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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.app.cyprus;
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import java.io.FileNotFoundException;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.common.ExcelUtils;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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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.reference.ReferenceFactory;
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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.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.mueller
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* @created 16.12.2010
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*/
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public class CyprusAltitudeActivator {
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private static final Logger logger = Logger.getLogger(CyprusAltitudeActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
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// static final URI source = cyprus_distribution();
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static final URI source = cyprus_altitude();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
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//feature tree uuid
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public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");
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//classification
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static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");
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private static final String sourceReferenceTitle = "Cyprus Excel Altitude Import";
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//TODO move to Feature vocabulary
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private static final UUID uuidAltitudeFeature = UUID.fromString("1a28ed59-e15f-4001-b5c2-ea89f0012671");
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//check - import
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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private void doImport(ICdmDataSource cdmDestination){
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ArrayList<HashMap<String, String>> excel;
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try {
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excel = ExcelUtils.parseXLS(source, "coreTax");
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} catch (FileNotFoundException e) {
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e.printStackTrace();
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return;
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}
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CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, hbm2dll);
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Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
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TransactionStatus tx = app.startTransaction();
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UUID uuidMikle77 = UUID.fromString("9f5fa7ee-538b-4ae5-bd82-2a9503fea1d6");
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UUID uuidMikle85 = UUID.fromString("994403c4-c400-413d-9a1a-8531a40bfd8c");
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Reference mikle77 = app.getReferenceService().find(uuidMikle77);
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Reference mikle85 = app.getReferenceService().find(uuidMikle85);
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Feature altitudeFeature = (Feature) app.getTermService().find(uuidAltitudeFeature);
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if (altitudeFeature == null){
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// altitudeFeature = Feature.NewInstance("Altitude", "Altitude", "alt.");
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// altitudeFeature.setUuid(uuidAltitudeFeature);
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// featureVoc = app.getVocabularyService().find(UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8"));
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// featureVoc.addTerm(altitudeFeature);
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throw new RuntimeException("Could not find altitudinal range feature");
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}
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MeasurementUnit meter = (MeasurementUnit)app.getTermService().find(UUID.fromString("8bef5055-789c-41e5-bea2-8dc2ea8ecdf6"));
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// NamedArea cyprus = (NamedArea)app.getTermService().find(UUID.fromString("da4cce9a-439b-4cc4-8073-85dc75bae169"));
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int count =1;
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for (HashMap<String, String> row : excel){
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count++;
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UUID baseUuid = makeUuid(row, "uuid");
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UUID acceptedUuid = makeUuid(row, "acceptedNameUuid");
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UUID parentUuid = makeUuid(row, "parentUuid");
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// String altitude = row.get("Altitude-kumuliert");
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String altitudeMin = row.get("Min");
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String altitudeMax = row.get("Max");
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String acceptedName = row.get("AcceptedName");
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String source = row.get("Source");
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if (StringUtils.isBlank(altitudeMin)){
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continue;
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}
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boolean hasAltitude = false;
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Reference sourceRef = getSource(source, mikle77, mikle85);
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Taxon taxon = getTaxon(app, baseUuid, acceptedUuid, parentUuid, acceptedName, count);
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if (taxon != null){
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TaxonDescription desc = getDescription(taxon, sourceRef);
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hasAltitude = makeAltitude(altitudeMin, altitudeMax, altitudeFeature, sourceRef, desc, meter, count);
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// hasAltitude = makeAltitudeOld(altitude, altitudeFeature, sourceRef, desc, meter, count);
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if (hasAltitude){
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if(desc.getTaxon() == null){
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taxon.addDescription(desc);
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}
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taxaToSave.add(taxon);
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}else{
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logger.warn("HasALtitude is false in " + count);
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}
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}else{
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logger.warn("Taxon not recognized in line " + count);
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}
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}
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app.getTaxonService().saveOrUpdate(taxaToSave);
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// tx.setRollbackOnly();
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app.commitTransaction(tx);
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}
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private Taxon getTaxon(CdmApplicationController app, UUID baseUuid, UUID acceptedUuid, UUID parentUuid, String acceptedName, int row) {
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TaxonBase<?> base = app.getTaxonService().find(baseUuid);
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// TaxonBase<?> parent = app.getTaxonService().find(parentUuid);
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//TODO
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Taxon result = null;
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if (base.isInstanceOf(Taxon.class)){
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Taxon t = CdmBase.deproxy(base, Taxon.class);
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if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){
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result = t;
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}else{
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logger.warn("Base taxon (uuid) not in classification. Row: " + row + ", Taxon: " + base.getTitleCache());
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}
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}
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if (result == null){
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TaxonBase<?> accepted = app.getTaxonService().find(acceptedUuid);
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Taxon t = CdmBase.deproxy(accepted, Taxon.class);;
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if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){
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if (hasSynonym(t, base)){
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result = t;
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}else{
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logger.warn("Synonym relation has changed somehow. Row: " + row + ", Taxon: " + base.getTitleCache());
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}
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}else{
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logger.warn("Accepted taxon not in classification. Row: " + row + ", Taxon: " + base.getTitleCache());
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}
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}
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if (result != null){
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if (! result.getName().getTitleCache().equals(acceptedName)){
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logger.warn("AcceptedName and taxon name is not equal in " + row + ".\n" +
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" Accepted Name: " + acceptedName + ";\n" +
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" Taxon Name: " + result.getName().getTitleCache());
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}
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}
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return result;
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}
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private boolean hasSynonym(Taxon t, TaxonBase<?> base) {
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if (base.isInstanceOf(Synonym.class)){
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for (SynonymRelationship rel : t.getSynonymRelations()){
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if (rel.getSynonym().equals(base)){
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return true;
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}
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}
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}
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return false;
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}
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// private static final Pattern altitudePattern = Pattern.compile("\\d{1,4}(-\\d{1,4})?");
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private boolean makeAltitude(String altitudeMin, String altitudeMax, Feature altitudeFeature,
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Reference sourceRef, TaxonDescription desc, MeasurementUnit meter, int row) {
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QuantitativeData data = QuantitativeData.NewInstance(altitudeFeature);
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//Meikle
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if (source != null){
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TaxonNameBase<?,?> nameUsedInSource = null; //TODO
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data.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef, null, nameUsedInSource, null);
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}
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// //Excel //excel source not wanted by Ralf
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// TaxonNameBase<?,?> nameUsedInSource = null; //TODO probably we don't want this
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// data.addSource(OriginalSourceType.Import, String.valueOf(row), "row", getSourceReference(), null, nameUsedInSource, null);
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data.setUnit(meter);
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Integer min = Integer.valueOf(altitudeMin);
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StatisticalMeasurementValue minValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min);
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data.addStatisticalValue(minValue);
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Integer max = Integer.valueOf(altitudeMax);
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StatisticalMeasurementValue maxValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max);
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data.addStatisticalValue(maxValue);
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desc.addElement(data);
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return true;
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}
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// private boolean makeAltitudeOld(String altitudeOrig, Feature feature, Reference source, TaxonDescription desc, MeasurementUnit meter, int row) {
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// String altitude = altitudeOrig.trim().replace(" ", "");
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// Matcher matcher = altitudePattern.matcher(altitude);
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//
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// if (matcher.matches()){
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// QuantitativeData data = QuantitativeData.NewInstance(feature);
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//
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// //Meikle
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// if (source != null){
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// TaxonNameBase<?,?> nameUsedInSource = null; //TODO
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// data.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, source, null, nameUsedInSource, null);
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// }
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// //Excel
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// TaxonNameBase<?,?> nameUsedInSource = null; //TODO probably we don't want this
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// data.addSource(OriginalSourceType.Import, String.valueOf(row), "row", getSourceReference(), null, nameUsedInSource, null);
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// data.setUnit(meter);
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//
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// String[] split = altitude.split("-");
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//
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// Integer min = Integer.valueOf(split[0]);
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// StatisticalMeasurementValue minValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min);
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// data.addStatisticalValue(minValue);
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//
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// if (split.length > 1){
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// Integer max = Integer.valueOf(split[1]);
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// StatisticalMeasurementValue maxValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max);
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// data.addStatisticalValue(maxValue);
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// }
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// desc.addElement(data);
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// return true;
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// }else{
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// logger.warn("Altitude does not match in row " + row + ": " + altitudeOrig);
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// return false;
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// }
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// }
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private TaxonDescription getDescription(Taxon taxon, Reference sourceRef) {
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if (taxon != null){
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//TODO Mikle existiert derzeit nicht also Source
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TaxonDescription desc = TaxonDescription.NewInstance();
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desc.setTitleCache("Import from " + getSourceReference().getTitleCache(), true);
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desc.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef,null);
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desc.addSource(OriginalSourceType.Import, null, null, getSourceReference(), null);
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return desc;
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}
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return null;
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}
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private Reference getSource(String source, Reference m77, Reference m85) {
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if(StringUtils.isNotBlank(source)){
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if (source.equals("Meikle 1977")){
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return m77;
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}else if (source.equals("Meikle 1985")){
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return m85;
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}else{
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logger.warn("Source not recognized: " + source);
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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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* @param row
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* @return
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*/
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private UUID makeUuid(HashMap<String, String> row, String colName) {
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if (StringUtils.isBlank(row.get(colName))){
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return null;
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}else{
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return UUID.fromString(row.get(colName));
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}
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}
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// private void getRowValues(HashMap<String, String> row) {
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// // TODO Auto-generated method stub
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// HashMap<String, Object> = new HashM
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// row
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//
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//
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// }
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Reference sourceReference;
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private Reference getSourceReference() {
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if (sourceReference == null){
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sourceReference = ReferenceFactory.newGeneric();
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sourceReference.setTitleCache(sourceReferenceTitle, true);
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}
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return sourceReference;
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}
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//Cyprus
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public static URI cyprus_altitude() {
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URI sourceUrl;
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try {
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sourceUrl = new URI("file:/F:/data/cyprus/Cyprus-altitude-import-neu.xls");
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// sourceUrl = new URI("file:/F:/data/cyprus/Zypern-Altitude.xls");
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return sourceUrl;
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} catch (URISyntaxException e) {
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e.printStackTrace();
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return null;
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}
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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CyprusAltitudeActivator me = new CyprusAltitudeActivator();
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me.doImport(cdmDestination);
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me.testMatcher();
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}
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private void testMatcher() {
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// makeAltitude("0-4400", null, null);
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}
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}
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