Revision 892efc69
Added by Andreas Kohlbecker almost 14 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
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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.Source; |
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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.common.IdentifiableSource; |
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import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
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public class BerlinModelTaxonRelationImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationImport.class); |
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public static final String TREE_NAMESPACE = "PTRefFk"; |
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private static int modCount = 30000; |
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private static final String pluralString = "taxon relations"; |
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private static final String dbTableName = "RelPTaxon"; |
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//biblio reference map |
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nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE; |
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cdmClass = ReferenceBase.class; |
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idSet = new HashSet<String>(); |
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// idSet = new HashSet<String>();
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Map<String, ReferenceBase> biblioRefMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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ResultSet rs = source.getResultSet(getTaxonomicTreeQuery()) ; |
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Object ptRefFkObj = rs.getObject("PTRefFk");
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String ptRefFk= String.valueOf(ptRefFkObj); |
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ReferenceBase<?> ref = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, ptRefFk); |
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//FIXME treeName
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rs.getString("RefCache");
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String treeName = "TaxonTree - No Name"; |
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String refCache = rs.getString("RefCache");
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if (CdmUtils.isNotEmpty(refCache)){
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treeName = refCache; |
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} |
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if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){
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treeName = ref.getTitleCache(); |
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} |
| ... | ... | |
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if (i == 1 && state.getConfig().getTaxonomicTreeUuid() != null){
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tree.setUuid(state.getConfig().getTaxonomicTreeUuid()); |
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} |
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IdentifiableSource identifiableSource = IdentifiableSource.NewInstance(ptRefFk, TREE_NAMESPACE); |
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tree.addSource(identifiableSource); |
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getTaxonTreeService().save(tree); |
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state.putTaxonomicTreeUuidInt((Integer)ptRefFkObj, tree); |
| ... | ... | |
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} |
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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.berlinModel.in.BerlinModelImportBase#getIdQuery() |
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*/ |
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@Override |
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protected String getIdQuery() {
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String result = " " + |
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" SELECT RelPTaxon.RelPTaxonId " + |
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" FROM RelPTaxon LEFT JOIN Name AS toName ON RelPTaxon.PTNameFk1 = toName.NameId " + |
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" ORDER BY toName.RankFk "; |
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return result; |
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} |
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/** |
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* @return |
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*/ |
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private String getTaxonomicTreeQuery() {
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String strQuery = "SELECT PTaxon.PTRefFk " + |
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String strQuery = "SELECT PTaxon.PTRefFk, Reference.RefCache " +
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" FROM RelPTaxon INNER JOIN " + |
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" PTaxon AS PTaxon ON RelPTaxon.PTNameFk2 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon.PTRefFk " + |
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" PTaxon AS PTaxon ON RelPTaxon.PTNameFk2 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon.PTRefFk INNER JOIN " + |
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" Reference ON PTaxon.PTRefFk = Reference.RefId " + |
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" WHERE (RelPTaxon.RelQualifierFk = 1) " + |
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" GROUP BY PTaxon.PTRefFk "; |
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" GROUP BY PTaxon.PTRefFk, Reference.RefCache ";
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return strQuery; |
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} |
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Map<String, ReferenceBase> nomRefMap = (Map<String, ReferenceBase>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE); |
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ResultSet rs = partitioner.getResultSet(); |
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try{
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int i = 0; |
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//for each reference |
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Object relRefFkObj = rs.getObject("relRefFk");
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int treeRefFk = rs.getInt("treeRefFk");
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int relQualifierFk = rs.getInt("relQualifierFk");
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String notes = rs.getString("notes");
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boolean isConceptRelationship = rs.getBoolean("is_concept_relation");
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TaxonBase taxon1 = taxonMap.get(String.valueOf(taxon1Id)); |
| ... | ... | |
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success = false; |
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continue; |
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} |
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AnnotatableEntity taxonRelationship = null; |
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Taxon toTaxon = (Taxon)taxon2; |
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if (isTaxonRelationship(relQualifierFk)){
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if (!(taxon1 instanceof Taxon)){
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} |
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Taxon fromTaxon = (Taxon)taxon1; |
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if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){
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makeTaxonomicallyIncluded(state, taxonTreeMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation); |
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taxonRelationship = makeTaxonomicallyIncluded(state, taxonTreeMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation);
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}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
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toTaxon.addMisappliedName(fromTaxon, citation, microcitation); |
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taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation);
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} |
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}else if (isSynonymRelationship(relQualifierFk)){
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if (!(taxon1 instanceof Synonym)){
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| ... | ... | |
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} |
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Synonym synonym = (Synonym)taxon1; |
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SynonymRelationship synRel = getSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation); |
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taxonRelationship = synRel; |
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if (relQualifierFk == TAX_REL_IS_SYNONYM_OF || |
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relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || |
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relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
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logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Taxon");
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}else{
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Taxon fromTaxon = (Taxon)taxon1; |
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fromTaxon.addTaxonRelation(toTaxon, relType, citation, microcitation); |
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taxonRelationship = fromTaxon.addTaxonRelation(toTaxon, relType, citation, microcitation);
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} |
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} catch (UnknownCdmTypeException e) {
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//TODO other relationships |
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logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented");
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success = false; |
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} |
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doNotes(taxonRelationship, notes); |
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taxaToSave.add(taxon2); |
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//TODO |
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getTaxonService().save(taxaToSave); |
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taxonTreeMap = null; |
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taxaToSave = null; |
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return success; |
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return success;
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} |
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|
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handleForeignKey(rs, taxonIdSet, "taxon2Id"); |
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// handleForeignKey(rs, taxonTreeIdSet, "treeRefFk"); |
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handleForeignKey(rs, referenceIdSet, "RelRefFk"); |
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}
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} |
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//taxon map |
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nameSpace = BerlinModelTaxonImport.NAMESPACE; |
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cdmClass = TaxonBase.class; |
| ... | ... | |
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} |
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} |
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private boolean makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, TaxonomicTree> taxonTreeMap, int treeRefFk, Taxon child, Taxon parent, ReferenceBase citation, String microCitation){
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private TaxonNode makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, TaxonomicTree> taxonTreeMap, int treeRefFk, Taxon child, Taxon parent, ReferenceBase citation, String microCitation){
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TaxonomicTree tree = taxonTreeMap.get(treeRefFk); |
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if (tree == null){
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UUID treeUuid = state.getTreeUuidByIntTreeKey(treeRefFk); |
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