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Revision daa58548

Added by Andreas Müller almost 6 years ago

ID daa5854856aeaf81f8b8d902fc7e378662e3c37d
Parent 76a5e528
Child a13538c8

cleanup

      */
     @Component
     public class BerlinModelCommonNamesImport  extends BerlinModelImportBase {
     	private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);
         private static final long serialVersionUID = -8921948187177864321L;
         private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);
     	public static final UUID REFERENCE_LANGUAGE_ISO639_2_UUID = UUID.fromString("40c4f8dd-3d9c-44a4-b77a-76e137a89a5f");
     	public static final UUID REFERENCE_LANGUAGE_STRING_UUID = UUID.fromString("2a1b678f-c27d-48c1-b43e-98fd0d426305");
-...
     	//map that stores the regions (named areas) and makes them accessible via the regionFk
     	private Map<String, NamedArea> regionMap = new HashMap<String, NamedArea>();
     	private Map<String, NamedArea> regionMap = new HashMap<>();
     	public BerlinModelCommonNamesImport(){
     		super(dbTableName, pluralString);
-...
     	@Override
     	protected String getIdQuery(BerlinModelImportState state) {
     		String result = " SELECT CommonNameId FROM emCommonName WHERE (1=1) ";
     		if (StringUtils.isNotBlank(state.getConfig().getCommonNameFilter())){
     		if (isNotBlank(state.getConfig().getCommonNameFilter())){
     			result += " AND " + state.getConfig().getCommonNameFilter();
+    		}
-...
     	 */
     	private void makeRegions(BerlinModelImportState state) {
     		try {
     			SortedSet<Integer> regionFks = new TreeSet<Integer>();
     			SortedSet<Integer> regionFks = new TreeSet<>();
     			Source source = state.getConfig().getSource();
     			//fill set with all regionFk from emCommonName.regionFks
-...
     		boolean success = true ;
     		Set<TaxonBase> taxaToSave = new HashSet<>();
     		Map<String, Taxon> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
     		Map<String, TaxonName> taxonNameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
     		Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
     		@SuppressWarnings("unchecked")
             Map<String, Taxon> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
     		@SuppressWarnings("unchecked")
             Map<String, TaxonName> taxonNameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
     		@SuppressWarnings("unchecked")
             Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
     		Map<String, Language> iso6392Map = new HashMap<String, Language>();
     		Map<String, Language> iso6392Map = new HashMap<>();
     	//	logger.warn("MisappliedNameRefFk  not yet implemented for Common Names");
-...
     					regionFk = regionFk.trim();
     					NamedArea area = regionMap.get(regionFk);
     					if (area == null){
     						if (regionFkSplit.length > 1 && StringUtils.isNotBlank(regionFk)){
     						if (regionFkSplit.length > 1 && isNotBlank(regionFk)){
     							logger.warn("Area for " + regionFk + " not defined in regionMap.");
     						}else{
     							//no region is defined
-...
     			}else if (splitRegion.length == 2){
     				String emCode = splitRegion[1].trim();
     				String tdwgCode = emTdwgMap.get(emCode);
     				if (StringUtils.isNotBlank(tdwgCode) ){
     				if (isNotBlank(tdwgCode) ){
     					NamedArea tdwgArea = getNamedArea(state, tdwgCode);
     					regionMap.put(String.valueOf(regionId), tdwgArea);
     				}else {
-...
     	private Map<String, String> getEmTdwgMap(Source source) throws SQLException {
     		String sql;
     		ResultSet rs;
     		Map<String, String> emTdwgMap = new HashMap<String, String>();
     		Map<String, String> emTdwgMap = new HashMap<>();
     		sql = " SELECT EmCode, TDWGCode FROM emArea ";
     		rs = source.getResultSet(sql);
     		while (rs.next()){
     			String emCode = rs.getString("EMCode");
     			String TDWGCode = rs.getString("TDWGCode");
     			if (StringUtils.isNotBlank(emCode) ){
     			if (isNotBlank(emCode) ){
     				emCode = emCode.trim();
     				if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")||
     						emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")){
     					emTdwgMap.put(emCode, emCode);
     				}else if (StringUtils.isNotBlank(TDWGCode)){
     				}else if (isNotBlank(TDWGCode)){
     					emTdwgMap.put(emCode, TDWGCode.trim());
+    				}
+    			}
-...
     			nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
     			cdmClass = TaxonName.class;
     			idSet = nameIdSet;
     			Map<String, TaxonName> nameMap = (Map<String, TaxonName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			@SuppressWarnings("unchecked")
                 Map<String, TaxonName> nameMap = (Map<String, TaxonName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			result.put(nameSpace, nameMap);
     			//taxon map
     			nameSpace = BerlinModelTaxonImport.NAMESPACE;
     			cdmClass = TaxonBase.class;
     			idSet = taxonIdSet;
     			Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			@SuppressWarnings("unchecked")
                 Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			result.put(nameSpace, taxonMap);
     			//reference map
     			nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
     			cdmClass = Reference.class;
     			idSet = referenceIdSet;
     			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			@SuppressWarnings("unchecked")
                 Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     			result.put(nameSpace, referenceMap);
     			// TODO remove if problem with duplicate DescElement_Annot id is solved
     		} catch (SQLException e) {

app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportBase.java
43	43	/**
44	44	* @author a.mueller
45	45	* @created 20.03.2008
46		* @version 1.0
47	46	*/
48	47	public abstract class BerlinModelImportBase extends DbImportBase<BerlinModelImportState, BerlinModelImportConfigurator> implements ICdmIO<BerlinModelImportState>, IPartitionedIO<BerlinModelImportState> {
49	48	private static final long serialVersionUID = -4982506434258587864L;

+    					}
     					//
     					if (resultSetHasColumn(rs,"LastScrutiny")){
     					if (resultSetHasColumn(rs, "LastScrutiny")){
     						String lastScrutiny = rs.getString("LastScrutiny");
     						//TODO strange, why not Extension last scrutiny? To match PESI? Is there a difference
     						//to LastScrutinyFK and SpeciesExpertFK?
-...
     		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> nameIdSet = new HashSet<String>();
     			Set<String> referenceIdSet = new HashSet<String>();
     			Set<String> nameIdSet = new HashSet<>();
     			Set<String> referenceIdSet = new HashSet<>();
     			while (rs.next()){
     				handleForeignKey(rs, nameIdSet, "PTNameFk");
     				handleForeignKey(rs, referenceIdSet, "PTRefFk");

     		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> nameIdSet = new HashSet<String>();
     			Set<String> referenceIdSet = new HashSet<String>();
     			Set<String> refDetailIdSet = new HashSet<String>();
     			Set<String> nameIdSet = new HashSet<>();
     			Set<String> referenceIdSet = new HashSet<>();
     			Set<String> refDetailIdSet = new HashSet<>();
     			while (rs.next()){
     				handleForeignKey(rs, nameIdSet, "name1Id");
     				handleForeignKey(rs, nameIdSet, "name2Id");
-...
     		return result;
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
     	 */
     	@Override
     	protected boolean doCheck(BerlinModelImportState state){
     		IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
     		return validator.validate(state);
+    	}
     	/* (non-Javadoc)
     	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
     	 */
     	@Override
         protected boolean isIgnore(BerlinModelImportState state){
     		return ! state.getConfig().isDoRelNames();

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Revision daa58548

Added by Andreas Müller almost 6 years ago