Revision 96533ef2
Added by Andreas Müller about 12 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivator.java | ||
|---|---|---|
| 98 | 98 |
|
| 99 | 99 |
//make PESI Source |
| 100 | 100 |
Source destination = pesiDestination; |
| 101 |
IExportTransformer transformer = new PesiTransformer(destination);
|
|
| 101 |
PesiTransformer transformer = new PesiTransformer(destination);
|
|
| 102 | 102 |
|
| 103 | 103 |
PesiExportConfigurator config = PesiExportConfigurator.NewInstance(destination, source, transformer); |
| 104 | 104 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorEM.java | ||
|---|---|---|
| 34 | 34 |
private static final Logger logger = Logger.getLogger(PesiExportActivatorEM.class); |
| 35 | 35 |
|
| 36 | 36 |
//database validation status (create, update, validate ...) |
| 37 |
static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI(); |
|
| 37 |
static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_EM2PESI_tmp();
|
|
| 38 | 38 |
// static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_FE2PESI(); |
| 39 | 39 |
// static final Source pesiDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI(); |
| 40 | 40 |
|
| 41 |
static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql(); |
|
| 41 |
static final ICdmDataSource cdmSource = CdmDestinations.cdm_test_local_mysql_test();
|
|
| 42 | 42 |
//Taxon names can't be mapped to their CDM ids as PESI Taxon table mainly holds taxa and there IDs. We ad nameIdStart to the TaxonName id to get a unique id |
| 43 | 43 |
static final int nameIdStart = 10000000; |
| 44 | 44 |
static final IdType idType = IdType.CDM_ID_WITH_EXCEPTIONS; |
| 45 | 45 |
|
| 46 |
static final int partitionSize = 2000;
|
|
| 46 |
static final int partitionSize = 1000;
|
|
| 47 | 47 |
|
| 48 | 48 |
//check - export |
| 49 | 49 |
static final CHECK check = CHECK.EXPORT_WITHOUT_CHECK; |
| ... | ... | |
| 62 | 62 |
//taxa |
| 63 | 63 |
static final boolean doTaxa = true; |
| 64 | 64 |
static final boolean doRelTaxa = true; |
| 65 |
static final boolean doTreeIndex = true;
|
|
| 66 |
static final boolean doRank = true;
|
|
| 65 |
static final boolean doTreeIndex = false;
|
|
| 66 |
static final boolean doRank = false;
|
|
| 67 | 67 |
static final boolean doInferredSynonyms = false; |
| 68 | 68 |
static final boolean doDescriptions = true; |
| 69 | 69 |
|
| ... | ... | |
| 99 | 99 |
|
| 100 | 100 |
//make PESI Source |
| 101 | 101 |
Source destination = pesiDestination; |
| 102 |
IExportTransformer transformer = new PesiTransformer(destination);
|
|
| 102 |
PesiTransformer transformer = new PesiTransformer(destination);
|
|
| 103 | 103 |
|
| 104 | 104 |
PesiExportConfigurator config = PesiExportConfigurator.NewInstance(destination, source, transformer); |
| 105 | 105 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorFE.java | ||
|---|---|---|
| 98 | 98 |
|
| 99 | 99 |
//make PESI Source |
| 100 | 100 |
Source destination = pesiDestination; |
| 101 |
IExportTransformer transformer = new PesiTransformer(destination);
|
|
| 101 |
PesiTransformer transformer = new PesiTransformer(destination);
|
|
| 102 | 102 |
|
| 103 | 103 |
PesiExportConfigurator config = PesiExportConfigurator.NewInstance(destination, source, transformer); |
| 104 | 104 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/ExpertsAndLastActionMapper.java | ||
|---|---|---|
| 21 | 21 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper; |
| 22 | 22 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbSingleAttributeExportMapperBase; |
| 23 | 23 |
import eu.etaxonomy.cdm.io.common.mapping.out.IDbExportMapper; |
| 24 |
import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer; |
|
| 24 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.out.IndexCounter; |
| 25 | 26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 26 | 27 |
|
| ... | ... | |
| 29 | 30 |
* @created 12.05.2009 |
| 30 | 31 |
* @version 1.0 |
| 31 | 32 |
*/ |
| 32 |
public class ExpertsAndLastActionMapper extends MultipleAttributeMapperBase<DbSingleAttributeExportMapperBase<DbExportStateBase<?>>> implements IDbExportMapper<DbExportStateBase<?>>{
|
|
| 33 |
public class ExpertsAndLastActionMapper extends MultipleAttributeMapperBase<DbSingleAttributeExportMapperBase<DbExportStateBase<?, IExportTransformer>>> implements IDbExportMapper<DbExportStateBase<?, IExportTransformer>, IExportTransformer>{
|
|
| 33 | 34 |
@SuppressWarnings("unused")
|
| 34 | 35 |
private static final Logger logger = Logger.getLogger(ExpertsAndLastActionMapper.class); |
| 35 | 36 |
|
| ... | ... | |
| 55 | 56 |
/* (non-Javadoc) |
| 56 | 57 |
* @see eu.etaxonomy.cdm.io.berlinModel.out.mapper.IDbExportMapper#initialize(java.sql.PreparedStatement, eu.etaxonomy.cdm.io.berlinModel.out.mapper.IndexCounter, eu.etaxonomy.cdm.io.berlinModel.out.DbExportState) |
| 57 | 58 |
*/ |
| 58 |
public void initialize(PreparedStatement stmt, IndexCounter index, DbExportStateBase<?> state, String tableName) {
|
|
| 59 |
for (DbSingleAttributeExportMapperBase<DbExportStateBase<?>> mapper : singleMappers){
|
|
| 59 |
public void initialize(PreparedStatement stmt, IndexCounter index, DbExportStateBase<?, IExportTransformer> state, String tableName) {
|
|
| 60 |
for (DbSingleAttributeExportMapperBase<DbExportStateBase<?, IExportTransformer>> mapper : singleMappers){
|
|
| 60 | 61 |
mapper.initialize(stmt, index, state, tableName); |
| 61 | 62 |
} |
| 62 | 63 |
} |
| ... | ... | |
| 67 | 68 |
*/ |
| 68 | 69 |
public boolean invoke(CdmBase cdmBase) throws SQLException {
|
| 69 | 70 |
boolean result = true; |
| 70 |
for (DbSingleAttributeExportMapperBase<DbExportStateBase<?>> mapper : singleMappers){
|
|
| 71 |
for (DbSingleAttributeExportMapperBase<DbExportStateBase<?, IExportTransformer>> mapper : singleMappers){
|
|
| 71 | 72 |
result &= mapper.invoke(cdmBase); |
| 72 | 73 |
} |
| 73 | 74 |
return result; |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiCollectionExportMapping.java | ||
|---|---|---|
| 80 | 80 |
}else if (mapper == this.sequenceMapper){
|
| 81 | 81 |
this.sequenceMapper.invoke(null); |
| 82 | 82 |
}else if (mapper instanceof IDbExportMapper){
|
| 83 |
IDbExportMapper<DbExportStateBase<?>> dbMapper = (IDbExportMapper)mapper;
|
|
| 83 |
IDbExportMapper<DbExportStateBase<?, PesiTransformer>, PesiTransformer> dbMapper = (IDbExportMapper)mapper;
|
|
| 84 | 84 |
try {
|
| 85 | 85 |
result &= dbMapper.invoke(collectionObject); |
| 86 | 86 |
} catch (Exception e) {
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java | ||
|---|---|---|
| 9 | 9 |
*/ |
| 10 | 10 |
package eu.etaxonomy.cdm.io.pesi.out; |
| 11 | 11 |
|
| 12 |
import static java.util.EnumSet.of; |
|
| 13 |
|
|
| 12 | 14 |
import java.sql.Connection; |
| 13 | 15 |
import java.sql.PreparedStatement; |
| 14 | 16 |
import java.sql.SQLException; |
| ... | ... | |
| 22 | 24 |
import org.springframework.transaction.TransactionStatus; |
| 23 | 25 |
|
| 24 | 26 |
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
| 25 |
import eu.etaxonomy.cdm.io.berlinModel.out.mapper.RefDetailMapper; |
|
| 26 | 27 |
import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
| 27 | 28 |
import eu.etaxonomy.cdm.io.common.Source; |
| 28 | 29 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 29 | 30 |
import eu.etaxonomy.cdm.io.common.mapping.out.CollectionExportMapping; |
| 30 |
import eu.etaxonomy.cdm.io.common.mapping.out.CreatedAndNotesMapper; |
|
| 31 | 31 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbAreaMapper; |
| 32 | 32 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbDescriptionElementTaxonMapper; |
| 33 | 33 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbDistributionStatusMapper; |
| 34 | 34 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbExportIgnoreMapper; |
| 35 | 35 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbExportNotYetImplementedMapper; |
| 36 | 36 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbLanguageMapper; |
| 37 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbMarkerMapper; |
|
| 38 | 37 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper; |
| 39 | 38 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbOriginalNameMapper; |
| 40 | 39 |
import eu.etaxonomy.cdm.io.common.mapping.out.DbSimpleFilterMapper; |
| ... | ... | |
| 48 | 47 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 49 | 48 |
import eu.etaxonomy.cdm.model.common.Language; |
| 50 | 49 |
import eu.etaxonomy.cdm.model.common.LanguageString; |
| 51 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
|
| 52 | 50 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 53 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
| 54 | 51 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 55 | 52 |
import eu.etaxonomy.cdm.model.description.Distribution; |
| 56 | 53 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 57 | 54 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
| 58 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
|
| 59 | 55 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 60 | 56 |
import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
| 61 | 57 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 62 | 58 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 63 | 59 |
import eu.etaxonomy.cdm.model.location.TdwgArea; |
| 64 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
|
| 65 | 60 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 66 | 61 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 67 |
import static java.util.EnumSet.of; |
|
| 68 | 62 |
/** |
| 69 | 63 |
* The export class for {@link eu.etaxonomy.cdm.model.description.DescriptionElementBase DescriptionElements}.<p>
|
| 70 | 64 |
* Inserts into DataWarehouse database table <code>Note</code>.<p> |
| ... | ... | |
| 609 | 603 |
* @param state The {@link DbExportStateBase DbExportState}.
|
| 610 | 604 |
* @return |
| 611 | 605 |
*/ |
| 612 |
private static Integer getTaxonFk(TaxonNameBase<?,?> taxonName, DbExportStateBase<?> state) {
|
|
| 606 |
private static Integer getTaxonFk(TaxonNameBase<?,?> taxonName, DbExportStateBase<?, PesiTransformer> state) {
|
|
| 613 | 607 |
return state.getDbId(taxonName); |
| 614 | 608 |
} |
| 615 | 609 |
|
| ... | ... | |
| 632 | 626 |
// mapping.addMapper(MethodMapper.NewInstance("Region", this));
|
| 633 | 627 |
mapping.addMapper(DbDescriptionElementTaxonMapper.NewInstance("taxonFk"));
|
| 634 | 628 |
mapping.addMapper(ExpertsAndLastActionMapper.NewInstance()); |
| 629 |
mapping.addCollectionMapping(getNoteSourceMapping()); |
|
| 630 |
return mapping; |
|
| 631 |
} |
|
| 632 |
|
|
| 633 |
private CollectionExportMapping<PesiExportState, PesiExportConfigurator,PesiTransformer> getNoteSourceMapping() {
|
|
| 634 |
String tableName = "NoteSource"; |
|
| 635 |
String collectionAttribute = "sources"; |
|
| 636 |
IdMapper parentMapper = IdMapper.NewInstance("NoteFk");
|
|
| 637 |
CollectionExportMapping<PesiExportState, PesiExportConfigurator, PesiTransformer> mapping = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper); |
|
| 638 |
mapping.addMapper(DbSimpleFilterMapper.NewSingleNullAttributeInstance("idInSource", "Sources with idInSource currently handle data lineage"));
|
|
| 639 |
mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceFk"));
|
|
| 640 |
mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceNameCache", IS_CACHE));
|
|
| 641 |
mapping.addMapper(DbStringMapper.NewInstance("CitationMicroReference", "SourceDetail"));
|
|
| 635 | 642 |
return mapping; |
| 636 | 643 |
} |
| 637 | 644 |
|
| ... | ... | |
| 663 | 670 |
return mapping; |
| 664 | 671 |
} |
| 665 | 672 |
|
| 666 |
private CollectionExportMapping<PesiExportState, PesiExportConfigurator> getOccurrenceSourceMapping() {
|
|
| 673 |
private CollectionExportMapping<PesiExportState, PesiExportConfigurator, PesiTransformer> getOccurrenceSourceMapping() {
|
|
| 667 | 674 |
String tableName = "OccurrenceSource"; |
| 668 | 675 |
String collectionAttribute = "sources"; |
| 669 | 676 |
IdMapper parentMapper = IdMapper.NewInstance("OccurrenceFk");
|
| 670 |
CollectionExportMapping<PesiExportState, PesiExportConfigurator> mapping = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper); |
|
| 677 |
CollectionExportMapping<PesiExportState, PesiExportConfigurator, PesiTransformer> mapping = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper);
|
|
| 671 | 678 |
mapping.addMapper(DbSimpleFilterMapper.NewSingleNullAttributeInstance("idInSource", "Sources with idInSource currently handle data lineage"));
|
| 672 | 679 |
mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceFk"));
|
| 673 | 680 |
mapping.addMapper(DbObjectMapper.NewInstance("Citation", "SourceNameCache", IS_CACHE));
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportBase.java | ||
|---|---|---|
| 24 | 24 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.common.Marker; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 27 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
|
| 28 |
import eu.etaxonomy.cdm.model.name.HybridRelationship; |
|
| 27 | 29 |
import eu.etaxonomy.cdm.model.name.NameRelationship; |
| 28 | 30 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 29 | 31 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 30 | 32 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 33 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
| 31 | 34 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 32 | 35 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 33 | 36 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
| ... | ... | |
| 39 | 42 |
* @date 12.02.2010 |
| 40 | 43 |
* |
| 41 | 44 |
*/ |
| 42 |
public abstract class PesiExportBase extends DbExportBase<PesiExportConfigurator, PesiExportState> {
|
|
| 43 |
@SuppressWarnings("unused")
|
|
| 45 |
public abstract class PesiExportBase extends DbExportBase<PesiExportConfigurator, PesiExportState, PesiTransformer> {
|
|
| 44 | 46 |
private static final Logger logger = Logger.getLogger(PesiExportBase.class); |
| 45 | 47 |
|
| 46 | 48 |
public PesiExportBase() {
|
| ... | ... | |
| 89 | 91 |
} |
| 90 | 92 |
return list; |
| 91 | 93 |
} |
| 94 |
|
|
| 95 |
protected <CLASS extends RelationshipBase> List<CLASS> getNextNameRelationshipPartition(Class<CLASS> clazz, int limit, int partitionCount, List<String> propertyPath) {
|
|
| 96 |
List<CLASS> result = new ArrayList<CLASS>(); |
|
| 97 |
String[] propertyPaths = null; |
|
| 98 |
String orderHints = null; |
|
| 99 |
List<CLASS> list = (List<CLASS>)getNameService().getAllRelationships(limit, partitionCount * limit); |
|
| 100 |
for (CLASS rel : list){
|
|
| 101 |
if (isPesiNameRelationship(rel)){
|
|
| 102 |
result.add(rel); |
|
| 103 |
} |
|
| 104 |
} |
|
| 105 |
return result; |
|
| 106 |
} |
|
| 107 |
|
|
| 108 |
protected <CLASS extends RelationshipBase> List<CLASS> getNextTaxonRelationshipPartition(Class<CLASS> clazz, int limit, int partitionCount, List<String> propertyPath) {
|
|
| 109 |
List<CLASS> result = new ArrayList<CLASS>(); |
|
| 110 |
String[] propertyPaths = null; |
|
| 111 |
String orderHints = null; |
|
| 112 |
List<CLASS> list = (List<CLASS>)getTaxonService().getAllRelationships(limit, partitionCount * limit); |
|
| 113 |
for (CLASS rel : list){
|
|
| 114 |
if (isPesiTaxonOrSynonymRelationship(rel)){
|
|
| 115 |
result.add(rel); |
|
| 116 |
} |
|
| 117 |
} |
|
| 118 |
return result; |
|
| 119 |
} |
|
| 120 |
|
|
| 121 |
protected boolean isPesiNameRelationship(RelationshipBase rel){
|
|
| 122 |
TaxonNameBase<?,?> name1; |
|
| 123 |
TaxonNameBase<?,?> name2; |
|
| 124 |
if (rel.isInstanceOf(HybridRelationship.class)){
|
|
| 125 |
HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class); |
|
| 126 |
name1 = hybridRel.getParentName(); |
|
| 127 |
name2 = hybridRel.getHybridName(); |
|
| 128 |
}else if (rel.isInstanceOf(NameRelationship.class)){
|
|
| 129 |
NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class); |
|
| 130 |
name1 = nameRel.getFromName(); |
|
| 131 |
name2 = nameRel.getToName(); |
|
| 132 |
}else{
|
|
| 133 |
logger.warn ("Only hybrid- and name-relationships alowed here");
|
|
| 134 |
return false; |
|
| 135 |
} |
|
| 136 |
return (isPesiName(name1) && isPesiName(name2)); |
|
| 137 |
|
|
| 138 |
} |
|
| 139 |
|
|
| 140 |
private boolean isPesiName(TaxonNameBase<?,?> name) {
|
|
| 141 |
return hasPesiTaxon(name) || isPurePesiName(name); |
|
| 142 |
} |
|
| 143 |
|
|
| 144 |
protected boolean isPesiTaxonOrSynonymRelationship(RelationshipBase rel){
|
|
| 145 |
TaxonBase<?> taxonBase; |
|
| 146 |
Taxon taxon; |
|
| 147 |
if (rel.isInstanceOf(SynonymRelationship.class)){
|
|
| 148 |
SynonymRelationship synRel = CdmBase.deproxy(rel, SynonymRelationship.class); |
|
| 149 |
taxonBase = synRel.getSynonym(); |
|
| 150 |
taxon = synRel.getAcceptedTaxon(); |
|
| 151 |
}else if (rel.isInstanceOf(TaxonRelationship.class)){
|
|
| 152 |
TaxonRelationship taxRel = CdmBase.deproxy(rel, TaxonRelationship.class); |
|
| 153 |
taxonBase = taxRel.getFromTaxon(); |
|
| 154 |
taxon = taxRel.getToTaxon(); |
|
| 155 |
}else{
|
|
| 156 |
logger.warn ("Only synonym - and taxon-relationships alowed here");
|
|
| 157 |
return false; |
|
| 158 |
} |
|
| 159 |
return (isPesiTaxon(taxonBase) && isPesiTaxon(taxon)); |
|
| 160 |
|
|
| 161 |
} |
|
| 92 | 162 |
|
| 93 | 163 |
|
| 164 |
|
|
| 94 | 165 |
/** |
| 95 | 166 |
* Decides if a name is not used as the name part of a PESI taxon (and therefore is |
| 96 | 167 |
* exported to PESI as taxon already) but is related to a name used as a PESI taxon |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportConfigurator.java | ||
|---|---|---|
| 24 | 24 |
* @date 12.02.2010 |
| 25 | 25 |
* |
| 26 | 26 |
*/ |
| 27 |
public class PesiExportConfigurator extends DbExportConfiguratorBase<PesiExportState> implements IExportConfigurator<PesiExportState> {
|
|
| 27 |
public class PesiExportConfigurator extends DbExportConfiguratorBase<PesiExportState, PesiTransformer> implements IExportConfigurator<PesiExportState, PesiTransformer> {
|
|
| 28 | 28 |
@SuppressWarnings("unused")
|
| 29 | 29 |
private static Logger logger = Logger.getLogger(PesiExportConfigurator.class); |
| 30 | 30 |
private int limitSave = 2000; |
| ... | ... | |
| 49 | 49 |
|
| 50 | 50 |
private int nameIdStart = 10000000; |
| 51 | 51 |
|
| 52 |
public static PesiExportConfigurator NewInstance(Source pesiDestination, ICdmDataSource source, IExportTransformer transformer) {
|
|
| 52 |
public static PesiExportConfigurator NewInstance(Source pesiDestination, ICdmDataSource source, PesiTransformer transformer) {
|
|
| 53 | 53 |
return new PesiExportConfigurator(pesiDestination, source, transformer); |
| 54 | 54 |
} |
| 55 | 55 |
|
| ... | ... | |
| 75 | 75 |
* @param cdmSource |
| 76 | 76 |
* @param transformer |
| 77 | 77 |
*/ |
| 78 |
private PesiExportConfigurator(Source pesiSource, ICdmDataSource cdmSource, IExportTransformer transformer) {
|
|
| 78 |
private PesiExportConfigurator(Source pesiSource, ICdmDataSource cdmSource, PesiTransformer transformer) {
|
|
| 79 | 79 |
super(transformer); |
| 80 | 80 |
setSource(cdmSource); |
| 81 | 81 |
setDestination(pesiSource); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportMapping.java | ||
|---|---|---|
| 18 | 18 |
* @date 24.02.2010 |
| 19 | 19 |
* |
| 20 | 20 |
*/ |
| 21 |
public class PesiExportMapping extends CdmDbExportMapping<PesiExportState,PesiExportConfigurator> {
|
|
| 21 |
public class PesiExportMapping extends CdmDbExportMapping<PesiExportState,PesiExportConfigurator, PesiTransformer> {
|
|
| 22 | 22 |
private static final Logger logger = Logger.getLogger(PesiExportMapping.class); |
| 23 | 23 |
|
| 24 | 24 |
public PesiExportMapping(String tableName) {
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportState.java | ||
|---|---|---|
| 25 | 25 |
* @date 12.02.2010 |
| 26 | 26 |
* |
| 27 | 27 |
*/ |
| 28 |
public class PesiExportState extends DbExportStateBase<PesiExportConfigurator>{
|
|
| 28 |
public class PesiExportState extends DbExportStateBase<PesiExportConfigurator, PesiTransformer>{
|
|
| 29 | 29 |
@SuppressWarnings("unused")
|
| 30 | 30 |
private static final Logger logger = Logger.getLogger(PesiExportState.class); |
| 31 | 31 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiNoteExport.java | ||
|---|---|---|
| 495 | 495 |
* @see MethodMapper |
| 496 | 496 |
*/ |
| 497 | 497 |
@SuppressWarnings("unused")
|
| 498 |
private static Integer getTaxonFk(DescriptionElementBase descriptionElement, DbExportStateBase<?> state) {
|
|
| 498 |
private static Integer getTaxonFk(DescriptionElementBase descriptionElement, DbExportStateBase<?, PesiTransformer> state) {
|
|
| 499 | 499 |
Integer result = null; |
| 500 | 500 |
DescriptionBase<?> inDescription = descriptionElement.getInDescription(); |
| 501 | 501 |
if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) {
|
| ... | ... | |
| 512 | 512 |
* @param state The {@link DbExportStateBase DbExportState}.
|
| 513 | 513 |
* @return |
| 514 | 514 |
*/ |
| 515 |
private static Integer getTaxonFk(TaxonNameBase<?,?> taxonName, DbExportStateBase<?> state) {
|
|
| 515 |
private static Integer getTaxonFk(TaxonNameBase<?,?> taxonName, DbExportStateBase<?, PesiTransformer> state) {
|
|
| 516 | 516 |
return state.getDbId(taxonName); |
| 517 | 517 |
} |
| 518 | 518 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java | ||
|---|---|---|
| 26 | 26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 27 | 27 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 28 | 28 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
| 29 |
import eu.etaxonomy.cdm.model.name.HybridRelationship; |
|
| 29 | 30 |
import eu.etaxonomy.cdm.model.name.NameRelationship; |
| 30 | 31 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 31 | 32 |
import eu.etaxonomy.cdm.model.name.Rank; |
| ... | ... | |
| 54 | 55 |
private static final String dbTableName = "RelTaxon"; |
| 55 | 56 |
private static final String pluralString = "Relationships"; |
| 56 | 57 |
private static PreparedStatement synonymsStmt; |
| 58 |
|
|
| 57 | 59 |
private HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>(); |
| 58 | 60 |
private List<Rank> rankList = new ArrayList<Rank>(); |
| 59 | 61 |
private PesiExportMapping mapping; |
| 60 | 62 |
private int count = 0; |
| 61 |
private static NomenclaturalCode nomenclaturalCode2; |
|
| 62 | 63 |
|
| 63 | 64 |
public PesiRelTaxonExport() {
|
| 64 | 65 |
super(); |
| ... | ... | |
| 81 | 82 |
return result; |
| 82 | 83 |
} |
| 83 | 84 |
|
| 85 |
|
|
| 84 | 86 |
/* (non-Javadoc) |
| 85 | 87 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
| 86 | 88 |
*/ |
| 87 | 89 |
@Override |
| 88 | 90 |
protected void doInvoke(PesiExportState state) {
|
| 91 |
try {
|
|
| 92 |
logger.info("*** Started Making " + pluralString + " ...");
|
|
| 93 |
|
|
| 94 |
Connection connection = state.getConfig().getDestination().getConnection(); |
|
| 95 |
String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?"; |
|
| 96 |
synonymsStmt = connection.prepareStatement(synonymsSql); |
|
| 97 |
|
|
| 98 |
// Stores whether this invoke was successful or not. |
|
| 99 |
boolean success = true; |
|
| 100 |
|
|
| 101 |
// PESI: Clear the database table RelTaxon. |
|
| 102 |
doDelete(state); |
|
| 103 |
|
|
| 104 |
// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon |
|
| 105 |
mapping = getMapping(); |
|
| 106 |
|
|
| 107 |
// Initialize the db mapper |
|
| 108 |
mapping.initialize(state); |
|
| 109 |
|
|
| 110 |
//Export Taxa.. |
|
| 111 |
// success &= doPhase01(state, mapping); |
|
| 112 |
|
|
| 113 |
|
|
| 114 |
|
|
| 115 |
// 2nd Round: Add ParentTaxonFk, TreeIndex to each Taxon |
|
| 116 |
success &= doPhase02(state, mapping); |
|
| 117 |
|
|
| 118 |
} catch (SQLException e) {
|
|
| 119 |
e.printStackTrace(); |
|
| 120 |
logger.error(e.getMessage()); |
|
| 121 |
state.setUnsuccessfull(); |
|
| 122 |
return; |
|
| 123 |
} |
|
| 124 |
} |
|
| 125 |
|
|
| 126 |
|
|
| 127 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
|
|
| 128 |
logger.info("PHASE 1: Relationships ...");
|
|
| 129 |
boolean success = true; |
|
| 130 |
|
|
| 131 |
int limit = state.getConfig().getLimitSave(); |
|
| 132 |
// Start transaction |
|
| 133 |
TransactionStatus txStatus = startTransaction(true); |
|
| 134 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 135 |
|
|
| 136 |
List<RelationshipBase> list; |
|
| 137 |
|
|
| 138 |
//taxon relations |
|
| 139 |
int partitionCount = 0; |
|
| 140 |
while ((list = getNextTaxonRelationshipPartition(null, limit, partitionCount++, null)).size() > 0 ) {
|
|
| 141 |
for (RelationshipBase rel : list){
|
|
| 142 |
try {
|
|
| 143 |
mapping.invoke(rel); |
|
| 144 |
} catch (Exception e) {
|
|
| 145 |
logger.error(e.getMessage() + ". Relationship: " + rel.getUuid()); |
|
| 146 |
e.printStackTrace(); |
|
| 147 |
} |
|
| 148 |
} |
|
| 149 |
} |
|
| 150 |
|
|
| 151 |
return success; |
|
| 152 |
} |
|
| 153 |
|
|
| 154 |
private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
|
|
| 155 |
logger.info("PHASE 1: Relationships ...");
|
|
| 156 |
boolean success = true; |
|
| 157 |
|
|
| 158 |
int limit = state.getConfig().getLimitSave(); |
|
| 159 |
// Start transaction |
|
| 160 |
TransactionStatus txStatus = startTransaction(true); |
|
| 161 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 162 |
|
|
| 163 |
List<RelationshipBase> list; |
|
| 164 |
|
|
| 165 |
//name relations |
|
| 166 |
int partitionCount = 0; |
|
| 167 |
while ((list = getNextNameRelationshipPartition(null, limit, partitionCount++, null)).size() > 0 ) {
|
|
| 168 |
for (RelationshipBase rel : list){
|
|
| 169 |
try {
|
|
| 170 |
TaxonNameBase<?,?> name1; |
|
| 171 |
TaxonNameBase<?,?> name2; |
|
| 172 |
if (rel.isInstanceOf(HybridRelationship.class)){
|
|
| 173 |
HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class); |
|
| 174 |
name1 = hybridRel.getParentName(); |
|
| 175 |
name2 = hybridRel.getHybridName(); |
|
| 176 |
}else if (rel.isInstanceOf(NameRelationship.class)){
|
|
| 177 |
NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class); |
|
| 178 |
name1 = nameRel.getFromName(); |
|
| 179 |
name2 = nameRel.getToName(); |
|
| 180 |
}else{
|
|
| 181 |
logger.warn ("Only hybrid- and name-relationships alowed here");
|
|
| 182 |
continue; |
|
| 183 |
} |
|
| 184 |
List<IdentifiableEntity> fromList = new ArrayList<IdentifiableEntity>(); |
|
| 185 |
List<IdentifiableEntity> toList = new ArrayList<IdentifiableEntity>(); |
|
| 186 |
makeList(name1, fromList); |
|
| 187 |
makeList(name2, toList); |
|
| 188 |
|
|
| 189 |
for (IdentifiableEntity fromEntity : fromList){
|
|
| 190 |
for (IdentifiableEntity toEntity : toList){
|
|
| 191 |
//TODO set entities to state |
|
| 192 |
state.setCurrentFromObject(fromEntity); |
|
| 193 |
state.setCurrentToObject(toEntity); |
|
| 194 |
mapping.invoke(rel); |
|
| 195 |
} |
|
| 196 |
} |
|
| 197 |
|
|
| 198 |
} catch (Exception e) {
|
|
| 199 |
logger.error(e.getMessage() + ". Relationship: " + rel.getUuid()); |
|
| 200 |
e.printStackTrace(); |
|
| 201 |
} |
|
| 202 |
} |
|
| 203 |
} |
|
| 204 |
|
|
| 205 |
|
|
| 206 |
return success; |
|
| 207 |
} |
|
| 208 |
|
|
| 209 |
private void makeList(TaxonNameBase<?, ?> name, List<IdentifiableEntity> list) {
|
|
| 210 |
if (! hasPesiTaxon(name)){
|
|
| 211 |
list.add(name); |
|
| 212 |
}else{
|
|
| 213 |
for (TaxonBase taxon: getPesiTaxa(name)){
|
|
| 214 |
list.add(taxon); |
|
| 215 |
} |
|
| 216 |
} |
|
| 217 |
} |
|
| 218 |
|
|
| 219 |
/* (non-Javadoc) |
|
| 220 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
|
| 221 |
*/ |
|
| 222 |
protected void doInvoke_Old(PesiExportState state) {
|
|
| 89 | 223 |
try {
|
| 90 | 224 |
logger.info("*** Started Making " + pluralString + " ...");
|
| 91 | 225 |
|
| ... | ... | |
| 483 | 617 |
* @see MethodMapper |
| 484 | 618 |
*/ |
| 485 | 619 |
@SuppressWarnings("unused")
|
| 486 |
private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship) {
|
|
| 620 |
private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
|
| 487 | 621 |
String result = null; |
| 488 | 622 |
NomenclaturalCode code = null; |
| 489 | 623 |
if (relationship.isInstanceOf(TaxonRelationship.class)){
|
| ... | ... | |
| 494 | 628 |
code = CdmBase.deproxy(relationship, NameRelationship.class).getFromName().getNomenclaturalCode(); |
| 495 | 629 |
} |
| 496 | 630 |
if (code != null) {
|
| 497 |
result = PesiTransformer.taxonRelation2RelTaxonQualifierCache(relationship, code);
|
|
| 631 |
result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);
|
|
| 498 | 632 |
} else {
|
| 499 | 633 |
logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());
|
| 500 | 634 |
} |
| ... | ... | |
| 528 | 662 |
} else if (relationship.isInstanceOf(SynonymRelationship.class)) {
|
| 529 | 663 |
SynonymRelationship sr = (SynonymRelationship)relationship; |
| 530 | 664 |
taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon(); |
| 531 |
} else if (relationship.isInstanceOf(NameRelationship.class)) {
|
|
| 665 |
} else if (relationship.isInstanceOf(NameRelationship.class) || relationship.isInstanceOf(HybridRelationship.class)) {
|
|
| 532 | 666 |
if (isFrom){
|
| 533 | 667 |
return state.getDbId(state.getCurrentFromObject()); |
| 534 | 668 |
}else{
|
| ... | ... | |
| 594 | 728 |
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", standardMethodParameter, PesiExportState.class));
|
| 595 | 729 |
mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", standardMethodParameter, PesiExportState.class));
|
| 596 | 730 |
mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this));
|
| 597 |
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this));
|
|
| 731 |
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));
|
|
| 598 | 732 |
mapping.addMapper(MethodMapper.NewInstance("Notes", this));
|
| 599 | 733 |
|
| 600 | 734 |
return mapping; |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.location.TdwgArea; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry; |
| 41 |
import eu.etaxonomy.cdm.model.name.HybridRelationshipType; |
|
| 41 | 42 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
| 42 | 43 |
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| 43 | 44 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| ... | ... | |
| 47 | 48 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 48 | 49 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
| 49 | 50 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 51 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
| 50 | 52 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
| 51 | 53 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 52 | 54 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 219 | 221 |
public static int IS_INFERRED_GENUS_FOR = 302; |
| 220 | 222 |
public static int IS_POTENTIAL_COMBINATION_FOR = 303; |
| 221 | 223 |
|
| 222 |
public static String STR_IS_BASIONYM_FOR = "is basionym for"; |
|
| 223 | 224 |
public static String STR_IS_BASIONYM_FOR_ZOOL = "is original combination for"; |
| 224 |
public static String STR_IS_LATER_HOMONYM_OF = "is later homonym of"; |
|
| 225 |
public static String STR_IS_REPLACED_SYNONYM_FOR = "is replaced synonym for"; |
|
| 226 |
public static String STR_IS_VALIDATION_OF = "is validation of"; |
|
| 227 |
public static String STR_IS_LATER_VALIDATION_OF = "is later validation of"; |
|
| 228 |
public static String STR_IS_TYPE_OF = "is type of"; |
|
| 229 |
public static String STR_IS_CONSERVED_TYPE_OF = "is conserved type of"; |
|
| 230 |
public static String STR_IS_REJECTED_TYPE_OF = "is rejected type of"; |
|
| 231 |
public static String STR_IS_FIRST_PARENT_OF = "is first parent of"; |
|
| 232 |
public static String STR_IS_SECOND_PARENT_OF = "is second parent of"; |
|
| 233 |
public static String STR_IS_FEMALE_PARENT_OF = "is female parent of"; |
|
| 234 |
public static String STR_IS_MALE_PARENT_OF = "is male parent of"; |
|
| 235 |
public static String STR_IS_CONSERVED_AGAINST = "is conserved against"; |
|
| 236 |
public static String STR_IS_REJECTED_IN_FAVOUR_OF = "is rejected in favour of"; |
|
| 237 |
public static String STR_IS_TREATED_AS_LATER_HOMONYM_OF = "is treated as later homonym of"; |
|
| 238 |
public static String STR_IS_ORTHOGRAPHIC_VARIANT_OF = "is orthographic variant of"; |
|
| 239 |
public static String STR_IS_ALTERNATIVE_NAME_FOR = "is alternative name for"; |
|
| 240 |
public static String STR_HAS_SAME_TYPE_AS = "has same type as"; |
|
| 241 |
public static String STR_IS_LECTOTYPE_OF = "is lectotype of"; |
|
| 242 |
public static String STR_TYPE_NOT_DESIGNATED = "type not designated"; |
|
| 243 |
public static String STR_IS_TAXONOMICALLY_INCLUDED_IN = "is taxonomically included in"; |
|
| 244 |
public static String STR_IS_SYNONYM_OF = "is synonym of"; |
|
| 245 |
public static String STR_IS_MISAPPLIED_NAME_FOR = "is misapplied name for"; |
|
| 246 |
public static String STR_IS_PRO_PARTE_SYNONYM_OF = "is pro parte synonym of"; |
|
| 247 |
public static String STR_IS_PARTIAL_SYNONYM_OF = "is partial synonym of"; |
|
| 248 |
public static String STR_IS_HETEROTYPIC_SYNONYM_OF = "is heterotypic synonym of"; |
|
| 249 | 225 |
public static String STR_IS_HETEROTYPIC_SYNONYM_OF_ZOOL = "is subjective synonym of"; |
| 250 |
public static String STR_IS_HOMOTYPIC_SYNONYM_OF = "is homotypic synonym of"; |
|
| 251 | 226 |
private static final String STR_IS_HOMOTYPIC_SYNONYM_OF_ZOOL = "is objective synonym of"; |
| 252 |
public static String STR_IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF = "is pro parte and homotypic synonym of"; |
|
| 253 |
public static String STR_IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF = "is pro parte and heterotypic synonym of"; |
|
| 254 |
public static String STR_IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF = "is partial and homotypic synonym of"; |
|
| 255 |
public static String STR_IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF = "is partial and heterotypic synonym of"; |
|
| 256 |
public static String STR_IS_INFERRED_EPITHET_FOR = "is inferred epithet for"; |
|
| 257 |
public static String STR_IS_INFERRED_GENUS_FOR = "is inferred genus for"; |
|
| 258 |
public static String STR_IS_POTENTIAL_COMBINATION_FOR = "is potential combination for"; |
|
| 259 | 227 |
|
| 228 |
|
|
| 229 |
//namespaces |
|
| 260 | 230 |
public static String STR_NAMESPACE_NOMINAL_TAXON = "Nominal taxon from TAX_ID:"; |
| 261 | 231 |
public static String STR_NAMESPACE_INFERRED_EPITHET = "Inferred epithet from TAX_ID:"; |
| 262 | 232 |
public static String STR_NAMESPACE_INFERRED_GENUS = "Inferred genus from TAX_ID:"; |
| 263 | 233 |
public static String STR_NAMESPACE_POTENTIAL_COMBINATION = "Potential combination from TAX_ID:"; |
| 264 | 234 |
|
| 235 |
|
|
| 265 | 236 |
// Kingdoms |
| 266 | 237 |
public static int KINGDOM_NULL = 0; |
| 267 | 238 |
public static int KINGDOM_ANIMALIA = 2; |
| ... | ... | |
| 1253 | 1224 |
private Map<String, String> tdwgLabelMap = new HashMap<String, String>(); |
| 1254 | 1225 |
private Map<Integer, String> nameStatusCacheMap = new HashMap<Integer, String>(); |
| 1255 | 1226 |
private Map<Integer, String> qualityStatusCacheMap = new HashMap<Integer, String>(); |
| 1227 |
private Map<Integer, String> taxRelQualifierCacheMap = new HashMap<Integer, String>(); |
|
| 1256 | 1228 |
|
| 1257 | 1229 |
|
| 1258 | 1230 |
private Source destination; |
| ... | ... | |
| 1298 | 1270 |
this.qualityStatusCacheMap.put(key, cache); |
| 1299 | 1271 |
} |
| 1300 | 1272 |
} |
| 1273 |
//qualityStatusCache |
|
| 1274 |
sql = " SELECT QualifierId, Qualifier FROM RelTaxonQualifier "; |
|
| 1275 |
rs = destination.getResultSet(sql); |
|
| 1276 |
while (rs.next()){
|
|
| 1277 |
Integer key = rs.getInt("QualifierId");
|
|
| 1278 |
String cache = rs.getString("Qualifier");
|
|
| 1279 |
if (StringUtils.isNotBlank(cache)){
|
|
| 1280 |
this.taxRelQualifierCacheMap.put(key, cache); |
|
| 1281 |
} |
|
| 1282 |
} |
|
| 1283 |
|
|
| 1284 |
|
|
| 1301 | 1285 |
|
| 1302 | 1286 |
} catch (SQLException e) {
|
| 1303 | 1287 |
logger.error("SQLException when trying to read area map", e);
|
| ... | ... | |
| 3514 | 3498 |
* @param relation |
| 3515 | 3499 |
* @return |
| 3516 | 3500 |
*/ |
| 3517 |
public static String taxonRelation2RelTaxonQualifierCache(RelationshipBase<?,?,?> relation, NomenclaturalCode code){
|
|
| 3518 |
if (relation == null) {
|
|
| 3501 |
public String getCacheByRelationshipType(RelationshipBase relation, NomenclaturalCode code){
|
|
| 3502 |
if (relation == null){
|
|
| 3519 | 3503 |
return null; |
| 3520 |
} |
|
| 3521 |
RelationshipTermBase<?> type = relation.getType(); |
|
| 3522 |
if (type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {
|
|
| 3523 |
return STR_IS_MISAPPLIED_NAME_FOR; |
|
| 3524 |
} else if (type.equals(SynonymRelationshipType.SYNONYM_OF())) {
|
|
| 3525 |
return STR_IS_SYNONYM_OF; |
|
| 3526 |
} else if (type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {
|
|
| 3527 |
if (code.equals(NomenclaturalCode.ICZN)){
|
|
| 3528 |
return STR_IS_HOMOTYPIC_SYNONYM_OF_ZOOL; |
|
| 3529 |
}else{
|
|
| 3530 |
return STR_IS_HOMOTYPIC_SYNONYM_OF; |
|
| 3531 |
} |
|
| 3532 |
} else if (type.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())) {
|
|
| 3533 |
if (code.equals(NomenclaturalCode.ICZN)){
|
|
| 3534 |
return STR_IS_HETEROTYPIC_SYNONYM_OF_ZOOL; |
|
| 3535 |
}else{
|
|
| 3536 |
return STR_IS_HETEROTYPIC_SYNONYM_OF; |
|
| 3537 |
} |
|
| 3538 |
} else if (type.equals(SynonymRelationshipType.INFERRED_EPITHET_OF())) {
|
|
| 3539 |
return STR_IS_INFERRED_EPITHET_FOR; |
|
| 3540 |
} else if (type.equals(SynonymRelationshipType.INFERRED_GENUS_OF())) {
|
|
| 3541 |
return STR_IS_INFERRED_GENUS_FOR; |
|
| 3542 |
} else if (type.equals(SynonymRelationshipType.POTENTIAL_COMBINATION_OF())) {
|
|
| 3543 |
return STR_IS_POTENTIAL_COMBINATION_FOR; |
|
| 3544 |
} else if (type.equals(NameRelationshipType.BASIONYM())) {
|
|
| 3504 |
}else{
|
|
| 3505 |
//preliminary until #2816 is fixed |
|
| 3506 |
RelationshipTermBase<?> type = relation.getType(); |
|
| 3545 | 3507 |
if (code.equals(NomenclaturalCode.ICZN)){
|
| 3546 |
return STR_IS_BASIONYM_FOR_ZOOL; |
|
| 3547 |
}else{
|
|
| 3548 |
return STR_IS_BASIONYM_FOR; |
|
| 3508 |
if (type.equals(NameRelationshipType.BASIONYM())) {
|
|
| 3509 |
return STR_IS_BASIONYM_FOR_ZOOL; |
|
| 3510 |
}else if (type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {
|
|
| 3511 |
return STR_IS_HOMOTYPIC_SYNONYM_OF_ZOOL; |
|
| 3512 |
} else if (type.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())) {
|
|
| 3513 |
return STR_IS_HETEROTYPIC_SYNONYM_OF_ZOOL; |
|
| 3514 |
} |
|
| 3549 | 3515 |
} |
| 3550 |
} else if (type.equals(NameRelationshipType.LATER_HOMONYM())) {
|
|
| 3551 |
return STR_IS_LATER_HOMONYM_OF; |
|
| 3552 |
} else if (type.equals(NameRelationshipType.REPLACED_SYNONYM())) {
|
|
| 3553 |
return STR_IS_REPLACED_SYNONYM_FOR; |
|
| 3554 |
} else if (type.equals(NameRelationshipType.VALIDATED_BY_NAME())) {
|
|
| 3555 |
return STR_IS_VALIDATION_OF; |
|
| 3556 |
} else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {
|
|
| 3557 |
return STR_IS_LATER_VALIDATION_OF; |
|
| 3558 |
} else if (type.equals(NameRelationshipType.CONSERVED_AGAINST())) {
|
|
| 3559 |
return STR_IS_CONSERVED_AGAINST; |
|
| 3560 |
} else if (type.equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())) {
|
|
| 3561 |
return STR_IS_TREATED_AS_LATER_HOMONYM_OF; |
|
| 3562 |
} else if (type.equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())) {
|
|
| 3563 |
return STR_IS_ORTHOGRAPHIC_VARIANT_OF; |
|
| 3564 |
} else if (type.equals(NameRelationshipType.ALTERNATIVE_NAME())) {
|
|
| 3565 |
return STR_IS_ALTERNATIVE_NAME_FOR; |
|
| 3566 |
} else {
|
|
| 3567 |
logger.warn("No equivalent RelationshipType found in datawarehouse for: " + type.getTitleCache());
|
|
| 3568 |
} |
|
| 3516 |
//end preliminary |
|
| 3569 | 3517 |
|
| 3570 |
// The following have no equivalent attribute in CDM |
|
| 3571 |
// IS_TYPE_OF |
|
| 3572 |
// IS_CONSERVED_TYPE_OF |
|
| 3573 |
// IS_REJECTED_TYPE_OF |
|
| 3574 |
// IS_FIRST_PARENT_OF |
|
| 3575 |
// IS_SECOND_PARENT_OF |
|
| 3576 |
// IS_FEMALE_PARENT_OF |
|
| 3577 |
// IS_MALE_PARENT_OF |
|
| 3578 |
// IS_REJECTED_IN_FAVOUR_OF |
|
| 3579 |
// HAS_SAME_TYPE_AS |
|
| 3580 |
// IS_LECTOTYPE_OF |
|
| 3581 |
// TYPE_NOT_DESIGNATED |
|
| 3582 |
// IS_PRO_PARTE_SYNONYM_OF |
|
| 3583 |
// IS_PARTIAL_SYNONYM_OF |
|
| 3584 |
// IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF |
|
| 3585 |
// IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF |
|
| 3586 |
// IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF |
|
| 3587 |
// IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF |
|
| 3588 |
|
|
| 3589 |
return null; |
|
| 3518 |
Integer key = taxonRelation2RelTaxonQualifierFk(relation); |
|
| 3519 |
return this.taxRelQualifierCacheMap.get(key); |
|
| 3520 |
} |
|
| 3590 | 3521 |
} |
| 3591 | 3522 |
|
| 3592 | 3523 |
/** |
| ... | ... | |
| 3602 | 3533 |
if (type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {
|
| 3603 | 3534 |
return IS_MISAPPLIED_NAME_FOR; |
| 3604 | 3535 |
} else if (type.equals(SynonymRelationshipType.SYNONYM_OF())) {
|
| 3605 |
return IS_SYNONYM_OF; |
|
| 3536 |
SynonymRelationship synRel = CdmBase.deproxy(relation, SynonymRelationship.class); |
|
| 3537 |
if (synRel.isProParte()){
|
|
| 3538 |
return IS_PRO_PARTE_SYNONYM_OF; |
|
| 3539 |
}else if (synRel.isPartial()){
|
|
| 3540 |
return IS_PARTIAL_SYNONYM_OF; |
|
| 3541 |
}else{
|
|
| 3542 |
return IS_SYNONYM_OF; |
|
| 3543 |
} |
|
| 3606 | 3544 |
} else if (type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {
|
| 3607 |
return IS_HOMOTYPIC_SYNONYM_OF; |
|
| 3545 |
SynonymRelationship synRel = CdmBase.deproxy(relation, SynonymRelationship.class); |
|
| 3546 |
if (synRel.isProParte()){
|
|
| 3547 |
return IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF; |
|
| 3548 |
}else if (synRel.isPartial()){
|
|
| 3549 |
return IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF; |
|
| 3550 |
}else{
|
|
| 3551 |
return IS_HOMOTYPIC_SYNONYM_OF; |
|
| 3552 |
} |
|
| 3608 | 3553 |
} else if (type.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())) {
|
| 3609 |
return IS_HETEROTYPIC_SYNONYM_OF; |
|
| 3554 |
SynonymRelationship synRel = CdmBase.deproxy(relation, SynonymRelationship.class); |
|
| 3555 |
if (synRel.isProParte()){
|
|
| 3556 |
return IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF; |
|
| 3557 |
}else if (synRel.isPartial()){
|
|
| 3558 |
return IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF; |
|
| 3559 |
}else{
|
|
| 3560 |
return IS_HETEROTYPIC_SYNONYM_OF; |
|
| 3561 |
} |
|
| 3610 | 3562 |
} else if (type.equals(SynonymRelationshipType.INFERRED_EPITHET_OF())) {
|
| 3611 | 3563 |
return IS_INFERRED_EPITHET_FOR; |
| 3612 | 3564 |
} else if (type.equals(SynonymRelationshipType.INFERRED_GENUS_OF())) {
|
| ... | ... | |
| 3631 | 3583 |
return IS_ORTHOGRAPHIC_VARIANT_OF; |
| 3632 | 3584 |
} else if (type.equals(NameRelationshipType.ALTERNATIVE_NAME())) {
|
| 3633 | 3585 |
return IS_ALTERNATIVE_NAME_FOR; |
| 3586 |
} else if (type.equals(HybridRelationshipType.FEMALE_PARENT())) {
|
|
| 3587 |
return IS_FEMALE_PARENT_OF; |
|
| 3588 |
} else if (type.equals(HybridRelationshipType.MALE_PARENT())) {
|
|
| 3589 |
return IS_MALE_PARENT_OF; |
|
| 3590 |
} else if (type.equals(HybridRelationshipType.FIRST_PARENT())) {
|
|
| 3591 |
return IS_FIRST_PARENT_OF; |
|
| 3592 |
} else if (type.equals(HybridRelationshipType.SECOND_PARENT())) {
|
|
| 3593 |
return IS_SECOND_PARENT_OF; |
|
| 3594 |
|
|
| 3634 | 3595 |
} else {
|
| 3635 | 3596 |
logger.warn("No equivalent RelationshipType found in datawarehouse for: " + type.getTitleCache());
|
| 3636 | 3597 |
} |
| ... | ... | |
| 3639 | 3600 |
// IS_TYPE_OF |
| 3640 | 3601 |
// IS_CONSERVED_TYPE_OF |
| 3641 | 3602 |
// IS_REJECTED_TYPE_OF |
| 3642 |
// IS_FIRST_PARENT_OF |
|
| 3643 |
// IS_SECOND_PARENT_OF |
|
| 3644 |
// IS_FEMALE_PARENT_OF |
|
| 3645 |
// IS_MALE_PARENT_OF |
|
| 3646 | 3603 |
// IS_REJECTED_IN_FAVOUR_OF |
| 3647 | 3604 |
// HAS_SAME_TYPE_AS |
| 3648 | 3605 |
// IS_LECTOTYPE_OF |
| 3649 | 3606 |
// TYPE_NOT_DESIGNATED |
| 3650 |
// IS_PRO_PARTE_SYNONYM_OF |
|
| 3651 |
// IS_PARTIAL_SYNONYM_OF |
|
| 3652 |
// IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF |
|
| 3653 |
// IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF |
|
| 3654 |
// IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF |
|
| 3655 |
// IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF |
|
| 3607 |
|
|
| 3656 | 3608 |
|
| 3657 | 3609 |
return null; |
| 3658 | 3610 |
} |
| ... | ... | |
| 3748 | 3700 |
}else{
|
| 3749 | 3701 |
return this.qualityStatusCacheMap.get(qualityStatusId); |
| 3750 | 3702 |
} |
| 3751 |
|
|
| 3752 | 3703 |
} |
| 3753 | 3704 |
|
| 3754 | 3705 |
public static String getOriginalDbBySources(BitSet sources) {
|
Also available in: Unified diff
getAllRelationships reimplemented to match only relevant relationship classes,
Export generics include Transformer type