Revision 5947a91a
Added by Andreas Müller almost 12 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java | ||
|---|---|---|
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import java.sql.Connection; |
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import java.sql.PreparedStatement; |
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import java.sql.SQLException; |
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import java.sql.Types; |
|
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import java.util.Arrays; |
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import java.util.HashSet; |
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import java.util.List; |
| ... | ... | |
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer; |
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import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.mapping.DbIgnoreMapper; |
|
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
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import eu.etaxonomy.cdm.io.common.mapping.out.CollectionExportMapping; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbAreaMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper; |
|
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import eu.etaxonomy.cdm.io.common.mapping.out.DbDescriptionElementTaxonMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbDistributionStatusMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbExportIgnoreMapper; |
| ... | ... | |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbSingleSourceMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbTextDataMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbTimePeriodMapper; |
|
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import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
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import eu.etaxonomy.cdm.io.profiler.ProfilerController; |
| ... | ... | |
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import eu.etaxonomy.cdm.model.location.TdwgArea; |
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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.Reference; |
|
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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/** |
| ... | ... | |
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occurrenceMapping.initialize(state); |
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|
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// Get specific mappings: (CDM) DescriptionElement -> (PESI) Additional taxon source |
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PesiExportMapping addittionalSourceMapping = getAdditionalTaxonSourceMapping(); |
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addittionalSourceMapping.initialize(state); |
|
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PesiExportMapping addSourceSourceMapping = getAddTaxonSourceSourceMapping(); |
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addSourceSourceMapping.initialize(state); |
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PesiExportMapping additionalSourceMapping = getAdditionalTaxonSourceMapping(); |
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additionalSourceMapping.initialize(state); |
|
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|
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// Get specific mappings: (CDM) DescriptionElement -> (PESI) Additional taxon source |
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PesiExportMapping vernacularMapping = getVernacularNamesMapping(); |
| ... | ... | |
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for (Taxon taxon : list) {
|
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countTaxa++; |
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doCount(count++, modCount, pluralString); |
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success &= handleSingleTaxon(taxon, state, notesMapping, occurrenceMapping, addittionalSourceMapping, vernacularMapping, imageMapping); |
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success &= handleSingleTaxon(taxon, state, notesMapping, occurrenceMapping, addSourceSourceMapping, |
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additionalSourceMapping, vernacularMapping, imageMapping); |
|
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} |
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list = null; |
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state.setCurrentTaxon(null); |
| ... | ... | |
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} |
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|
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private boolean handleSingleTaxon(Taxon taxon, PesiExportState state, PesiExportMapping notesMapping, PesiExportMapping occurrenceMapping, |
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PesiExportMapping addittionalSourceMapping, PesiExportMapping vernacularMapping, PesiExportMapping imageMapping) throws SQLException {
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|
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PesiExportMapping addSourceSourceMapping, PesiExportMapping additionalSourceMapping, |
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PesiExportMapping vernacularMapping, PesiExportMapping imageMapping) throws SQLException {
|
|
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boolean success = true; |
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Set<DescriptionBase<?>> descriptions = new HashSet<DescriptionBase<?>>(); |
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descriptions.addAll(taxon.getDescriptions()); |
| ... | ... | |
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boolean isImageGallery = desc.isImageGallery(); |
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for (DescriptionElementBase element : desc.getElements()){
|
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success &= handleDescriptionElement(state, notesMapping, occurrenceMapping, vernacularMapping, imageMapping, |
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isImageGallery, element); |
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addSourceSourceMapping, additionalSourceMapping, isImageGallery, element);
|
|
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} |
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} |
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return success; |
| ... | ... | |
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|
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private boolean handleDescriptionElement(PesiExportState state, PesiExportMapping notesMapping, |
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PesiExportMapping occurrenceMapping, PesiExportMapping vernacularMapping, PesiExportMapping imageMapping, |
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boolean isImageGallery, DescriptionElementBase element) throws SQLException {
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|
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PesiExportMapping addSourceSourceMapping, PesiExportMapping additionalSourceMapping, boolean isImageGallery, DescriptionElementBase element) throws SQLException {
|
|
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try {
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boolean success = true; |
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if (isImageGallery){
|
| ... | ... | |
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}else if (isCommonName(element)){
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countCommonName++; |
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if (element.isInstanceOf(TextData.class)){
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// |
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//we do not import text data common names
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}else{
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success &= vernacularMapping.invoke(element); |
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} |
| ... | ... | |
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} |
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}else if (isAdditionalTaxonSource(element)){
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countAdditionalSources++; |
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// success &= addittionalSourceMapping.invoke(element); |
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success &= addSourceSourceMapping.invoke(element); |
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success &= additionalSourceMapping.invoke(element); |
|
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}else if (isExcludedNote(element)){
|
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//do nothing |
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}else if (isPesiNote(element)){
|
| ... | ... | |
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if (feature == null){
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return false; |
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} |
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return (feature.equals(Feature.CITATION())); |
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return (feature.equals(Feature.CITATION()) || feature.equals(Feature.ADDITIONAL_PUBLICATION()));
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} |
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|
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private boolean isOccurrence(DescriptionElementBase element) {
|
| ... | ... | |
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* @return The <code>Note_2</code> attribute. |
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* @see MethodMapper |
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*/ |
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@SuppressWarnings("unused")
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private static String getNote_2(DescriptionElementBase descriptionElement) {
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logger.warn("Not yet implemented");
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@SuppressWarnings("unused") //used for mapper
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private static String getNote_2(DescriptionElementBase element) {
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//E+M map links -> medium |
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if (element.getFeature() != null && element.getFeature().getUuid().equals(BerlinModelTransformer.uuidFeatureMaps)){
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String text = CdmBase.deproxy(element, TextData.class).getText(Language.ENGLISH()); |
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if (text.contains("medium")){
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return "medium"; |
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} |
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} |
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return null; |
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} |
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|
| ... | ... | |
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mapping.addMapper(IdMapper.NewInstance("NoteId"));
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mapping.addMapper(DbTextDataMapper.NewInstance(Language.ENGLISH(), "Note_1")); |
| 784 | 800 |
//TODO |
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mapping.addMapper(DbExportNotYetImplementedMapper.NewInstance("Note_2", "Need to research what Note_2 is for"));
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mapping.addMapper(MethodMapper.NewInstance("Note_2", this, DescriptionElementBase.class));
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mapping.addMapper(MethodMapper.NewInstance("NoteCategoryFk", this, DescriptionElementBase.class ));
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mapping.addMapper(MethodMapper.NewInstance("NoteCategoryCache", this, DescriptionElementBase.class, PesiExportState.class ));
|
| ... | ... | |
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return mapping; |
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} |
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|
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/** |
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* Returns the CDM to PESI specific export mappings for additional taxon sources to create a new |
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* source for the additional source |
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* @see #{@link PesiDescriptionExport#getAdditionalTaxonSourceMapping()}
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* @return The {@link PesiExportMapping PesiExportMapping}.
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*/ |
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private PesiExportMapping getAddTaxonSourceSourceMapping() {
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PesiExportMapping sourceMapping = new PesiExportMapping(PesiSourceExport.dbTableName); |
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sourceMapping.addMapper(IdMapper.NewInstance("SourceId"));
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sourceMapping.addMapper(DbConstantMapper.NewInstance("SourceCategoryFk", Types.INTEGER, PesiTransformer.REF_UNRESOLVED));
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sourceMapping.addMapper(DbConstantMapper.NewInstance("SourceCategoryCache", Types.VARCHAR, PesiTransformer.REF_STR_UNRESOLVED));
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// sourceMapping.addMapper(MethodMapper.NewInstance("NomRefCache", PesiSourceExport.class, "getNomRefCache", Reference.class));
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sourceMapping.addMapper(DbTextDataMapper.NewInstance(Language.ENGLISH(), "NomRefCache")); |
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return sourceMapping; |
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} |
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/** |
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* Returns the CDM to PESI specific export mappings for additional taxon sources. |
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* @see #{@link PesiDescriptionExport#getAddTaxonSourceSourceMapping()}
|
|
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* @return The {@link PesiExportMapping PesiExportMapping}.
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*/ |
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private PesiExportMapping getAdditionalTaxonSourceMapping() {
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PesiExportMapping mapping = new PesiExportMapping(dbAdditionalSourceTableName); |
| 859 | 899 |
|
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this, DescriptionElementBase.class, PesiExportState.class));
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mapping.addMapper(DbSingleSourceMapper.NewInstance("SourceFk", of (DbSingleSourceMapper.EXCLUDE.WITH_ID) , ! IS_CACHE));
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mapping.addMapper(DbSingleSourceMapper.NewInstance("SourceNameCache", of(DbSingleSourceMapper.EXCLUDE.WITH_ID) , ! IS_CACHE));
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mapping.addMapper(IdMapper.NewInstance("SourceFk"));
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mapping.addMapper(DbTextDataMapper.NewInstance(Language.ENGLISH(), "SourceNameCache")); |
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|
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mapping.addMapper(DbConstantMapper.NewInstance("SourceUseFk", Types.INTEGER, PesiTransformer.NOMENCLATURAL_REFERENCE));
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mapping.addMapper(DbConstantMapper.NewInstance("SourceUseCache", Types.VARCHAR, PesiTransformer.STR_NOMENCLATURAL_REFERENCE));
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// mapping.addMapper(MethodMapper.NewInstance("SourceUseFk", this));
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// mapping.addMapper(MethodMapper.NewInstance("SourceUseCache", this));
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// mapping.addMapper(MethodMapper.NewInstance("SourceFk", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));
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// mapping.addMapper(MethodMapper.NewInstance("SourceNameCache", this));
|
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// mapping.addMapper(MethodMapper.NewInstance("SourceDetail", this));
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// mapping.addMapper(DbIgnoreMapper.NewInstance("SourceDetail", "SourceDetails not available for additional sources"));
|
|
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|
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return mapping; |
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} |
Also available in: Unified diff
latest changes for PESI export, moving old IOs to extra package