
     				// Add an empty description
                     List<Variable> vars = XPApp.getCurrentBase().getVariables();
     				for(Variable var : vars){
     					individual.addMatrix(var, new ArrayList<Mode>());
+    				}
     				loadDescription(individual, taxonBase);
     				XPApp.getCurrentBase().addIndividual(individual);
+    			}
     	/**
     	 * Load taxa and convert to individuals.
     	 * Loads the
     	 *  - uuid
     	 *  - name
     	 *  - varModMatrix,
     	 *  - varNumValuesMatrix
     	 *  - varComment (TODO)
     	 *  - varUnknown (TODO)
     	 */
     	public void loadTaxa(){
     		//categorical data
     		logger.warn("load categorical data");
     		Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> categoricalData = getCategoricalData();
     		handleCategoricalData(categoricalData);
     		logger.warn("load categorical data :::");
     		//quantitative data
     		logger.warn("load quantitative data");
     		Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> quantitativeData = getQuantitativeData();
     		handleQuantitativeData(quantitativeData);
     		logger.warn("load quantitative data :::");
     		//TODO
     		//descriptions with no data
     		//TODO varComment
     		//TODO varUnknown
     		//TODO Resources
     //		TODO private String index;
     //		TODO private String description;
+    	}
     	/**
     	 * @return
     	 */
     	private Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> getCategoricalData() {
     		Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> data = getWorkingSetService().getTaxonFeatureDescriptionElementMap(
     				CategoricalData.class, uuidWorkingSet, null, null, null, null);
     		return data;
+    	}
     	private Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> getQuantitativeData() {
     		Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> data = getWorkingSetService().getTaxonFeatureDescriptionElementMap(
     				QuantitativeData.class, uuidWorkingSet, null, null, null, null);
     		return data;
+    	}
     	private void handleCategoricalData(Map<UuidAndTitleCache, Map<UUID, Set<CategoricalData>>> categoricalData) {
     		for (UuidAndTitleCache taxon : categoricalData.keySet()){
     			Map<UUID, Set<CategoricalData>> variableMap = categoricalData.get(taxon);
     			Individual individual = getIndividualByUuidAndTitleCache(taxon);
     			handleCategoricalData(variableMap, individual);
+    		}
+    	}
     	private void handleQuantitativeData(Map<UuidAndTitleCache, Map<UUID, Set<QuantitativeData>>> quantitativeData) {
     		for (UuidAndTitleCache taxon : quantitativeData.keySet()){
     			Map<UUID, Set<QuantitativeData>> variableMap = quantitativeData.get(taxon);
     			Individual individual = getIndividualByUuidAndTitleCache(taxon);
     			handleQuantitativeData(variableMap, individual);
+    		}
     		commitTransaction(tx);
+    	}
     	// Load the first taxonDescription
     	public void loadDescription(Individual individual, TaxonBase taxonBase) {
     		Pager<TaxonDescription> taxonDescriptionPager = cdmApplicationController.getDescriptionService().getTaxonDescriptions((Taxon)taxonBase, null, null, null, 0, Arrays.asList(new String[]{"elements.states", "elements.feature"} ));
     		List<TaxonDescription> taxonDescriptionList = taxonDescriptionPager.getRecords();
     		TaxonDescription taxonDescription = taxonDescriptionList.get(0);
     		Set<DescriptionElementBase> DescriptionElementBaseList = taxonDescription.getElements();
     		for(DescriptionElementBase descriptionElementBase : DescriptionElementBaseList){
     			if(descriptionElementBase instanceof CategoricalData){
     				// find the xper variable corresponding
     				Variable variable = null;
     				List<Variable> vars = XPApp.getCurrentBase().getVariables();
     				for(Variable var : vars){
     					if(var.getUuid().equals(((CategoricalData)descriptionElementBase).getFeature().getUuid())){
     						variable = var;
+    					}
+    				}
     				if(variable != null){
     	private void handleCategoricalData(Map<UUID, Set<CategoricalData>> variableMap, Individual individual) {
     		for (UUID featureUuid : variableMap.keySet()){
     			Variable variable = baseController.findVariableByUuid(featureUuid);
     			if (variable != null){
     				for (CategoricalData categorical : variableMap.get(featureUuid)) {
     					// create a list of xper Mode corresponding
     					List<Mode> modesList = variable.getModes();
     					List<StateData> stateList = ((CategoricalData)descriptionElementBase).getStates();
     					for(StateData state : stateList){
     						for(Mode mode : modesList){
     							if(state.getState().getUuid().equals(mode.getUuid())){
     					List<StateData> stateDataList = categorical.getStates();
     					for (StateData state : stateDataList) {
     						for (Mode mode : modesList) {
     							if (state.getState().getUuid().equals(mode.getUuid())) {
     								// Add state to the Description
     								individual.addModeMatrix(variable, mode);
+    							}
+    						}
+    					}
+    				}
     			}else if(descriptionElementBase instanceof QuantitativeData){
     				// find the xper variable corresponding
     				Variable variable = null;
     				List<Variable> vars = XPApp.getCurrentBase().getVariables();
     				for(Variable var : vars){
     					if(var.getUuid().equals(((QuantitativeData)descriptionElementBase).getFeature().getUuid())){
     						variable = var;
+    					}
+    				}
     				if(variable != null){
     					fr_jussieu_snv_lis.base.QuantitativeData qdXper = new fr_jussieu_snv_lis.base.QuantitativeData();
     					QuantitativeData qdCDM = ((QuantitativeData)descriptionElementBase);
     					if(qdCDM.getMax() != null)
     						qdXper.setMax(new Double(qdCDM.getMax()));
     					if(qdCDM.getMin() != null)
     						qdXper.setMin(new Double(qdCDM.getMin()));
     					if(qdCDM.getTypicalLowerBoundary() != null)
     						qdXper.setUmethLower(new Double(qdCDM.getTypicalLowerBoundary()));
     					if(qdCDM.getTypicalUpperBoundary() != null)
     						qdXper.setUmethUpper(new Double(qdCDM.getTypicalUpperBoundary()));
     					// Does not work
     					//qdXper.setMean(new Double(qdCDM.getAverage()));
     					//qdXper.setSd(new Double(qdCDM.getStandardDeviation()));
     					//qdXper.setNSample(new Double(qdCDM.getSampleSize()));
     			}else{
     				logger.warn("Variable not found for uuid " +  featureUuid.toString());
+    			}
+    		}
+    	}
     	private void handleQuantitativeData(Map<UUID, Set<QuantitativeData>> variableMap, Individual individual) {
     		for (UUID featureUuid : variableMap.keySet()){
     			Variable variable = baseController.findVariableByUuid(featureUuid);
     			if (variable != null){
     				for (QuantitativeData qdCDM : variableMap.get(featureUuid)){
     					fr_jussieu_snv_lis.base.QuantitativeData qdXper = adaptQdCdm2QdXper(qdCDM);
     					individual.addNumMatrix(variable, qdXper);
+    				}
     			}else{
     				logger.warn("Variable not found for uuid " +  featureUuid.toString());
+    			}
+    		}
+    	}
     	// Create a workingSet if not exist
     	public void createWorkingSet(){
     	/**
     	 * @param qdCDM
     	 * @return
     	 */
     	private fr_jussieu_snv_lis.base.QuantitativeData adaptQdCdm2QdXper(
     			QuantitativeData qdCDM) {
     		fr_jussieu_snv_lis.base.QuantitativeData qdXper = new fr_jussieu_snv_lis.base.QuantitativeData();
     		if(cdmApplicationController.getWorkingSetService().list(WorkingSet.class, null, null, null, null).size() <= 0){
     			WorkingSet ws = WorkingSet.NewInstance();
     			UUID featureTreeUUID = UUID.fromString("47eda782-89c7-4c69-9295-e4052ebe16c6");
     			List<String> featureTreeInit = Arrays.asList(new String[]{"root.children.feature.representations"});
     			FeatureTree featureTree = cdmApplicationController.getFeatureTreeService().load(featureTreeUUID, featureTreeInit);
     			ws.setDescriptiveSystem(featureTree);
     			List<TaxonBase> taxonList = cdmApplicationController.getTaxonService().list(Taxon.class , null, null, null, null);
     			for(TaxonBase taxonBase : taxonList){
     				Pager<TaxonDescription> taxonDescriptionPager = cdmApplicationController.getDescriptionService().getTaxonDescriptions((Taxon)taxonBase, null, null, null, 0, Arrays.asList(new String[]{"elements.states", "elements.feature"} ));
     				List<TaxonDescription> taxonDescriptionList = taxonDescriptionPager.getRecords();
     				TaxonDescription taxonDescription = taxonDescriptionList.get(0);
     				ws.addDescription(taxonDescription);
     				System.out.println(taxonDescription.getUuid());
+    			}
     			cdmApplicationController.getWorkingSetService().save(ws);
     		if (qdCDM.getMax() != null){
     			qdXper.setMax(new Double(qdCDM.getMax()));
+    		}
     		if (qdCDM.getMin() != null){
     			qdXper.setMin(new Double(qdCDM.getMin()));
+    		}
     		if (qdCDM.getTypicalLowerBoundary() != null){
     			qdXper.setUmethLower(new Double(qdCDM
     					.getTypicalLowerBoundary()));
+    		}
     		if (qdCDM.getTypicalUpperBoundary() != null){
     			qdXper.setUmethUpper(new Double(qdCDM
     					.getTypicalUpperBoundary()));
+    		}
     		if (qdCDM.getAverage() != null){
     			qdXper.setMean(new Double(qdCDM.getAverage()));
+    		}
     		if (qdCDM.getStandardDeviation() != null){
     			qdXper.setSd(new Double(qdCDM.getStandardDeviation()));
+    		}
     		if (qdCDM.getSampleSize() != null){
     			qdXper.setNSample(new Integer(Math.round(qdCDM.getSampleSize())));
+    		}
     		return qdXper;
+    	}
     	private Individual getIndividualByUuidAndTitleCache(UuidAndTitleCache taxon) {
     		Individual result = this.getBaseController().findIndividualByName(taxon.getTitleCache());
     		if (result == null){
     			result= new Individual(taxon.getTitleCache());
     			result.setUuid(taxon.getUuid());
     			this.getBaseController().addIndividual(result);
+    		}
     		return result;
+    	}
     //	// Create a workingSet if not exist
     //	public void createWorkingSet(){
     //
     //		if(getWorkingSetService().list(WorkingSet.class, null, null, null, null).size() <= 0){
     //			WorkingSet ws = WorkingSet.NewInstance();
     //
     //			UUID featureTreeUUID = UUID.fromString("47eda782-89c7-4c69-9295-e4052ebe16c6");
     //			List<String> featureTreeInit = Arrays.asList(new String[]{"root.children.feature.representations"});
     //
     //			FeatureTree featureTree = getFeatureTreeService().load(featureTreeUUID, featureTreeInit);
     //			ws.setDescriptiveSystem(featureTree);
     //
     //			List<TaxonBase> taxonList = getTaxonService().list(Taxon.class , null, null, null, null);
     //			for(TaxonBase taxonBase : taxonList){
     //				Pager<TaxonDescription> taxonDescriptionPager = getDescriptionService().getTaxonDescriptions((Taxon)taxonBase, null, null, null, 0, Arrays.asList(new String[]{"elements.states", "elements.feature"} ));
     //				List<TaxonDescription> taxonDescriptionList = taxonDescriptionPager.getRecords();
     //				TaxonDescription taxonDescription = taxonDescriptionList.get(0);
     //				ws.addDescription(taxonDescription);
     //				System.out.println(taxonDescription.getUuid());
     //			}
     //
     //			getWorkingSetService().save(ws);
     //		}
     //	}
     // ************************************ SAVE *************************************/
     	@Override
     	public void save() {
     		List<Variable> vars = XPApp.getCurrentBase().getVariables();
-...
     	 * @param vars
     	 */
     	private void saveFeatures(List<Variable> vars) {
     		tx = cdmApplicationController.startTransaction();
     		tx = startTransaction();
     		for (Variable variable : vars){
     			Feature feature = getFeature(variable);
     			if (Utils.numType.equals(variable.getType())){
-...
     				logger.warn("variable type undefined");
+    			}
+    		}
     		cdmApplicationController.commitTransaction(tx);
     		commitTransaction(tx);
+    	}
-...
     	 */
     	public Feature getFeature(Variable variable) {
     		UUID uuid = variable.getUuid();
     		ITermService termService = cdmApplicationController.getTermService();
     		ITermService termService = getTermService();
     		DefinedTermBase<?> term = termService.find(uuid);
     		Feature feature = CdmBase.deproxy(term, Feature.class);
     		return feature;
+    	}
     	private void saveCategoricalFeature(Variable variable, Feature feature) {
     		ITermService termService = cdmApplicationController.getTermService();
     		IVocabularyService vocService = cdmApplicationController.getVocabularyService();
     		ITermService termService = getTermService();
     		IVocabularyService vocService = getVocabularyService();
     		if (feature == null){
     			saveNewFeature(variable, termService, vocService);
     		}else{
-...
     	public void saveNewState(Mode mode, Feature feature) {
     		TransactionStatus ta = startTransaction();
     		ITermService termService = cdmApplicationController.getTermService();
     		IVocabularyService vocService = cdmApplicationController.getVocabularyService();
     		ITermService termService = getTermService();
     		IVocabularyService vocService = getVocabularyService();
     		termService.saveOrUpdate(feature);
     		int numberOfVocs = feature.getSupportedCategoricalEnumerations().size();
-...
     	private void saveNumericalFeature(Variable variable, Feature feature) {
     		ITermService termService = cdmApplicationController.getTermService();
     		IVocabularyService vocService = cdmApplicationController.getVocabularyService();
     //		IVocabularyService vocService = getVocabularyService();
     		String variableUnit = variable.getUnit();
     		Set<MeasurementUnit> units = feature.getRecommendedMeasurementUnits();
     		//preliminary
-...
+    			}
     			if (! unitExists){
     				units.clear();
     				MeasurementUnit existingUnit = findExistingUnit(variableUnit, termService);
     				MeasurementUnit existingUnit = findExistingUnit(variableUnit);
     				if (existingUnit == null){
     					String unitDescription = null;
     					String unitLabel = variableUnit;
     					String labelAbbrev = null;
     					MeasurementUnit newUnit = MeasurementUnit.NewInstance(unitDescription, unitLabel, labelAbbrev);
     					termService.save(newUnit);
     					getTermService().save(newUnit);
     					UUID defaultMeasurmentUnitVocabularyUuid = UUID.fromString("3b82c375-66bb-4636-be74-dc9cd087292a");
     					TermVocabulary voc = vocService.find(defaultMeasurmentUnitVocabularyUuid);
     					TermVocabulary voc = getVocabularyService().find(defaultMeasurmentUnitVocabularyUuid);
     					if (voc == null){
     						logger.warn("Could not find MeasurementService vocabulary");
     					}else{
     						voc.addTerm(newUnit);
     						vocService.saveOrUpdate(voc);
     						getVocabularyService().saveOrUpdate(voc);
+    					}
     					existingUnit = newUnit;
+    				}
-...
+    	}
     	private MeasurementUnit findExistingUnit(String variableUnit, ITermService termService) {
     		Pager<MeasurementUnit> existingUnits = termService.findByRepresentationText(variableUnit, MeasurementUnit.class, null, null);
     	private MeasurementUnit findExistingUnit(String variableUnit) {
     		Pager<MeasurementUnit> existingUnits = getTermService().findByRepresentationText(variableUnit, MeasurementUnit.class, null, null);
     		for (MeasurementUnit exUnit : existingUnits.getRecords()){
     			if (variableUnit.equals(exUnit.getLabel())){
     				return exUnit;
-...
+    	}
     	/**
     	 * @param tx
     	 */
     	private void commitTransaction(TransactionStatus tx) {
     		cdmApplicationController.commitTransaction(tx);
     // ************************** Override ********************************/
     	@Override
     	protected boolean doInvoke(IoStateBase state) {
     		//not needed
     		return false;
+    	}
     	/**
     	 * @return
     	 */
     	private TransactionStatus startTransaction() {
     		TransactionStatus tx = cdmApplicationController.startTransaction();
     		return tx;
     	@Override
     	protected boolean doCheck(IoStateBase state) {
     		//not needed
     		return false;
+    	}
     	@Override
     	protected boolean isIgnore(IoStateBase state) {
     		//not needed
     		return false;
+    	}
     	@Override
     	public String toString() {
     		String ws = uuidWorkingSet == null ?"-" : uuidWorkingSet.toString();
     		return "CdmXperAdapter (" + ws + ")";
+    	}
+    }

     package eu.etaxonomy.cdm.io.xper;
     import java.util.List;
     import java.util.UUID;
     import org.apache.log4j.Logger;
-...
     	 */
     	@Override
     	public boolean matchNumValue(Individual ind, Variable var, Double value) {
     		logger.warn("matchNumValue Not yet implemented");
     		return false;
     		logger.info("matchNumValue implemented by using super");
     		return super.matchNumValue(ind, var, value);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public void addIndividual(Individual ind) {
     		logger.warn("addIndividual Not yet implemented");
     		super.addIndividual(ind);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public Individual findIndividualByName(String ind) {
     		logger.warn("findIndividualByName Not yet implemented");
     		return null;
     		return super.findIndividualByName(ind);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public boolean checkingUnknown(Variable var, Individual ind) {
     		logger.warn("checkingUnknown Not yet implemented");
     		return false;
     		return super.checkingUnknown(var, ind);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public void checkUnknown(Variable var, Individual ind, boolean b, boolean withDaughters) {
     		logger.warn("checkUnknown Not yet implemented");
     		super.checkUnknown(var, ind, b, withDaughters);
+    	}
     	/* (non-Javadoc)
     	 * @see fr_jussieu_snv_lis.base.IControlerBase#checkUnknown(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual[], boolean, boolean)
     	 */
     	@Override
     	public void checkUnknown(Variable var, Individual[] tab, boolean b,
     			boolean withDaughters) {
     		logger.warn("checkUnknown(var,tab, b, withDaughters) Not yet implemented");
     	public void checkUnknown(Variable var, Individual[] tab, boolean b, boolean withDaughters) {
     		super.checkUnknown(var, tab, b, withDaughters);
+    	}
     	/* (non-Javadoc)
-...
     	 */
     	@Override
     	public Variable findVariableByName(String str) {
     		logger.warn("findVariableByName Not yet implemented");
     		logger.warn("findVariableByName implemented as super");
     		return super.findVariableByName(str);
+    	}
     	/**
     	 * Returns the variable with variable.uuid equal to uuid.
     	 * Returns <code>null</code> if no such variable exists or
     	 * if <code>uuid == null</code>
     	 * @param uuid
     	 * @return
     	 */
     	public Variable findVariableByUuid(UUID uuid) {
     		if (uuid == null){
     			return null;
+    		}
     		//TODO improve performance by storing variables also in a
     		//hashmap
     		for (Variable var : base.getVariables()) {
     			if (uuid.equals(var.getUuid())) {
     				return var;
+    			}
+    		}
     		return null;
+    	}
-...
     	 */
     	@Override
     	public boolean checkExistanceOneVariable(String s) {
     		logger.warn("checkExistanceOneVariable Not yet implemented");
     		return false;
     		logger.warn("checkExistanceOneVariable implemented as super");
     		return super.checkExistanceOneVariable(s);
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void addNewVariableAndItsModesToMatrix(Variable newVariable) {
     		logger.warn("addNewVariableAndItsModesToMatrix Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void addNewVariableNumAndItsModesToMatrix(Variable newVariable) {
     		logger.warn("addNewVariableNumAndItsModesToMatrix Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void deleteVariableFromMatrix(Variable variable) {
     		logger.warn("deleteVariableFromMatrix Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void deleteVariable(Variable va) {
     		logger.warn("deleteVariable Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void deleteVariableAndAllDaughters(Variable v) {
     		logger.warn("deleteVariableAndAllDaughters Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void deleteVariablesAndAllDaughters(Variable[] tab) {
     		logger.warn("deleteVariablesAndAllDaughters Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     	@Override
     	public void deleteVariablesWithoutDaughters(Variable[] tab) {
     		logger.warn("deleteVariablesWithoutDaughters Not yet implemented");
+    	}
     	/* (non-Javadoc)
-...
     		return null;
+    	}
     	/* (non-Javadoc)
     	 * @see fr_jussieu_snv_lis.base.IControlerBase#getVariableDaughters(java.util.List, fr_jussieu_snv_lis.base.Variable)
     	 */
     	@Override
     	public List<Variable> getVariableDaughters(List<Variable> listDaugther,
     			Variable v) {
     		logger.warn("getVariableDaughters Not yet implemented");
     		return null;
+    	}
     	/* (non-Javadoc)
     	 * @see fr_jussieu_snv_lis.base.IControlerBase#getVariableDaughters(fr_jussieu_snv_lis.base.Variable)
     	 */
     	@Override
     	public List<Variable> getVariableDaughters(Variable v) {
     		logger.warn("getVariableDaughters Not yet implemented");
     		return null;
     		return super.getVariableDaughters(v);
+    	}
     	/* (non-Javadoc)

+    	 *
     	 */
     	private boolean startApplications() {
     		boolean result = false;
     		DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;
     		ICdmDataSource datasource = CdmDestinations.cdm_test_local_xper();
     		System.out.println("cdm start");
-...
     			return false;
     		}else{
     			UUID uuidWorkingSet =  workingSets.iterator().next().getUuid();
     			adapterCdmXper = new CdmXperAdapter(appCtr, uuidWorkingSet);
     			adapterCdmXper = (CdmXperAdapter)appCtr.getBean("cdmXperAdapter");
     //			adapterCdmXper = new CdmXperAdapter(appCtr, uuidWorkingSet);
     			result =  adapterCdmXper.startXper(uuidWorkingSet);
+    		}
     		return result;
     		Thread t = new Thread() {
     			public void run() {
     				new Xper(adapterCdmXper);
+    			}
     		};
     		System.out.println("xper2 start");
     		t.start();
     		while(!XPApp.xperReady){
     			//TODO wait
+    		}
     		System.out.println("xper2 started :::");
     		return true;
+    	}
     	public void xperloadDataFromCdm(){
-...
     	 * @param args
     	 */
     	public static void main(String[] args) {
     		System.out.println("start test");
     		System.out.println("start test adapter");
     		//start CDM and Xper
     		TestAdapterCdmXper testAdapter = new TestAdapterCdmXper();
     		boolean success = testAdapter.startApplications();
     		while(!XPApp.xperReady){
     			try {
     				Thread.sleep(200);
     			} catch (InterruptedException e) {
     				e.printStackTrace();
+    			}
+    		}
     		System.out.println("xper2 started :::");
     		if (success){
     			testAdapter.createThumbnailDirectory();
     			if (args.length >= 1 && "-p".equals(args[0]) ){
-...
     				testAdapter.generateThumbnails();
+    			}
     		}else{
     			System.out.println("end test adapter with errors");
     			System.exit(-1);
+    		}
     		System.out.println("end test adapter");
+    	}

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Revision 3dff50a1

Added by Andreas Müller about 13 years ago