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/**
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*
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*/
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package eu.etaxonomy.cdm.io.common;
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import java.lang.reflect.InvocationTargetException;
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import java.lang.reflect.Method;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Calendar;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.joda.time.DateTime;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OriginalSource;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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/**
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* @author a.mueller
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*
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*/
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public class ImportHelper {
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private static final Logger logger = Logger.getLogger(ImportHelper.class);
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public static final boolean OVERWRITE = true;
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public static final boolean NO_OVERWRITE = false;
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public static final boolean OBLIGATORY = true;
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public static final boolean FACULTATIVE = false;
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public static boolean setOriginalSource(IdentifiableEntity idEntity, ReferenceBase sourceReference, long sourceId, String namespace){
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return setOriginalSource(idEntity, sourceReference, String.valueOf(sourceId), namespace);
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}
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/**
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* Adds an original source object to the identifiable entity.
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* @param idEntity
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* @param sourceReference
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* @param sourceId
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* @return
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*/
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public static boolean setOriginalSource(IdentifiableEntity idEntity, ReferenceBase sourceReference, String sourceId, String namespace){
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OriginalSource originalSource = new OriginalSource();
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originalSource.setIdInSource(sourceId);
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originalSource.setCitation(sourceReference);
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originalSource.setIdNamespace(namespace);
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idEntity.addSource(originalSource);
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return true;
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}
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public static boolean addStringValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName){
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return addValue(rs, cdmBase, dbAttrName, cdmAttrName, String.class, OVERWRITE);
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}
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public static boolean addStringValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, boolean overwriteNull){
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return addValue(rs, cdmBase, dbAttrName, cdmAttrName, String.class, overwriteNull);
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}
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public static boolean addBooleanValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName){
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return addValue(rs, cdmBase, dbAttrName, cdmAttrName, boolean.class, OVERWRITE);
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}
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public static boolean addValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, Class clazz, boolean overwriteNull){
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Object strValue;
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try {
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strValue = rs.getObject(dbAttrName);
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return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
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}catch (SQLException e) {
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logger.error("SQLException: " + e);
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return false;
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}
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}
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public static boolean addXmlStringValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName){
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return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, String.class, OVERWRITE);
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}
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public static boolean addXmlStringValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, boolean overwriteNull){
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return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, String.class, overwriteNull);
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}
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public static boolean addXmlBooleanValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName){
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return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, boolean.class, OVERWRITE);
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}
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public static boolean addXmlValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, Class clazz, boolean overwriteNull){
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return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
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}
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public static boolean addXmlValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, Class clazz, boolean overwriteNull, boolean obligat){
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Object strValue;
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strValue = getXmlInputValue(root, xmlElementName, namespace);
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return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, obligat);
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}
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public static boolean addValue(Object sourceValue, CdmBase cdmBase, String cdmAttrName, Class clazz, boolean overwriteNull, boolean obligat){
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String methodName;
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// Object strValue;
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try {
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if (overwriteNull == NO_OVERWRITE && sourceValue == null ){
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if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
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return true;
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}
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if (logger.isDebugEnabled()) { logger.debug("addValue: " + sourceValue);}
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if (clazz == boolean.class || clazz == Boolean.class){
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if (cdmAttrName == null || cdmAttrName.length() < 1 ){
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throw new IllegalArgumentException("boolean CdmAttributeName should have atleast 3 characters");
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}
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methodName = "set" + cdmAttrName.substring(2, 3).toUpperCase() + cdmAttrName.substring(3) ;
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}else if(clazz == String.class) {
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if (cdmAttrName == null || cdmAttrName.length() < 1 ){
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throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
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}
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methodName = "set" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
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}else{
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logger.error("Class not supported: " + clazz.toString());
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return false;
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}
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Method cdmMethod = cdmBase.getClass().getMethod(methodName, clazz);
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cdmMethod.invoke(cdmBase, sourceValue);
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return true;
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} catch (NullPointerException e) {
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logger.error("NullPointerException: " + e.getMessage());
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return false;
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} catch (IllegalArgumentException e) {
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logger.error("IllegalArgumentException: " + e.getMessage());
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return false;
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} catch (IllegalAccessException e) {
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logger.error("IllegalAccessException: " + e.getMessage());
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return false;
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} catch (InvocationTargetException e) {
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logger.error("InvocationTargetException: " + e.getMessage());
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return false;
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}catch (SecurityException e) {
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logger.error("SecurityException: " + e.getMessage());
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return false;
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} catch (NoSuchMethodException e) {
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if (obligat){
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logger.error("NoSuchMethod: " + e.getMessage());
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return false;
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}else{
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if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
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return true;
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}
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}
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}
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private static boolean valuesAreNull(List<Object> values){
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for (Object sourceValue : values.toArray()){
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if (sourceValue != null){
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return false;
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}
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}
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return true;
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}
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public static boolean addMultipleValues(List<Object> sourceValues, CdmBase cdmBase, String cdmAttrName, List<Class> classes, boolean overwriteNull, boolean obligat){
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String methodName;
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// Object strValue;
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try {
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if (overwriteNull == NO_OVERWRITE && valuesAreNull(sourceValues)){
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if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
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return true;
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}
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if (logger.isDebugEnabled()) { logger.debug("addValues: " + sourceValues.toString());}
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if (cdmAttrName == null || cdmAttrName.length() < 1 ){
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throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
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}
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methodName = "add" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
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Class[] classArray = classes.toArray(new Class[0]);
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Method cdmMethod = cdmBase.getClass().getMethod(methodName, classArray);
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cdmMethod.invoke(cdmBase, sourceValues.toArray());
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return true;
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} catch (NullPointerException e) {
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logger.error("NullPointerException: " + e.getMessage());
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return false;
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} catch (IllegalArgumentException e) {
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logger.error("IllegalArgumentException: " + e.getMessage());
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return false;
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} catch (IllegalAccessException e) {
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logger.error("IllegalAccessException: " + e.getMessage());
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return false;
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} catch (InvocationTargetException e) {
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logger.error("InvocationTargetException: " + e.getMessage());
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return false;
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}catch (SecurityException e) {
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logger.error("SecurityException: " + e.getMessage());
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return false;
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} catch (NoSuchMethodException e) {
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if (obligat){
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logger.error("NoSuchMethod: " + e.getMessage());
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return false;
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}else{
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if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
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return true;
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}
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}
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}
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public static boolean addAnnotationFromResultSet(ResultSet rs, String attributeName, AnnotatableEntity cdmBase, Language language){
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try {
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String value = rs.getString(attributeName);
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if (CdmUtils.Nz(value).equals("")){
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String strAnnotation = attributeName + ": " + value;
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Annotation annoatation = Annotation.NewInstance(strAnnotation, language);
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cdmBase.addAnnotation(annoatation);
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}
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return true;
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} catch (SQLException e) {
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logger.warn(e);
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e.printStackTrace();
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return false;
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}
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}
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237
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238
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239
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public static Object getXmlInputValue(Element root, String xmlElementName, Namespace namespace){
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Object result = null;
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Element child = root.getChild(xmlElementName, namespace);
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if (child != null){
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result = child.getText().trim();
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}
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return result;
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}
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248
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249
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250
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public static TimePeriod getDatePublished(String refYear){
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//FIXME until now only quick and dirty and wrong
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if (refYear == null){
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return null;
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}
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String[] years = refYear.split("-");
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DateTime dtStart = null;
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DateTime dtEnd = null;
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258
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259
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if (years.length > 2 || years.length <= 0){
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logger.warn("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX getDatePublished");
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261
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}else {
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dtStart = parseSingleDate(years[0]);
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263
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if (years.length >= 2){
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dtEnd = parseSingleDate(years[1]);
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}
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}
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TimePeriod result = TimePeriod.NewInstance(dtStart, dtEnd);
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return result;
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270
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}
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271
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272
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private static DateTime parseSingleDate(String singleDateString){
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273
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//FIXME until now only quick and dirty and wrong
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DateTime dt = new DateTime(9999, 12, 30, 0,0,0,0);
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275
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if (CdmUtils.isNumeric(singleDateString)){
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276
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try {
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Integer year = Integer.valueOf(singleDateString.trim());
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if (year > 1750 && year < 2050){
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dt = dt.withYear(year);
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}
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} catch (NumberFormatException e) {
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logger.debug("Not a Integer format in getCalendar()");
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}
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284
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}
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return dt;
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286
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287
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}
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288
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289
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290
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//******* old *****************
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291
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292
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// private static Calendar getCalendar(String strYear){
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293
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// //FIXME until now only quick and dirty and wrong
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294
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// Calendar cal = Calendar.getInstance();
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// cal.set(9999, Calendar.DECEMBER, 30, 0, 0, 0);
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296
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// if (CdmUtils.isNumeric(strYear)){
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297
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// try {
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// Integer year = Integer.valueOf(strYear.trim());
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299
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// if (year > 1750 && year < 2030){
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300
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// cal.set(year, Calendar.JANUARY, 1, 0, 0, 0);
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// }
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// } catch (NumberFormatException e) {
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303
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// logger.debug("Not a Integer format in getCalendar()");
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// }
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// }
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// return cal;
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// }
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308
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309
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310
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}
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