Revision 892efc69
Added by Andreas Kohlbecker almost 14 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonNameRelationImport.java | ||
|---|---|---|
| 40 | 40 |
import eu.etaxonomy.cdm.io.common.IOValidator; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.model.agent.Person; |
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity; |
|
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
| 47 | 48 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
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import eu.etaxonomy.cdm.model.name.NonViralName; |
|
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| ... | ... | |
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*/ |
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@Override |
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = |
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" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " + |
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" FROM Name as FromName INNER JOIN " + |
|
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" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " + |
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" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+ |
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" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " + |
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String strQuery =
|
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" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
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" FROM Name as FromName INNER JOIN " +
|
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" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
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" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
|
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" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
|
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" WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
|
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return strQuery; |
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} |
| ... | ... | |
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Map<String, ReferenceBase> biblioRefMap = partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE); |
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Map<String, ReferenceBase> nomRefMap = partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE); |
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ResultSet rs = partitioner.getResultSet(); |
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try {
|
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|
| ... | ... | |
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//get nomRef |
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citation = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, |
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relRefFk); |
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} |
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}
|
|
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|
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//TODO (preliminaryFlag = true testen |
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String microcitation = details; |
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String rule = null; |
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|
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if (nameFrom != null && nameTo != null){
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if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
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nameTo.addBasionym(nameFrom, citation, microcitation, rule); |
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}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
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nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
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nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
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nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());//nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ; |
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}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF || relQualifierFk == NAME_REL_IS_LECTOTYPE_OF || relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED ){
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boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF); |
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boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF); |
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boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF); |
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boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED); |
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|
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NameTypeDesignationStatus status = null; |
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String originalNameString = null; |
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//TODO addToAllNames true or false? |
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boolean addToAllNames = false; |
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if (config.getNameTypeDesignationStatusMethod() != null){
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Method method = config.getNameTypeDesignationStatusMethod(); |
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method.setAccessible(true); |
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try {
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status = (NameTypeDesignationStatus)method.invoke(null, notes); |
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nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames); |
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} catch (Exception e) {
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throw new RuntimeException(e); |
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} |
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}else{
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if (isLectoType){
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status = NameTypeDesignationStatus.LECTOTYPE(); |
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} |
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nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames); |
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} |
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}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
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nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_IS_FIRST_PARENT_OF || relQualifierFk == NAME_REL_IS_SECOND_PARENT_OF || relQualifierFk == NAME_REL_IS_FEMALE_PARENT_OF || relQualifierFk == NAME_REL_IS_MALE_PARENT_OF){
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//HybridRelationships |
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if (! (nameTo instanceof BotanicalName) || ! (nameFrom instanceof BotanicalName)){
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logger.warn("HybridrelationshipNames ("+name1Id +"," + name2Id +") must be of type BotanicalName but are not");
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success = false; |
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} |
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try {
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HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk); |
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BotanicalName parent = (BotanicalName)nameFrom; |
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BotanicalName child = (BotanicalName)nameTo; |
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//TODO bug when trying to persist |
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//parent.addHybridChild(child, hybridRelType, rule); |
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logger.warn("HybridRelationships not yet implemented");
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} catch (UnknownCdmTypeException e) {
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logger.warn(e); |
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success = false; |
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} |
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}else {
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//TODO |
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Method method = config.getNamerelationshipTypeMethod(); |
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if (method != null){
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try {
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method.invoke(null, relQualifierFk, nameTo, nameFrom); |
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} catch (Exception e) {
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logger.error(e.getMessage()); |
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logger.warn("NameRelationship could not be imported");
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success = false; |
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} |
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}else{
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logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
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success = false; |
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} |
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} |
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success = handleNameRelationship(success, config, name1Id, name2Id, |
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relQualifierFk, notes, nameFrom, nameTo, citation, |
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microcitation, rule); |
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nameToSave.add(nameFrom); |
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|
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//TODO |
| ... | ... | |
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success = false; |
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} |
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} |
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partitioner.startDoSave(); |
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getNameService().save(nameToSave); |
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|
| ... | ... | |
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} |
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} |
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|
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/** |
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* @param success |
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* @param config |
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* @param name1Id |
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* @param name2Id |
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* @param relQualifierFk |
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* @param notes |
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* @param nameFrom |
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* @param nameTo |
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* @param citation |
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* @param microcitation |
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* @param rule |
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* @return |
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*/ |
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private boolean handleNameRelationship(boolean success, |
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BerlinModelImportConfigurator config, int name1Id, int name2Id, |
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int relQualifierFk, String notes, TaxonNameBase nameFrom, |
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TaxonNameBase nameTo, ReferenceBase<?> citation, |
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String microcitation, String rule) {
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AnnotatableEntity nameRelationship = null; |
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if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
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nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule); |
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}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
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nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup()); |
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}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF || relQualifierFk == NAME_REL_IS_LECTOTYPE_OF || relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED ){
|
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boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF); |
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boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF); |
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boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF); |
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boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED); |
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|
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NameTypeDesignationStatus status = null; |
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String originalNameString = null; |
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//TODO addToAllNames true or false? |
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boolean addToAllNames = false; |
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if (config.getNameTypeDesignationStatusMethod() != null){
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Method method = config.getNameTypeDesignationStatusMethod(); |
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method.setAccessible(true); |
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try {
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status = (NameTypeDesignationStatus)method.invoke(null, notes); |
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nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames); |
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} catch (Exception e) {
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throw new RuntimeException(e); |
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} |
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}else{
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if (isLectoType){
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status = NameTypeDesignationStatus.LECTOTYPE(); |
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} |
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nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames); |
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} |
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|
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}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
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nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ; |
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}else if (relQualifierFk == NAME_REL_IS_FIRST_PARENT_OF || relQualifierFk == NAME_REL_IS_SECOND_PARENT_OF || relQualifierFk == NAME_REL_IS_FEMALE_PARENT_OF || relQualifierFk == NAME_REL_IS_MALE_PARENT_OF){
|
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//HybridRelationships |
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if (! (nameTo instanceof NonViralName ) || ! (nameFrom instanceof NonViralName)){
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logger.warn("HybridrelationshipNames ("+name1Id +"," + name2Id +") must be of type NonViralNameName but are not");
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success = false; |
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} |
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try {
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HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk); |
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BotanicalName parent = (BotanicalName)nameFrom; |
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BotanicalName child = (BotanicalName)nameTo; |
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|
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nameRelationship = parent.addHybridChild(child, hybridRelType, rule); |
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|
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} catch (UnknownCdmTypeException e) {
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logger.warn(e); |
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success = false; |
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} |
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}else {
|
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//TODO |
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Method method = config.getNamerelationshipTypeMethod(); |
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if (method != null){
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try {
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method.invoke(null, relQualifierFk, nameTo, nameFrom); |
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} catch (Exception e) {
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logger.error(e.getMessage()); |
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logger.warn("NameRelationship could not be imported");
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success = false; |
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} |
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}else{
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logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
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success = false; |
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} |
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} |
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doNotes(nameRelationship, notes); |
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return success; |
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} |
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|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
| 230 | 259 |
*/ |
| ... | ... | |
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handleForeignKey(rs, nameIdSet, "name2Id"); |
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handleForeignKey(rs, referenceIdSet, "RefFk"); |
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handleForeignKey(rs, refDetailIdSet, "RefDetailFk"); |
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}
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|
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} |
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|
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//name map |
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nameSpace = BerlinModelTaxonNameImport.NAMESPACE; |
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cdmClass = TaxonNameBase.class; |
| ... | ... | |
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idSet = referenceIdSet; |
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Map<String, ReferenceBase> biblioReferenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, biblioReferenceMap); |
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|
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//nom refDetail map |
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nameSpace = BerlinModelRefDetailImport.NOM_REFDETAIL_NAMESPACE; |
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cdmClass = ReferenceBase.class; |
| ... | ... | |
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|
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} catch (SQLException e) {
|
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throw new RuntimeException(e); |
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} |
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}
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return result; |
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} |
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|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| 292 | 320 |
*/ |
| ... | ... | |
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IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator(); |
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return validator.validate(state); |
| 297 | 325 |
} |
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|
|
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|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName() |
| ... | ... | |
| 312 | 339 |
@Override |
| 313 | 340 |
public String getPluralString() {
|
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return pluralString; |
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} |
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|
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}
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|
|
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
| 319 | 346 |
*/ |
| 320 | 347 |
protected boolean isIgnore(BerlinModelImportState state){
|
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return ! state.getConfig().isDoRelNames(); |
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} |
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}
|
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| 323 | 350 |
|
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|
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} |
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merging /branches/cdmlib/SPRINT-Chichorieae1/ to trunk