Revision 008ae587
Added by Andreas Müller over 9 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/RoteListeDbTaxonImport.java | ||
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import org.apache.log4j.Logger; |
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import org.springframework.stereotype.Component; |
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import eu.etaxonomy.cdm.api.service.IClassificationService; |
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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.io.common.TdwgAreaProvider; |
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping; |
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import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.IMappingImport; |
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import eu.etaxonomy.cdm.io.redlist.validation.RoteListeDbTaxonImportValidator; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.description.Distribution; |
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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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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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
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/** |
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* TODO do we still need this class? |
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* @author a.mueller |
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* @created 27.08.2012 |
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*/ |
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@Component |
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public class RoteListeDbTaxonImport extends RoteListeDbImportBase<TaxonBase> implements IMappingImport<TaxonBase, RoteListeDbImportState>{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(RoteListeDbTaxonImport.class); |
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private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| ... | ... | |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery() |
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*/ |
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@Override |
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protected String getIdQuery() {
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String strQuery = " SELECT pk FROM " + dbTableName + |
| ... | ... | |
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return strQuery; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping() |
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*/ |
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@Override |
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protected DbImportMapping getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping(); |
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return mapping; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator) |
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*/ |
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@Override |
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protected String getRecordQuery(RoteListeDbImportConfigurator config) {
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String strSelect = " SELECT * "; |
| ... | ... | |
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@Override |
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public boolean doPartition(ResultSetPartitioner partitioner, RoteListeDbImportState state) {
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// higherTaxonMap = new HashMap<UUID, Taxon>(); |
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// Reference genevaReference = getReferenceService().find(state.getConfig().getUuidGenevaReference()); |
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// if (genevaReference == null){
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// genevaReference = makeGenevaReference(state); |
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// getReferenceService().save(genevaReference); |
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// } |
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// state.setGenevaReference(genevaReference); |
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boolean success = super.doPartition(partitioner, state); |
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// higherTaxonMap = new HashMap<UUID, Taxon>(); |
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// state.setGenevaReference(null); |
| ... | ... | |
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// speciesTaxon.addSource(sourceId, REFERENCE_NAMESPACE, sourceRef, null); |
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// |
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// |
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// //geneva id |
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// Reference genevaReference = state.getGenevaReference(); |
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// Object genevaId = rs.getObject("geneva_ID");
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// speciesTaxon.addSource(String.valueOf(genevaId), null, genevaReference, null); |
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// |
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// //distribution |
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// handleDistribution(rs, speciesTaxon); |
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// |
| ... | ... | |
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return null; |
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} |
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private void handleDistribution(ResultSet rs, Taxon speciesTaxon) throws SQLException {
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TaxonDescription description = TaxonDescription.NewInstance(speciesTaxon); |
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Boolean isCongo = rs.getBoolean("drc");
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Boolean isBurundi = rs.getBoolean("burundi");
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Boolean isRwanda = rs.getBoolean("rwanda");
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addDistribution(description, isCongo, "ZAI"); |
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addDistribution(description, isBurundi, "BUR"); |
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addDistribution(description, isRwanda, "RWA"); |
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} |
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/** |
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* @param description |
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* @param isCongo |
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*/ |
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private void addDistribution(TaxonDescription description, Boolean exists, String label) {
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if (exists == true){
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NamedArea namedArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(label); |
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Distribution distribution = Distribution.NewInstance(namedArea, PresenceAbsenceTerm.PRESENT()); |
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description.addElement(distribution); |
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} |
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} |
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//TODO use Mapper |
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private boolean makeTaxonomicallyIncluded(RoteListeDbImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
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String treeKey; |
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UUID treeUuid; |
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if (treeRefFk == null){
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treeKey = "1"; // there is only one tree and it gets the map key '1' |
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treeUuid = state.getConfig().getClassificationUuid(); |
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}else{
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treeKey =String.valueOf(treeRefFk); |
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treeUuid = state.getTreeUuidByTreeKey(treeKey); |
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} |
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Classification tree = (Classification)state.getRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey); |
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if (tree == null){
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IClassificationService service = state.getCurrentIO().getClassificationService(); |
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tree = service.find(treeUuid); |
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if (tree == null){
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String treeName = state.getConfig().getClassificationName(); |
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tree = Classification.NewInstance(treeName); |
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tree.setUuid(treeUuid); |
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//FIXME tree reference |
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//tree.setReference(ref); |
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service.save(tree); |
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} |
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state.addRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey, tree); |
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} |
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TaxonNode childNode = tree.addParentChild(parent, child, citation, microCitation); |
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return (childNode != null); |
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} |
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// private Reference makeGenevaReference(RoteListeDbImportState state) {
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// Reference result = ReferenceFactory.newDatabase(); |
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// result.setTitleCache(state.getConfig().getGenevaReferenceTitle(), true); |
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// result.setUuid(state.getConfig().getUuidGenevaReference()); |
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// return result; |
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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) |
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*/ |
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@Override |
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protected boolean doCheck(RoteListeDbImportState state){
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IOValidator<RoteListeDbImportState> validator = new RoteListeDbTaxonImportValidator(); |
| ... | ... | |
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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) |
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*/ |
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@Override |
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protected boolean isIgnore(RoteListeDbImportState state){
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return ! state.getConfig().isDoTaxa(); |
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} |
Also available in: Unified diff
cleanup RoteListeDbTaxonImport