Revision 75f6d666
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java | ||
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbAnnotationMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedIntegerMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedStringMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper; |
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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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.model.taxon.TaxonRelationship; |
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/** |
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private PesiExportMapping mapping; |
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private PesiExportMapping synonymMapping; |
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private PesiExportMapping taxonNodeMapping; |
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public PesiRelTaxonExport() {
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super(); |
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synonymMapping = getSynonymMapping(); |
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synonymMapping.initialize(state); |
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// Get specific mappings: (CDM) Synonym -> (PESI) RelTaxon |
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taxonNodeMapping = getTaxonNodeMapping(); |
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taxonNodeMapping.initialize(state); |
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//Export taxon relations |
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success &= doPhase01(state, mapping); |
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//Export taxon nodes |
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success &= doPhase01b(state, taxonNodeMapping); |
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// Export name relations |
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success &= doPhase02(state, mapping); |
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|
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return success; |
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} |
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private boolean doPhase01b(PesiExportState state, PesiExportMapping taxonNodeMapping) {
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logger.info("PHASE 1b: Taxonnodes ...");
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boolean success = true; |
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int limit = state.getConfig().getLimitSave(); |
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// Start transaction |
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TransactionStatus txStatus = startTransaction(true); |
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logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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List<TaxonNode> list; |
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//taxon nodes |
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int partitionCount = 0; |
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int totalCount = 0; |
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while ((list = getNextTaxonNodePartition(limit, partitionCount++, null)) != null) {
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totalCount = totalCount + list.size(); |
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logger.info("Read " + list.size() + " PESI taxon nodes. Limit: " + limit + ". Total: " + totalCount );
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for (TaxonNode tn : list){
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try {
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taxonNodeMapping.invoke(tn); |
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} catch (Exception e) {
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logger.error(e.getMessage() + ". TaxonNode: " + tn.getUuid()); |
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e.printStackTrace(); |
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} |
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} |
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commitTransaction(txStatus); |
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txStatus = startTransaction(); |
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} |
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commitTransaction(txStatus); |
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return success; |
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} |
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private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) {
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logger.info("PHASE 2: Name Relationships ...");
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boolean success = true; |
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return state.getDbId(synonym); |
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} |
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/** |
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* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>Synonym</code>. |
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* @param synonym The {@link Synonym synonym}.
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* @param state The {@link PesiExportState PesiExportState}.
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* @return The <code>TaxonFk1</code> attribute. |
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* @see MethodMapper |
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*/ |
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@SuppressWarnings("unused")
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private static Integer getParent(TaxonNode taxonNode, PesiExportState state) {
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TaxonNode parent = taxonNode == null? null : taxonNode.getParent(); |
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Taxon parentTaxon = parent == null? null: parent.getTaxon(); |
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return state.getDbId(parentTaxon); |
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} |
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/** |
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* Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>. |
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* @param relationship The {@link RelationshipBase Relationship}.
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return mapping; |
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} |
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PesiExportMapping getTaxonNodeMapping() {
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PesiExportMapping mapping = new PesiExportMapping(dbTableName); |
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getParent", TaxonNode.class, PesiExportState.class));
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mapping.addMapper(DbObjectMapper.NewInstance("taxon", "TaxonFk1"));
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mapping.addMapper(DbFixedIntegerMapper.NewInstance(101, "RelTaxonQualifierFk")); |
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mapping.addMapper(DbFixedStringMapper.NewInstance("is taxonomically included in", "RelQualifierCache"));
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// mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes")); |
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return mapping; |
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} |
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@Override |
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protected boolean doCheck(PesiExportState state) {
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Also available in: Unified diff
ref #8509 add included taxon relationship export to PESI