| 1 |
d427288b
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Andreas Müller
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/**
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| 2 |
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*
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| 3 |
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*/
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| 4 |
43b78563
|
Andreas Müller
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package eu.etaxonomy.cdm.io.common;
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| 5 |
d427288b
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Andreas Müller
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| 6 |
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import java.lang.reflect.InvocationTargetException;
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| 7 |
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import java.lang.reflect.Method;
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| 8 |
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import java.sql.ResultSet;
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| 9 |
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import java.sql.SQLException;
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| 10 |
79bcb889
|
Andreas Müller
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import java.util.Calendar;
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| 11 |
e133b83b
|
Andreas Müller
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import java.util.List;
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| 12 |
d427288b
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Andreas Müller
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| 13 |
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import org.apache.log4j.Logger;
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| 14 |
43b78563
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Andreas Müller
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import org.jdom.Element;
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| 15 |
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import org.jdom.Namespace;
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| 16 |
bcdc633e
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Andreas Müller
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import org.joda.time.DateTime;
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| 17 |
d427288b
|
Andreas Müller
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| 18 |
79bcb889
|
Andreas Müller
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import eu.etaxonomy.cdm.common.CdmUtils;
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| 19 |
b42eac28
|
Andreas Müller
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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| 20 |
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import eu.etaxonomy.cdm.model.common.Annotation;
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| 21 |
d427288b
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.CdmBase;
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| 22 |
4e4722d3
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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| 23 |
b42eac28
|
Andreas Müller
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import eu.etaxonomy.cdm.model.common.Language;
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| 24 |
4e4722d3
|
Andreas Müller
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import eu.etaxonomy.cdm.model.common.OriginalSource;
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| 25 |
79bcb889
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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| 26 |
4e4722d3
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Andreas Müller
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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| 27 |
d427288b
|
Andreas Müller
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/**
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| 28 |
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* @author a.mueller
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| 29 |
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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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| 34 |
8160c112
|
Andreas Müller
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public static final boolean OVERWRITE = true;
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| 35 |
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public static final boolean NO_OVERWRITE = false;
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| 37 |
79bcb889
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Andreas Müller
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public static final boolean OBLIGATORY = true;
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| 38 |
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public static final boolean FACULTATIVE = false;
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| 40 |
8160c112
|
Andreas Müller
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| 41 |
57c46d2e
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Andreas Müller
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| 42 |
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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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| 45 |
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| 46 |
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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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| 51 |
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* @return
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*/
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| 53 |
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public static boolean setOriginalSource(IdentifiableEntity idEntity, ReferenceBase sourceReference, String sourceId, String namespace){
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| 54 |
4e4722d3
|
Andreas Müller
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OriginalSource originalSource = new OriginalSource();
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| 55 |
57c46d2e
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Andreas Müller
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originalSource.setIdInSource(sourceId);
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| 56 |
43b78563
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Andreas Müller
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originalSource.setCitation(sourceReference);
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| 57 |
57c46d2e
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Andreas Müller
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originalSource.setIdNamespace(namespace);
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| 58 |
4e4722d3
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Andreas Müller
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idEntity.addSource(originalSource);
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return true;
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}
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| 62 |
d427288b
|
Andreas Müller
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| 63 |
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public static boolean addStringValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName){
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| 64 |
8160c112
|
Andreas Müller
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return addValue(rs, cdmBase, dbAttrName, cdmAttrName, String.class, OVERWRITE);
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| 65 |
d427288b
|
Andreas Müller
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}
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8160c112
|
Andreas Müller
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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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| 71 |
d427288b
|
Andreas Müller
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public static boolean addBooleanValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName){
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| 72 |
8160c112
|
Andreas Müller
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return addValue(rs, cdmBase, dbAttrName, cdmAttrName, boolean.class, OVERWRITE);
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| 73 |
d427288b
|
Andreas Müller
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}
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| 74 |
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| 75 |
8160c112
|
Andreas Müller
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public static boolean addValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, Class clazz, boolean overwriteNull){
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| 76 |
51c93ed3
|
Andreas Müller
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Object strValue;
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| 77 |
d427288b
|
Andreas Müller
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try {
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| 78 |
51c93ed3
|
Andreas Müller
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strValue = rs.getObject(dbAttrName);
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| 79 |
79bcb889
|
Andreas Müller
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return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
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| 80 |
43b78563
|
Andreas Müller
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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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| 83 |
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}
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| 84 |
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| 85 |
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}
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| 86 |
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| 88 |
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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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| 90 |
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}
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| 91 |
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| 92 |
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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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| 94 |
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}
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| 96 |
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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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| 100 |
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| 101 |
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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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| 102 |
79bcb889
|
Andreas Müller
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return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
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}
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| 104 |
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| 105 |
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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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| 106 |
43b78563
|
Andreas Müller
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Object strValue;
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| 107 |
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strValue = getXmlInputValue(root, xmlElementName, namespace);
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| 108 |
79bcb889
|
Andreas Müller
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return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, obligat);
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| 109 |
43b78563
|
Andreas Müller
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}
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| 110 |
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| 111 |
79bcb889
|
Andreas Müller
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public static boolean addValue(Object sourceValue, CdmBase cdmBase, String cdmAttrName, Class clazz, boolean overwriteNull, boolean obligat){
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| 112 |
43b78563
|
Andreas Müller
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String methodName;
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| 113 |
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// Object strValue;
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| 114 |
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try {
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| 115 |
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if (overwriteNull == NO_OVERWRITE && sourceValue == null ){
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| 116 |
8160c112
|
Andreas Müller
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if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
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| 117 |
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return true;
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| 118 |
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}
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| 119 |
43b78563
|
Andreas Müller
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if (logger.isDebugEnabled()) { logger.debug("addValue: " + sourceValue);}
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| 120 |
d427288b
|
Andreas Müller
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if (clazz == boolean.class || clazz == Boolean.class){
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| 121 |
dd9ecdbd
|
Andreas Müller
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
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| 122 |
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throw new IllegalArgumentException("boolean CdmAttributeName should have atleast 3 characters");
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| 123 |
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}
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| 124 |
d427288b
|
Andreas Müller
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methodName = "set" + cdmAttrName.substring(2, 3).toUpperCase() + cdmAttrName.substring(3) ;
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| 125 |
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}else if(clazz == String.class) {
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| 126 |
dd9ecdbd
|
Andreas Müller
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
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| 127 |
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throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
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| 128 |
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}
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| 129 |
d427288b
|
Andreas Müller
|
methodName = "set" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
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| 130 |
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}else{
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| 131 |
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logger.error("Class not supported: " + clazz.toString());
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| 132 |
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return false;
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| 133 |
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}
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| 134 |
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Method cdmMethod = cdmBase.getClass().getMethod(methodName, clazz);
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| 135 |
43b78563
|
Andreas Müller
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cdmMethod.invoke(cdmBase, sourceValue);
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| 136 |
d427288b
|
Andreas Müller
|
return true;
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| 137 |
4406daca
|
Andreas Müller
|
} catch (NullPointerException e) {
|
| 138 |
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logger.error("NullPointerException: " + e.getMessage());
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| 139 |
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return false;
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| 140 |
d427288b
|
Andreas Müller
|
} catch (IllegalArgumentException e) {
|
| 141 |
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logger.error("IllegalArgumentException: " + e.getMessage());
|
| 142 |
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return false;
|
| 143 |
|
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} catch (IllegalAccessException e) {
|
| 144 |
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logger.error("IllegalAccessException: " + e.getMessage());
|
| 145 |
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return false;
|
| 146 |
|
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} catch (InvocationTargetException e) {
|
| 147 |
|
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logger.error("InvocationTargetException: " + e.getMessage());
|
| 148 |
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return false;
|
| 149 |
|
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}catch (SecurityException e) {
|
| 150 |
|
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logger.error("SecurityException: " + e.getMessage());
|
| 151 |
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return false;
|
| 152 |
|
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} catch (NoSuchMethodException e) {
|
| 153 |
79bcb889
|
Andreas Müller
|
if (obligat){
|
| 154 |
|
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logger.error("NoSuchMethod: " + e.getMessage());
|
| 155 |
b42eac28
|
Andreas Müller
|
return false;
|
| 156 |
79bcb889
|
Andreas Müller
|
}else{
|
| 157 |
b42eac28
|
Andreas Müller
|
if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
|
| 158 |
|
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return true;
|
| 159 |
79bcb889
|
Andreas Müller
|
}
|
| 160 |
d427288b
|
Andreas Müller
|
}
|
| 161 |
e133b83b
|
Andreas Müller
|
|
| 162 |
|
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}
|
| 163 |
|
|
|
| 164 |
|
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private static boolean valuesAreNull(List<Object> values){
|
| 165 |
|
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for (Object sourceValue : values.toArray()){
|
| 166 |
|
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if (sourceValue != null){
|
| 167 |
|
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return false;
|
| 168 |
|
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}
|
| 169 |
|
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}
|
| 170 |
|
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return true;
|
| 171 |
|
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}
|
| 172 |
|
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|
| 173 |
|
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public static boolean addMultipleValues(List<Object> sourceValues, CdmBase cdmBase, String cdmAttrName, List<Class> classes, boolean overwriteNull, boolean obligat){
|
| 174 |
|
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String methodName;
|
| 175 |
|
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// Object strValue;
|
| 176 |
|
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try {
|
| 177 |
|
|
|
| 178 |
|
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if (overwriteNull == NO_OVERWRITE && valuesAreNull(sourceValues)){
|
| 179 |
|
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if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
|
| 180 |
|
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return true;
|
| 181 |
|
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}
|
| 182 |
|
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if (logger.isDebugEnabled()) { logger.debug("addValues: " + sourceValues.toString());}
|
| 183 |
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| 184 |
|
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|
| 185 |
|
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if (cdmAttrName == null || cdmAttrName.length() < 1 ){
|
| 186 |
|
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throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
|
| 187 |
|
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}
|
| 188 |
|
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methodName = "add" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
|
| 189 |
|
|
|
| 190 |
|
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Class[] classArray = classes.toArray(new Class[0]);
|
| 191 |
|
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Method cdmMethod = cdmBase.getClass().getMethod(methodName, classArray);
|
| 192 |
|
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cdmMethod.invoke(cdmBase, sourceValues.toArray());
|
| 193 |
|
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return true;
|
| 194 |
|
|
} catch (NullPointerException e) {
|
| 195 |
|
|
logger.error("NullPointerException: " + e.getMessage());
|
| 196 |
|
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return false;
|
| 197 |
|
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} catch (IllegalArgumentException e) {
|
| 198 |
|
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logger.error("IllegalArgumentException: " + e.getMessage());
|
| 199 |
|
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return false;
|
| 200 |
|
|
} catch (IllegalAccessException e) {
|
| 201 |
|
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logger.error("IllegalAccessException: " + e.getMessage());
|
| 202 |
|
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return false;
|
| 203 |
|
|
} catch (InvocationTargetException e) {
|
| 204 |
|
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logger.error("InvocationTargetException: " + e.getMessage());
|
| 205 |
|
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return false;
|
| 206 |
|
|
}catch (SecurityException e) {
|
| 207 |
|
|
logger.error("SecurityException: " + e.getMessage());
|
| 208 |
|
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return false;
|
| 209 |
|
|
} catch (NoSuchMethodException e) {
|
| 210 |
|
|
if (obligat){
|
| 211 |
|
|
logger.error("NoSuchMethod: " + e.getMessage());
|
| 212 |
|
|
return false;
|
| 213 |
|
|
}else{
|
| 214 |
|
|
if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
|
| 215 |
|
|
return true;
|
| 216 |
|
|
}
|
| 217 |
|
|
}
|
| 218 |
|
|
|
| 219 |
b42eac28
|
Andreas Müller
|
}
|
| 220 |
|
|
|
| 221 |
|
|
public static boolean addAnnotationFromResultSet(ResultSet rs, String attributeName, AnnotatableEntity cdmBase, Language language){
|
| 222 |
|
|
try {
|
| 223 |
|
|
String value = rs.getString(attributeName);
|
| 224 |
|
|
if (CdmUtils.Nz(value).equals("")){
|
| 225 |
|
|
String strAnnotation = attributeName + ": " + value;
|
| 226 |
|
|
Annotation annoatation = Annotation.NewInstance(strAnnotation, language);
|
| 227 |
|
|
cdmBase.addAnnotation(annoatation);
|
| 228 |
d427288b
|
Andreas Müller
|
|
| 229 |
b42eac28
|
Andreas Müller
|
}
|
| 230 |
|
|
return true;
|
| 231 |
|
|
} catch (SQLException e) {
|
| 232 |
|
|
logger.warn(e);
|
| 233 |
|
|
e.printStackTrace();
|
| 234 |
|
|
return false;
|
| 235 |
|
|
}
|
| 236 |
43b78563
|
Andreas Müller
|
}
|
| 237 |
|
|
|
| 238 |
b42eac28
|
Andreas Müller
|
|
| 239 |
|
|
|
| 240 |
43b78563
|
Andreas Müller
|
public static Object getXmlInputValue(Element root, String xmlElementName, Namespace namespace){
|
| 241 |
|
|
Object result = null;
|
| 242 |
|
|
Element child = root.getChild(xmlElementName, namespace);
|
| 243 |
|
|
if (child != null){
|
| 244 |
|
|
result = child.getText().trim();
|
| 245 |
|
|
}
|
| 246 |
|
|
return result;
|
| 247 |
|
|
}
|
| 248 |
79bcb889
|
Andreas Müller
|
|
| 249 |
|
|
|
| 250 |
|
|
public static TimePeriod getDatePublished(String refYear){
|
| 251 |
|
|
//FIXME until now only quick and dirty and wrong
|
| 252 |
|
|
if (refYear == null){
|
| 253 |
|
|
return null;
|
| 254 |
|
|
}
|
| 255 |
|
|
String[] years = refYear.split("-");
|
| 256 |
bcdc633e
|
Andreas Müller
|
DateTime dtStart = null;
|
| 257 |
|
|
DateTime dtEnd = null;
|
| 258 |
79bcb889
|
Andreas Müller
|
|
| 259 |
|
|
if (years.length > 2 || years.length <= 0){
|
| 260 |
b42eac28
|
Andreas Müller
|
logger.warn("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX getDatePublished");
|
| 261 |
79bcb889
|
Andreas Müller
|
}else {
|
| 262 |
bcdc633e
|
Andreas Müller
|
dtStart = parseSingleDate(years[0]);
|
| 263 |
|
|
|
| 264 |
79bcb889
|
Andreas Müller
|
if (years.length >= 2){
|
| 265 |
bcdc633e
|
Andreas Müller
|
dtEnd = parseSingleDate(years[1]);
|
| 266 |
79bcb889
|
Andreas Müller
|
}
|
| 267 |
|
|
}
|
| 268 |
bcdc633e
|
Andreas Müller
|
TimePeriod result = TimePeriod.NewInstance(dtStart, dtEnd);
|
| 269 |
79bcb889
|
Andreas Müller
|
return result;
|
| 270 |
|
|
}
|
| 271 |
|
|
|
| 272 |
bcdc633e
|
Andreas Müller
|
private static DateTime parseSingleDate(String singleDateString){
|
| 273 |
79bcb889
|
Andreas Müller
|
//FIXME until now only quick and dirty and wrong
|
| 274 |
bcdc633e
|
Andreas Müller
|
DateTime dt = new DateTime(9999, 12, 30, 0,0,0,0);
|
| 275 |
|
|
if (CdmUtils.isNumeric(singleDateString)){
|
| 276 |
79bcb889
|
Andreas Müller
|
try {
|
| 277 |
bcdc633e
|
Andreas Müller
|
Integer year = Integer.valueOf(singleDateString.trim());
|
| 278 |
|
|
if (year > 1750 && year < 2050){
|
| 279 |
|
|
dt = dt.withYear(year);
|
| 280 |
79bcb889
|
Andreas Müller
|
}
|
| 281 |
|
|
} catch (NumberFormatException e) {
|
| 282 |
|
|
logger.debug("Not a Integer format in getCalendar()");
|
| 283 |
|
|
}
|
| 284 |
|
|
}
|
| 285 |
bcdc633e
|
Andreas Müller
|
return dt;
|
| 286 |
|
|
|
| 287 |
79bcb889
|
Andreas Müller
|
}
|
| 288 |
43b78563
|
Andreas Müller
|
|
| 289 |
bcdc633e
|
Andreas Müller
|
|
| 290 |
|
|
//******* old *****************
|
| 291 |
|
|
|
| 292 |
|
|
// private static Calendar getCalendar(String strYear){
|
| 293 |
|
|
// //FIXME until now only quick and dirty and wrong
|
| 294 |
|
|
// Calendar cal = Calendar.getInstance();
|
| 295 |
|
|
// cal.set(9999, Calendar.DECEMBER, 30, 0, 0, 0);
|
| 296 |
|
|
// if (CdmUtils.isNumeric(strYear)){
|
| 297 |
|
|
// try {
|
| 298 |
|
|
// Integer year = Integer.valueOf(strYear.trim());
|
| 299 |
|
|
// if (year > 1750 && year < 2030){
|
| 300 |
|
|
// cal.set(year, Calendar.JANUARY, 1, 0, 0, 0);
|
| 301 |
|
|
// }
|
| 302 |
|
|
// } catch (NumberFormatException e) {
|
| 303 |
|
|
// logger.debug("Not a Integer format in getCalendar()");
|
| 304 |
|
|
// }
|
| 305 |
|
|
// }
|
| 306 |
|
|
// return cal;
|
| 307 |
|
|
// }
|
| 308 |
|
|
|
| 309 |
d427288b
|
Andreas Müller
|
|
| 310 |
|
|
}
|