/ - Diff - EDIT - EDIT Project Management

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
-...
     /**
      * @author a.mueller
      * @since 03.07.2008
      * @version 1.0
      */
     public class TreeCreator {
     	@SuppressWarnings("unused")
-...
     	public static FeatureTree flatTree(UUID featureTreeUuid, Map<Integer, Feature> featureMap, Object[] featureKeyList){
     		FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
     		FeatureNode root = result.getRoot();
     		for (Object featureKey : featureKeyList){
     			Feature feature = featureMap.get(featureKey);
     			if (feature != null){
     				FeatureNode child = FeatureNode.NewInstance(feature);
     				root.addChild(child);
     				root.addChild(child);
+    			}
+    		}
     		return result;
+    	}
     	/**
     	 * @param args
     	 */
     	public static void main(String[] args) {
     		Map<Integer, Feature>  map = new HashMap<Integer, Feature>(null);
     		Map<Integer, Feature>  map = new HashMap<>(null);
     		map.put(1, Feature.DISTRIBUTION());
     		map.put(2, Feature.ECOLOGY());
     		Object[] strFeatureList = new Integer[]{1,2};
     		Object[] strFeatureList = new Integer[]{1,2};
     		FeatureTree tree = TreeCreator.flatTree(UUID.randomUUID(), map, strFeatureList);
     		System.out.println(tree.getRootChildren());

+    	}
     	@Override
         public boolean doPartition(ResultSetPartitioner partitioner, ErmsImportState state) {
         public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, ErmsImportState state) {
     		boolean success = true ;
     		Set<CdmBase> objectsToSave = new HashSet<>();
-...
     		ResultSet rs = partitioner.getResultSet();
     		try{
     			while (rs.next()){
     				success &= mapping.invoke(rs,objectsToSave);
     				success &= mapping.invoke(rs, objectsToSave);
+    			}
     		} catch (SQLException e) {
     			logger.error("SQLException:" +  e);
-...
     		return success;
+    	}
     	/**
     	 * @return
     	 */

     import eu.etaxonomy.cdm.model.reference.Reference;
     import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
     /**
      * @author a.mueller
      * @since 20.03.2008
      */
     public class ErmsImportConfigurator
             extends DbImportConfiguratorBase<ErmsImportState>{
         private static final long serialVersionUID = 5434106058744720246L;
         @SuppressWarnings("unused")
     	private static Logger logger = Logger.getLogger(ErmsImportConfigurator.class);
     	public static ErmsImportConfigurator NewInstance(Source ermsSource, ICdmDataSource destination){
     			return new ErmsImportConfigurator(ermsSource, destination);
     	    return new ErmsImportConfigurator(ermsSource, destination);
+    	}
     	/* Max number of records to be saved with one service call */
-...
     	private static IInputTransformer defaultTransformer = new ErmsTransformer();
     	@Override
     	@SuppressWarnings("unchecked")
         @Override
         protected void makeIoClassList(){
     		ioClassList = new Class[]{
     				ErmsGeneralImportValidator.class
-...
     		};
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
     	 */
     	@Override
         public ImportStateBase getNewState() {
     		return new ErmsImportState(this);
+    	}
     	/**
     	 * @param berlinModelSource
     	 * @param sourceReference
-...
     	   super(ermsSource, destination, NomenclaturalCode.ICZN, defaultTransformer);//default for ERMS
+    	}
     	@Override
         public Source getSource() {
     		return super.getSource();
-...
     		super.setSource(berlinModelSource);
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#getSourceReference()
     	 */
     	@Override
         public Reference getSourceReference() {
     		if (sourceReference == null){
-...
     		return sourceReference;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getSourceNameString()
     	 */
     	@Override
         public String getSourceNameString() {
     		if (this.getSource() == null){
-...
+    		}
+    	}
     	/**
     	 * @return the userTransformationMethod
     	 */
     	@Override
         public Method getUserTransformationMethod() {
     		return userTransformationMethod;
+    	}
     	/**
     	 * @param userTransformationMethod the userTransformationMethod to set
     	 */
     	@Override
         public void setUserTransformationMethod(Method userTransformationMethod) {
     		this.userTransformationMethod = userTransformationMethod;
+    	}
     	/**
     	 * @return the limitSave
     	 */
     	@Override
         public int getRecordsPerTransaction() {
     		return recordsPerTransaction;
+    	}
     	/**
     	 * @param limitSave the limitSave to set
     	 */
     	@Override
         public void setRecordsPerTransaction(int recordsPerTransaction) {
     		this.recordsPerTransaction = recordsPerTransaction;
+    	}
     	/**
     	 * @param doVernaculars the doVernaculars to set
     	 */
     	public void setDoVernaculars(boolean doVernaculars) {
     		this.doVernaculars = doVernaculars;
+    	}
     	/**
     	 * @return the doVernaculars
     	 */
     	public boolean isDoVernaculars() {
     		return doVernaculars;
+    	}
     	/**
     	 * @param doLinks the doLinks to set
     	 */
     	public void setDoLinks(boolean doLinks) {
     		this.doLinks = doLinks;
+    	}
     	/**
     	 * @return the doLinks
     	 */
     	public boolean isDoLinks() {
     		return doLinks;
+    	}
     	/**
     	 * @param doNotes the doNotes to set
     	 */
     	public void setDoNotes(boolean doNotes) {
     		this.doNotes = doNotes;
+    	}
     	/**
     	 * @return the doNotes
     	 */
     	public boolean isDoNotes() {
     		return doNotes;
+    	}
     	/**
     	 * @param doImages the doImages to set
     	 */
     	public void setDoImages(boolean doImages) {
     		this.doImages = doImages;
+    	}
     	/**
     	 * @return the doImages
     	 */
     	public boolean isDoImages() {
     		return doImages;
+    	}
     	public boolean isDoOccurrence() {
     		return doOccurrence;
+    	}
-...
     		this.doOccurrence = doOccurrence;
+    	}
     	public DO_REFERENCES getDoReferences() {
     		return doReferences;
+    	}
-...
     		this.doRelTaxa = doRelTaxa;
+    	}
+    }

     	private Map<Integer, Rank> makeKingdomMap(Map<Integer, Map<Integer, Rank>> rankMap, Integer rankId) {
     		Map<Integer, Rank> result = rankMap.get(rankId);
     		if (result == null){
     			result = new HashMap<Integer, Rank>();
     			result = new HashMap<>();
     			rankMap.put(rankId, result);
+    		}
     		return result;
+    	}
     	@Override
     	protected boolean doCheck(ErmsImportState state) {
     		IOValidator<ErmsImportState> rankImport = new ErmsRankImportValidator();
     		return rankImport.validate(state);
+    	}
     	@Override
     	protected String getRecordQuery(ErmsImportConfigurator config) {
     		// TODO Auto-generated method stub
     		return null;
+    	}
     	@Override
     	protected boolean isIgnore(ErmsImportState state) {
     		return false;  //should always be called
     		return null;   // not needed
+    	}
     	@Override
-...
     		return null;  // not needed
+    	}
     	public Rank createObject(ResultSet rs, ErmsImportState state)
     			throws SQLException {
     		return null;  // not needed
+    	}
     	@Override
     	protected DbImportMapping<?, ?> getMapping() {
     		return null;  //not needed
+    	}
         @Override
         protected boolean doCheck(ErmsImportState state) {
             IOValidator<ErmsImportState> rankImport = new ErmsRankImportValidator();
             return rankImport.validate(state);
+        }
         @Override
         protected boolean isIgnore(ErmsImportState state) {
             return false;  //should always be called
+        }
+    }

     import eu.etaxonomy.cdm.model.taxon.TaxonBase;
     import eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy;
     /**
      * @author a.mueller
      * @since 20.02.2010
-...
     	@Override
         protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
     		if (mapping == null){
     			mapping = new DbImportMapping<ErmsImportState, ErmsImportConfigurator>();
     			mapping = new DbImportMapping<>();
     			mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "id", TAXON_NAMESPACE)); //id + tu_status
     			UUID tsnUuid = ErmsTransformer.uuidTsn;
-...
     			mapping.addMapper(DbImportExtensionMapper.NewInstance("tu_displayname", displayNameExtType));
     			ExtensionType fuzzyNameExtType = getExtensionType(ErmsTransformer.uuidFuzzyName, "fuzzy name", "fuzzy name", "fuzzy name");
     		//	mapping.addMapper(DbImportExtensionMapper.NewInstance("tu_fuzzyname", fuzzyNameExtType));
     			mapping.addMapper(DbImportStringMapper.NewInstance("tu_authority", "(NonViralName)name.authorshipCache"));
     			mapping.addMapper(DbImportStringMapper.NewInstance("tu_authority", "name.authorshipCache"));
     			ExtensionType fossilStatusExtType = getExtensionType(ErmsTransformer.uuidFossilStatus, "fossil status", "fossil status", "fos. stat.");
     			mapping.addMapper(DbImportExtensionMapper.NewInstance("fossil_name", fossilStatusExtType));
-...
     			mapping.addMapper(DbImportMarkerMapper.NewInstance("tu_fresh", ErmsTransformer.uuidMarkerFreshwater, "freshwater", "fresh", "fresh", null));
     			mapping.addMapper(DbImportMarkerMapper.NewInstance("tu_terrestrial", ErmsTransformer.uuidMarkerTerrestrial, "terrestrial", "terrestrial", "terrestrial", null));
     //			UUID hiddenUuid = ErmsTransformer.uuidHidden;
     //			mapping.addMapper(DbImportMarkerCreationMapper.Mapper.NewInstance("qualitystatus_name", qualityUuid, "quality status", "quality status", "quality status")); //checked by Tax Editor ERMS1.1, Added by db management team (2x), checked by Tax Editor
-...
+    	}
     	private Set<Integer> getAcceptedTaxaKeys(ErmsImportState state) {
     		Set<Integer> result = new HashSet<Integer>();
     		Set<Integer> result = new HashSet<>();
     		String parentCol = "tu_parent";
     		String accCol = " tu_acctaxon";
     		String idCol = " id ";
-...
     		String taxonTable = "tu";
     		String vernacularsTable = "vernaculars";
     		String distributionTable = "dr";
     		String sql = " SELECT DISTINCT %s FROM %s  " +
     				" UNION  SELECT %s FROM %s WHERE %s is NULL" +
     				" UNION  SELECT DISTINCT %s FROM %s " +
     				" UNION  SELECT DISTINCT %s FROM %s " +
     				" UNION  SELECT DISTINCT %s FROM %s ";
     		String sql =
     		        " SELECT DISTINCT %s FROM %s  "  //fk to parent
     		        + " UNION  SELECT %s FROM %s WHERE %s is NULL" //id of taxa not having accepted taxon
     		        + " UNION  SELECT DISTINCT %s FROM %s "  //fk to accepted taxon
     		        + " UNION  SELECT DISTINCT %s FROM %s " //vernaculars
     		        + " UNION  SELECT DISTINCT %s FROM %s ";  //distributions
     		sql = String.format(sql,
     				parentCol, taxonTable,
     				idCol, taxonTable, accCol,

     		super(pluralString, dbTableName, cdmTargetClass);
+    	}
     	@Override
     	protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
     		if (mapping == null){
-...
     		String nameSpace;
     		Class<?> cdmClass;
     		Set<String> idSet;
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
     		try{
     			Set<String> taxonIdSet = new HashSet<String>();
     			Set<String> nameIdSet = new HashSet<String>();
     			Set<String> taxonIdSet = new HashSet<>();
     			Set<String> nameIdSet = new HashSet<>();
     			while (rs.next()){
     				handleForeignKey(rs, taxonIdSet, "parentId");
     				handleForeignKey(rs, taxonIdSet, "accParentId");
-...
                 Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			result.put(nameSpace, taxonMap);
     			return result;
     		} catch (SQLException e) {
     			throw new RuntimeException(e);
+    		}
     		return result;
+    	}
     	@Override

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
-...
     import org.apache.log4j.Logger;
     import eu.etaxonomy.cdm.io.common.IOValidator;
     import eu.etaxonomy.cdm.io.common.Source;
     import eu.etaxonomy.cdm.io.pesi.erms.ErmsImportConfigurator;
     import eu.etaxonomy.cdm.io.pesi.erms.ErmsImportState;
     /**
      * ERMS reference validator.
      * NOT YET USED.
+     *
      * @author a.mueller
      * @since 17.02.2010
      * @version 1.0
      */
     public class ErmsReferenceImportValidator implements IOValidator<ErmsImportState>{
     	private static final Logger logger = Logger.getLogger(ErmsReferenceImportValidator.class);
     	public boolean validate(ErmsImportState state){
     	@Override
         public boolean validate(ErmsImportState state){
     		boolean result = true;
     		ErmsImportConfigurator config = state.getConfig();
     		logger.info("Checking for references not yet fully implemented");
     //		result &= checkTaxonStatus(config);
     //		result &= checkInactivated(config);
     		return result;
+    	}
     	private boolean checkTaxonStatus(ErmsImportConfigurator bmiConfig){
     		try {
     			boolean result = true;
     			Source source = bmiConfig.getSource();
     			String strSQL = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache "  +
     				" FROM RelPTaxon " +
     					" INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
     					" INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk  " +
     				" FROM RelPTaxon " +
     					" INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
     					" INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk  " +
     					" INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
     				" WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) ";
     			ResultSet rs = source.getResultSet(strSQL);
-...
     				int refFk = rs.getInt("PTRefFk");
     				int relPTaxonId = rs.getInt("relPTaxonId");
     				String taxonName = rs.getString("FullNameCache");
     				System.out.println("RIdentifier:" + rIdentifier + "\n  name: " + nameFk +
     				System.out.println("RIdentifier:" + rIdentifier + "\n  name: " + nameFk +
     						"\n  taxonName: " + taxonName + "\n  refId: " + refFk + "\n  RelPTaxonId: " + relPTaxonId );
     				result = firstRow = false;
+    			}
     			if (i > 0){
     				System.out.println(" ");
+    			}
     			return result;
     		} catch (SQLException e) {
     			e.printStackTrace();
-...
+    		}
+    	}
+    }

     /**
     * Copyright (C) 2007 EDIT
     * European Distributed Institute of Taxonomy
     * European Distributed Institute of Taxonomy
     * http://www.e-taxonomy.eu
+    *
+    *
     * The contents of this file are subject to the Mozilla Public License Version 1.1
     * See LICENSE.TXT at the top of this package for the full license terms.
     */
-...
     /**
      * @author a.mueller
      * @since 12.03.2010
      * @version 1.0
      */
     public class ErmsVernacularImportValidator  implements IOValidator<ErmsImportState>{
     	private static final Logger logger = Logger.getLogger(ErmsVernacularImportValidator.class);
     	public boolean validate(ErmsImportState state){
     	@Override
         public boolean validate(ErmsImportState state){
     		boolean result = true;
     		ErmsImportConfigurator config = state.getConfig();
     		logger.info("Checking for vernaculars not yet implemented");

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Revision 4d0649fd

Added by Andreas Müller over 5 years ago