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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.redlist.gefaesspflanzen;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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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.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.DbImportBase;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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.TaxonRelationshipType;
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/**
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*
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* @author pplitzner
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* @date Mar 1, 2016
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*
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*/
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@Component
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@SuppressWarnings("serial")
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public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
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private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
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private static final String tableName = "Rote Liste Gefäßpflanzen";
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private static final String pluralString = "classifications";
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public RedListGefaesspflanzenImportClassification() {
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super(tableName, pluralString);
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}
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@Override
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protected String getIdQuery(RedListGefaesspflanzenImportState state) {
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return "SELECT NAMNR "
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+ "FROM V_TAXATLAS_D20_EXPORT t "
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+ " ORDER BY NAMNR";
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}
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@Override
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protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
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String result = " SELECT * "
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+ " FROM V_TAXATLAS_D20_EXPORT t "
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+ " WHERE t.NAMNR IN (@IDSET)";
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result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
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return result;
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}
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@Override
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protected void doInvoke(RedListGefaesspflanzenImportState state) {
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makeClassification("Gesamtliste", state.getConfig().getClassificationUuid(), "Gesamtliste", null, RedListUtil.gesamtListeReferenceUuid, state);
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makeClassification("Checkliste", RedListUtil.checkListClassificationUuid, "Checkliste", null, RedListUtil.checkListReferenceUuid, state);
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makeClassification("E", RedListUtil.uuidClassificationE, "Ehrendorfer", null, RedListUtil.uuidClassificationReferenceE, state);
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makeClassification("W", RedListUtil.uuidClassificationW, "Wisskirchen (Standardliste)", 1998, RedListUtil.uuidClassificationReferenceW, state);
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makeClassification("K", RedListUtil.uuidClassificationK, "Korneck (Rote Liste)", 1996, RedListUtil.uuidClassificationReferenceK, state);
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makeClassification("AW", RedListUtil.uuidClassificationAW, "Atlas (Westdeutschland)", 1988, RedListUtil.uuidClassificationReferenceAW, state);
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makeClassification("AO", RedListUtil.uuidClassificationAO, "Atlas (Ostdeutschland)", 1996, RedListUtil.uuidClassificationReferenceAO, state);
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makeClassification("R", RedListUtil.uuidClassificationR, "Rothmaler", 2011, RedListUtil.uuidClassificationReferenceR, state);
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makeClassification("O", RedListUtil.uuidClassificationO, "Oberdorfer", 2001, RedListUtil.uuidClassificationReferenceO, state);
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makeClassification("S", RedListUtil.uuidClassificationS, "Schmeil-Fitschen", 2011, RedListUtil.uuidClassificationReferenceS, state);
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super.doInvoke(state);
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
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ResultSet rs = partitioner.getResultSet();
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Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());
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Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);
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Classification classificationE = getClassificationService().load(RedListUtil.uuidClassificationE);
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Classification classificationW = getClassificationService().load(RedListUtil.uuidClassificationW);
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Classification classificationK = getClassificationService().load(RedListUtil.uuidClassificationK);
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Classification classificationAW = getClassificationService().load(RedListUtil.uuidClassificationAW);
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Classification classificationAO = getClassificationService().load(RedListUtil.uuidClassificationAO);
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Classification classificationR = getClassificationService().load(RedListUtil.uuidClassificationR);
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Classification classificationO = getClassificationService().load(RedListUtil.uuidClassificationO);
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Classification classificationS = getClassificationService().load(RedListUtil.uuidClassificationS);
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try {
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while (rs.next()){
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makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification,
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classificationE, classificationW, classificationK, classificationAW
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, classificationAO, classificationR, classificationO, classificationS);
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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logger.info("Update classification (1000 nodes)");
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getClassificationService().saveOrUpdate(gesamtListeClassification);
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getClassificationService().saveOrUpdate(checklistClassification);
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return true;
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}
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private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs,
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Classification gesamtListeClassification, Classification checklistClassification,
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Classification classificationE, Classification classificationW, Classification classificationK,
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Classification classificationAW, Classification classificationAO, Classification classificationR,
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Classification classificationO, Classification classificationS)
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throws SQLException {
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long id = rs.getLong(RedListUtil.NAMNR);
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String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
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String gueltString = rs.getString(RedListUtil.GUELT);
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String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
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String relationE = rs.getString(RedListUtil.E);
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String relationW = rs.getString(RedListUtil.W);
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String relationK = rs.getString(RedListUtil.K);
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String relationAW = rs.getString(RedListUtil.AW);
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String relationAO = rs.getString(RedListUtil.AO);
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String relationR = rs.getString(RedListUtil.R);
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String relationO = rs.getString(RedListUtil.O);
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String relationS = rs.getString(RedListUtil.S);
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//Gesamtliste
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TaxonBase<?> taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
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TaxonBase<?> parentBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
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if(parentBaseGL!=null && !parentBaseGL.isInstanceOf(Taxon.class)){
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RedListUtil.logMessage(id, parentBaseGL+" is no taxon but is a parent of "+taxonBaseGL+" (Gesamtliste)", logger);
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}
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Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
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createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);
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//Checkliste
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TaxonBase<?> taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
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TaxonBase<?> parentBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
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if(parentBaseCL!=null && !parentBaseCL.isInstanceOf(Taxon.class)){
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RedListUtil.logMessage(id, parentBaseCL+" is no taxon but is a parent of "+taxonBaseCL+" (Checkliste)", logger);
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}
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Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
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if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist
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createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);
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}
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if(taxonBaseGL!= null && taxonBaseCL!=null
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&& taxonBaseGL.getUuid().equals(taxonBaseCL.getUuid())){
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RedListUtil.logMessage(id, "Same UUID for "+taxonBaseGL+ " (Gesamtliste) and "+taxonBaseCL+" (Checkliste)", logger);
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}
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if(parentGL!=null && parentCL!=null && parentGL.getUuid().equals(parentCL.getUuid())){
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RedListUtil.logMessage(id, "Same UUID for "+parentGL+ " (Gesamtliste) and "+parentCL+" (Checkliste)", logger);
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}
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//add taxa for concept relationships to E, W, K, AW, AO, R, O, S
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addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, relationE, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, relationW, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, relationK, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, relationAW, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, relationAO, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, relationR, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, relationO, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, relationS, taxonBaseGL, taxonBaseCL, id, state);
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}
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private void addTaxonToClassification(Classification classification, String classificationNamespace, String relationString, final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, long id, RedListGefaesspflanzenImportState state){
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Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class);
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//add concept relation to gesamtliste and checkliste
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if(taxon!=null && CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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//if the related concept in gesamtliste/checkliste is a synonym then we
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//create a relation to the accepted taxon
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Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon);
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Taxon acceptedChecklistTaxon = getAcceptedTaxon(checklisteTaxon);
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String relationSubstring = relationString.substring(relationString.length()-1, relationString.length());
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TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(relationSubstring);
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if(taxonRelationshipTypeByKey==null){
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RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+gesamtListeTaxon.generateTitle(), logger);
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}
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//there is no type "included in" so we have to reverse the direction
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if(relationSubstring.equals("<")){
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if(acceptedGesamtListeTaxon!=null){
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acceptedGesamtListeTaxon.addTaxonRelation(taxon, taxonRelationshipTypeByKey, null, null);
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}
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if(acceptedChecklistTaxon!=null) {
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acceptedChecklistTaxon.addTaxonRelation(taxon, taxonRelationshipTypeByKey, null, null);
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}
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}
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else{
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if(acceptedGesamtListeTaxon!=null){
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taxon.addTaxonRelation(acceptedGesamtListeTaxon, taxonRelationshipTypeByKey, null, null);
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}
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if(acceptedChecklistTaxon!=null) {
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taxon.addTaxonRelation(acceptedChecklistTaxon, taxonRelationshipTypeByKey, null, null);
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}
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}
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taxon.setSec(classification.getReference());
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classification.addChildTaxon(taxon, null, null);
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//TODO is saving and setting the title cache to null neccessary?
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getTaxonService().saveOrUpdate(taxon);
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getTaxonService().saveOrUpdate(gesamtListeTaxon);
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if(checklisteTaxon!=null){
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getTaxonService().saveOrUpdate(checklisteTaxon);
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}
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taxon.setTitleCache(null);//Reset title cache to see sec ref in title
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}
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}
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private void createParentChildNodes(Classification classification, long id, String gueltString,
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String taxZusatzString, TaxonBase<?> taxonBase, Taxon parent) {
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if(taxonBase==null){
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RedListUtil.logMessage(id, "child taxon/synonym of "+parent+" is null. ("+classification.generateTitle()+")" , logger);
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return;
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}
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//taxon
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if(taxonBase.isInstanceOf(Taxon.class)){
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//misapplied name
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String appendedPhrase = taxonBase.getAppendedPhrase();
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if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){
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if(parent==null){
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RedListUtil.logMessage(id, "parent taxon of misapplied name "+taxonBase+" is null. ("+classification.getTitleCache()+")" , logger);
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return;
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}
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parent.addMisappliedName((Taxon) taxonBase, null, null);
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}
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else{
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classification.addParentChild(parent, (Taxon)taxonBase, null, null);
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}
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if(CdmUtils.isNotBlank(taxZusatzString)){
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if(taxZusatzString.trim().equals("p. p.")){
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RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);
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}
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}
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}
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//synonym
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else if(taxonBase.isInstanceOf(Synonym.class)){
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if(parent==null){
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RedListUtil.logMessage(id, "parent taxon of synonym "+taxonBase+" is null. ("+classification.getTitleCache()+")" , logger);
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return;
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}
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//basionym
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if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
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parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
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parent.getName().addBasionym(taxonBase.getName());
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}
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//regular synonym
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else{
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SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
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//TAX_ZUSATZ
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if(CdmUtils.isNotBlank(taxZusatzString)){
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if(taxZusatzString.trim().equals("p. p.")){
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synonymRelationship.setProParte(true);
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}
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else if(taxZusatzString.trim().equals("s. l. p. p.")){
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synonymRelationship.setProParte(true);
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taxonBase.setAppendedPhrase("s. l.");
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}
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else if(taxZusatzString.trim().equals("s. str. p. p.")){
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synonymRelationship.setProParte(true);
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taxonBase.setAppendedPhrase("s. str.");
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}
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else if(taxZusatzString.trim().equals("s. l.")
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|| taxZusatzString.trim().equals("s. str.")){
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taxonBase.setAppendedPhrase(taxZusatzString);
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}
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else{
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RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);
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}
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}
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}
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}
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//set sec reference
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taxonBase.setSec(classification.getReference());
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taxonBase.setTitleCache(null, false);//refresh title cache
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
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RedListGefaesspflanzenImportState state) {
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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Set<String> idSet = new HashSet<String>();
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try {
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while (rs.next()){
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idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
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idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE));
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result.put(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_CHECKLISTE_NAMESPACE));
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result.put(RedListUtil.CLASSIFICATION_NAMESPACE_E, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_E));
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result.put(RedListUtil.CLASSIFICATION_NAMESPACE_W, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_W));
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result.put(RedListUtil.CLASSIFICATION_NAMESPACE_K, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_K));
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result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AW, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AW));
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316
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result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AO, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AO));
|
317
|
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_R, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_R));
|
318
|
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_O, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_O));
|
319
|
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_S, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_S));
|
320
|
return result;
|
321
|
}
|
322
|
|
323
|
private void makeClassification(String classificationName, UUID classificationUuid, String referenceName, Integer yearPublished, UUID referenceUuid, RedListGefaesspflanzenImportState state) {
|
324
|
Classification classification = Classification.NewInstance(classificationName, Language.DEFAULT());
|
325
|
classification.setUuid(classificationUuid);
|
326
|
Reference reference = ReferenceFactory.newGeneric();
|
327
|
reference.setTitle(referenceName);
|
328
|
reference.setUuid(referenceUuid);
|
329
|
classification.setReference(reference);
|
330
|
if(yearPublished!=null){
|
331
|
reference.setDatePublished(TimePeriod.NewInstance(yearPublished));
|
332
|
}
|
333
|
getClassificationService().save(classification);
|
334
|
}
|
335
|
|
336
|
@Override
|
337
|
protected boolean doCheck(RedListGefaesspflanzenImportState state) {
|
338
|
return false;
|
339
|
}
|
340
|
|
341
|
@Override
|
342
|
protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
|
343
|
return false;
|
344
|
}
|
345
|
|
346
|
}
|